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

Zhang, Qibin; Monroe, Matthew E.; Schepmoes, Athena A.

Non-enzymatic glycation of proteins is implicated in diabetes mellitus and its related complications. In this report, we extend our previous development and refinement of proteomics-based methods for the analysis of non-enzymatically glycated proteins to comprehensively identify glycated proteins in normal and diabetic human plasma and erythrocytes. Using immunodepletion, enrichment, and fractionation strategies, we identified 7749 unique glycated peptides, corresponding to 3742 unique glycated proteins. Semi-quantitative comparisons revealed a number of proteins with glycation levels significantly increased in diabetes relative to control samples and that erythrocyte proteins are more extensively glycated than plasma proteins. A glycation motif analysis revealed amino acidsmore » that are favored more than others in the protein primary structures in the vicinity of the glycation sites in both sample types. The glycated peptides and corresponding proteins reported here provide a foundation for the potential identification of novel markers for diabetes, glycemia, or diabetic complications.« less

Revealing the ultrafast outflow in IRAS 13224-3809 through spectral variability

NASA Astrophysics Data System (ADS)

Parker, M. L.; Alston, W. N.; Buisson, D. J. K.; Fabian, A. C.; Jiang, J.; Kara, E.; Lohfink, A.; Pinto, C.; Reynolds, C. S.

2017-08-01

We present an analysis of the long-term X-ray variability of the extreme narrow-line Seyfert 1 galaxy IRAS 13224-3809 using principal component analysis (PCA) and fractional excess variability (Fvar) spectra to identify model-independent spectral components. We identify a series of variability peaks in both the first PCA component and Fvar spectrum which correspond to the strongest predicted absorption lines from the ultrafast outflow (UFO) discovered by Parker et al. (2017). We also find higher order PCA components, which correspond to variability of the soft excess and reflection features. The subtle differences between RMS and PCA results argue that the observed flux-dependence of the absorption is due to increased ionization of the gas, rather than changes in column density or covering fraction. This result demonstrates that we can detect outflows from variability alone and that variability studies of UFOs are an extremely promising avenue for future research.

Urban transport safety assessment in akure based on corresponding performance indicators

NASA Astrophysics Data System (ADS)

Oye, Adedamola; Aderinlewo, Olufikayo; Croope, Silvana

2013-03-01

The level of safety of the transportation system in Akure, Nigeria was assessed by identifying the associated road safety problems and developing the corresponding safety performance indicators. These indicators were analysed with respect to accidents that occurred within the city from the year 2005 to 2009 based on the corresponding attributable risk measures. The results of the analysis showed the state of existing safety programs in Akure town. Six safety performance indicators were identified namely alcohol and drug use, excessive speeds, protection system (use of seat belts and helmets), use of day time running lights, state of vehicles (passive safety) and road condition. These indicators were used to determine the percentage of injury accidents as follows: 83.33% and 86.36% for years 2005 and 2006 respectively, 81.46% for year 2007 while years 2008 and 2009 had 82.86% and 78.12% injury accidents respectively.

Identification of CRASH, a gene deregulated in gynecological tumors.

PubMed

Evtimova, Vesna; Zeillinger, Robert; Kaul, Sepp; Weidle, Ulrich H

2004-01-01

We have identified CRASH, a human asparaginase-like protein which is composed of 308 amino acids and exhibits 32% homology to human aspartylglucosaminadase at the amino acid level. Database analysis revealed that the gene corresponding to CRASH is composed of 7 exons and 6 introns. Steady-state level of CRASH mRNA was found to be increased in 5 cell lines derived from metastatic lesions compared with 2 cell lines derived from primary mammary carcinoma and HMEC (human mammary epithelial cells). We found that the mRNA level of CRASH correlates with the metastatic propensity of several isogenic human colon cancer and pancreatic carcinoma cell lines. CRASH corresponds to a recently identified sperm autoantigen and furthermore we have demonstrated inducibility of CRASH mRNA by androgen and progesterone. Investigation of several types of human cancers and their corresponding normal tissues revealed high levels of CRASH mRNA in uterine, mammary and ovarian tumors compared with the corresponding normal tissues. CRASH mRNA expression was analysed in breast cancer samples with disclosed clinico-pathological features and corresponding normal tissues. The levels of CRASH mRNA were significantly up-regulated in tumors compared with normal breast tissues and correlate with lack of estrogen receptor expression of the tumors.

Non-destructive analysis of the conformational differences among feedstock sources and their corresponding co-products from bioethanol production with molecular spectroscopy.

PubMed

Gamage, I H; Jonker, A; Zhang, X; Yu, P

2014-01-24

The objective of this study was to determine the possibility of using molecular spectroscopy with multivariate technique as a fast method to detect the source effects among original feedstock sources of wheat and their corresponding co-products, wheat DDGS, from bioethanol production. Different sources of the bioethanol feedstock and their corresponding bioethanol co-products, three samples per source, were collected from the same newly-built bioethanol plant with current bioethanol processing technology. Multivariate molecular spectral analyses were carried out using agglomerative hierarchical cluster analysis (AHCA) and principal component analysis (PCA). The molecular spectral data of different feedstock sources and their corresponding co-products were compared at four different regions of ca. 1800-1725 cm(-1) (carbonyl CO ester, mainly related to lipid structure conformation), ca. 1725-1482 cm(-1) (amide I and amide II region mainly related to protein structure conformation), ca. 1482-1180 cm(-1) (mainly associated with structural carbohydrate) and ca. 1180-800 cm(-1) (mainly related to carbohydrates) in complex plant-based system. The results showed that the molecular spectroscopy with multivariate technique could reveal the structural differences among the bioethanol feedstock sources and among their corresponding co-products. The AHCA and PCA analyses were able to distinguish the molecular structure differences associated with chemical functional groups among the different sources of the feedstock and their corresponding co-products. The molecular spectral differences indicated the differences in functional, biomolecular and biopolymer groups which were confirmed by wet chemical analysis. These biomolecular and biopolymer structural differences were associated with chemical and nutrient profiles and nutrient utilization and availability. Molecular spectral analyses had the potential to identify molecular structure difference among bioethanol feedstock sources and their corresponding co-products. Copyright © 2013 Elsevier B.V. All rights reserved.

Non-destructive analysis of the conformational differences among feedstock sources and their corresponding co-products from bioethanol production with molecular spectroscopy

NASA Astrophysics Data System (ADS)

Gamage, I. H.; Jonker, A.; Zhang, X.; Yu, P.

2014-01-01

The objective of this study was to determine the possibility of using molecular spectroscopy with multivariate technique as a fast method to detect the source effects among original feedstock sources of wheat and their corresponding co-products, wheat DDGS, from bioethanol production. Different sources of the bioethanol feedstock and their corresponding bioethanol co-products, three samples per source, were collected from the same newly-built bioethanol plant with current bioethanol processing technology. Multivariate molecular spectral analyses were carried out using agglomerative hierarchical cluster analysis (AHCA) and principal component analysis (PCA). The molecular spectral data of different feedstock sources and their corresponding co-products were compared at four different regions of ca. 1800-1725 cm-1 (carbonyl Cdbnd O ester, mainly related to lipid structure conformation), ca. 1725-1482 cm-1 (amide I and amide II region mainly related to protein structure conformation), ca. 1482-1180 cm-1 (mainly associated with structural carbohydrate) and ca. 1180-800 cm-1 (mainly related to carbohydrates) in complex plant-based system. The results showed that the molecular spectroscopy with multivariate technique could reveal the structural differences among the bioethanol feedstock sources and among their corresponding co-products. The AHCA and PCA analyses were able to distinguish the molecular structure differences associated with chemical functional groups among the different sources of the feedstock and their corresponding co-products. The molecular spectral differences indicated the differences in functional, biomolecular and biopolymer groups which were confirmed by wet chemical analysis. These biomolecular and biopolymer structural differences were associated with chemical and nutrient profiles and nutrient utilization and availability. Molecular spectral analyses had the potential to identify molecular structure difference among bioethanol feedstock sources and their corresponding co-products.

An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant.

PubMed

Ortseifen, Vera; Stolze, Yvonne; Maus, Irena; Sczyrba, Alexander; Bremges, Andreas; Albaum, Stefan P; Jaenicke, Sebastian; Fracowiak, Jochen; Pühler, Alfred; Schlüter, Andreas

2016-08-10

To study the metaproteome of a biogas-producing microbial community, fermentation samples were taken from an agricultural biogas plant for microbial cell and protein extraction and corresponding metagenome analyses. Based on metagenome sequence data, taxonomic community profiling was performed to elucidate the composition of bacterial and archaeal sub-communities. The community's cytosolic metaproteome was represented in a 2D-PAGE approach. Metaproteome databases for protein identification were compiled based on the assembled metagenome sequence dataset for the biogas plant analyzed and non-corresponding biogas metagenomes. Protein identification results revealed that the corresponding biogas protein database facilitated the highest identification rate followed by other biogas-specific databases, whereas common public databases yielded insufficient identification rates. Proteins of the biogas microbiome identified as highly abundant were assigned to the pathways involved in methanogenesis, transport and carbon metabolism. Moreover, the integrated metagenome/-proteome approach enabled the examination of genetic-context information for genes encoding identified proteins by studying neighboring genes on the corresponding contig. Exemplarily, this approach led to the identification of a Methanoculleus sp. contig encoding 16 methanogenesis-related gene products, three of which were also detected as abundant proteins within the community's metaproteome. Thus, metagenome contigs provide additional information on the genetic environment of identified abundant proteins. Copyright © 2016 Elsevier B.V. All rights reserved.

Functional Path Analysis as a Multivariate Technique in Developing a Theory of Participation in Adult Education.

ERIC Educational Resources Information Center

Martin, James L.

This paper reports on attempts by the author to construct a theoretical framework of adult education participation using a theory development process and the corresponding multivariate statistical techniques. Two problems are identified: the lack of theoretical framework in studying problems, and the limiting of statistical analysis to univariate…

Proteomic analysis of the excretory/secretory products and antigenic proteins of Echinococcus granulosus adult worms from infected dogs.

PubMed

Wang, Ying; Xiao, Di; Shen, Yujuan; Han, Xiuming; Zhao, Fei; Li, Xiaohong; Wu, Weiping; Zhou, Hejun; Zhang, Jianzhong; Cao, Jianping

2015-05-21

Cystic echinococcosis, which is caused by Echinococcus granulosus, is one of the most widespread zoonotic helminth diseases that affects humans and livestock. Dogs, which harbor adult worms in their small intestines, are a pivotal source of E. granulosus infection in humans and domestic animals. Therefore, novel molecular approaches for the prevention and diagnosis of this parasite infection in dogs need to be developed. In this study, we performed proteomic analysis to identify excretory/secretory products (ES) and antigenic proteins of E. granulosus adult worms using two-dimensional electrophoresis, tandem matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF/TOF), and Western blotting of sera from infected dogs. This study identified 33 ES product spots corresponding to 9 different proteins and 21 antigenic protein spots corresponding to 13 different proteins. Six antigenic proteins were identified for the first time. The present study extended the existing proteomic data of E. granulosus and provides further information regarding host-parasite interactions and survival mechanisms. The results of this study contribute to vaccination and immunodiagnoses for E. granulosus infections.

A new transform for the analysis of complex fractionated atrial electrograms

PubMed Central

2011-01-01

Background Representation of independent biophysical sources using Fourier analysis can be inefficient because the basis is sinusoidal and general. When complex fractionated atrial electrograms (CFAE) are acquired during atrial fibrillation (AF), the electrogram morphology depends on the mix of distinct nonsinusoidal generators. Identification of these generators using efficient methods of representation and comparison would be useful for targeting catheter ablation sites to prevent arrhythmia reinduction. Method A data-driven basis and transform is described which utilizes the ensemble average of signal segments to identify and distinguish CFAE morphologic components and frequencies. Calculation of the dominant frequency (DF) of actual CFAE, and identification of simulated independent generator frequencies and morphologies embedded in CFAE, is done using a total of 216 recordings from 10 paroxysmal and 10 persistent AF patients. The transform is tested versus Fourier analysis to detect spectral components in the presence of phase noise and interference. Correspondence is shown between ensemble basis vectors of highest power and corresponding synthetic drivers embedded in CFAE. Results The ensemble basis is orthogonal, and efficient for representation of CFAE components as compared with Fourier analysis (p ≤ 0.002). When three synthetic drivers with additive phase noise and interference were decomposed, the top three peaks in the ensemble power spectrum corresponded to the driver frequencies more closely as compared with top Fourier power spectrum peaks (p ≤ 0.005). The synthesized drivers with phase noise and interference were extractable from their corresponding ensemble basis with a mean error of less than 10%. Conclusions The new transform is able to efficiently identify CFAE features using DF calculation and by discerning morphologic differences. Unlike the Fourier transform method, it does not distort CFAE signals prior to analysis, and is relatively robust to jitter in periodic events. Thus the ensemble method can provide a useful alternative for quantitative characterization of CFAE during clinical study. PMID:21569421

On-Line 1D and 2D PLOT/LC-ESI-MS Using 10 μm i.d. Poly(styrene–divinylbenzene) Porous Layer Open Tubular (PLOT) Columns For Ultrasensitive Proteomic Analysis

PubMed Central

Luo, Quanzhou; Yue, Guihua; Valaskovic, Gary A; Gu, Ye; Wu, Shiaw-Lin; Karger, Barry L.

2008-01-01

Following on our recent work, on-line one dimensional (1D) and two dimensional (2D) PLOT/LC-ESI-MS platforms using 3.2 m × 10 μm i.d. poly(styrenedivinylbenzene) (PS-DVB) porous layer open tubular (PLOT) columns have been developed to provide robust, high performance and ultrasensitive proteomic analysis. Using a PicoClear tee, the dead volume connection between a 50 μm i.d. PS-DVB monolithic microSPE column and the PLOT column was minimized. The microSPE/PLOT column assembly provided a separation performance similar to that obtained with direct injection onto the PLOT column at a mobile phase flow rate of 20 nL/min. The trace analysis potential of the platform was evaluated using an in-gel tryptic digest sample of a gel fraction (15 to 40 kDa) of a cervical cancer (SiHa) cell line. As an example of the sensitivity of the system, ∼2.5 ng of protein in 2 μL solution, an amount corresponding to 20 SiHa cells, was subjected to on-line microSPE-PLOT/LC-ESIMS/MS analysis using a linear ion trap MS. 237 peptides associated with 163 unique proteins were identified from a single analysis when using stringent criteria associated with a false positive rate less than 1% . The number of identified peptides and proteins increased to 638 and 343, respectively, as the injection amount was raised to ∼45 ng of protein, an amount corresponding to 350 SiHa cells. In comparison, only 338 peptides and 231 unique proteins were identified (false positive rate again less than 1%) from 750 ng of protein from the identical gel fraction, an amount corresponding to 6000 SiHa cells, using a typical 15 cm × 75 μm i.d. packed capillary column. The greater sensitivity, higher recovery, and higher resolving power of the PLOT column resulted in the increased number of identifications from only ∼5% of the injected sample amount. The resolving power of the microSPE/PLOT assembly was further extended by 2D chromatography via combination of the high-efficiency reversed phase PLOT column with strong cation exchange chromatography (SCX). As an example, 1071 peptides associated with 536 unique proteins were identified from 75 ng of protein from the same gel fraction, an amount corresponding to 600 cells, using 5 ion exchange fractions in online 2D SCX-PLOT/LC-MS. The 2D system, implemented in an automated format, led to simple and robust operation for proteomic analysis. These promising results demonstrate the potential of the PLOT column for ultratrace analysis. PMID:17625912

Software reliability: Application of a reliability model to requirements error analysis

NASA Technical Reports Server (NTRS)

Logan, J.

1980-01-01

The application of a software reliability model having a well defined correspondence of computer program properties to requirements error analysis is described. Requirements error categories which can be related to program structural elements are identified and their effect on program execution considered. The model is applied to a hypothetical B-5 requirement specification for a program module.

Identify the ability to purchase a house in the five major cities of Java for the Indonesian middle class using correspondence analysis

NASA Astrophysics Data System (ADS)

Ginanjar, Irlandia; Indratno, Sapto W.

2015-12-01

Ministry of Housing Republic of Indonesia explained that the Constitution mandates that every citizen has the right to reside. Jakarta, Surabaya, Bandung, Semarang, and Yogyakarta are five of Java's major cities with high population and investment opportunities, so the housing needs in that five cities is very high. Market sentiment analysis recorded the average of property purchasing power for Indonesian society around Rp 250 million, which the author assumes that the highest price for Indonesian middle class. Based on the fact, does the Indonesian middle class have the ability to purchase a house in the five major cities of Java? What facilities do they get? Both questions can be answered using the results of correspondence analysis.

Metabolomic determinants of metabolic risk in Mexican adolescents

PubMed Central

Perng, Wei; Hector, Emily C.; Song, Peter X.K.; Rojo, Martha Maria Tellez; Raskind, Sasha; Kachman, Maureen; Cantoral, Alejandra; Burant, Charles F.; Peterson, Karen E.

2017-01-01

Objective To identify metabolites associated with metabolic risk, separately by sex, in Mexican adolescents. Methods We carried out untargeted metabolomic profiling on fasting serum of 238 youth age 8–14 years, and identified metabolites associated with a metabolic syndrome risk z-score (MetRisk z-score), separately for boys and girls using the simulation and extrapolation (SIMEX) algorithm. We examined associations of each metabolite with MetRisk z-score using linear regression models that accounted for maternal education, child’s age, and pubertal status. Results Of the 938 features identified in metabolomics analysis, 7 named compounds (of 27 identified metabolites) were associated with MetRisk z-score in girls, and 3 named compounds (of 14 identified) were associated with MetRisk z-score in boys. In girls, diacylglycerol (DG) 16:0/16:0, 1,3-dielaidin, myo-inositol, and urate corresponded with higher MetRisk z-score, whereas N-acetylglycine, thymine, and dodecenedioic acid were associated with lower MetRisk z-score. For example, each z-score increment in DG 16:0/16:0 corresponded with 0.60 (0.47, 0.74). In boys, we found positive associations of DG 16:0/16:0, tyrosine, and 5′-methylthioadenosine with MetRisk z-score. Conclusions Metabolites on lipid, amino acid, and carbohydrate metabolism pathways are associated with metabolic risk in girls. Compounds on lipid and DNA pathways correspond with metabolic risk in boys. PMID:28758362

PDA survey of quality risk management practices in the pharmaceutical, devices, & biotechnology industries.

PubMed

Ahmed, Ruhi; Baseman, Harold; Ferreira, Jorge; Genova, Thomas; Harclerode, William; Hartman, Jeffery; Kim, Samuel; Londeree, Nanette; Long, Michael; Miele, William; Ramjit, Timothy; Raschiatore, Marlene; Tomonto, Charles

2008-01-01

In July 2006 the Parenteral Drug Association's Risk Management Task Force for Aseptic Processes, conducted an electronic survey of PDA members to determine current industry practices regarding implementation of Quality Risk Management in their organizations. This electronic survey was open and publicly available via the PDA website and targeted professionals in our industry who are involved in initiating, implementing, or reviewing risk management programs or decisions in their organizations. One hundred twenty-nine members participated and their demographics are presented in the sidebar "Correspondents Profile". Among the major findings are: *The "Aseptic Processing/Filling" operation is the functional area identified as having the greatest need for risk assessment and quality risk management. *The most widely used methodology in industry to identify risk is Failure Mode and Effects Analysis (FMEA). This tool was most widely applied in assessing change control and for adverse event, complaint, or failure investigations. *Despite the fact that personnel training was identified as the strategy most used for controlling/minimizing risk, the largest contributors to sterility failure in operations are still "Personnel". *Most companies still rely on "Manufacturing Controls" to mitigate risk and deemed the utilization of Process Analytical Technology (PAT) least important in this aspect. *A majority of correspondents verified that they did not periodically assess their risk management programs. *A majority of the correspondents desired to see case studies or examples of risk analysis implementation (as applicable to aseptic processing) in future PDA technical reports on risk management.

Determining the trophic guilds of fishes and macroinvertebrates in a seagrass food web

USGS Publications Warehouse

Luczkovich, J.J.; Ward, G.P.; Johnson, J.C.; Christian, R.R.; Baird, D.; Neckles, H.; Rizzo, W.M.

2002-01-01

We established trophic guilds of macroinvertebrate and fish taxa using correspondence analysis and a hierarchical clustering strategy for a seagrass food web in winter in the northeastern Gulf of Mexico. To create the diet matrix, we characterized the trophic linkages of macroinvertebrate and fish taxa present in Halodule wrightii seagrass habitat areas within the St. Marks National Wildlife Refuge (Florida) using binary data, combining dietary links obtained from relevant literature for macroinvertebrates with stomach analysis of common fishes collected during January and February of 1994. Heirarchical average-linkage cluster analysis of the 73 taxa of fishes and macroinvertebrates in the diet matrix yielded 14 clusters with diet similarity ??? 0.60. We then used correspondence analysis with three factors to jointly plot the coordinates of the consumers (identified by cluster membership) and of the 33 food sources. Correspondence analysis served as a visualization tool for assigning each taxon to one of eight trophic guilds: herbivores, detritivores, suspension feeders, omnivores, molluscivores, meiobenthos consumers, macrobenthos consumers, and piscivores. These trophic groups, cross-classified with major taxonomic groups, were further used to develop consumer compartments in a network analysis model of carbon flow in this seagrass ecosystem. The method presented here should greatly improve the development of future network models of food webs by providing an objective procedure for aggregating trophic groups.

Comprehensive Identification of Glycated Peptides and Their Glycation Motifs in Plasma and Erythrocytes of Control and Diabetic Subjects

PubMed Central

Zhang, Qibin; Monroe, Matthew E.; Schepmoes, Athena A.; Clauss, Therese R. W.; Gritsenko, Marina A.; Meng, Da; Petyuk, Vladislav A.; Smith, Richard D.; Metz, Thomas O.

2011-01-01

Non-enzymatic glycation of proteins sets the stage for formation of advanced glycation end-products and development of chronic complications of diabetes. In this report, we extended our previous methods on proteomics analysis of glycated proteins to comprehensively identify glycated proteins in control and diabetic human plasma and erythrocytes. Using immunodepletion, enrichment, and fractionation strategies, we identified 7749 unique glycated peptides, corresponding to 3742 unique glycated proteins. Semi-quantitative comparisons showed that glycation levels of a number of proteins were significantly increased in diabetes and that erythrocyte proteins were more extensively glycated than plasma proteins. A glycation motif analysis revealed that some amino acids were favored more than others in the protein primary structures in the vicinity of the glycation sites in both sample types. The glycated peptides and corresponding proteins reported here provide a foundation for potential identification of novel markers for diabetes, hyperglycemia, and diabetic complications in future studies. PMID:21612289

Perceived Challenges in Primary Literature in a Master’s Class: Effects of Experience and Instruction

PubMed Central

Lie, Richard; Abdullah, Christopher; He, Wenliang; Tour, Ella

2016-01-01

Primary literature offers rich opportunities to teach students how to “think like a scientist,” but the challenges students face when they attempt to read research articles are not well understood. Here, we present an analysis of what master’s students perceive as the most challenging aspects of engaging with primary literature. We examined 69 pairs of pre- and postcourse responses from students enrolled in a master’s-level course that offered a structured analysis of primary literature. On the basis of these responses, we identified six categories of challenges. Before instruction, “techniques” and “experimental data” were the most frequently identified categories of challenges. The majority of difficulties students perceived in the primary literature corresponded to Bloom’s lower-order cognitive skills. After instruction, “conclusions” were identified as the most difficult aspect of primary literature, and the frequency of challenges that corresponded to higher-order cognitive skills increased significantly among students who reported less experience with primary literature. These changes are consistent with a more competent perception of the primary literature, in which these students increasingly focus on challenges requiring critical thinking. Students’ difficulties identified here can inform the design of instructional approaches aimed to teach students how to critically read scientific papers. PMID:27909027

Temperature analysis with voltage-current time differential operation of electrochemical sensors

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

Woo, Leta Yar-Li; Glass, Robert Scott; Fitzpatrick, Joseph Jay

A method for temperature analysis of a gas stream. The method includes identifying a temperature parameter of an affected waveform signal. The method also includes calculating a change in the temperature parameter by comparing the affected waveform signal with an original waveform signal. The method also includes generating a value from the calculated change which corresponds to the temperature of the gas stream.

Mass Balance Analysis of Contaminated Heparin Product

PubMed Central

Liu, Zhenling; Xiao, Zhongping; Masuko, Sayaka; Zhao, Wenjing; Sterner, Eric; Bansal, Vinod; Fareed, Jawed; Dordick, Jonathan; Zhang, Fuming; Linhardt, Robert J.

2011-01-01

A quantitative analysis of a recalled contaminated lot of heparin (HP) sodium injection United States Pharmacopeial (USP) was undertaken in response to the controversy regarding the exact nature of the contaminant involved in the HP crisis. A mass balance analysis of the formulated drug product was performed. After freeze-drying, a 1 ml vial for injection afforded 54.8 ± 0.3 mg of dry solids. The excipients, sodium chloride and residual benzyl alcohol, accounted for 11.4 ± 0.5 mg and 0.9 ± 0.5 mg, respectively. Active pharmaceutical ingredient (API) represented 41.5 ± 1.0 mg, corresponding to 75.7 wt% of dry mass. Exhaustive treatment of API with specific enzymes, heparin lyases and/or chondroitin lyases was used to close mass balance. HP represented 30.5 ± 0.5 mg, corresponding to 73.5 wt% of the API. Dermatan sulfate (DS) impurity represented 1.7 ± 0.3 mg, corresponding to 4.1 wt% of the API. Contaminant, 9.3 ± 0.1 mg corresponding to 22.4 wt% of API, was found in the contaminated formulated drug product. The recovery of contaminant was close to quantitative (95.6-100 wt%). A single contaminant was unambiguously identified as oversulfated chondroitin sulfate (OSCS). PMID:20850409

Above Saddle-Point Regions of Order in a Sea of Chaos in the Vibrational Dynamics of KCN.

PubMed

Párraga, H; Arranz, F J; Benito, R M; Borondo, F

2018-04-05

The dynamical characteristics of a region of regular vibrational motion in the sea of chaos above the saddle point corresponding to the linear C-N-K configuration is examined in detail. To explain the origin of this regularity, the associated phase space structures were characterized using suitably defined Poincaré surfaces of section, identifying the different resonances between the stretching and bending modes, as a function of excitation energy. The corresponding topology is elucidated by means of periodic orbit analysis.

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

Rohrbaugh, Wayne Joseph

Results are reported from an investigation of correlations between molecular structural parameters of selected organophosphorus insecticides and their corresponding toxic effectiveness. The crystal and molecular structures of azinphos-methyl, emidithion, and tetrachlorvinphos were determined via three-dimensional x-ray analysis. Acetylcholinesterase (AChE) in nerve cells was identified as the target for organophosphorus insecticides.

Identification of atmospheric organic sources using the carbon hollow tube-gas chromatography method and factor analysis

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

Cobb, G.P.; Braman, R.S.; Gilbert, R.A.

Atmospheric organics were sampled and analyzed by using the carbon hollow tube-gas chromatography method. Chromatograms from spice mixtures, cigarettes, and ambient air were analyzed. Principal factor analysis of row order chromatographic data produces factors which are eigenchromatograms of the components in the samples. Component sources are identified from the eigenchromatograms in all experiments and the individual eigenchromatogram corresponding to a particular source is determined in most cases. Organic sources in ambient air and in cigaretts are identified with 87% certainty. Analysis of clove cigarettes allows the determination of the relative amount of clove in different cigarettes. A new nondestructive qualitymore » control method using the hollow tube-gas chromatography analysis is discussed.« less

Analysis of stability and bifurcations of fixed points and periodic solutions of a lumped model of neocortex with two delays

PubMed Central

2012-01-01

A lumped model of neural activity in neocortex is studied to identify regions of multi-stability of both steady states and periodic solutions. Presence of both steady states and periodic solutions is considered to correspond with epileptogenesis. The model, which consists of two delay differential equations with two fixed time lags is mainly studied for its dependency on varying connection strength between populations. Equilibria are identified, and using linear stability analysis, all transitions are determined under which both trivial and non-trivial fixed points lose stability. Periodic solutions arising at some of these bifurcations are numerically studied with a two-parameter bifurcation analysis. PMID:22655859

Serial analysis of gene expression identifies connective tissue growth factor expression as a prognostic biomarker in gallbladder cancer.

PubMed

Alvarez, Hector; Corvalan, Alejandro; Roa, Juan C; Argani, Pedram; Murillo, Francisco; Edwards, Jennifer; Beaty, Robert; Feldmann, Georg; Hong, Seung-Mo; Mullendore, Michael; Roa, Ivan; Ibañez, Luis; Pimentel, Fernando; Diaz, Alfonso; Riggins, Gregory J; Maitra, Anirban

2008-05-01

Gallbladder cancer (GBC) is an uncommon neoplasm in the United States, but one with high mortality rates. This malignancy remains largely understudied at the molecular level such that few targeted therapies or predictive biomarkers exist. We built the first series of serial analysis of gene expression (SAGE) libraries from GBC and nonneoplastic gallbladder mucosa, composed of 21-bp long-SAGE tags. SAGE libraries were generated from three stage-matched GBC patients (representing Hispanic/Latino, Native American, and Caucasian ethnicities, respectively) and one histologically alithiasic gallbladder. Real-time quantitative PCR was done on microdissected epithelium from five matched GBC and corresponding nonneoplastic gallbladder mucosa. Immunohistochemical analysis was done on a panel of 182 archival GBC in high-throughput tissue microarray format. SAGE tags corresponding to connective tissue growth factor (CTGF) transcripts were identified as differentially overexpressed in all pairwise comparisons of GBC (P < 0.001). Real-time quantitative PCR confirmed significant overexpression of CTGF transcripts in microdissected primary GBC (P < 0.05), but not in metastatic GBC, compared with nonneoplastic gallbladder epithelium. By immunohistochemistry, 66 of 182 (36%) GBC had high CTGF antigen labeling, which was significantly associated with better survival on univariate analysis (P = 0.0069, log-rank test). An unbiased analysis of the GBC transcriptome by SAGE has identified CTGF expression as a predictive biomarker of favorable prognosis in this malignancy. The SAGE libraries from GBC and nonneoplastic gallbladder mucosa are publicly available at the Cancer Genome Anatomy Project web site and should facilitate much needed research into this lethal neoplasm.

Analysis of University Management of Emerging Technologies and Recommendations for Developing Countries

ERIC Educational Resources Information Center

Villa Enciso, Eliana María; Picón Jácome, Edgar; Valencia-Arias, Alejandro; Jiménez Hernández, Claudia Nelcy

2017-01-01

University management seeks to achieve the objectives established by higher education's institutions, including their third mission, which corresponds to the transfer of research results into the industry; in this regard, emerging technologies play an important role to solve problems identified in the industry. Emerging technologies are those…

ARCHITECTURAL PROGRAMMING--STATE OF THE ART.

ERIC Educational Resources Information Center

EVANS, BENJAMIN H.

IN RESPONSE TO A NEED FOR A MORE THOROUGH AND RIGOROUS STUDY AND ANALYSIS PROCESS IN ENVIRONMENTAL FUNCTIONS PRIOR TO THE DESIGN OF NEW BUILDINGS, A STUDY WAS UNDERTAKEN TO IDENTIFY THE EMERGING TECHNIQUES OF ARCHITECTURAL PROGRAMING PRACTICE. THE STUDY INCLUDED CORRESPONDENCE AND REVIEW OF PERIODICALS, QUESTIONNAIRES AND VISITATIONS, AND A…

The Use of Multiple Correspondence Analysis to Explore Associations between Categories of Qualitative Variables in Healthy Ageing.

PubMed

Costa, Patrício Soares; Santos, Nadine Correia; Cunha, Pedro; Cotter, Jorge; Sousa, Nuno

2013-01-01

The main focus of this study was to illustrate the applicability of multiple correspondence analysis (MCA) in detecting and representing underlying structures in large datasets used to investigate cognitive ageing. Principal component analysis (PCA) was used to obtain main cognitive dimensions, and MCA was used to detect and explore relationships between cognitive, clinical, physical, and lifestyle variables. Two PCA dimensions were identified (general cognition/executive function and memory), and two MCA dimensions were retained. Poorer cognitive performance was associated with older age, less school years, unhealthier lifestyle indicators, and presence of pathology. The first MCA dimension indicated the clustering of general/executive function and lifestyle indicators and education, while the second association was between memory and clinical parameters and age. The clustering analysis with object scores method was used to identify groups sharing similar characteristics. The weaker cognitive clusters in terms of memory and executive function comprised individuals with characteristics contributing to a higher MCA dimensional mean score (age, less education, and presence of indicators of unhealthier lifestyle habits and/or clinical pathologies). MCA provided a powerful tool to explore complex ageing data, covering multiple and diverse variables, showing if a relationship exists and how variables are related, and offering statistical results that can be seen both analytically and visually.

Multiple loci and genetic interactions involving flowering time genes regulate stem branching among natural variants of Arabidopsis.

PubMed

Huang, Xueqing; Ding, Jia; Effgen, Sigi; Turck, Franziska; Koornneef, Maarten

2013-08-01

Shoot branching is a major determinant of plant architecture. Genetic variants for reduced stem branching in the axils of cauline leaves of Arabidopsis were found in some natural accessions and also at low frequency in the progeny of multiparent crosses. Detailed genetic analysis using segregating populations derived from backcrosses with the parental lines and bulked segregant analysis was used to identify the allelic variation controlling reduced stem branching. Eight quantitative trait loci (QTLs) contributing to natural variation for reduced stem branching were identified (REDUCED STEM BRANCHING 1-8 (RSB1-8)). Genetic analysis showed that RSB6 and RSB7, corresponding to flowering time genes FLOWERING LOCUS C (FLC) and FRIGIDA (FRI), epistatically regulate stem branching. Furthermore, FLOWERING LOCUS T (FT), which corresponds to RSB8 as demonstrated by fine-mapping, transgenic complementation and expression analysis, caused pleiotropic effects not only on flowering time, but, in the specific background of active FRI and FLC alleles, also on the RSB trait. The consequence of allelic variation only expressed in late-flowering genotypes revealed novel and thus far unsuspected roles of several genes well characterized for their roles in flowering time control. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

Determining the trophic guilds of fishes and macroinvertebrates in a seagrass food web

USGS Publications Warehouse

Luczkovich, J.J.; Ward, G.P.; Johnson, J.C.; Christian, R.R.; Baird, D.; Neckles, H.; Rizzo, W.M.

2002-01-01

We established trophic guilds of macroinvertebrate and fish taxa using correspondence analysis and a hierarchical clustering strategy for a seagrass food web in winter in the northeastern Gulf of Mexico. To create the diet matrix, we characterized the trophic linkages of macroinvertebrate and fish taxa. present in Hatodule wrightii seagrass habitat areas within the St. Marks National Wildlife Refuge (Florida) using binary data, combining dietary links obtained from relevant literature for macroinvertebrates with stomach analysis of common fishes collected during January and February of 1994. Heirarchical average-linkage cluster analysis of the 73 taxa of fishes and macroinvertebrates in the diet matrix yielded 14 clusters with diet similarity greater than or equal to 0.60. We then used correspondence analysis with three factors to jointly plot the coordinates of the consumers (identified by cluster membership) and of the 33 food sources. Correspondence analysis served as a visualization tool for assigning each taxon to one of eight trophic guilds: herbivores, detritivores, suspension feeders, omnivores, molluscivores, meiobenthos consumers, macrobenthos consumers, and piscivores. These trophic groups, cross-classified with major taxonomic groups, were further used to develop consumer compartments in a network analysis model of carbon flow in this seagrass ecosystem. The method presented here should greatly improve the development of future network models of food webs by providing an objective procedure for aggregating trophic groups.

A scene-analysis approach to remote sensing. [San Francisco, California

NASA Technical Reports Server (NTRS)

Tenenbaum, J. M. (Principal Investigator); Fischler, M. A.; Wolf, H. C.

1978-01-01

The author has identified the following significant results. Geometric correspondance between a sensed image and a symbolic map is established in an initial stage of processing by adjusting parameters of a sensed model so that the image features predicted from the map optimally match corresponding features extracted from the sensed image. Information in the map is then used to constrain where to look in an image, what to look for, and how to interpret what is seen. For simple monitoring tasks involving multispectral classification, these constraints significantly reduce computation, simplify interpretation, and improve the utility of the resulting information. Previously intractable tasks requiring spatial and textural analysis may become straightforward in the context established by the map knowledge. The use of map-guided image analysis in monitoring the volume of water in a reservoir, the number of boxcars in a railyard, and the number of ships in a harbor is demonstrated.

Utility of correlation techniques in gravity and magnetic interpretation

NASA Technical Reports Server (NTRS)

Chandler, V. W.; Koski, J. S.; Braice, L. W.; Hinze, W. J.

1977-01-01

Internal correspondence uses Poisson's Theorem in a moving-window linear regression analysis between the anomalous first vertical derivative of gravity and total magnetic field reduced to the pole. The regression parameters provide critical information on source characteristics. The correlation coefficient indicates the strength of the relation between magnetics and gravity. Slope value gives delta j/delta sigma estimates of the anomalous source. The intercept furnishes information on anomaly interference. Cluster analysis consists of the classification of subsets of data into groups of similarity based on correlation of selected characteristics of the anomalies. Model studies are used to illustrate implementation and interpretation procedures of these methods, particularly internal correspondence. Analysis of the results of applying these methods to data from the midcontinent and a transcontinental profile shows they can be useful in identifying crustal provinces, providing information on horizontal and vertical variations of physical properties over province size zones, validating long wavelength anomalies, and isolating geomagnetic field removal problems.

Plasma Glycoproteomics Reveals Sepsis Outcomes Linked to Distinct Proteins in Common Pathways

PubMed Central

DeLeon-Pennell, Kristine Y.; Nguyen, Nguyen T.; de Castro Brás, Lisandra E.; Flynn, Elizabeth R.; Cannon, Presley L.; Griswold, Michael E.; Jin, Yu-Fang; Puskarich, Michael A.; Jones, Alan E.; Lindsey, Merry L.

2015-01-01

Objective Sepsis remains a predominant cause of mortality in the ICU, yet strategies to increase survival have proved largely unsuccessful. This study aimed to identify proteins linked to sepsis outcomes using a glycoproteomic approach to target extracellular proteins that trigger downstream pathways and direct patient outcomes. Design Plasma was obtained from the LacTATEs cohort. N-linked plasma glycopeptides were quantified by solid-phase extraction coupled with mass spectrometry. Glycopeptides were assigned to proteins using RefSeq and visualized in a heat map. Protein differences were validated by immunoblotting, and proteins were mapped for biological processes using Database for Annotation, Visualization and Integrated Discovery and for functional pathways using Kyoto Encyclopedia of Genes and Genomes databases. Setting Hospitalized care. Measurements and Main Results A total of 501 glycopeptides corresponding to 234 proteins were identified. Of these, 66 glycopeptides were unique to the survivor group and corresponded to 54 proteins, 60 were unique to the nonsurvivor group and corresponded to 43 proteins, and 375 were common responses between groups and corresponded to 137 proteins. Immunoblotting showed that nonsurvivors had increased total kininogen; decreased total cathepsin-L1, vascular cell adhesion molecule, periostin, and neutrophil gelatinase–associated lipocalin; and a two-fold decrease in glycosylated clusterin (all p < 0.05). Kyoto Encyclopedia of Genes and Genomes analysis identified six enriched pathways. Interestingly, survivors relied on the extrinsic pathway of the complement and coagulation cascade, whereas nonsurvivors relied on the intrinsic pathway. Conclusion This study identifies proteins linked to patient outcomes and provides insight into unexplored mechanisms that can be investigated for the identification of novel therapeutic targets. (Crit Care Med 2015; XX:00–00) PMID:26086942

Synthesis, structural, thermal and Hirshfeld surface analysis of novel [1,2,4]triazolo[3,4-b][1,3,4] thiadiazine carrying 1,4-benzothiazine-3-one moiety

NASA Astrophysics Data System (ADS)

Shruthi, C.; Ravindrachary, V.; Guruswamy, B.; Lokanath, N. K.; Kumara, Karthik; Goveas, Janet

2018-05-01

Needle shaped single crystal of the title compound was grown by slow evaporation solution growth technique using ethanol as solvent. The grown single crystal was characterized using FT-IR, Single crystal XRD and Thermal analysis. The FT-IR spectrum confirms the molecular structure and identifies the different functional groups present in the compound. Single crystal XRD study reveals that the crystallized compound belongs to the monoclinic crystal system with P21/c space group and the corresponding cell parameters were identified. The thermal stability of the material was determined using both TGA and DTA analysis. The intermolecular interaction of each individual atom in the crystal lattice was estimated using Hirshfeld surface and finger print analysis.

Deregulation of HIF1-alpha and hypoxia-regulated pathways in hepatocellular carcinoma and corresponding non-malignant liver tissue--influence of a modulated host stroma on the prognosis of HCC.

PubMed

Simon, Frank; Bockhorn, Maximilian; Praha, Christian; Baba, Hideo A; Broelsch, Christoph E; Frilling, Andrea; Weber, Frank

2010-04-01

The aim of this study was to elucidate the role of HIF1A expression in hepatocellular carcinoma (HCC) and the corresponding non-malignant liver tissue and to correlate it with the clinical outcome of HCC patients after curative liver resection. HIF1A expression was determined by quantitative RT-PCR in HCC and corresponding non-malignant liver tissue of 53 patients surgically treated for HCC. High-density gene expression analysis and pathway analysis was performed on a selected subset of patients with high and low HIF1A expression in the non-malignant liver tissue. HIF1A over-expression in the apparently non-malignant liver tissue was a predictor of tumor recurrence and survival. The estimated 1-year and 5-year disease-free survival was significantly better in patients with low HIF1A expression in the non-malignant liver tissue when compared to those patients with high HIF1 expression (88.9% vs. 67.9% and 61.0% vs. 22.6%, respectively, p = 0.008). Based on molecular pathway analysis utilizing high-density gene-expression profiling, HIF1A related molecular networks were identified that contained genes involved in cell migration, cell homing, and cell-cell interaction. Our study identified a potential novel mechanism contributing to prognosis of HCC. The deregulation of HIF1A and its related pathways in the apparently non-malignant liver tissue provides for a modulated environment that potentially enhances or allows for HCC recurrence after curative resection.

Development and characterization of mouse monoclonal antibodies reactive with chicken IL-1ß

USDA-ARS?s Scientific Manuscript database

Two mouse monoclonal antibodies (mAbs) specific for chicken interleukin-1ß (chIL-1ß) were produced and characterized. Both mAbs identified a 66.0 kDa recombinant protein expressed in Escherichia coli by Western blot analysis that corresponded to the expected molecular weight of a recombinant fusion ...

Factor Structure of the Children's Behavior Questionnaire in Children with Williams Syndrome

ERIC Educational Resources Information Center

Leyfer, Ovsanna; John, Angela E.; Woodruff-Borden, Janet; Mervis, Carolyn B.

2012-01-01

To examine the factor structure of temperament in 5-10-year-olds with Williams syndrome, an exploratory factor analysis was conducted on the responses of parents of 192 children on the children's behavior questionnaire. Four factors were identified. Two corresponded to factors reported for typically developing children: effortful control and…

Development and characterization of mouse monoclonal antibodies reactive with chicken IL1 Beta

USDA-ARS?s Scientific Manuscript database

Two mouse monoclonal antibodies (mAbs) specific for chicken interleukin-1 Beta (chIL-1 Beta) were produced and characterized. Both mAbs identified a 66.0 kDa recombinant protein expressed in Escherichia coli by Western blot analysis that corresponded to the expected molecular weight of a recombinant...

Molecular Typing of Australian Scedosporium Isolates Showing Genetic Variability and Numerous S. aurantiacum

PubMed Central

Delhaes, Laurence; Harun, Azian; Chen, Sharon C.A.; Nguyen, Quoc; Slavin, Monica; Heath, Christopher H.; Maszewska, Krystyna; Halliday, Catriona; Robert, Vincent; Sorrell, Tania C.

2008-01-01

One hundred clinical isolates from a prospective nationwide study of scedosporiosis in Australia (2003–2005) and 46 additional isolates were genotyped by internal transcribed spacer–restriction fragment length polymorphism (ITS-RFLP) analysis, ITS sequencing, and M13 PCR fingerprinting. ITS-RFLP and PCR fingerprinting identified 3 distinct genetic groups. The first group corresponded to Scedosporium prolificans (n = 83), and the other 2 comprised isolates previously identified as S. apiospermum: one of these corresponded to S. apiospermum (n = 33) and the other to the newly described species S. aurantiacum (n = 30). Intraspecies variation was highest for S. apiospermum (58%), followed by S. prolificans (45%) and S. aurantiacum (28%) as determined by PCR fingerprinting. ITS sequence variation of 2.2% was observed among S. apiospermum isolates. No correlation was found between genotype of strains and their geographic origin, body site from which they were cultured, or colonization versus invasive disease. Twelve S. prolificans isolates from 2 suspected case clusters were examined by amplified fragment length polymorphism analysis. No specific clusters were confirmed. PMID:18258122

Probabilistic characterization of sleep architecture: home based study on healthy volunteers.

PubMed

Garcia-Molina, Gary; Vissapragada, Sreeram; Mahadevan, Anandi; Goodpaster, Robert; Riedner, Brady; Bellesi, Michele; Tononi, Giulio

2016-08-01

The quantification of sleep architecture has high clinical value for diagnostic purposes. While the clinical standard to assess sleep architecture is in-lab based polysomnography, higher ecological validity can be obtained with multiple sleep recordings at home. In this paper, we use a dataset composed of fifty sleep EEG recordings at home (10 per study participant for five participants) to analyze the sleep stage transition dynamics using Markov chain based modeling. The statistical analysis of the duration of continuous sleep stage bouts is also analyzed to identify the speed of transition between sleep stages. This analysis identified two types of NREM states characterized by fast and slow exit rates which from the EEG analysis appear to correspond to shallow and deep sleep respectively.

Big Bang Bifurcation Analysis and Allee Effect in Generic Growth Functions

NASA Astrophysics Data System (ADS)

Leonel Rocha, J.; Taha, Abdel-Kaddous; Fournier-Prunaret, D.

2016-06-01

The main purpose of this work is to study the dynamics and bifurcation properties of generic growth functions, which are defined by the population size functions of the generic growth equation. This family of unimodal maps naturally incorporates a principal focus of ecological and biological research: the Allee effect. The analysis of this kind of extinction phenomenon allows to identify a class of Allee’s functions and characterize the corresponding Allee’s effect region and Allee’s bifurcation curve. The bifurcation analysis is founded on the performance of fold and flip bifurcations. The dynamical behavior is rich with abundant complex bifurcation structures, the big bang bifurcations of the so-called “box-within-a-box” fractal type being the most outstanding. Moreover, these bifurcation cascades converge to different big bang bifurcation curves with distinct kinds of boxes, where for the corresponding parameter values several attractors are associated. To the best of our knowledge, these results represent an original contribution to clarify the big bang bifurcation analysis of continuous 1D maps.

Analysis of waterborne paints by gas chromatography-mass spectrometry with a temperature-programmable pyrolyzer.

PubMed

Nakamura, S; Takino, M; Daishima, S

2001-04-06

Gas chromatography-mass spectrometry (GC-MS) with a temperature-programmable pyrolyzer was used for the analysis of waterborne paints. Evolved gas analysis (EGA) profiles of the waterborne paints were obtained by this temperature-programmed pyrolysis directly coupled with MS via a deactivated metal capillary tube. The EGA profile suggested the optimal thermal desorption conditions for solvents and additives and the subsequent optimal pyrolysis temperature for the remaining polymeric material. Polymers were identified from pyrograms with the assistance of a new polymer library. The solvents were identified from the electron ionization mass spectra with the corresponding chemical ionization mass spectra. The additive was identified as zinc pyrithione by comparison with authentic standard. Zinc pyrithione cannot be analyzed by GC-MS as it is. However, the thermal decomposition products of zinc pyrithione could be detected. The information on the decomposition temperature and products was useful for the identification of the original compound.

Area estimation using multiyear designs and partial crop identification

NASA Technical Reports Server (NTRS)

Sielken, R. L., Jr.

1984-01-01

Statistical procedures were developed for large area assessments using both satellite and conventional data. Crop acreages, other ground cover indices, and measures of change were the principal characteristics of interest. These characteristics are capable of being estimated from samples collected possibly from several sources at varying times, with different levels of identification. Multiyear analysis techniques were extended to include partially identified samples; the best current year sampling design corresponding to a given sampling history was determined; weights reflecting the precision or confidence in each observation were identified and utilized, and the variation in estimates incorporating partially identified samples were quantified.

Individual Differences in Dynamic Functional Brain Connectivity across the Human Lifespan.

PubMed

Davison, Elizabeth N; Turner, Benjamin O; Schlesinger, Kimberly J; Miller, Michael B; Grafton, Scott T; Bassett, Danielle S; Carlson, Jean M

2016-11-01

Individual differences in brain functional networks may be related to complex personal identifiers, including health, age, and ability. Dynamic network theory has been used to identify properties of dynamic brain function from fMRI data, but the majority of analyses and findings remain at the level of the group. Here, we apply hypergraph analysis, a method from dynamic network theory, to quantify individual differences in brain functional dynamics. Using a summary metric derived from the hypergraph formalism-hypergraph cardinality-we investigate individual variations in two separate, complementary data sets. The first data set ("multi-task") consists of 77 individuals engaging in four consecutive cognitive tasks. We observe that hypergraph cardinality exhibits variation across individuals while remaining consistent within individuals between tasks; moreover, the analysis of one of the memory tasks revealed a marginally significant correspondence between hypergraph cardinality and age. This finding motivated a similar analysis of the second data set ("age-memory"), in which 95 individuals, aged 18-75, performed a memory task with a similar structure to the multi-task memory task. With the increased age range in the age-memory data set, the correlation between hypergraph cardinality and age correspondence becomes significant. We discuss these results in the context of the well-known finding linking age with network structure, and suggest that hypergraph analysis should serve as a useful tool in furthering our understanding of the dynamic network structure of the brain.

Floral Biosynthesis of Mn3O4 and Fe2O3 Nanoparticles Using Chaenomeles sp. Flower Extracts for Efficient Medicinal Applications

NASA Astrophysics Data System (ADS)

Karunakaran, Gopalu; Jagathambal, Matheswaran; Kolesnikov, Evgeny; Dmitry, Arkhipov; Ishteev, Artur; Gusev, Alexander; Kuznetsov, Denis

2017-08-01

Manganese oxide (Mn3O4) and iron oxide (Fe2O3) nanoparticles were successfully synthesized with the flower extracts of Chaenomeles sp. This is the first ever approach to synthesize nanoparticles from Chaenomeles sp. flower extracts. The organic molecules present in the flower extracts actively converted the nitrate precursor into its corresponding nanoparticles. The organic molecules that are involved in the synthesis of nanoparticles are identified using different phytochemical and gas chromatography-mass spectrometry analyses. The identified components are glycosides, alkaloids, terpenoids, saponins, flavonoids, quinines, and steroids. The structural and chemical compositions of the synthesized powder were also analyzed. The x-ray powder diffraction analysis revealed that the particles show tetragonal and rhombohedral crystalline phases. The Fourier transform infrared spectroscopy analysis showed the functional groups that are involved in the reduction of nitrates into the corresponding nanoparticles. Energy-dispersive x-ray spectroscopy analysis confirmed the presence of the elements in the synthesized nanoparticles. Transmission electron microscopy images showed the formation of spherical nanoparticles with an average size of 30-100 nm. Antioxidant analysis showed that the synthesized nanoparticles had excellent antioxidant potential. The antibacterial study showed that they inhibit the growth of harmful bacteria such as Pseudomonas aeruginosa and Streptococcus pyogenes. Thus, this study proposes a new eco-friendly and nontoxic method to synthesize nanoparticles for medicinal applications.

Quantitative Phosphoproteomic Analysis Provides Insight into the Response to Short-Term Drought Stress in Ammopiptanthus mongolicus Roots.

PubMed

Sun, Huigai; Xia, Bolin; Wang, Xue; Gao, Fei; Zhou, Yijun

2017-10-17

Drought is one of the major abiotic stresses that negatively affects plant growth and development. Ammopiptanthus mongolicus is an ecologically important shrub in the mid-Asia desert region and used as a model for abiotic tolerance research in trees. Protein phosphorylation participates in the regulation of various biological processes, however, phosphorylation events associated with drought stress signaling and response in plants is still limited. Here, we conducted a quantitative phosphoproteomic analysis of the response of A. mongolicus roots to short-term drought stress. Data are available via the iProx database with project ID IPX0000971000. In total, 7841 phosphorylation sites were found from the 2019 identified phosphopeptides, corresponding to 1060 phosphoproteins. Drought stress results in significant changes in the abundance of 103 phosphopeptides, corresponding to 90 differentially-phosphorylated phosphoproteins (DPPs). Motif-x analysis identified two motifs, including [pSP] and [RXXpS], from these DPPs. Functional enrichment and protein-protein interaction analysis showed that the DPPs were mainly involved in signal transduction and transcriptional regulation, osmotic adjustment, stress response and defense, RNA splicing and transport, protein synthesis, folding and degradation, and epigenetic regulation. These drought-corresponsive phosphoproteins, and the related signaling and metabolic pathways probably play important roles in drought stress signaling and response in A. mongolicus roots. Our results provide new information for understanding the molecular mechanism of the abiotic stress response in plants at the posttranslational level.

Relationships between protein-encoding gene abundance and corresponding process are commonly assumed yet rarely observed

USGS Publications Warehouse

Rocca, Jennifer D.; Hall, Edward K.; Lennon, Jay T.; Evans, Sarah E.; Waldrop, Mark P.; Cotner, James B.; Nemergut, Diana R.; Graham, Emily B.; Wallenstein, Matthew D.

2015-01-01

For any enzyme-catalyzed reaction to occur, the corresponding protein-encoding genes and transcripts are necessary prerequisites. Thus, a positive relationship between the abundance of gene or transcripts and corresponding process rates is often assumed. To test this assumption, we conducted a meta-analysis of the relationships between gene and/or transcript abundances and corresponding process rates. We identified 415 studies that quantified the abundance of genes or transcripts for enzymes involved in carbon or nitrogen cycling. However, in only 59 of these manuscripts did the authors report both gene or transcript abundance and rates of the appropriate process. We found that within studies there was a significant but weak positive relationship between gene abundance and the corresponding process. Correlations were not strengthened by accounting for habitat type, differences among genes or reaction products versus reactants, suggesting that other ecological and methodological factors may affect the strength of this relationship. Our findings highlight the need for fundamental research on the factors that control transcription, translation and enzyme function in natural systems to better link genomic and transcriptomic data to ecosystem processes.

Relationship between body fat and BMI in a U.S. Hispanic population-based cohort study: Results from HCHS/SOL

USDA-ARS?s Scientific Manuscript database

To evaluate the percentage of body fat (%BF)-BMI relationship, identify %BF levels corresponding to adult BMI cut points, and examine %BF-BMI agreement in a diverse Hispanic/Latino population. %BF by bioelectrical impedance analysis was corrected against %BF by 18O dilution in 434 participants of th...

Using Geographical Information Systems (GIS) to Identify the Geographic Regions Where People That Use Ground Water are Most Vulnerable to Impacts from Underground Storage

EPA Science Inventory

Using Geographic Information Systems (GIS), the vulnerability of ground water supplies to contamination from underground storage tanks (USTs) was assessed. The analysis was conducted for the 48 contiguous states, and then again for groups of states corresponding to the EPA Regio...

Correlative feature analysis of FFDM images

NASA Astrophysics Data System (ADS)

Yuan, Yading; Giger, Maryellen L.; Li, Hui; Sennett, Charlene

2008-03-01

Identifying the corresponding image pair of a lesion is an essential step for combining information from different views of the lesion to improve the diagnostic ability of both radiologists and CAD systems. Because of the non-rigidity of the breasts and the 2D projective property of mammograms, this task is not trivial. In this study, we present a computerized framework that differentiates the corresponding images from different views of a lesion from non-corresponding ones. A dual-stage segmentation method, which employs an initial radial gradient index(RGI) based segmentation and an active contour model, was initially applied to extract mass lesions from the surrounding tissues. Then various lesion features were automatically extracted from each of the two views of each lesion to quantify the characteristics of margin, shape, size, texture and context of the lesion, as well as its distance to nipple. We employed a two-step method to select an effective subset of features, and combined it with a BANN to obtain a discriminant score, which yielded an estimate of the probability that the two images are of the same physical lesion. ROC analysis was used to evaluate the performance of the individual features and the selected feature subset in the task of distinguishing between corresponding and non-corresponding pairs. By using a FFDM database with 124 corresponding image pairs and 35 non-corresponding pairs, the distance feature yielded an AUC (area under the ROC curve) of 0.8 with leave-one-out evaluation by lesion, and the feature subset, which includes distance feature, lesion size and lesion contrast, yielded an AUC of 0.86. The improvement by using multiple features was statistically significant as compared to single feature performance. (p<0.001)

Surface shape analysis with an application to brain surface asymmetry in schizophrenia.

PubMed

Brignell, Christopher J; Dryden, Ian L; Gattone, S Antonio; Park, Bert; Leask, Stuart; Browne, William J; Flynn, Sean

2010-10-01

Some methods for the statistical analysis of surface shapes and asymmetry are introduced. We focus on a case study where magnetic resonance images of the brain are available from groups of 30 schizophrenia patients and 38 controls, and we investigate large-scale brain surface shape differences. Key aspects of shape analysis are to remove nuisance transformations by registration and to identify which parts of one object correspond with the parts of another object. We introduce maximum likelihood and Bayesian methods for registering brain images and providing large-scale correspondences of the brain surfaces. Brain surface size-and-shape analysis is considered using random field theory, and also dimension reduction is carried out using principal and independent components analysis. Some small but significant differences are observed between the the patient and control groups. We then investigate a particular type of asymmetry called torque. Differences in asymmetry are observed between the control and patient groups, which add strength to other observations in the literature. Further investigations of the midline plane location in the 2 groups and the fitting of nonplanar curved midlines are also considered.

Historical Analysis of Bibliometric Trends in the Journal of Pediatric Orthopaedics With a Particular Focus on Sex.

PubMed

Fischer, James P; Wininger, Austin E; Scofield, David C; Tucker, Aamir; Kacena-Merrell, Ethan J; Whipple, Elizabeth C; Kacena, Melissa A; Loder, Randall T

2018-03-01

Orthopaedics is the clinical discipline with the lowest percentage of female residents and faculty. Pediatric orthopaedics has a higher percentage of women than other orthopaedic subspecialties. It was the purpose of this study to examine bibliometric trends in the Journal of Pediatric Orthopaedics (JPO) with a specific focus on sex. A bibliometeric analysis for the years 2015, 2005, 1995, 1985, 1981 was performed. The names of first and corresponding authors; corresponding author position; country of origin; number of institutions, countries, authors, printed pages, and references was tabulated. Author sex was identified for the first and corresponding authors using the "Baby Name Guesser" (www.gpeters.com/names/baby-names.php). A P<0.05 was considered significant. There were 746 publications; 68.7% were from North America. The average number of authors, corresponding author position, collaborating institutions, countries, and number of references increased, whereas the number of printed pages decreased. Asia had the greatest number of authors (4.4), with Australia/New Zealand the fewest (3.4). Sex was determined for 98.3% of the first authors and 98.5% of the corresponding authors. There was a significant increase in the number of female first authors over time (5.9% to 25.6%, P<10), especially in Europe and North America. There were significant increase in the number of female corresponding authors over time (5.8% to 17.6%, P=0.000009). There was a significant trend to have a greater percentage of both female first and corresponding authors over time (P=0.0005) with a reverse trend for both male first and corresponding authors (P<10). In this study, we noted that the number of female first and corresponding authors in Journal of Pediatric Orthopaedics has been steadily increasing. This should result in more female pediatric orthopaedic surgeons in academic faculty positions.

Expediting Combinatorial Data Set Analysis by Combining Human and Algorithmic Analysis.

PubMed

Stein, Helge Sören; Jiao, Sally; Ludwig, Alfred

2017-01-09

A challenge in combinatorial materials science remains the efficient analysis of X-ray diffraction (XRD) data and its correlation to functional properties. Rapid identification of phase-regions and proper assignment of corresponding crystal structures is necessary to keep pace with the improved methods for synthesizing and characterizing materials libraries. Therefore, a new modular software called htAx (high-throughput analysis of X-ray and functional properties data) is presented that couples human intelligence tasks used for "ground-truth" phase-region identification with subsequent unbiased verification by an algorithm to efficiently analyze which phases are present in a materials library. Identified phases and phase-regions may then be correlated to functional properties in an expedited manner. For the functionality of htAx to be proven, two previously published XRD benchmark data sets of the materials systems Al-Cr-Fe-O and Ni-Ti-Cu are analyzed by htAx. The analysis of ∼1000 XRD patterns takes less than 1 day with htAx. The proposed method reliably identifies phase-region boundaries and robustly identifies multiphase structures. The method also addresses the problem of identifying regions with previously unpublished crystal structures using a special daisy ternary plot.

Gene Expression Profiling of Gastric Cancer

PubMed Central

Marimuthu, Arivusudar; Jacob, Harrys K.C.; Jakharia, Aniruddha; Subbannayya, Yashwanth; Keerthikumar, Shivakumar; Kashyap, Manoj Kumar; Goel, Renu; Balakrishnan, Lavanya; Dwivedi, Sutopa; Pathare, Swapnali; Dikshit, Jyoti Bajpai; Maharudraiah, Jagadeesha; Singh, Sujay; Sameer Kumar, Ghantasala S; Vijayakumar, M.; Veerendra Kumar, Kariyanakatte Veeraiah; Premalatha, Chennagiri Shrinivasamurthy; Tata, Pramila; Hariharan, Ramesh; Roa, Juan Carlos; Prasad, T.S.K; Chaerkady, Raghothama; Kumar, Rekha Vijay; Pandey, Akhilesh

2015-01-01

Gastric cancer is the second leading cause of cancer death worldwide, both in men and women. A genomewide gene expression analysis was carried out to identify differentially expressed genes in gastric adenocarcinoma tissues as compared to adjacent normal tissues. We used Agilent’s whole human genome oligonucleotide microarray platform representing ~41,000 genes to carry out gene expression analysis. Two-color microarray analysis was employed to directly compare the expression of genes between tumor and normal tissues. Through this approach, we identified several previously known candidate genes along with a number of novel candidate genes in gastric cancer. Testican-1 (SPOCK1) was one of the novel molecules that was 10-fold upregulated in tumors. Using tissue microarrays, we validated the expression of testican-1 by immunohistochemical staining. It was overexpressed in 56% (160/282) of the cases tested. Pathway analysis led to the identification of several networks in which SPOCK1 was among the topmost networks of interacting genes. By gene enrichment analysis, we identified several genes involved in cell adhesion and cell proliferation to be significantly upregulated while those corresponding to metabolic pathways were significantly downregulated. The differentially expressed genes identified in this study are candidate biomarkers for gastric adenoacarcinoma. PMID:27030788

Reduced structural connectivity within a prefrontal-motor-subcortical network in amyotrophic lateral sclerosis.

PubMed

Buchanan, Colin R; Pettit, Lewis D; Storkey, Amos J; Abrahams, Sharon; Bastin, Mark E

2015-05-01

To investigate white matter structural connectivity changes associated with amyotrophic lateral sclerosis (ALS) using network analysis and compare the results with those obtained using standard voxel-based methods, specifically Tract-based Spatial Statistics (TBSS). MRI data were acquired from 30 patients with ALS and 30 age-matched healthy controls. For each subject, 85 grey matter regions (network nodes) were identified from high resolution structural MRI, and network connections formed from the white matter tracts generated by diffusion MRI and probabilistic tractography. Whole-brain networks were constructed using strong constraints on anatomical plausibility and a weighting reflecting tract-averaged fractional anisotropy (FA). Analysis using Network-based Statistics (NBS), without a priori selected regions, identified an impaired motor-frontal-subcortical subnetwork (10 nodes and 12 bidirectional connections), consistent with upper motor neuron pathology, in the ALS group compared with the controls (P = 0.020). Reduced FA in three of the impaired network connections, which involved fibers of the corticospinal tract, correlated with rate of disease progression (P ≤ 0.024). A novel network-tract comparison revealed that the connections involved in the affected network had a strong correspondence (mean overlap of 86.2%) with white matter tracts identified as having reduced FA compared with the control group using TBSS. These findings suggest that white matter degeneration in ALS is strongly linked to the motor cortex, and that impaired structural networks identified using NBS have a strong correspondence to affected white matter tracts identified using more conventional voxel-based methods. © 2014 Wiley Periodicals, Inc.

Multi-Morbidity in Hospitalised Older Patients: Who Are the Complex Elderly?

PubMed Central

Ruiz, Milagros; Bottle, Alex; Long, Susannah; Aylin, Paul

2015-01-01

Background No formal definition for the “complex elderly” exists; moreover, these older patients with high levels of multi-morbidity are not readily identified as such at point of hospitalisation, thus missing a valuable opportunity to manage the older patient appropriately within the hospital setting. Objectives To empirically identify the complex elderly patient based on degree of multi-morbidity. Design Retrospective observational study using administrative data. Setting English hospitals during the financial year 2012–13. Subjects All admitted patients aged 65 years and over. Methods By using exploratory analysis (correspondence analysis) we identify multi-morbidity groups based on 20 target conditions whose hospital prevalence was ≥ 1%. Results We examined a total of 2788900 hospital admissions. Multi-morbidity was highly prevalent, 62.8% had 2 or more of the targeted conditions while 4.7% had six or more. Multi-morbidity increased with age from 56% (65-69yr age-groups) up to 67% (80-84yr age-group). The average multi-morbidity was 3.2±1.2 (SD). Correspondence analysis revealed 3 distinct groups of older patients. Group 1 (multi-morbidity ≤2), associated with cancer and/or metastasis; Group 2 (multi-morbidity of 3, 4 or 5), associated with chronic pulmonary disease, lung disease, rheumatism and osteoporosis; finally Group 3 with the highest level of multi-morbidity (≥6) and associated with heart failure, cerebrovascular accident, diabetes, hypertension and myocardial infarction. Conclusions By using widely available hospital administrative data, we propose patients in Groups 2 and 3 to be identified as the complex elderly. Identification of multi-morbidity patterns can help to predict the needs of the older patient and improve resource provision. PMID:26716440

Automatic generation of endocardial surface meshes with 1-to-1 correspondence from cine-MR images

NASA Astrophysics Data System (ADS)

Su, Yi; Teo, S.-K.; Lim, C. W.; Zhong, L.; Tan, R. S.

2015-03-01

In this work, we develop an automatic method to generate a set of 4D 1-to-1 corresponding surface meshes of the left ventricle (LV) endocardial surface which are motion registered over the whole cardiac cycle. These 4D meshes have 1- to-1 point correspondence over the entire set, and is suitable for advanced computational processing, such as shape analysis, motion analysis and finite element modelling. The inputs to the method are the set of 3D LV endocardial surface meshes of the different frames/phases of the cardiac cycle. Each of these meshes is reconstructed independently from border-delineated MR images and they have no correspondence in terms of number of vertices/points and mesh connectivity. To generate point correspondence, the first frame of the LV mesh model is used as a template to be matched to the shape of the meshes in the subsequent phases. There are two stages in the mesh correspondence process: (1) a coarse matching phase, and (2) a fine matching phase. In the coarse matching phase, an initial rough matching between the template and the target is achieved using a radial basis function (RBF) morphing process. The feature points on the template and target meshes are automatically identified using a 16-segment nomenclature of the LV. In the fine matching phase, a progressive mesh projection process is used to conform the rough estimate to fit the exact shape of the target. In addition, an optimization-based smoothing process is used to achieve superior mesh quality and continuous point motion.

Microarray analysis of genes associated with cell surface NIS protein levels in breast cancer.

PubMed

Beyer, Sasha J; Zhang, Xiaoli; Jimenez, Rafael E; Lee, Mei-Ling T; Richardson, Andrea L; Huang, Kun; Jhiang, Sissy M

2011-10-11

Na+/I- symporter (NIS)-mediated iodide uptake allows radioiodine therapy for thyroid cancer. NIS is also expressed in breast tumors, raising potential for radionuclide therapy of breast cancer. However, NIS expression in most breast cancers is low and may not be sufficient for radionuclide therapy. We aimed to identify biomarkers associated with NIS expression such that mechanisms underlying NIS modulation in human breast tumors may be elucidated. Published oligonucleotide microarray data within the National Center for Biotechnology Information Gene Expression Omnibus database were analyzed to identify gene expression tightly correlated with NIS mRNA level among human breast tumors. NIS immunostaining was performed in a tissue microarray composed of 28 human breast tumors which had corresponding oligonucleotide microarray data available for each tumor such that gene expression associated with cell surface NIS protein level could be identified. NIS mRNA levels do not vary among breast tumors or when compared to normal breast tissues when detected by Affymetrix oligonucleotide microarray platforms. Cell surface NIS protein levels are much more variable than their corresponding NIS mRNA levels. Despite a limited number of breast tumors examined, our analysis identified cysteinyl-tRNA synthetase as a biomarker that is highly associated with cell surface NIS protein levels in the ER-positive breast cancer subtype. Further investigation on genes associated with cell surface NIS protein levels within each breast cancer molecular subtype may lead to novel targets for selectively increasing NIS expression/function in a subset of breast cancers patients.

Structural equation modeling assessing relationship between mathematics beliefs, teachers' attitudes and teaching practices among novice teachers in Malaysia

NASA Astrophysics Data System (ADS)

Borhan, Noziati; Zakaria, Effandi

2017-05-01

This quantitative study was conducted to investigate the perception level of novice teachers about mathematics belief, teachers' attitude towards mathematics and teaching practices of mathematics in the classroom. In addition, it also aims to identify whether there is a correspondence model with the data obtained and to identify the relationship between the variables of beliefs, attitudes and practices among novice teachers in Malaysia. A total of 263 primary novice teachers throughout the country were involved in this study were selected randomly. Respondents are required to provide a response to the questionnaire of 66 items related to mathematics beliefs, attitudes and practices of the teaching mathematics. There are ten sub-factors which have been established in this instrument for three major constructs using a Likert scale rating of five points. The items of the constructs undergo the exploratory factor analysis (EFA) and confirmatory factor analysis (CFA) procedure involve of unidimensionality test, convergent validity, construct validity and discriminant validity. Descriptive statistics were used to describe the frequency, percentage, the mean and standard deviation for completing some research questions that have been expressed. As for inferential statistical analysis, the researchers used structural equation modeling (SEM) to answer the question of correspondents model and the relationship between these three variables. The results of the study were found that there exist a correspondence measurement and structural model with the data obtained. While the relationship between variable found that mathematics beliefs have a significant influence on teachers' attitudes towards mathematics as well as the relationship between the attitudes with teaching practices. Meanwhile, mathematics belief had no significant relationship with mathematics teaching practices among novice teachers in Malaysia.

Preliminary analysis of the potential of LANDSAT imagery to study desertification. [Xique-Xique, Brazil

NASA Technical Reports Server (NTRS)

Dejesusparada, N. (Principal Investigator); Lombardo, M. A.; Decarvalho, V. C.

1980-01-01

The use of LANDSAT imagery to define and delimit areas under process of desertification was investigated. Imagery for two different years (1973 and 1978) and two different seasons (dry and rainy seasons in 1976), were used to identify terrain morphology and vegetation cover. The analysis of LANDSAT interpretation, combined with geological and soil information obtained from published literature, allowed the identification of eleven ecological units which were classified corresponding to the degree of the Xique Xique region of Rio Sao Francisco.

Epigenome overlap measure (EPOM) for comparing tissue/cell types based on chromatin states.

PubMed

Li, Wei Vivian; Razaee, Zahra S; Li, Jingyi Jessica

2016-01-11

The dynamics of epigenomic marks in their relevant chromatin states regulate distinct gene expression patterns, biological functions and phenotypic variations in biological processes. The availability of high-throughput epigenomic data generated by next-generation sequencing technologies allows a data-driven approach to evaluate the similarities and differences of diverse tissue and cell types in terms of epigenomic features. While ChromImpute has allowed for the imputation of large-scale epigenomic information to yield more robust data to capture meaningful relationships between biological samples, widely used methods such as hierarchical clustering and correlation analysis cannot adequately utilize epigenomic data to accurately reveal the distinction and grouping of different tissue and cell types. We utilize a three-step testing procedure-ANOVA, t test and overlap test to identify tissue/cell-type- associated enhancers and promoters and to calculate a newly defined Epigenomic Overlap Measure (EPOM). EPOM results in a clear correspondence map of biological samples from different tissue and cell types through comparison of epigenomic marks evaluated in their relevant chromatin states. Correspondence maps by EPOM show strong capability in distinguishing and grouping different tissue and cell types and reveal biologically meaningful similarities between Heart and Muscle, Blood & T-cell and HSC & B-cell, Brain and Neurosphere, etc. The gene ontology enrichment analysis both supports and explains the discoveries made by EPOM and suggests that the associated enhancers and promoters demonstrate distinguishable functions across tissue and cell types. Moreover, the tissue/cell-type-associated enhancers and promoters show enrichment in the disease-related SNPs that are also associated with the corresponding tissue or cell types. This agreement suggests the potential of identifying causal genetic variants relevant to cell-type-specific diseases from our identified associated enhancers and promoters. The proposed EPOM measure demonstrates superior capability in grouping and finding a clear correspondence map of biological samples from different tissue and cell types. The identified associated enhancers and promoters provide a comprehensive catalog to study distinct biological processes and disease variants in different tissue and cell types. Our results also find that the associated promoters exhibit more cell-type-specific functions than the associated enhancers do, suggesting that the non-associated promoters have more housekeeping functions than the non-associated enhancers.

Mass spectrometric analysis of electrophoretically separated allergens and proteases in grass pollen diffusates

PubMed Central

Raftery, Mark J; Saldanha, Rohit G; Geczy, Carolyn L; Kumar, Rakesh K

2003-01-01

Background Pollens are important triggers for allergic asthma and seasonal rhinitis, and proteases released by major allergenic pollens can injure airway epithelial cells in vitro. Disruption of mucosal epithelial integrity by proteases released by inhaled pollens could promote allergic sensitisation. Methods Pollen diffusates from Kentucky blue grass (Poa pratensis), rye grass (Lolium perenne) and Bermuda grass (Cynodon dactylon) were assessed for peptidase activity using a fluorogenic substrate, as well as by gelatin zymography. Following one- or two-dimensional gel electrophoresis, Coomassie-stained individual bands/spots were excised, subjected to tryptic digestion and analysed by mass spectrometry, either MALDI reflectron TOF or microcapillary liquid chromatography MS-MS. Database searches were used to identify allergens and other plant proteins in pollen diffusates. Results All pollen diffusates tested exhibited peptidase activity. Gelatin zymography revealed high Mr proteolytic activity at ~ 95,000 in all diffusates and additional proteolytic bands in rye and Bermuda grass diffusates, which appeared to be serine proteases on the basis of inhibition studies. A proteolytic band at Mr ~ 35,000 in Bermuda grass diffusate, which corresponded to an intense band detected by Western blotting using a monoclonal antibody to the timothy grass (Phleum pratense) group 1 allergen Phl p 1, was identified by mass spectrometric analysis as the group 1 allergen Cyn d 1. Two-dimensional analysis similarly demonstrated proteolytic activity corresponding to protein spots identified as Cyn d 1. Conclusion One- and two-dimensional electrophoretic separation, combined with analysis by mass spectrometry, is useful for rapid determination of the identities of pollen proteins. A component of the proteolytic activity in Bermuda grass diffusate is likely to be related to the allergen Cyn d 1. PMID:14577842

The information filter: how dentists use diet diary information to give patients clear and simple advice.

PubMed

Arheiam, Arheiam; Brown, Stephen L; Higham, Susan M; Albadri, Sondos; Harris, Rebecca V

2016-12-01

Diet diaries are recommended for dentists to monitor children's sugar consumption. Diaries provide multifaceted dietary information, but patients respond better to simpler advice. We explore how dentists integrate information from diet diaries to deliver useable advice to patients. As part of a questionnaire study of general dental practitioners (GDPs) in Northwest England, we asked dentists to specify the advice they would give a hypothetical patient based upon a diet diary case vignette. A sequential mixed method approach was used for data analysis: an initial inductive content analysis (ICA) to develop coding system to capture the complexity of dietary assessment and delivered advice. Using these codes, a quantitative analysis was conducted to examine correspondences between identified dietary problems and advice given. From these correspondences, we inferred how dentists reduced problems to give simple advice. A total of 229 dentists' responses were analysed. ICA on 40 questionnaires identified two distinctive approaches of developing diet advice: a summative (summary of issues into an all-encompassing message) and a selective approach (selection of a main message approach). In the quantitative analysis of all responses, raw frequencies indicated that dentists saw more problems than they advised on and provided highly specific advice on a restricted number of problems (e.g. not eating sugars before bedtime 50.7% or harmful items 42.4%, rather than simply reducing the amount of sugar 9.2%). Binary logistic regression models indicate that dentists provided specific advice that was tailored to the key problems that they identified. Dentists provided specific recommendations to address what they felt were key problems, whilst not intervening to address other problems that they may have felt less pressing. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

In silico identification of miRNAs and their target genes and analysis of gene co-expression network in saffron (Crocus sativus L.) stigma

PubMed Central

Zinati, Zahra; Shamloo-Dashtpagerdi, Roohollah; Behpouri, Ali

2016-01-01

As an aromatic and colorful plant of substantive taste, saffron (Crocus sativus L.) owes such properties of matter to growing class of the secondary metabolites derived from the carotenoids, apocarotenoids. Regarding the critical role of microRNAs in secondary metabolic synthesis and the limited number of identified miRNAs in C. sativus, on the other hand, one may see the point how the characterization of miRNAs along with the corresponding target genes in C. sativus might expand our perspectives on the roles of miRNAs in carotenoid/apocarotenoid biosynthetic pathway. A computational analysis was used to identify miRNAs and their targets using EST (Expressed Sequence Tag) library from mature saffron stigmas. Then, a gene co- expression network was constructed to identify genes which are potentially involved in carotenoid/apocarotenoid biosynthetic pathways. EST analysis led to the identification of two putative miRNAs (miR414 and miR837-5p) along with the corresponding stem- looped precursors. To our knowledge, this is the first report on miR414 and miR837-5p in C. sativus. Co-expression network analysis indicated that miR414 and miR837-5p may play roles in C. sativus metabolic pathways and led to identification of candidate genes including six transcription factors and one protein kinase probably involved in carotenoid/apocarotenoid biosynthetic pathway. Presence of transcription factors, miRNAs and protein kinase in the network indicated multiple layers of regulation in saffron stigma. The candidate genes from this study may help unraveling regulatory networks underlying the carotenoid/apocarotenoid biosynthesis in saffron and designing metabolic engineering for enhanced secondary metabolites. PMID:28261627

Systemic Analysis of Foodborne Disease Outbreak in Korea.

PubMed

Lee, Jong-Kyung; Kwak, No-Seong; Kim, Hyun Jung

2016-02-01

This study systemically analyzed data on the prevalence of foodborne pathogens and foodborne disease outbreaks to identify the priorities of foodborne infection risk management in Korea. Multiple correspondence analysis was applied to three variables: origin of food source, phase of food supply chain, and 12 pathogens using 358 cases from 76 original papers and official reports published in 1998-2012. In addition, correspondence analysis of two variables--place and pathogen--was conducted based on epidemiological data of 2357 foodborne outbreaks in 2002-2011 provided by the Korean Ministry of Food and Drug Safety. The results of this study revealed three distinct areas of food monitoring: (1) livestock-derived raw food contaminated with Campylobacter spp., pathogenic Escherichia coli, Salmonella spp., and Listeria monocytogenes; (2) multi-ingredient and ready-to-eat food related to Staphylococcus aureus; and (3) water associated with norovirus. Our findings emphasize the need to track the sources and contamination pathways of foodborne pathogens for more effective risk management.

Does the Factor Structure of Military Sexual Stressors in Men Correspond to Women's? A Confirmatory Factor Analysis Using the Sexual Harassment Inventory.

PubMed

Reddy, Madhavi K; Murdoch, Maureen

2016-02-01

Unwanted sexual stressors experienced by military men and women are associated with a host of negative physical and mental health problems. Government officials are making it a priority to put a stop to these unwanted sexual experiences. However, the measure typically used measures sexual stressors much better for women than for men. The purpose of the present study was to test the factor structure of an alternative measure, the Sexual Harassment Inventory (SHI), to examine whether sexual stressors experienced by men correspond to women's experiences. We used three preexisting datasets in which the SHI was used to assess active and former military members' sexual stressor experiences. We conducted an exploratory factor analysis to identify women's response patterns and a confirmatory factor analysis to determine whether men's response patterns corresponded to women's. Findings showed that the SHI has evidence of factorial validity in female service members and adequate, but not exceptional, factorial fit for male service members. It is imperative that more work be done to better understand how men experience and perceive potential military sexual stressors and how those perceptions and experiences compare to women's. Reprint & Copyright © 2016 Association of Military Surgeons of the U.S.

Systemic family psychotherapy in China: a qualitative analysis of therapy process.

PubMed

Liu, Liang; Miller, John K; Zhao, Xudong; Ma, Xiquan; Wang, Jikun; Li, Wentian

2013-12-01

Although the procedure of systemic family therapy has been extensively researched in Western culture, few studies on this subject have been conducted in China. The aim of this study was to specify the therapy-delivered interventions in Chinese systemic family therapy and to explore how Western-imported systemic therapy model is delivered in Chinese culture. A qualitative and exploratory research approach was taken in which thematic analysis was used to analyse the transcribed psychotherapy videotapes with Chinese families. Twenty-six hours of video-recorded systemic family therapy sessions from 14 Chinese family cases were sampled. Thematic analysis was used to analyse the transcriptions of therapy sessions and identify therapist-generated interventions in therapy. Frequencies of different interventions were counted, and correspondence analysis (CA) was used to reveal the corresponding relationships between different interventions. Analysis led to two main themes related to therapists-delivered interventions: Therapist's intention and therapy technique. Results revealed 15 types of therapist's intentions and 16 categories of therapy techniques. CA indicated that therapists' intentions changed across different therapy stages and specific techniques were used to achieve corresponding intentions. Interventions delivered in Chinese systemic therapy are mainly adherent with Milan and post-Milan systemic models. Due to the shortage in systemic therapy service in China and Chinese culture advocating reverence to authority, components of psycho-education, guidance, and metaphor are adopted in Chinese systemic practice. Some directions for future research are suggested. © 2012 The British Psychological Society.

Learner Acquisition and Its Relationship with Constructivist Learner Roles in a Secondary Education Chemistry Curriculum in Québec/Canada

ERIC Educational Resources Information Center

Aydin, Abdullah

2013-01-01

This study aims to identify constructivist learner roles in acquisitions in the secondary education chemistry curriculum of the province of Québec/Canada. This research used document analysis as a qualitative research method. According to our findings; the "learner roles" in curriculum correspond with the "student roles"…

Combined magnetic and gravity analysis

NASA Technical Reports Server (NTRS)

Hinze, W. J.; Braile, L. W.; Chandler, V. W.; Mazella, F. E.

1975-01-01

Efforts are made to identify methods of decreasing magnetic interpretation ambiguity by combined gravity and magnetic analysis, to evaluate these techniques in a preliminary manner, to consider the geologic and geophysical implications of correlation, and to recommend a course of action to evaluate methods of correlating gravity and magnetic anomalies. The major thrust of the study was a search and review of the literature. The literature of geophysics, geology, geography, and statistics was searched for articles dealing with spatial correlation of independent variables. An annotated bibliography referencing the Germane articles and books is presented. The methods of combined gravity and magnetic analysis techniques are identified and reviewed. A more comprehensive evaluation of two types of techniques is presented. Internal correspondence of anomaly amplitudes is examined and a combined analysis is done utilizing Poisson's theorem. The geologic and geophysical implications of gravity and magnetic correlation based on both theoretical and empirical relationships are discussed.

Subgroup analyses in randomised controlled trials: cohort study on trial protocols and journal publications.

PubMed

Kasenda, Benjamin; Schandelmaier, Stefan; Sun, Xin; von Elm, Erik; You, John; Blümle, Anette; Tomonaga, Yuki; Saccilotto, Ramon; Amstutz, Alain; Bengough, Theresa; Meerpohl, Joerg J; Stegert, Mihaela; Olu, Kelechi K; Tikkinen, Kari A O; Neumann, Ignacio; Carrasco-Labra, Alonso; Faulhaber, Markus; Mulla, Sohail M; Mertz, Dominik; Akl, Elie A; Bassler, Dirk; Busse, Jason W; Ferreira-González, Ignacio; Lamontagne, Francois; Nordmann, Alain; Gloy, Viktoria; Raatz, Heike; Moja, Lorenzo; Rosenthal, Rachel; Ebrahim, Shanil; Vandvik, Per O; Johnston, Bradley C; Walter, Martin A; Burnand, Bernard; Schwenkglenks, Matthias; Hemkens, Lars G; Bucher, Heiner C; Guyatt, Gordon H; Briel, Matthias

2014-07-16

To investigate the planning of subgroup analyses in protocols of randomised controlled trials and the agreement with corresponding full journal publications. Cohort of protocols of randomised controlled trial and subsequent full journal publications. Six research ethics committees in Switzerland, Germany, and Canada. 894 protocols of randomised controlled trial involving patients approved by participating research ethics committees between 2000 and 2003 and 515 subsequent full journal publications. Of 894 protocols of randomised controlled trials, 252 (28.2%) included one or more planned subgroup analyses. Of those, 17 (6.7%) provided a clear hypothesis for at least one subgroup analysis, 10 (4.0%) anticipated the direction of a subgroup effect, and 87 (34.5%) planned a statistical test for interaction. Industry sponsored trials more often planned subgroup analyses compared with investigator sponsored trials (195/551 (35.4%) v 57/343 (16.6%), P<0.001). Of 515 identified journal publications, 246 (47.8%) reported at least one subgroup analysis. In 81 (32.9%) of the 246 publications reporting subgroup analyses, authors stated that subgroup analyses were prespecified, but this was not supported by 28 (34.6%) corresponding protocols. In 86 publications, authors claimed a subgroup effect, but only 36 (41.9%) corresponding protocols reported a planned subgroup analysis. Subgroup analyses are insufficiently described in the protocols of randomised controlled trials submitted to research ethics committees, and investigators rarely specify the anticipated direction of subgroup effects. More than one third of statements in publications of randomised controlled trials about subgroup prespecification had no documentation in the corresponding protocols. Definitive judgments regarding credibility of claimed subgroup effects are not possible without access to protocols and analysis plans of randomised controlled trials. © The DISCO study group 2014.

Serum Autoantibodies in Chronic Prostate Inflammation in Prostate Cancer Patients.

PubMed

Schlick, Bettina; Massoner, Petra; Lueking, Angelika; Charoentong, Pornpimol; Blattner, Mirjam; Schaefer, Georg; Marquart, Klaus; Theek, Carmen; Amersdorfer, Peter; Zielinski, Dirk; Kirchner, Matthias; Trajanoski, Zlatko; Rubin, Mark A; Müllner, Stefan; Schulz-Knappe, Peter; Klocker, Helmut

2016-01-01

Chronic inflammation is frequently observed on histological analysis of malignant and non-malignant prostate specimens. It is a suspected supporting factor for prostate diseases and their progression and a main cause of false positive PSA tests in cancer screening. We hypothesized that inflammation induces autoantibodies, which may be useful biomarkers. We aimed to identify and validate prostate inflammation associated serum autoantibodies in prostate cancer patients and evaluate the expression of corresponding autoantigens. Radical prostatectomy specimens of prostate cancer patients (N = 70) were classified into high and low inflammation groups according to the amount of tissue infiltrating lymphocytes. The corresponding pre-surgery blood serum samples were scrutinized for autoantibodies using a low-density protein array. Selected autoantigens were identified in prostate tissue and their expression pattern analyzed by immunohistochemistry and qPCR. The identified autoantibody profile was cross-checked in an independent sample set (N = 63) using the Luminex-bead protein array technology. Protein array screening identified 165 autoantibodies differentially abundant in the serum of high compared to low inflammation patients. The expression pattern of three corresponding antigens were established in benign and cancer tissue by immunohistochemistry and qPCR: SPAST (Spastin), STX18 (Syntaxin 18) and SPOP (speckle-type POZ protein). Of these, SPAST was significantly increased in prostate tissue with high inflammation. All three autoantigens were differentially expressed in primary and/or castration resistant prostate tumors when analyzed in an inflammation-independent tissue microarray. Cross-validation of the inflammation autoantibody profile on an independent sample set using a Luminex-bead protein array, retrieved 51 of the significantly discriminating autoantibodies. Three autoantibodies were significantly upregulated in both screens, MUT, RAB11B and CSRP2 (p>0.05), two, SPOP and ZNF671, close to statistical significance (p = 0.051 and 0.076). We provide evidence of an inflammation-specific autoantibody profile and confirm the expression of corresponding autoantigens in prostate tissue. This supports evaluation of autoantibodies as non-invasive markers for prostate inflammation.

Serum Autoantibodies in Chronic Prostate Inflammation in Prostate Cancer Patients

PubMed Central

Schlick, Bettina; Massoner, Petra; Lueking, Angelika; Charoentong, Pornpimol; Blattner, Mirjam; Schaefer, Georg; Marquart, Klaus; Theek, Carmen; Amersdorfer, Peter; Zielinski, Dirk; Kirchner, Matthias; Trajanoski, Zlatko; Rubin, Mark A.; Müllner, Stefan; Schulz-Knappe, Peter; Klocker, Helmut

2016-01-01

Background Chronic inflammation is frequently observed on histological analysis of malignant and non-malignant prostate specimens. It is a suspected supporting factor for prostate diseases and their progression and a main cause of false positive PSA tests in cancer screening. We hypothesized that inflammation induces autoantibodies, which may be useful biomarkers. We aimed to identify and validate prostate inflammation associated serum autoantibodies in prostate cancer patients and evaluate the expression of corresponding autoantigens. Methods Radical prostatectomy specimens of prostate cancer patients (N = 70) were classified into high and low inflammation groups according to the amount of tissue infiltrating lymphocytes. The corresponding pre-surgery blood serum samples were scrutinized for autoantibodies using a low-density protein array. Selected autoantigens were identified in prostate tissue and their expression pattern analyzed by immunohistochemistry and qPCR. The identified autoantibody profile was cross-checked in an independent sample set (N = 63) using the Luminex-bead protein array technology. Results Protein array screening identified 165 autoantibodies differentially abundant in the serum of high compared to low inflammation patients. The expression pattern of three corresponding antigens were established in benign and cancer tissue by immunohistochemistry and qPCR: SPAST (Spastin), STX18 (Syntaxin 18) and SPOP (speckle-type POZ protein). Of these, SPAST was significantly increased in prostate tissue with high inflammation. All three autoantigens were differentially expressed in primary and/or castration resistant prostate tumors when analyzed in an inflammation-independent tissue microarray. Cross-validation of the inflammation autoantibody profile on an independent sample set using a Luminex-bead protein array, retrieved 51 of the significantly discriminating autoantibodies. Three autoantibodies were significantly upregulated in both screens, MUT, RAB11B and CSRP2 (p>0.05), two, SPOP and ZNF671, close to statistical significance (p = 0.051 and 0.076). Conclusions We provide evidence of an inflammation-specific autoantibody profile and confirm the expression of corresponding autoantigens in prostate tissue. This supports evaluation of autoantibodies as non-invasive markers for prostate inflammation. PMID:26863016

Determining conduction patterns on a sparse electrode grid: Implications for the analysis of clinical arrhythmias

NASA Astrophysics Data System (ADS)

Vidmar, David; Narayan, Sanjiv M.; Krummen, David E.; Rappel, Wouter-Jan

2016-11-01

We present a general method of utilizing bioelectric recordings from a spatially sparse electrode grid to compute a dynamic vector field describing the underlying propagation of electrical activity. This vector field, termed the wave-front flow field, permits quantitative analysis of the magnitude of rotational activity (vorticity) and focal activity (divergence) at each spatial point. We apply this method to signals recorded during arrhythmias in human atria and ventricles using a multipolar contact catheter and show that the flow fields correlate with corresponding activation maps. Further, regions of elevated vorticity and divergence correspond to sites identified as clinically significant rotors and focal sources where therapeutic intervention can be effective. These flow fields can provide quantitative insights into the dynamics of normal and abnormal conduction in humans and could potentially be used to enhance therapies for cardiac arrhythmias.

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

Hernandez, Y.; Carriazo, J.G.; Almanza, O.

Materials from a mining process, in which ferronickel metal extraction is the principal aim, were studied. The residual solid (scum) obtained in this process leads to large-scale accumulation of a vitreous material (pollutant) which creates an environmental problem. These materials were characterized by EPR, X-ray diffraction and X-ray fluorescence. The results indicate that the analyzed solids are rich in Fe{sub 2}O{sub 3} and NiO among other oxides. The scum material shows diffraction signals corresponding to the minerals enstatite (pyroxene) and {alpha}-alumina. Moreover, the scum EPR analysis showed a broad line around g = 2.1 corresponding to Fe{sup 3+} clusters inmore » a complex glassy matrix. An analysis of EPR at different temperatures was also performed. The objective of this work, as a first exploratory stage, is to develop a better understanding of the residual solids in order to identify potential applications.« less

The Identification of the Deformation Stage of a Metal Specimen Based on Acoustic Emission Data Analysis

PubMed Central

Zou, Shenao; Yan, Fengying; Yang, Guoan; Sun, Wei

2017-01-01

The acoustic emission (AE) signals of metal materials have been widely used to identify the deformation stage of a pressure vessel. In this work, Q235 steel samples with different propagation distances and geometrical structures are stretched to get the corresponding acoustic emission signals. Then the obtained acoustic emission signals are de-noised by empirical mode decomposition (EMD), and then decomposed into two different frequency ranges, i.e., one mainly corresponding to metal deformation and the other mainly corresponding to friction signals. The ratio of signal energy between two frequency ranges is defined as a new acoustic emission characteristic parameter. Differences can be observed at different deformation stages in both magnitude and data distribution range. Compared with other acoustic emission parameters, the proposed parameter is valid in different setups of the propagation medium and the coupled stiffness. PMID:28387703

A Genetic and Molecular Analysis of the 46c Chromosomal Region Surrounding the Fmrfamide Neuropeptide Gene in Drosophila Melanogaster

PubMed Central

O'Brien, M. A.; Roberts, M. S.; Taghert, P. H.

1994-01-01

We have analyzed the FMRFamide neuropeptide gene region of Drosophila melanogaster. This gene maps to the 46C region of chromosome 2R; this interval previously was not well characterized. For this genetic and molecular analysis, we have used X-ray mutagenesis, EMS mutagenesis, and the recently reported local P element transposition method. We identified four overlapping deletions, two of which have proximal breakpoints that define a 50-60-kb region surrounding the FMRFamide gene in 46C. To this small region, we mapped three lethal complementation groups; 10 additional lethal complementation groups were mapped to more distal regions of 46CD. One of these groups corresponds to even-skipped, the other 12 are previously unidentified. Using various lines of evidence we excluded the possibility that FMRFamide corresponds to any of the three lethal complementation groups mapping to its immediate 50-60-kb vicinity. The positions of two of the three lethal complementation groups were identified with P elements using a local transposition scheme. The third lethal complementation group was excluded as being FMRFamide mutants by sequence analysis and by immunocytochemistry with proFMRFamide precursor-specific antibodies. This analysis has (1) provided a genetic map of the 46CD chromosomal region and a detailed molecular map of a portion of the 46C region and (2) provided additional evidence of the utility of local transposition for targeting nearby genes. PMID:8056304

Individual Differences in Dynamic Functional Brain Connectivity across the Human Lifespan

PubMed Central

Davison, Elizabeth N.; Turner, Benjamin O.; Miller, Michael B.; Carlson, Jean M.

2016-01-01

Individual differences in brain functional networks may be related to complex personal identifiers, including health, age, and ability. Dynamic network theory has been used to identify properties of dynamic brain function from fMRI data, but the majority of analyses and findings remain at the level of the group. Here, we apply hypergraph analysis, a method from dynamic network theory, to quantify individual differences in brain functional dynamics. Using a summary metric derived from the hypergraph formalism—hypergraph cardinality—we investigate individual variations in two separate, complementary data sets. The first data set (“multi-task”) consists of 77 individuals engaging in four consecutive cognitive tasks. We observe that hypergraph cardinality exhibits variation across individuals while remaining consistent within individuals between tasks; moreover, the analysis of one of the memory tasks revealed a marginally significant correspondence between hypergraph cardinality and age. This finding motivated a similar analysis of the second data set (“age-memory”), in which 95 individuals, aged 18–75, performed a memory task with a similar structure to the multi-task memory task. With the increased age range in the age-memory data set, the correlation between hypergraph cardinality and age correspondence becomes significant. We discuss these results in the context of the well-known finding linking age with network structure, and suggest that hypergraph analysis should serve as a useful tool in furthering our understanding of the dynamic network structure of the brain. PMID:27880785

Visualising nursing data using correspondence analysis.

PubMed

Kokol, Peter; Blažun Vošner, Helena; Železnik, Danica

2016-09-01

Digitally stored, large healthcare datasets enable nurses to use 'big data' techniques and tools in nursing research. Big data is complex and multi-dimensional, so visualisation may be a preferable approach to analyse and understand it. To demonstrate the use of visualisation of big data in a technique called correspondence analysis. In the authors' study, relations among data in a nursing dataset were shown visually in graphs using correspondence analysis. The case presented demonstrates that correspondence analysis is easy to use, shows relations between data visually in a form that is simple to interpret, and can reveal hidden associations between data. Correspondence analysis supports the discovery of new knowledge. Implications for practice Knowledge obtained using correspondence analysis can be transferred immediately into practice or used to foster further research.

Efficacy of neck circumference to identify metabolic syndrome in 3-10 year-old European children: Results from IDEFICS study.

PubMed

Formisano, A; Bammann, K; Fraterman, A; Hadjigeorgiou, C; Herrmann, D; Iacoviello, L; Marild, S; Moreno, L A; Nagy, P; Van Den Bussche, K; Veidebaum, T; Lauria, F; Siani, A

2016-06-01

Several studies demonstrated that larger neck circumference (NC) in children and adolescents may help to identify obesity and cardio-metabolic abnormalities. We aimed to evaluate the correlation between NC and metabolic syndrome (MetS) risk factors and to determine the utility of this anthropometric index to identify MetS in European children. The present cross-sectional analysis includes 15,673 children (3-10 years) participating in the IDEFICS study. A continuous MetS (cMetS) score was calculated summing age and sex standardized z-scores of specific MetS risk factors. Receiver Operating Characteristic analysis, stratified by one-year age groups, was used to determine the ability of NC to identify children with unfavorable metabolic profile, corresponding to cMetS score ≥ 90th percentile. The areas under the curve values for NC associated with cMetS score values ≥ 90th percentile were significantly greater in girls than in boys (p < 0.001), except for 5 < 6 years group. For boys, optimal NC cut-off values ranged from 26.2 cm for the lowest age group (3 < 4 years), up to 30.9 cm for the highest age group (9 < 10 years). In girls, corresponding values varied from 24.9 cm to 29.6 cm. The study demonstrated the efficacy of NC in identifying European children with an unfavorable metabolic profile. Copyright © 2016 The Italian Society of Diabetology, the Italian Society for the Study of Atherosclerosis, the Italian Society of Human Nutrition, and the Department of Clinical Medicine and Surgery, Federico II University. Published by Elsevier B.V. All rights reserved.

Identification of speech transients using variable frame rate analysis and wavelet packets.

PubMed

Rasetshwane, Daniel M; Boston, J Robert; Li, Ching-Chung

2006-01-01

Speech transients are important cues for identifying and discriminating speech sounds. Yoo et al. and Tantibundhit et al. were successful in identifying speech transients and, emphasizing them, improving the intelligibility of speech in noise. However, their methods are computationally intensive and unsuitable for real-time applications. This paper presents a method to identify and emphasize speech transients that combines subband decomposition by the wavelet packet transform with variable frame rate (VFR) analysis and unvoiced consonant detection. The VFR analysis is applied to each wavelet packet to define a transitivity function that describes the extent to which the wavelet coefficients of that packet are changing. Unvoiced consonant detection is used to identify unvoiced consonant intervals and the transitivity function is amplified during these intervals. The wavelet coefficients are multiplied by the transitivity function for that packet, amplifying the coefficients localized at times when they are changing and attenuating coefficients at times when they are steady. Inverse transform of the modified wavelet packet coefficients produces a signal corresponding to speech transients similar to the transients identified by Yoo et al. and Tantibundhit et al. A preliminary implementation of the algorithm runs more efficiently.

Perturbation analyses of intermolecular interactions

NASA Astrophysics Data System (ADS)

Koyama, Yohei M.; Kobayashi, Tetsuya J.; Ueda, Hiroki R.

2011-08-01

Conformational fluctuations of a protein molecule are important to its function, and it is known that environmental molecules, such as water molecules, ions, and ligand molecules, significantly affect the function by changing the conformational fluctuations. However, it is difficult to systematically understand the role of environmental molecules because intermolecular interactions related to the conformational fluctuations are complicated. To identify important intermolecular interactions with regard to the conformational fluctuations, we develop herein (i) distance-independent and (ii) distance-dependent perturbation analyses of the intermolecular interactions. We show that these perturbation analyses can be realized by performing (i) a principal component analysis using conditional expectations of truncated and shifted intermolecular potential energy terms and (ii) a functional principal component analysis using products of intermolecular forces and conditional cumulative densities. We refer to these analyses as intermolecular perturbation analysis (IPA) and distance-dependent intermolecular perturbation analysis (DIPA), respectively. For comparison of the IPA and the DIPA, we apply them to the alanine dipeptide isomerization in explicit water. Although the first IPA principal components discriminate two states (the α state and PPII (polyproline II) + β states) for larger cutoff length, the separation between the PPII state and the β state is unclear in the second IPA principal components. On the other hand, in the large cutoff value, DIPA eigenvalues converge faster than that for IPA and the top two DIPA principal components clearly identify the three states. By using the DIPA biplot, the contributions of the dipeptide-water interactions to each state are analyzed systematically. Since the DIPA improves the state identification and the convergence rate with retaining distance information, we conclude that the DIPA is a more practical method compared with the IPA. To test the feasibility of the DIPA for larger molecules, we apply the DIPA to the ten-residue chignolin folding in explicit water. The top three principal components identify the four states (native state, two misfolded states, and unfolded state) and their corresponding eigenfunctions identify important chignolin-water interactions to each state. Thus, the DIPA provides the practical method to identify conformational states and their corresponding important intermolecular interactions with distance information.

Perturbation analyses of intermolecular interactions.

PubMed

Koyama, Yohei M; Kobayashi, Tetsuya J; Ueda, Hiroki R

2011-08-01

Conformational fluctuations of a protein molecule are important to its function, and it is known that environmental molecules, such as water molecules, ions, and ligand molecules, significantly affect the function by changing the conformational fluctuations. However, it is difficult to systematically understand the role of environmental molecules because intermolecular interactions related to the conformational fluctuations are complicated. To identify important intermolecular interactions with regard to the conformational fluctuations, we develop herein (i) distance-independent and (ii) distance-dependent perturbation analyses of the intermolecular interactions. We show that these perturbation analyses can be realized by performing (i) a principal component analysis using conditional expectations of truncated and shifted intermolecular potential energy terms and (ii) a functional principal component analysis using products of intermolecular forces and conditional cumulative densities. We refer to these analyses as intermolecular perturbation analysis (IPA) and distance-dependent intermolecular perturbation analysis (DIPA), respectively. For comparison of the IPA and the DIPA, we apply them to the alanine dipeptide isomerization in explicit water. Although the first IPA principal components discriminate two states (the α state and PPII (polyproline II) + β states) for larger cutoff length, the separation between the PPII state and the β state is unclear in the second IPA principal components. On the other hand, in the large cutoff value, DIPA eigenvalues converge faster than that for IPA and the top two DIPA principal components clearly identify the three states. By using the DIPA biplot, the contributions of the dipeptide-water interactions to each state are analyzed systematically. Since the DIPA improves the state identification and the convergence rate with retaining distance information, we conclude that the DIPA is a more practical method compared with the IPA. To test the feasibility of the DIPA for larger molecules, we apply the DIPA to the ten-residue chignolin folding in explicit water. The top three principal components identify the four states (native state, two misfolded states, and unfolded state) and their corresponding eigenfunctions identify important chignolin-water interactions to each state. Thus, the DIPA provides the practical method to identify conformational states and their corresponding important intermolecular interactions with distance information.

Perceived Challenges in Primary Literature in a Master's Class: Effects of Experience and Instruction.

PubMed

Lie, Richard; Abdullah, Christopher; He, Wenliang; Tour, Ella

Primary literature offers rich opportunities to teach students how to "think like a scientist," but the challenges students face when they attempt to read research articles are not well understood. Here, we present an analysis of what master's students perceive as the most challenging aspects of engaging with primary literature. We examined 69 pairs of pre- and postcourse responses from students enrolled in a master's-level course that offered a structured analysis of primary literature. On the basis of these responses, we identified six categories of challenges. Before instruction, "techniques" and "experimental data" were the most frequently identified categories of challenges. The majority of difficulties students perceived in the primary literature corresponded to Bloom's lower-order cognitive skills. After instruction, "conclusions" were identified as the most difficult aspect of primary literature, and the frequency of challenges that corresponded to higher-order cognitive skills increased significantly among students who reported less experience with primary literature. These changes are consistent with a more competent perception of the primary literature, in which these students increasingly focus on challenges requiring critical thinking. Students' difficulties identified here can inform the design of instructional approaches aimed to teach students how to critically read scientific papers. © 2016 R. Lie, C. Abdullah, et al. CBE—Life Sciences Education © 2016 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Integrated genetic and epigenetic analysis identifies three different subclasses of colon cancer

PubMed Central

Shen, Lanlan; Toyota, Minoru; Kondo, Yutaka; Lin, E; Zhang, Li; Guo, Yi; Hernandez, Natalie Supunpong; Chen, Xinli; Ahmed, Saira; Konishi, Kazuo; Hamilton, Stanley R.; Issa, Jean-Pierre J.

2007-01-01

Colon cancer has been viewed as the result of progressive accumulation of genetic and epigenetic abnormalities. However, this view does not fully reflect the molecular heterogeneity of the disease. We have analyzed both genetic (mutations of BRAF, KRAS, and p53 and microsatellite instability) and epigenetic alterations (DNA methylation of 27 CpG island promoter regions) in 97 primary colorectal cancer patients. Two clustering analyses on the basis of either epigenetic profiling or a combination of genetic and epigenetic profiling were performed to identify subclasses with distinct molecular signatures. Unsupervised hierarchical clustering of the DNA methylation data identified three distinct groups of colon cancers named CpG island methylator phenotype (CIMP) 1, CIMP2, and CIMP negative. Genetically, these three groups correspond to very distinct profiles. CIMP1 are characterized by MSI (80%) and BRAF mutations (53%) and rare KRAS and p53 mutations (16% and 11%, respectively). CIMP2 is associated with 92% KRAS mutations and rare MSI, BRAF, or p53 mutations (0, 4, and 31% respectively). CIMP-negative cases have a high rate of p53 mutations (71%) and lower rates of MSI (12%) or mutations of BRAF (2%) or KRAS (33%). Clustering based on both genetic and epigenetic parameters also identifies three distinct (and homogeneous) groups that largely overlap with the previous classification. The three groups are independent of age, gender, or stage, but CIMP1 and 2 are more common in proximal tumors. Together, our integrated genetic and epigenetic analysis reveals that colon cancers correspond to three molecularly distinct subclasses of disease. PMID:18003927

Statistical 3D shape analysis of gender differences in lateral ventricles

NASA Astrophysics Data System (ADS)

He, Qing; Karpman, Dmitriy; Duan, Ye

2010-03-01

This paper aims at analyzing gender differences in the 3D shapes of lateral ventricles, which will provide reference for the analysis of brain abnormalities related to neurological disorders. Previous studies mostly focused on volume analysis, and the main challenge in shape analysis is the required step of establishing shape correspondence among individual shapes. We developed a simple and efficient method based on anatomical landmarks. 14 females and 10 males with matching ages participated in this study. 3D ventricle models were segmented from MR images by a semiautomatic method. Six anatomically meaningful landmarks were identified by detecting the maximum curvature point in a small neighborhood of a manually clicked point on the 3D model. Thin-plate spline was used to transform a randomly selected template shape to each of the rest shape instances, and the point correspondence was established according to Euclidean distance and surface normal. All shapes were spatially aligned by Generalized Procrustes Analysis. Hotelling T2 twosample metric was used to compare the ventricle shapes between males and females, and False Discovery Rate estimation was used to correct for the multiple comparison. The results revealed significant differences in the anterior horn of the right ventricle.

Heritable DNA methylation marks associated with susceptibility to breast cancer.

PubMed

Joo, Jihoon E; Dowty, James G; Milne, Roger L; Wong, Ee Ming; Dugué, Pierre-Antoine; English, Dallas; Hopper, John L; Goldgar, David E; Giles, Graham G; Southey, Melissa C

2018-02-28

Mendelian-like inheritance of germline DNA methylation in cancer susceptibility genes has been previously reported. We aimed to scan the genome for heritable methylation marks associated with breast cancer susceptibility by studying 25 Australian multiple-case breast cancer families. Here we report genome-wide DNA methylation measured in 210 peripheral blood DNA samples provided by family members using the Infinium HumanMethylation450. We develop and apply a new statistical method to identify heritable methylation marks based on complex segregation analysis. We estimate carrier probabilities for the 1000 most heritable methylation marks based on family structure, and we use Cox proportional hazards survival analysis to identify 24 methylation marks with corresponding carrier probabilities significantly associated with breast cancer. We replicate an association with breast cancer risk for four of the 24 marks using an independent nested case-control study. Here, we report a novel approach for identifying heritable DNA methylation marks associated with breast cancer risk.

Who is having a voice? Journalists' selection of sources in a creationism controversy in the UK press

NASA Astrophysics Data System (ADS)

Allgaier, Joachim

2011-06-01

Media accounts of reality have the potential to influence public opinion and decision making processes. Therefore who has and who does not have access to the media and can make their voice heard is a crucial question with serious political consequences. In this article it is investigated whether the speciality of journalists influences their source selection procedures. The coverage of science in schools is an interesting example, since it can be covered by specialized science or education correspondents, but also by general news reporters. A public controversy in the UK about the inclusion of creationism in a school is used to identify which types of sources were selected by various journalists. The focus is upon the selection of sources and whether journalists with different specialties consider various sources relevant and credible. A content analysis of articles, featuring this controversy, is combined with an analysis of correspondent's strategies for selecting sources based on interviews with them. The findings suggest that compared to journalists that specialize in education issues, science correspondents employ a narrower scope when seeking sources. This might have important consequences for the representation of views on science education in the media.

Urea free and more efficient sample preparation method for mass spectrometry based protein identification via combining the formic acid-assisted chemical cleavage and trypsin digestion.

PubMed

Wu, Shuaibin; Yang, Kaiguang; Liang, Zhen; Zhang, Lihua; Zhang, Yukui

2011-10-30

A formic acid (FA)-assisted sample preparation method was presented for protein identification via mass spectrometry (MS). Detailedly, an aqueous solution containing 2% FA and dithiothreitol was selected to perform protein denaturation, aspartic acid (D) sites cleavage and disulfide linkages reduction simultaneously at 108°C for 2h. Subsequently, FA wiped off via vacuum concentration. Finally, iodoacetamide (IAA) alkylation and trypsin digestion could be performed ordinally. A series of model proteins (BSA, β-lactoglobulin and apo-Transferrin) were treated respectively using such method, followed by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) analysis. The identified peptide number was increased by ∼ 80% in comparison with the conventional urea-assisted sample preparation method. Moreover, BSA identification was achieved efficiently down to femtomole (25 ± 0 sequence coverage and 16 ± 1 peptides) via such method. In contrast, there were not peptides identified confidently via the urea-assisted method before desalination via the C18 zip tip. The absence of urea in this sample preparation method was an advantage for the more favorable digestion and MALDI-TOF MS analysis. The performances of two methods for the real sample (rat liver proteome) were also compared, followed by a nanoflow reversed-phase liquid chromatography with electrospray ionization tandem mass spectrometry system analysis. As a result, 1335 ± 43 peptides were identified confidently (false discovery rate <1%) via FA-assisted method, corresponding to 295 ± 12 proteins (of top match=1 and requiring 2 unique peptides at least). In contrast, there were only 1107 ± 16 peptides (corresponding to 231 ± 10 proteins) obtained from the conventional urea-assisted method. It was serving as a more efficient protein sample preparation method for researching specific proteomes better, and providing assistance to develop other proteomics analysis methods, such as, peptide quantitative analysis. Copyright © 2011 Elsevier B.V. All rights reserved.

MAISTAS: a tool for automatic structural evaluation of alternative splicing products.

PubMed

Floris, Matteo; Raimondo, Domenico; Leoni, Guido; Orsini, Massimiliano; Marcatili, Paolo; Tramontano, Anna

2011-06-15

Analysis of the human genome revealed that the amount of transcribed sequence is an order of magnitude greater than the number of predicted and well-characterized genes. A sizeable fraction of these transcripts is related to alternatively spliced forms of known protein coding genes. Inspection of the alternatively spliced transcripts identified in the pilot phase of the ENCODE project has clearly shown that often their structure might substantially differ from that of other isoforms of the same gene, and therefore that they might perform unrelated functions, or that they might even not correspond to a functional protein. Identifying these cases is obviously relevant for the functional assignment of gene products and for the interpretation of the effect of variations in the corresponding proteins. Here we describe a publicly available tool that, given a gene or a protein, retrieves and analyses all its annotated isoforms, provides users with three-dimensional models of the isoform(s) of his/her interest whenever possible and automatically assesses whether homology derived structural models correspond to plausible structures. This information is clearly relevant. When the homology model of some isoforms of a gene does not seem structurally plausible, the implications are that either they assume a structure unrelated to that of the other isoforms of the same gene with presumably significant functional differences, or do not correspond to functional products. We provide indications that the second hypothesis is likely to be true for a substantial fraction of the cases. http://maistas.bioinformatica.crs4.it/.

Determination of origin and sugars of citrus fruits using genetic algorithm, correspondence analysis and partial least square combined with fiber optic NIR spectroscopy

NASA Astrophysics Data System (ADS)

Tewari, Jagdish C.; Dixit, Vivechana; Cho, Byoung-Kwan; Malik, Kamal A.

2008-12-01

The capacity to confirm the variety or origin and the estimation of sucrose, glucose, fructose of the citrus fruits are major interests of citrus juice industry. A rapid classification and quantification technique was developed and validated for simultaneous and nondestructive quantifying the sugar constituent's concentrations and the origin of citrus fruits using Fourier Transform Near-Infrared (FT-NIR) spectroscopy in conjunction with Artificial Neural Network (ANN) using genetic algorithm, Chemometrics and Correspondences Analysis (CA). To acquire good classification accuracy and to present a wide range of concentration of sucrose, glucose and fructose, we have collected 22 different varieties of citrus fruits from the market during the entire season of citruses. FT-NIR spectra were recorded in the NIR region from 1100 to 2500 nm using the fiber optic probe and three types of data analysis were performed. Chemometrics analysis using Partial Least Squares (PLS) was performed in order to determine the concentration of individual sugars. Artificial Neural Network analysis was performed for classification, origin or variety identification of citrus fruits using genetic algorithm. Correspondence analysis was performed in order to visualize the relationship between the citrus fruits. To compute a PLS model based upon the reference values and to validate the developed method, high performance liquid chromatography (HPLC) was performed. Spectral range and the number of PLS factors were optimized for the lowest standard error of calibration (SEC), prediction (SEP) and correlation coefficient ( R2). The calibration model developed was able to assess the sucrose, glucose and fructose contents in unknown citrus fruit up to an R2 value of 0.996-0.998. Numbers of factors from F1 to F10 were optimized for correspondence analysis for relationship visualization of citrus fruits based on the output values of genetic algorithm. ANN and CA analysis showed excellent classification of citrus according to the variety to which they belong and well-classified citrus according to their origin. The technique has potential in rapid determination of sugars content and to identify different varieties and origins of citrus in citrus juice industry.

Determination of origin and sugars of citrus fruits using genetic algorithm, correspondence analysis and partial least square combined with fiber optic NIR spectroscopy.

PubMed

Tewari, Jagdish C; Dixit, Vivechana; Cho, Byoung-Kwan; Malik, Kamal A

2008-12-01

The capacity to confirm the variety or origin and the estimation of sucrose, glucose, fructose of the citrus fruits are major interests of citrus juice industry. A rapid classification and quantification technique was developed and validated for simultaneous and nondestructive quantifying the sugar constituent's concentrations and the origin of citrus fruits using Fourier Transform Near-Infrared (FT-NIR) spectroscopy in conjunction with Artificial Neural Network (ANN) using genetic algorithm, Chemometrics and Correspondences Analysis (CA). To acquire good classification accuracy and to present a wide range of concentration of sucrose, glucose and fructose, we have collected 22 different varieties of citrus fruits from the market during the entire season of citruses. FT-NIR spectra were recorded in the NIR region from 1,100 to 2,500 nm using the fiber optic probe and three types of data analysis were performed. Chemometrics analysis using Partial Least Squares (PLS) was performed in order to determine the concentration of individual sugars. Artificial Neural Network analysis was performed for classification, origin or variety identification of citrus fruits using genetic algorithm. Correspondence analysis was performed in order to visualize the relationship between the citrus fruits. To compute a PLS model based upon the reference values and to validate the developed method, high performance liquid chromatography (HPLC) was performed. Spectral range and the number of PLS factors were optimized for the lowest standard error of calibration (SEC), prediction (SEP) and correlation coefficient (R(2)). The calibration model developed was able to assess the sucrose, glucose and fructose contents in unknown citrus fruit up to an R(2) value of 0.996-0.998. Numbers of factors from F1 to F10 were optimized for correspondence analysis for relationship visualization of citrus fruits based on the output values of genetic algorithm. ANN and CA analysis showed excellent classification of citrus according to the variety to which they belong and well-classified citrus according to their origin. The technique has potential in rapid determination of sugars content and to identify different varieties and origins of citrus in citrus juice industry.

Predictors of in-hospital mortality amongst octogenarians undergoing emergency general surgery: a retrospective cohort study.

PubMed

Wilson, Iain; Paul Barrett, Michael; Sinha, Ashish; Chan, Shirley

2014-11-01

Elderly patients are often judged to be fit for emergency surgery based on age alone. This study identified risk factors predictive of in-hospital mortality amongst octogenarians undergoing emergency general surgery. A retrospective review of octogenarians undergoing emergency general surgery over 3 years was performed. Parametric survival analysis using Cox multivariate regression model was used to identify risk factors predictive of in-hospital mortality. Hazard ratios (HR) and corresponding 95% confidence interval were calculated. Seventy-three patients with a median age of 84 years were identified. Twenty-eight (38%) patients died post-operatively. Multivariate analysis identified ASA grade (ASA 5 HR 23.4 95% CI 2.38-230, p = 0.007) and chronic obstructive pulmonary disease (COPD) (HR 3.35 95% CI 1.15-9.69, p = 0.026) to be the only significant predictors of in-hospital mortality. Identification of high risk surgical patients should be based on physiological fitness for surgery rather than chronological age. Crown Copyright © 2014. Published by Elsevier Ltd. All rights reserved.

Immunoinformatic Analysis of Crimean Congo Hemorrhagic Fever Virus Glycoproteins and Epitope Prediction for Synthetic Peptide Vaccine.

PubMed

Tipu, Hamid Nawaz

2016-02-01

To determine the Crimean Congo Hemorrhagic Fever (CCHF) virus M segement glycoprotein's immunoinformatic parameters, and identify Human Leukocyte Antigen (HLA) class I binders as candidates for synthetic peptide vaccines. Cross-sectional study. Combined Military Hospital, Khuzdar Cantt, in May 2015. Data acquisition, antigenicity prediction, secondary and tertiary structure prediction, residue analysis were done using immunoinformatics tools. HLAclass I binders in glycoprotein's sequence were identified at nanomer length using NetMHC 3.4 and mapped onto tertiary structure. Docking was done for strongest binder against its corresponding allele with CABS-dock. HLAA*0101, 0201, 0301, 2402, 2601 and B*0702, 0801, 2705, 3901, 4001, 5801, 1501 were analyzed against two glycoprotein components of the virus. Atotal of 35 nanomers from GP1, and 3 from GP2 were identified. HLAB*0702 bound maximum number of peptides (6), while HLAB*4001 showed strongest binding affinity. HLAspecific glycoproteins epitope prediction can help identify synthetic peptide vaccine candidates.

Automated identification of best-quality coronary artery segments from multiple-phase coronary CT angiography (cCTA) for vessel analysis

NASA Astrophysics Data System (ADS)

Zhou, Chuan; Chan, Heang-Ping; Hadjiiski, Lubomir M.; Chughtai, Aamer; Wei, Jun; Kazerooni, Ella A.

2016-03-01

We are developing an automated method to identify the best quality segment among the corresponding segments in multiple-phase cCTA. The coronary artery trees are automatically extracted from different cCTA phases using our multi-scale vessel segmentation and tracking method. An automated registration method is then used to align the multiple-phase artery trees. The corresponding coronary artery segments are identified in the registered vessel trees and are straightened by curved planar reformation (CPR). Four features are extracted from each segment in each phase as quality indicators in the original CT volume and the straightened CPR volume. Each quality indicator is used as a voting classifier to vote the corresponding segments. A newly designed weighted voting ensemble (WVE) classifier is finally used to determine the best-quality coronary segment. An observer preference study is conducted with three readers to visually rate the quality of the vessels in 1 to 6 rankings. Six and 10 cCTA cases are used as training and test set in this preliminary study. For the 10 test cases, the agreement between automatically identified best-quality (AI-BQ) segments and radiologist's top 2 rankings is 79.7%, and between AI-BQ and the other two readers are 74.8% and 83.7%, respectively. The results demonstrated that the performance of our automated method was comparable to those of experienced readers for identification of the best-quality coronary segments.

Cross-scale analysis of cluster correspondence using different operational neighborhoods

NASA Astrophysics Data System (ADS)

Lu, Yongmei; Thill, Jean-Claude

2008-09-01

Cluster correspondence analysis examines the spatial autocorrelation of multi-location events at the local scale. This paper argues that patterns of cluster correspondence are highly sensitive to the definition of operational neighborhoods that form the spatial units of analysis. A subset of multi-location events is examined for cluster correspondence if they are associated with the same operational neighborhood. This paper discusses the construction of operational neighborhoods for cluster correspondence analysis based on the spatial properties of the underlying zoning system and the scales at which the zones are aggregated into neighborhoods. Impacts of this construction on the degree of cluster correspondence are also analyzed. Empirical analyses of cluster correspondence between paired vehicle theft and recovery locations are conducted on different zoning methods and across a series of geographic scales and the dynamics of cluster correspondence patterns are discussed.

Rmg8, a New Gene for Resistance to Triticum Isolates of Pyricularia oryzae in Hexaploid Wheat.

PubMed

Anh, Vu Lan; Anh, Nguyen Tuan; Tagle, Analiza Grubanzo; Vy, Trinh Thi Phuong; Inoue, Yoshihiro; Takumi, Shigeo; Chuma, Izumi; Tosa, Yukio

2015-12-01

Blast, caused by Pyricularia oryzae, is one of the major diseases of wheat in South America. We identified a new gene for resistance to Triticum isolates of P. oryzae in common wheat 'S-615', and designated it "resistance to Magnaporthe grisea 8" (Rmg8). Rmg8 was assigned to chromosome 2B through molecular mapping with simple-sequence repeat markers. To identify an avirulence gene corresponding to Rmg8, Triticum isolate Br48 (avirulent on S-615) was crossed with 200R29 (virulent on S-615), an F1 progeny derived from a cross between an Eleusine isolate (MZ5-1-6) and Br48. Segregation analysis of their progeny revealed that avirulence of Br48 on S-615 was conditioned by a single gene, which was designated AVR-Rmg8. AVR-Rmg8 was closely linked to AVR-Rmg7, which corresponded to Rmg7 located on chromosome 2A of tetraploid wheat.

Correlative feature analysis on FFDM

PubMed Central

Yuan, Yading; Giger, Maryellen L.; Li, Hui; Sennett, Charlene

2008-01-01

Identifying the corresponding images of a lesion in different views is an essential step in improving the diagnostic ability of both radiologists and computer-aided diagnosis (CAD) systems. Because of the nonrigidity of the breasts and the 2D projective property of mammograms, this task is not trivial. In this pilot study, we present a computerized framework that differentiates between corresponding images of the same lesion in different views and noncorresponding images, i.e., images of different lesions. A dual-stage segmentation method, which employs an initial radial gradient index (RGI) based segmentation and an active contour model, is applied to extract mass lesions from the surrounding parenchyma. Then various lesion features are automatically extracted from each of the two views of each lesion to quantify the characteristics of density, size, texture and the neighborhood of the lesion, as well as its distance to the nipple. A two-step scheme is employed to estimate the probability that the two lesion images from different mammographic views are of the same physical lesion. In the first step, a correspondence metric for each pairwise feature is estimated by a Bayesian artificial neural network (BANN). Then, these pairwise correspondence metrics are combined using another BANN to yield an overall probability of correspondence. Receiver operating characteristic (ROC) analysis was used to evaluate the performance of the individual features and the selected feature subset in the task of distinguishing corresponding pairs from noncorresponding pairs. Using a FFDM database with 123 corresponding image pairs and 82 noncorresponding pairs, the distance feature yielded an area under the ROC curve (AUC) of 0.81±0.02 with leave-one-out (by physical lesion) evaluation, and the feature metric subset, which included distance, gradient texture, and ROI-based correlation, yielded an AUC of 0.87±0.02. The improvement by using multiple feature metrics was statistically significant compared to single feature performance. PMID:19175108

Independent Orbiter Assessment (IOA): Analysis of the manned maneuvering unit

NASA Technical Reports Server (NTRS)

Bailey, P. S.

1986-01-01

Results of the Independent Orbiter Assessment (IOA) of the Failure Modes and Effects Analysis (FMEA) and Critical Items List (CIL) are presented. The IOA approach features a top-down analysis of the hardware to determine failure modes, criticality, and potential critical items (PCIs). To preserve indepedence, this analysis was accomplished without reliance upon the results contained within the NASA FMEA/CIL documentation. This report documents the independent analysis results corresponding to the Manned Maneuvering Unit (MMU) hardware. The MMU is a propulsive backpack, operated through separate hand controllers that input the pilot's translational and rotational maneuvering commands to the control electronics and then to the thrusters. The IOA analysis process utilized available MMU hardware drawings and schematics for defining hardware subsystems, assemblies, components, and hardware items. Final levels of detail were evaluated and analyzed for possible failure modes and effects. Criticality was assigned based upon the worst case severity of the effect for each identified failure mode. The IOA analysis of the MMU found that the majority of the PCIs identified are resultant from the loss of either the propulsion or control functions, or are resultant from inability to perform an immediate or future mission. The five most severe criticalities identified are all resultant from failures imposed on the MMU hand controllers which have no redundancy within the MMU.

Reducing power consumption during execution of an application on a plurality of compute nodes

DOEpatents

Archer, Charles J [Rochester, MN; Blocksome, Michael A [Rochester, MN; Peters, Amanda E [Rochester, MN; Ratterman, Joseph D [Rochester, MN; Smith, Brian E [Rochester, MN

2012-06-05

Methods, apparatus, and products are disclosed for reducing power consumption during execution of an application on a plurality of compute nodes that include: executing, by each compute node, an application, the application including power consumption directives corresponding to one or more portions of the application; identifying, by each compute node, the power consumption directives included within the application during execution of the portions of the application corresponding to those identified power consumption directives; and reducing power, by each compute node, to one or more components of that compute node according to the identified power consumption directives during execution of the portions of the application corresponding to those identified power consumption directives.

Blooming Trees: Substructures and Surrounding Groups of Galaxy Clusters

NASA Astrophysics Data System (ADS)

Yu, Heng; Diaferio, Antonaldo; Serra, Ana Laura; Baldi, Marco

2018-06-01

We develop the Blooming Tree Algorithm, a new technique that uses spectroscopic redshift data alone to identify the substructures and the surrounding groups of galaxy clusters, along with their member galaxies. Based on the estimated binding energy of galaxy pairs, the algorithm builds a binary tree that hierarchically arranges all of the galaxies in the field of view. The algorithm searches for buds, corresponding to gravitational potential minima on the binary tree branches; for each bud, the algorithm combines the number of galaxies, their velocity dispersion, and their average pairwise distance into a parameter that discriminates between the buds that do not correspond to any substructure or group, and thus eventually die, and the buds that correspond to substructures and groups, and thus bloom into the identified structures. We test our new algorithm with a sample of 300 mock redshift surveys of clusters in different dynamical states; the clusters are extracted from a large cosmological N-body simulation of a ΛCDM model. We limit our analysis to substructures and surrounding groups identified in the simulation with mass larger than 1013 h ‑1 M ⊙. With mock redshift surveys with 200 galaxies within 6 h ‑1 Mpc from the cluster center, the technique recovers 80% of the real substructures and 60% of the surrounding groups; in 57% of the identified structures, at least 60% of the member galaxies of the substructures and groups belong to the same real structure. These results improve by roughly a factor of two the performance of the best substructure identification algorithm currently available, the σ plateau algorithm, and suggest that our Blooming Tree Algorithm can be an invaluable tool for detecting substructures of galaxy clusters and investigating their complex dynamics.

The Multiple Correspondence Analysis Method and Brain Functional Connectivity: Its Application to the Study of the Non-linear Relationships of Motor Cortex and Basal Ganglia.

PubMed

Rodriguez-Sabate, Clara; Morales, Ingrid; Sanchez, Alberto; Rodriguez, Manuel

2017-01-01

The complexity of basal ganglia (BG) interactions is often condensed into simple models mainly based on animal data and that present BG in closed-loop cortico-subcortical circuits of excitatory/inhibitory pathways which analyze the incoming cortical data and return the processed information to the cortex. This study was aimed at identifying functional relationships in the BG motor-loop of 24 healthy-subjects who provided written, informed consent and whose BOLD-activity was recorded by MRI methods. The analysis of the functional interaction between these centers by correlation techniques and multiple linear regression showed non-linear relationships which cannot be suitably addressed with these methods. The multiple correspondence analysis (MCA), an unsupervised multivariable procedure which can identify non-linear interactions, was used to study the functional connectivity of BG when subjects were at rest. Linear methods showed different functional interactions expected according to current BG models. MCA showed additional functional interactions which were not evident when using lineal methods. Seven functional configurations of BG were identified with MCA, two involving the primary motor and somatosensory cortex, one involving the deepest BG (external-internal globus pallidum, subthalamic nucleus and substantia nigral), one with the input-output BG centers (putamen and motor thalamus), two linking the input-output centers with other BG (external pallidum and subthalamic nucleus), and one linking the external pallidum and the substantia nigral. The results provide evidence that the non-linear MCA and linear methods are complementary and should be best used in conjunction to more fully understand the nature of functional connectivity of brain centers.

Symbolic universes between present and future of Europe. First results of the map of European societies' cultural milieu.

PubMed

Salvatore, Sergio; Fini, Viviana; Mannarini, Terri; Veltri, Giuseppe Alessandro; Avdi, Evrinomi; Battaglia, Fiorella; Castro-Tejerina, Jorge; Ciavolino, Enrico; Cremaschi, Marco; Kadianaki, Irini; Kharlamov, Nikita A; Krasteva, Anna; Kullasepp, Katrin; Matsopoulos, Anastassios; Meschiari, Claudia; Mossi, Piergiorgio; Psinas, Polivios; Redd, Rozlyn; Rochira, Alessia; Santarpia, Alfonso; Sammut, Gordon; Valsiner, Jaan; Valmorbida, Antonella

2018-01-01

This paper reports the framework, method and main findings of an analysis of cultural milieus in 4 European countries (Estonia, Greece, Italy, and UK). The analysis is based on a questionnaire applied to a sample built through a two-step procedure of post-hoc random selection from a broader dataset based on an online survey. Responses to the questionnaire were subjected to multidimensional analysis-a combination of Multiple Correspondence Analysis and Cluster Analysis. We identified 5 symbolic universes, that correspond to basic, embodied, affect-laden, generalized worldviews. People in this study see the world as either a) an ordered universe; b) a matter of interpersonal bond; c) a caring society; d) consisting of a niche of belongingness; e) a hostile place (others' world). These symbolic universes were also interpreted as semiotic capital: they reflect the capacity of a place to foster social and civic development. Moreover, the distribution of the symbolic universes, and therefore social and civic engagement, is demonstrated to be variable across the 4 countries in the analysis. Finally, we develop a retrospective reconstruction of the distribution of symbolic universes as well as the interplay between their current state and past, present and future socio-institutional scenarios.

Comparing Help-Seeking Behavior of Male and Female Survivors of Sexual Assault: A Content Analysis of a Hotline.

PubMed

Young, Stephen M; Pruett, Jana A; Colvin, Marianna L

2018-06-01

This content analysis examines written documentation of telephone calls to a regional sexual assault hotline over a 5-year period. All male callers identified as primary victims were selected for analysis ( n = 58) and a corresponding sample of female primary victims ( n = 58) were randomly selected for comparison to better understand the help-seeking behavior of sexual assault survivors and inform services accordingly. A summative content analysis revealed significant contrasting themes between male and female victims, including females significantly receiving more referrals and males accessing the hotline to tell their experience of being sexually assaulted due to perceived limited support. Implications for training, practice, and future research are discussed.

Informative Feature Selection for Object Recognition via Sparse PCA

DTIC Science & Technology

2011-04-07

constraint on images collected from low-power camera net- works instead of high-end photography is that establishing wide-baseline feature correspondence of...variable selection tool for selecting informative features in the object images captured from low-resolution cam- era sensor networks. Firstly, we...More examples can be found in Figure 4 later. 3. Identifying Informative Features Classical PCA is a well established tool for the analysis of high

Human parietofrontal networks related to action observation detected at rest.

PubMed

Molinari, Elisa; Baraldi, Patrizia; Campanella, Martina; Duzzi, Davide; Nocetti, Luca; Pagnoni, Giuseppe; Porro, Carlo A

2013-01-01

Recent data show a broad correspondence between human resting-state and task-related brain networks. We performed a functional magnetic resonance imaging (fMRI) study to compare, in the same subjects, the spatial independent component analysis (ICA) maps obtained at rest and during the observation of either reaching/grasping hand actions or matching static pictures. Two parietofrontal networks were identified by ICA from action observation task data. One network, specific to reaching/grasping observation, included portions of the anterior intraparietal cortex and of the dorsal and ventral lateral premotor cortices. A second network included more posterior portions of the parietal lobe, the dorsomedial frontal cortex, and more anterior and ventral parts, respectively, of the dorsal and ventral premotor cortices, extending toward Broca's area; this network was more generally related to the observation of hand action and static pictures. A good spatial correspondence was found between the 2 observation-related ICA maps and 2 ICA maps identified from resting-state data. The anatomical connectivity among the identified clusters was tested in the same volunteers, using persistent angular structure-MRI and deterministic tractography. These findings extend available knowledge of human parietofrontal circuits and further support the hypothesis of a persistent coherence within functionally relevant networks during rest.

The pig CYP2E1 promoter is activated by COUP-TF1 and HNF-1 and is inhibited by androstenone.

PubMed

Tambyrajah, Winston S; Doran, Elena; Wood, Jeffrey D; McGivan, John D

2004-11-15

Functional analysis of the pig cytochrome P4502E1 (CYP2E1) promoter identified two major activating elements. One corresponded to the hepatic nuclear factor 1 (HNF-1) consensus binding sequence at nucleotides -128/-98 and the other was located in the region -292/-266. The binding of proteins in pig liver nuclear extracts to a synthetic double-stranded oligonucleotide corresponding to this more distal activating sequence was studied by electrophoretic mobility shift assay. The minimum protein binding sequence was identified as TGTTCTGACCTCTGGG. Gel super-shift assays identified the protein binding to this site as chick ovalbumin upstream promoter transcription factor 1 (COUP-TF1). Androstenone inhibited promoter activity in transfection experiments only with constructs which included the COUP-TF1 binding site. Androstenone inhibited COUP-TF1 binding to synthetic oligonucleotides but did not affect HNF-1 binding. The results offer an explanation for the inhibition of CYP2E1 protein expression by androstenone in isolated pig hepatocytes and may be relevant to the low expression of hepatic CYP2E1 in those pigs which accumulate high levels of androstenone in vivo.

Investigating the viral ecology of global bee communities with high-throughput metagenomics.

PubMed

Galbraith, David A; Fuller, Zachary L; Ray, Allyson M; Brockmann, Axel; Frazier, Maryann; Gikungu, Mary W; Martinez, J Francisco Iturralde; Kapheim, Karen M; Kerby, Jeffrey T; Kocher, Sarah D; Losyev, Oleksiy; Muli, Elliud; Patch, Harland M; Rosa, Cristina; Sakamoto, Joyce M; Stanley, Scott; Vaudo, Anthony D; Grozinger, Christina M

2018-06-11

Bee viral ecology is a fascinating emerging area of research: viruses exert a range of effects on their hosts, exacerbate impacts of other environmental stressors, and, importantly, are readily shared across multiple bee species in a community. However, our understanding of bee viral communities is limited, as it is primarily derived from studies of North American and European Apis mellifera populations. Here, we examined viruses in populations of A. mellifera and 11 other bee species from 9 countries, across 4 continents and Oceania. We developed a novel pipeline to rapidly and inexpensively screen for bee viruses. This pipeline includes purification of encapsulated RNA/DNA viruses, sequence-independent amplification, high throughput sequencing, integrated assembly of contigs, and filtering to identify contigs specifically corresponding to viral sequences. We identified sequences for (+)ssRNA, (-)ssRNA, dsRNA, and ssDNA viruses. Overall, we found 127 contigs corresponding to novel viruses (i.e. previously not observed in bees), with 27 represented by >0.1% of the reads in a given sample, and 7 contained an RdRp or replicase sequence which could be used for robust phylogenetic analysis. This study provides a sequence-independent pipeline for viral metagenomics analysis, and greatly expands our understanding of the diversity of viruses found in bee communities.

Mentha suaveolens Ehrh. Chemotypes in Eastern Iberian Peninsula: Essential Oil Variation and Relation with Ecological Factors.

PubMed

Llorens-Molina, Juan Antonio; Rivera Seclén, Cynthia Fiorella; Vacas Gonzalez, Sandra; Boira Tortajada, Herminio

2017-12-01

Essential oil (EO) extracts coming from two representative populations of Mentha suaveolens Ehrh. subesp. suaveolens in Eastern Iberian Peninsula were analyzed by gas chromatography coupled with mass spectrometry and flame ion detector. Plant sampling was carried out in the morning and evening in order to study diurnal variation in EO profiles. Likewise, leaves and inflorescences were analyzed separately. Two chemotypes corresponding to each one of the populations were identified, with piperitenone oxide (35.2 - 74.3%) and piperitone oxide (83.9 - 91.3%), respectively, as major compounds. Once different chemotypes were identified, canonical correspondence analysis was employed to evaluate the effect of the bioclimatic and edaphic factors recorded in each location on the observed differences. Statistical analysis suggested that these chemotypes were closely related to specific environmental factors, mainly the bioclimatic ones. Concretely, piperitenone oxide chemotype can be associated to supramediterranean bioclimatic conditions and soils with major salinity and water field capacity. On the other hand, the most volatile fraction (hydrocarbon monoterpenes) reached its higher level in the morning; specifically, a noticeable amount of limonene was found in morning samples of flowers (4.8 - 10.6%). This fact can be related to ecological role of volatile compounds in order to attract pollinator insects. © 2017 Wiley-VHCA AG, Zurich, Switzerland.

Suppression subtractive hybridization and comparative expression analysis to identify developmentally regulated genes in filamentous fungi.

PubMed

Gesing, Stefan; Schindler, Daniel; Nowrousian, Minou

2013-09-01

Ascomycetes differentiate four major morphological types of fruiting bodies (apothecia, perithecia, pseudothecia and cleistothecia) that are derived from an ancestral fruiting body. Thus, fruiting body differentiation is most likely controlled by a set of common core genes. One way to identify such genes is to search for genes with evolutionary conserved expression patterns. Using suppression subtractive hybridization (SSH), we selected differentially expressed transcripts in Pyronema confluens (Pezizales) by comparing two cDNA libraries specific for sexual and for vegetative development, respectively. The expression patterns of selected genes from both libraries were verified by quantitative real time PCR. Expression of several corresponding homologous genes was found to be conserved in two members of the Sordariales (Sordaria macrospora and Neurospora crassa), a derived group of ascomycetes that is only distantly related to the Pezizales. Knockout studies with N. crassa orthologues of differentially regulated genes revealed a functional role during fruiting body development for the gene NCU05079, encoding a putative MFS peptide transporter. These data indicate conserved gene expression patterns and a functional role of the corresponding genes during fruiting body development; such genes are candidates of choice for further functional analysis. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Secretomic survey of Trichoderma harzianum grown on plant biomass substrates.

PubMed

Gómez-Mendoza, Diana Paola; Junqueira, Magno; do Vale, Luis Henrique Ferreira; Domont, Gilberto Barbosa; Ferreira Filho, Edivaldo Ximenes; Sousa, Marcelo Valle de; Ricart, Carlos André Ornelas

2014-04-04

The present work aims at characterizing T. harzianum secretome when the fungus is grown in synthetic medium supplemented with one of the four substrates: glucose, cellulose, xylan, and sugarcane bagasse (SB). The characterization was done by enzymatic assays and proteomic analysis using 2-DE/MALDI-TOF and gel-free shotgun LC-MS/MS. The results showed that SB induced the highest cellulolytic and xylanolytic activities when compared with the other substrates, while remarkable differences in terms of number and distribution of protein spots in 2-DE gels were also observed among the samples. Additionally, treatment of the secretomes with PNGase F revealed that most spot trails in 2-DE gels corresponded to N-glycosylated proteoforms. The LC-MS/MS analysis of the samples identified 626 different protein groups, including carbohydrate-active enzymes and accessory, noncatalytic, and cell-wall-associated proteins. Although the SB-induced secretome displayed the highest cellulolytic and xylanolytic activities, it did not correspond to a higher proteome complexity because CM-cellulose-induced secretome was significantly more diverse. Among the identified proteins, 73% were exclusive to one condition, while only 5% were present in all samples. Therefore, this study disclosed the variation of T. harzianum secretome in response to different substrates and revealed the diversity of the fungus enzymatic toolbox.

Identification of linear and threshold responses in streams along a gradient of urbanization in Anchorage, Alaska

USGS Publications Warehouse

Ourso, R.T.; Frenzel, S.A.

2003-01-01

We examined biotic and physiochemical responses in urbanized Anchorage, Alaska, to the percent of impervious area within stream basins, as determined by high-resolution IKONOS satellite imagery and aerial photography. Eighteen of the 86 variables examined, including riparian and instream habitat, macroinvertebrate communities, and water/sediment chemistry, were significantly correlated with percent impervious area. Variables related to channel condition, instream substrate, water chemistry, and residential and transportation right-of-way land uses were identified by principal components analysis as significant factors separating site groups. Detrended canonical correspondence analysis indicated that the macroinvertebrate communities responded to an urbanization gradient closely paralleling the percent of impervious area within the subbasin. A sliding regression analysis of variables significantly correlated with percent impervious area revealed 8 variables exhibiting threshold responses that correspond to a mean of 4.4-5.8% impervious area, much lower than mean values reported in other, similar investigations. As contributing factors to a subbasin's impervious area, storm drains and roads appeared to be important elements influencing the degradation of water quality with respect to the biota.

Development of a Novel Technology for Label Free DNA Sequencing

DTIC Science & Technology

2012-05-21

of the C-H bond stretch vibrations in the planes of the corresponding DNA bases , and in the higher-frequency side, sequence-identifier region is...composed of the N-H bond stretch vibrations in the planes of the corresponding DNA bases . In addition, the sequence-identifier dividing region almost...regions are localized at the corresponding DNA bases and exhibit a definable dependence on the sequence form of the codons under study. Final

Elementary Mode Analysis: A Useful Metabolic Pathway Analysis Tool for Characterizing Cellular Metabolism

PubMed Central

Trinh, Cong T.; Wlaschin, Aaron; Srienc, Friedrich

2010-01-01

Elementary Mode Analysis is a useful Metabolic Pathway Analysis tool to identify the structure of a metabolic network that links the cellular phenotype to the corresponding genotype. The analysis can decompose the intricate metabolic network comprised of highly interconnected reactions into uniquely organized pathways. These pathways consisting of a minimal set of enzymes that can support steady state operation of cellular metabolism represent independent cellular physiological states. Such pathway definition provides a rigorous basis to systematically characterize cellular phenotypes, metabolic network regulation, robustness, and fragility that facilitate understanding of cell physiology and implementation of metabolic engineering strategies. This mini-review aims to overview the development and application of elementary mode analysis as a metabolic pathway analysis tool in studying cell physiology and as a basis of metabolic engineering. PMID:19015845

Construction of a genetic linkage map and analysis of quantitative trait loci associated with the agronomically important traits of Pleurotus eryngii.

PubMed

Im, Chak Han; Park, Young-Hoon; Hammel, Kenneth E; Park, Bokyung; Kwon, Soon Wook; Ryu, Hojin; Ryu, Jae-San

2016-07-01

Breeding new strains with improved traits is a long-standing goal of mushroom breeders that can be expedited by marker-assisted selection (MAS). We constructed a genetic linkage map of Pleurotus eryngii based on segregation analysis of markers in postmeiotic monokaryons from KNR2312. In total, 256 loci comprising 226 simple sequence-repeat (SSR) markers, 2 mating-type factors, and 28 insertion/deletion (InDel) markers were mapped. The map consisted of 12 linkage groups (LGs) spanning 1047.8cM, with an average interval length of 4.09cM. Four independent populations (Pd3, Pd8, Pd14, and Pd15) derived from crossing between four monokaryons from KNR2532 as a tester strain and 98 monokaryons from KNR2312 were used to characterize quantitative trait loci (QTL) for nine traits such as yield, quality, cap color, and earliness. Using composite interval mapping (CIM), 71 QTLs explaining between 5.82% and 33.17% of the phenotypic variations were identified. Clusters of more than five QTLs for various traits were identified in three genomic regions, on LGs 1, 7 and 9. Regardless of the population, 6 of the 9 traits studied and 18 of the 71 QTLs found in this study were identified in the largest cluster, LG1, in the range from 65.4 to 110.4cM. The candidate genes for yield encoding transcription factor, signal transduction, mycelial growth and hydrolase are suggested by using manual and computational analysis of genome sequence corresponding to QTL region with the highest likelihood odds (LOD) for yield. The genetic map and the QTLs established in this study will help breeders and geneticists to develop selection markers for agronomically important characteristics of mushrooms and to identify the corresponding genes. Copyright © 2016 Elsevier Inc. All rights reserved.

Clinical and Epidemiological Characteristics of Suicides Committed in Medellin, Colombia.

PubMed

Ortega, Paula Andrea; Manrique, Ruben Darío; Tovilla Zarate, Carlos Alfonso; López Jaramillo, Carlos; Cuartas, Jorge Mauricio

2014-01-01

The purpose of this study was to identify the characteristics of individuals who committed suicide in Medellín between 2008 and 2010, and to identify variables related to the type of events. A retrospective and descriptive analysis was conducted on data provided by the National Institute of Legal Medicine and Forensic Sciences. In addition, a univariate and bivariate analysis was used to identify the sociodemographic and medical-legal characteristics of the deceased. Multiple correspondence analysis was also used in order to establish typologies. The information was analyzed using STATA 11.0. Of the 389 cases occurring between 2008 and 2010, 84.6% (n=329) were men. The male to female ratio was 5:1; 64% of the cases occurred in people aged 18-45 years; 6.7% occurred in children under 18, with hanging being the method most chosen by the victims (48.3%). Exploratory analysis was used to identify a possible association between the use of violent methods and events occurring in the housing and social strata 1, 2 and 3. Some factors could be associated with suicide, providing data that could consolidate health intervention strategies in our population. Copyright © 2013 Asociación Colombiana de Psiquiatría. Publicado por Elsevier España. All rights reserved.

Real-time synchronization of kinematic and video data for the comprehensive assessment of surgical skills.

PubMed

Dosis, Aristotelis; Bello, Fernando; Moorthy, Krishna; Munz, Yaron; Gillies, Duncan; Darzi, Ara

2004-01-01

Surgical dexterity in operating theatres has traditionally been assessed subjectively. Electromagnetic (EM) motion tracking systems such as the Imperial College Surgical Assessment Device (ICSAD) have been shown to produce valid and accurate objective measures of surgical skill. To allow for video integration we have modified the data acquisition and built it within the ROVIMAS analysis software. We then used ActiveX 9.0 DirectShow video capturing and the system clock as a time stamp for the synchronized concurrent acquisition of kinematic data and video frames. Interactive video/motion data browsing was implemented to allow the user to concentrate on frames exhibiting certain kinematic properties that could result in operative errors. We exploited video-data synchronization to calculate the camera visual hull by identifying all 3D vertices using the ICSAD electromagnetic sensors. We also concentrated on high velocity peaks as a means of identifying potential erroneous movements to be confirmed by studying the corresponding video frames. The outcome of the study clearly shows that the kinematic data are precisely synchronized with the video frames and that the velocity peaks correspond to large and sudden excursions of the instrument tip. We validated the camera visual hull by both video and geometrical kinematic analysis and we observed that graphs containing fewer sudden velocity peaks are less likely to have erroneous movements. This work presented further developments to the well-established ICSAD dexterity analysis system. Synchronized real-time motion and video acquisition provides a comprehensive assessment solution by combining quantitative motion analysis tools and qualitative targeted video scoring.

Novel Loci for Metabolic Networks and Multi-Tissue Expression Studies Reveal Genes for Atherosclerosis

PubMed Central

Inouye, Michael; Ripatti, Samuli; Kettunen, Johannes; Lyytikäinen, Leo-Pekka; Oksala, Niku; Laurila, Pirkka-Pekka; Kangas, Antti J.; Soininen, Pasi; Savolainen, Markku J.; Viikari, Jorma; Kähönen, Mika; Perola, Markus; Salomaa, Veikko; Raitakari, Olli; Lehtimäki, Terho; Taskinen, Marja-Riitta; Järvelin, Marjo-Riitta; Ala-Korpela, Mika; Palotie, Aarno; de Bakker, Paul I. W.

2012-01-01

Association testing of multiple correlated phenotypes offers better power than univariate analysis of single traits. We analyzed 6,600 individuals from two population-based cohorts with both genome-wide SNP data and serum metabolomic profiles. From the observed correlation structure of 130 metabolites measured by nuclear magnetic resonance, we identified 11 metabolic networks and performed a multivariate genome-wide association analysis. We identified 34 genomic loci at genome-wide significance, of which 7 are novel. In comparison to univariate tests, multivariate association analysis identified nearly twice as many significant associations in total. Multi-tissue gene expression studies identified variants in our top loci, SERPINA1 and AQP9, as eQTLs and showed that SERPINA1 and AQP9 expression in human blood was associated with metabolites from their corresponding metabolic networks. Finally, liver expression of AQP9 was associated with atherosclerotic lesion area in mice, and in human arterial tissue both SERPINA1 and AQP9 were shown to be upregulated (6.3-fold and 4.6-fold, respectively) in atherosclerotic plaques. Our study illustrates the power of multi-phenotype GWAS and highlights candidate genes for atherosclerosis. PMID:22916037

UPLC-MSE Profiling of Phytoplankton Metabolites: Application to the Identification of Pigments and Structural Analysis of Metabolites in Porphyridium purpureum

PubMed Central

Juin, Camille; Bonnet, Antoine; Nicolau, Elodie; Bérard, Jean-Baptiste; Devillers, Romain; Thiéry, Valérie; Cadoret, Jean-Paul; Picot, Laurent

2015-01-01

A fast and high-resolution UPLC-MSE analysis was used to identify phytoplankton pigments in an ethanol extract of Porphyridium purpureum (Pp) devoid of phycobiliproteins. In a first step, 22 standard pigments were analyzed by UPLC-MSE to build a database including retention time and accurate masses of parent and fragment ions. Using this database, seven pigments or derivatives previously reported in Pp were unequivocally identified: β,β-carotene, chlorophyll a, zeaxanthin, chlorophyllide a, pheophorbide a, pheophytin a, and cryptoxanthin. Minor amounts of Divinyl chlorophyll a, a chemotaxonomic pigment marker for prochlorophytes, were also unequivocally identified using the database. Additional analysis of ionization and fragmentation patterns indicated the presence of ions that could correspond to hydroxylated derivatives of chlorophyll a and pheophytin a, produced during the ethanolic extraction, as well as previously described galactosyldiacylglycerols, the thylakoid coenzyme plastoquinone, and gracilamide B, a molecule previously reported in the red seaweed Gracillaria asiatica. These data point to UPLC-MSE as an efficient technique to identify phytoplankton pigments for which standards are available, and demonstrate its major interest as a complementary method for the structural elucidation of ionizable marine molecules. PMID:25913708

Source apportionment of 1 h semi-continuous data during the 2005 Study of Organic Aerosols in Riverside (SOAR) using positive matrix factorization

NASA Astrophysics Data System (ADS)

Eatough, Delbert J.; Grover, Brett D.; Woolwine, Woods R.; Eatough, Norman L.; Long, Russell; Farber, Robert

Positive matrix factorization (PMF2) was used to elucidate sources of fine particulate material (PM 2.5) for a study conducted during July and August 2005, in Riverside, CA. One-hour averaged semi-continuous measurements were made with a suite of instruments to provide PM 2.5 mass and chemical composition data. Total PM 2.5 mass concentrations (non-volatile plus semi-volatile) were measured with an R&P filter dynamic measurement system (FDMS TEOM) and a conventional TEOM monitor was used to measure non-volatile mass concentrations. PM 2.5 chemical species monitors included a dual-oven Sunset monitor to measure both non-volatile and semi-volatile carbonaceous material, an ion chromatographic-based monitor to measure sulfate and nitrate and an Anderson Aethalometer to measure black carbon (BC). Gas phase data including CO, NO 2, NO x and O 3 were also collected during the sampling period. In addition, single-particle measurements were made using aerosol time-of-flight mass spectrometry (ATOFMS). Twenty different single-particle types consistent with those observed in previous ATOFMS studies in Riverside were identified for the PMF2 analysis. Finally, time-of-flight aerosol mass spectrometry (ToF-AMS) provided data on markers of primary and secondary organic aerosol. Two distinct PMF2 analyses were performed. In analysis 1, all the data except for the ATOFMS and ToF-AMS data were used in an initial evaluation of sources at Riverside during the study. PMF2 was able to identify six factors from the data set corresponding to both primary and secondary sources, primarily from automobile emissions, diesel emissions, secondary nitrate formation, a secondary photochemical associated source, organic emissions and Basin transported pollutants. In analysis 2, the ATOFMS and ToF-AMS data were included in the analysis. In the second analysis, PMF2 was able to identify 16 factors with a variety of both primary and secondary factors being identified, corresponding to both primary and secondary material from both anthropogenic and natural sources. Based on relationships with Basin meteorology, the PMF identified source profiles and diurnal patterns in the source concentrations, sources were identified as being of local origin or resulting from transport of pollutants across the Basin due to onshore flow. Good agreement was observed between the PMF2 predicted mass and the FDMS measured mass for both analyses.

Bacterial community characterization and biogeochemistry of sediments from a tropical upwelling system (Cabo Frio, Southeastern Brazil)

NASA Astrophysics Data System (ADS)

Castelo-Branco, R.; Barreiro, A.; Silva, F. S.; Carvalhal-Gomes, S. B. V.; Fontana, L. F.; Mendonça-Filho, J. G.; Vasconcelos, V.

2016-11-01

The Cabo Frio Upwelling System is one of the largest and most productive areas in southeastern Brazil. Although it is well-known that bacterial communities play a crucial role in the biogeochemical cycles and food chain of marine ecosystems, little is known regarding the microbial communities in the sediments of this upwelling region. In this research, we address the effect of different hydrological conditions on the biogeochemistry of sediments and the diversity of bacterial communities. Biogeochemistry profiles of sediments from four sampling stations along an inner-outer transect on the continental shelf were evaluated and denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA gene fragments was used to study the bacterial community composition in these sediments. Our sequencing analysis of excised bands identified Alpha- and Gammaproteobacteria, Bacteroidetes and bacteria belonging to the Firmicutes phyla as the phylogenetic groups, indicating the existence of great diversity in these marine sediments. In this multidisciplinary study, the use of multivariate analysis was crucial for understanding how biogeochemical profiles influence bacterial community distribution. A Principal Component Analysis (PCA) indicated that the biogeochemical variables exhibited a clear spatial pattern that is mainly related to hydrological conditions. A Correspondence Analysis (CA) revealed an important association between certain taxonomic groups and specific sampling locations. Canonical Correspondence Analysis (CCA) demonstrated that the biogeochemistry influences the structure of the bacterial community in sediments. Among the bacterial groups identified, the most taxonomically diverse classes (Alphaproteobacteria and Gammaproteobacteria) were found to be distributed regardless of any studied biogeochemical variables influences, whereas other groups responded to biogeochemical conditions which, in turn, were influenced by hydrological conditions. This finding was observed for members of the two classes in the Bacteroidetes phylum, which were associated with either proteins or carbohydrates.

Comparative study of contrast-enhanced ultrasound qualitative and quantitative analysis for identifying benign and malignant breast tumor lumps.

PubMed

Liu, Jian; Gao, Yun-Hua; Li, Ding-Dong; Gao, Yan-Chun; Hou, Ling-Mi; Xie, Ting

2014-01-01

To compare the value of contrast-enhanced ultrasound (CEUS) qualitative and quantitative analysis in the identification of breast tumor lumps. Qualitative and quantitative indicators of CEUS for 73 cases of breast tumor lumps were retrospectively analyzed by univariate and multivariate approaches. Logistic regression was applied and ROC curves were drawn for evaluation and comparison. The CEUS qualitative indicator-generated regression equation contained three indicators, namely enhanced homogeneity, diameter line expansion and peak intensity grading, which demonstrated prediction accuracy for benign and malignant breast tumor lumps of 91.8%; the quantitative indicator-generated regression equation only contained one indicator, namely the relative peak intensity, and its prediction accuracy was 61.5%. The corresponding areas under the ROC curve for qualitative and quantitative analyses were 91.3% and 75.7%, respectively, which exhibited a statistically significant difference by the Z test (P<0.05). The ability of CEUS qualitative analysis to identify breast tumor lumps is better than with quantitative analysis.

Image analysis technique as a tool to identify morphological changes in Trametes versicolor pellets according to exopolysaccharide or laccase production.

PubMed

Tavares, Ana P M; Silva, Rui P; Amaral, António L; Ferreira, Eugénio C; Xavier, Ana M R B

2014-02-01

Image analysis technique was applied to identify morphological changes of pellets from white-rot fungus Trametes versicolor on agitated submerged cultures during the production of exopolysaccharide (EPS) or ligninolytic enzymes. Batch tests with four different experimental conditions were carried out. Two different culture media were used, namely yeast medium or Trametes defined medium and the addition of lignolytic inducers as xylidine or pulp and paper industrial effluent were evaluated. Laccase activity, EPS production, and final biomass contents were determined for batch assays and the pellets morphology was assessed by image analysis techniques. The obtained data allowed establishing the choice of the metabolic pathways according to the experimental conditions, either for laccase enzymatic production in the Trametes defined medium, or for EPS production in the rich Yeast Medium experiments. Furthermore, the image processing and analysis methodology allowed for a better comprehension of the physiological phenomena with respect to the corresponding pellets morphological stages.

Uncertainty Reduction using Bayesian Inference and Sensitivity Analysis: A Sequential Approach to the NASA Langley Uncertainty Quantification Challenge

NASA Technical Reports Server (NTRS)

Sankararaman, Shankar

2016-01-01

This paper presents a computational framework for uncertainty characterization and propagation, and sensitivity analysis under the presence of aleatory and epistemic un- certainty, and develops a rigorous methodology for efficient refinement of epistemic un- certainty by identifying important epistemic variables that significantly affect the overall performance of an engineering system. The proposed methodology is illustrated using the NASA Langley Uncertainty Quantification Challenge (NASA-LUQC) problem that deals with uncertainty analysis of a generic transport model (GTM). First, Bayesian inference is used to infer subsystem-level epistemic quantities using the subsystem-level model and corresponding data. Second, tools of variance-based global sensitivity analysis are used to identify four important epistemic variables (this limitation specified in the NASA-LUQC is reflective of practical engineering situations where not all epistemic variables can be refined due to time/budget constraints) that significantly affect system-level performance. The most significant contribution of this paper is the development of the sequential refine- ment methodology, where epistemic variables for refinement are not identified all-at-once. Instead, only one variable is first identified, and then, Bayesian inference and global sensi- tivity calculations are repeated to identify the next important variable. This procedure is continued until all 4 variables are identified and the refinement in the system-level perfor- mance is computed. The advantages of the proposed sequential refinement methodology over the all-at-once uncertainty refinement approach are explained, and then applied to the NASA Langley Uncertainty Quantification Challenge problem.

The identification of job opportunities for severely disabled sick-listed employees

PubMed Central

2012-01-01

Background Work disability is a major problem for both the worker and society. To explore the work opportunities in regular jobs of persons low in functional abilities, we tried to identify occupations low in task demands. Because of the variety of functional abilities and of the corresponding work demands, the disabled persons need to be classified by type of disability in a limited number of subgroups. Within each subgroup, occupations judged suitable for the most seriously disabled will be selected as having a very low level of the corresponding task demands. These occupations can be applied as reference occupations to assess the presence or absence of work capacity of sick-listed employees in regular jobs, and as job opportunities for people with a specific type of functional disability. Methods Registered data from 50,931 disability assessments within the Dutch social security system were used in a second order factor analysis to identify types of disabilities in claimants for a disability pension. Threshold values were chosen to classify claimants according to the severity of the disability. In the disability assessment procedure, a labour expert needs to select jobs with task demands not exceeding the functional abilities of the claimant. For each type of disability, the accessible jobs for the subgroup of the most severely disabled claimants were identified as lowest in the corresponding demand. Results The factor analysis resulted in four types of disabilities: general physical ability; autonomy; psychological ability; and manual skills. For each of these types of disablement, a set of four to six occupations low in task demands were selected for the subgroup of most severely disabled claimants. Because of an overlap of the sets of occupations, 13 occupations were selected in total. The percentage of claimants with at least one of the occupations of the corresponding set (the coverage), ranged from 84% to 93%. An alternative selection of six occupations for all subgroups with even less overlap had a coverage ranging from 84% to 89% per subgroup. Conclusion This study resulted in two proposals for a set of reference occupations. Further research will be needed to compare the results of the new method of disability assessment to the results of the method presently used in practice. PMID:22394686

Do key dimensions of seed and seedling functional trait variation capture variation in recruitment probability?

PubMed

Larson, Julie E; Sheley, Roger L; Hardegree, Stuart P; Doescher, Paul S; James, Jeremy J

2016-05-01

Seedling recruitment is a critical driver of population dynamics and community assembly, yet we know little about functional traits that define different recruitment strategies. For the first time, we examined whether trait relatedness across germination and seedling stages allows the identification of general recruitment strategies which share core functional attributes and also correspond to recruitment outcomes in applied settings. We measured six seed and eight seedling traits (lab- and field-collected, respectively) for 47 varieties of dryland grasses and used principal component analysis (PCA) and cluster analysis to identify major dimensions of trait variation and to isolate trait-based recruitment groups, respectively. PCA highlighted some links between seed and seedling traits, suggesting that relative growth rate and root elongation rate are simultaneously but independently associated with seed mass and initial root mass (first axis), and with leaf dry matter content, specific leaf area, coleoptile tissue density and germination rate (second axis). Third and fourth axes captured separate tradeoffs between hydrothermal time and base water potential for germination, and between specific root length and root mass ratio, respectively. Cluster analysis separated six recruitment types along dimensions of germination and growth rates, but classifications did not correspond to patterns of germination, emergence or recruitment in the field under either of two watering treatments. Thus, while we have begun to identify major threads of functional variation across seed and seedling stages, our understanding of how this variation influences demographic processes-particularly germination and emergence-remains a key gap in functional ecology.

AbsIDconvert: An absolute approach for converting genetic identifiers at different granularities

PubMed Central

2012-01-01

Background High-throughput molecular biology techniques yield vast amounts of data, often by detecting small portions of ribonucleotides corresponding to specific identifiers. Existing bioinformatic methodologies categorize and compare these elements using inferred descriptive annotation given this sequence information irrespective of the fact that it may not be representative of the identifier as a whole. Results All annotations, no matter the granularity, can be aligned to genomic sequences and therefore annotated by genomic intervals. We have developed AbsIDconvert, a methodology for converting between genomic identifiers by first mapping them onto a common universal coordinate system using an interval tree which is subsequently queried for overlapping identifiers. AbsIDconvert has many potential uses, including gene identifier conversion, identification of features within a genomic region, and cross-species comparisons. The utility is demonstrated in three case studies: 1) comparative genomic study mapping plasmodium gene sequences to corresponding human and mosquito transcriptional regions; 2) cross-species study of Incyte clone sequences; and 3) analysis of human Ensembl transcripts mapped by Affymetrix®; and Agilent microarray probes. AbsIDconvert currently supports ID conversion of 53 species for a given list of input identifiers, genomic sequence, or genome intervals. Conclusion AbsIDconvert provides an efficient and reliable mechanism for conversion between identifier domains of interest. The flexibility of this tool allows for custom definition identifier domains contingent upon the availability and determination of a genomic mapping interval. As the genomes and the sequences for genetic elements are further refined, this tool will become increasingly useful and accurate. AbsIDconvert is freely available as a web application or downloadable as a virtual machine at: http://bioinformatics.louisville.edu/abid/. PMID:22967011

Systems-level analysis of cell-specific AQP2 gene expression in renal collecting duct.

PubMed

Yu, Ming-Jiun; Miller, R Lance; Uawithya, Panapat; Rinschen, Markus M; Khositseth, Sookkasem; Braucht, Drew W W; Chou, Chung-Lin; Pisitkun, Trairak; Nelson, Raoul D; Knepper, Mark A

2009-02-17

We used a systems biology-based approach to investigate the basis of cell-specific expression of the water channel aquaporin-2 (AQP2) in the renal collecting duct. Computational analysis of the 5'-flanking region of the AQP2 gene (Genomatix) revealed 2 conserved clusters of putative transcriptional regulator (TR) binding elements (BEs) centered at -513 bp (corresponding to the SF1, NFAT, and FKHD TR families) and -224 bp (corresponding to the AP2, SRF, CREB, GATA, and HOX TR families). Three other conserved motifs corresponded to the ETS, EBOX, and RXR TR families. To identify TRs that potentially bind to these BEs, we carried out mRNA profiling (Affymetrix) in mouse mpkCCDc14 collecting duct cells, revealing expression of 25 TRs that are also expressed in native inner medullary collecting duct. One showed a significant positive correlation with AQP2 mRNA abundance among mpkCCD subclones (Ets1), and 2 showed a significant negative correlation (Elf1 and an orphan nuclear receptor Nr1h2). Transcriptomic profiling in native proximal tubules (PT), medullary thick ascending limbs (MTAL), and IMCDs from kidney identified 14 TRs (including Ets1 and HoxD3) expressed in the IMCD but not PT or MTAL (candidate AQP2 enhancer roles), and 5 TRs (including HoxA5, HoxA9 and HoxA10) expressed in PT and MTAL but not in IMCD (candidate AQP2 repressor roles). In luciferase reporter assays, overexpression of 3 ETS family TRs transactivated the mouse proximal AQP2 promoter. The results implicate ETS family TRs in cell-specific expression of AQP2 and point to HOX, RXR, CREB and GATA family TRs as playing likely additional roles.

Chiral Tagging of Verbenone with 3-BUTYN-2-OL for Establishing Absolute Configuration and Determining Enantiomeric Excess

NASA Astrophysics Data System (ADS)

Evangelisti, Luca; Mayer, Kevin J.; Holdren, Martin S.; Smart, Taylor; West, Channing; Pate, Brooks; Sedo, Galen; Marshall, Frank E.; Grubbs, G. S., II

2017-06-01

Chiral analysis of a commercial sample of (1S)-(-)-verbenone has been performed using the chiral tag approach. The chirped-pulse Fourier transform microwave spectrum of the verbenone-butynol complex is measured in the 2-8 GHz frequency range. Verbenone is placed in a nozzle reservoir heated to 333K (about 1 Torr vapor pressure). The complex is formed by using a carrier gas of neon with approximately 0.1% butynol. The expansion pressure is about 2 atm. A measurement using racemic butynol is performed to identify isomers of both diastereomer complexes. Quantum chemistry calculations using the B3LYP-D3BJ method with the def2TZVP basis set provided estimated spectroscopic constants for the homochiral and heterochiral complexes. This analysis included 8 isomers for each diastereomer. Four rotational spectra are identified for isomers of the homochiral complex and correspond to the four lowest energy isomers from the theoretical study. Three heterochiral complexes are identified and also correspond to the lowest energy isomers from theory. Subsequent measurements were made with enantiopure tag (both (R)-(+)-3-buty-2-nol and (S)-(-)-3-butyn-2-ol) to establish the absolute configuration of verbenone. The sensitivity of the measurement was sufficient to perform ^{13}C-isotopologue analysis of three of the homochiral complexes and two of the heterochiral complexes. These results provide definitive structures of verbenone with correct stereochemistry. The commercial sample has relatively low enantiomeric excess with the certificate of analysis reporting an EE of 53.6%. Using the intensities of assigned transitions of the chiral tag complexes, the enantiomeric excess was determined from the broadband rotational spectrum through the ratio of the intensities of pairs of transitions. A total of 2617 pairs of transitions were analyzed. The average EE was found to be 53.6% with a standard deviation of 2%.

Identification of a putative protein profile associated with tamoxifen therapy resistance in breast cancer.

PubMed

Umar, Arzu; Kang, Hyuk; Timmermans, Annemieke M; Look, Maxime P; Meijer-van Gelder, Marion E; den Bakker, Michael A; Jaitly, Navdeep; Martens, John W M; Luider, Theo M; Foekens, John A; Pasa-Tolić, Ljiljana

2009-06-01

Tamoxifen resistance is a major cause of death in patients with recurrent breast cancer. Current clinical factors can correctly predict therapy response in only half of the treated patients. Identification of proteins that are associated with tamoxifen resistance is a first step toward better response prediction and tailored treatment of patients. In the present study we intended to identify putative protein biomarkers indicative of tamoxifen therapy resistance in breast cancer using nano-LC coupled with FTICR MS. Comparative proteome analysis was performed on approximately 5,500 pooled tumor cells (corresponding to approximately 550 ng of protein lysate/analysis) obtained through laser capture microdissection (LCM) from two independently processed data sets (n = 24 and n = 27) containing both tamoxifen therapy-sensitive and therapy-resistant tumors. Peptides and proteins were identified by matching mass and elution time of newly acquired LC-MS features to information in previously generated accurate mass and time tag reference databases. A total of 17,263 unique peptides were identified that corresponded to 2,556 non-redundant proteins identified with > or = 2 peptides. 1,713 overlapping proteins between the two data sets were used for further analysis. Comparative proteome analysis revealed 100 putatively differentially abundant proteins between tamoxifen-sensitive and tamoxifen-resistant tumors. The presence and relative abundance for 47 differentially abundant proteins were verified by targeted nano-LC-MS/MS in a selection of unpooled, non-microdissected discovery set tumor tissue extracts. ENPP1, EIF3E, and GNB4 were significantly associated with progression-free survival upon tamoxifen treatment for recurrent disease. Differential abundance of our top discriminating protein, extracellular matrix metalloproteinase inducer, was validated by tissue microarray in an independent patient cohort (n = 156). Extracellular matrix metalloproteinase inducer levels were higher in therapy-resistant tumors and significantly associated with an earlier tumor progression following first line tamoxifen treatment (hazard ratio, 1.87; 95% confidence interval, 1.25-2.80; p = 0.002). In summary, comparative proteomics performed on laser capture microdissection-derived breast tumor cells using nano-LC-FTICR MS technology revealed a set of putative biomarkers associated with tamoxifen therapy resistance in recurrent breast cancer.

P-Element Insertion Alleles of Essential Genes on the Third Chromosome of Drosophila Melanogaster: Correlation of Physical and Cytogenetic Maps in Chromosomal Region 86e-87f

PubMed Central

Deak, P.; Omar, M. M.; Saunders, RDC.; Pal, M.; Komonyi, O.; Szidonya, J.; Maroy, P.; Zhang, Y.; Ashburner, M.; Benos, P.; Savakis, C.; Siden-Kiamos, I.; Louis, C.; Bolshakov, V. N.; Kafatos, F. C.; Madueno, E.; Modolell, J.; Glover, D. M.

1997-01-01

We have established a collection of 2460 lethal or semi-lethal mutant lines using a procedure thought to insert single P elements into vital genes on the third chromosome of Drosophila melanogaster. More than 1200 randomly selected lines were examined by in situ hybridization and 90% found to contain single insertions at sites that mark 89% of all lettered subdivisions of the Bridges' map. A set of chromosomal deficiencies that collectively uncover ~25% of the euchromatin of chromosome 3 reveal lethal mutations in 468 lines corresponding to 145 complementation groups. We undertook a detailed analysis of the cytogenetic interval 86E-87F and identified 87 P-element-induced mutations falling into 38 complementation groups, 16 of which correspond to previously known genes. Twenty-one of these 38 complementation groups have at least one allele that has a P-element insertion at a position consistent with the cytogenetics of the locus. We have rescued P elements and flanking chromosomal sequences from the 86E-87F region in 35 lines with either lethal or genetically silent P insertions, and used these as probes to identify cosmids and P1 clones from the Drosophila genome projects. This has tied together the physical and genetic maps and has linked 44 previously identified cosmid contigs into seven ``supercontigs'' that span the interval. STS data for sequences flanking one side of the P-element insertions in 49 lines has identified insertions in the αγ element at 87C, two known transposable elements, and the open reading frames of seven putative single copy genes. These correspond to five known genes in this interval, and two genes identified by the homology of their predicted products to known proteins from other organisms. PMID:9409831

The ribosomal protein genes and Minute loci of Drosophila melanogaster

PubMed Central

Marygold, Steven J; Roote, John; Reuter, Gunter; Lambertsson, Andrew; Ashburner, Michael; Millburn, Gillian H; Harrison, Paul M; Yu, Zhan; Kenmochi, Naoya; Kaufman, Thomas C; Leevers, Sally J; Cook, Kevin R

2007-01-01

Background Mutations in genes encoding ribosomal proteins (RPs) have been shown to cause an array of cellular and developmental defects in a variety of organisms. In Drosophila melanogaster, disruption of RP genes can result in the 'Minute' syndrome of dominant, haploinsufficient phenotypes, which include prolonged development, short and thin bristles, and poor fertility and viability. While more than 50 Minute loci have been defined genetically, only 15 have so far been characterized molecularly and shown to correspond to RP genes. Results We combined bioinformatic and genetic approaches to conduct a systematic analysis of the relationship between RP genes and Minute loci. First, we identified 88 genes encoding 79 different cytoplasmic RPs (CRPs) and 75 genes encoding distinct mitochondrial RPs (MRPs). Interestingly, nine CRP genes are present as duplicates and, while all appear to be functional, one member of each gene pair has relatively limited expression. Next, we defined 65 discrete Minute loci by genetic criteria. Of these, 64 correspond to, or very likely correspond to, CRP genes; the single non-CRP-encoding Minute gene encodes a translation initiation factor subunit. Significantly, MRP genes and more than 20 CRP genes do not correspond to Minute loci. Conclusion This work answers a longstanding question about the molecular nature of Minute loci and suggests that Minute phenotypes arise from suboptimal protein synthesis resulting from reduced levels of cytoribosomes. Furthermore, by identifying the majority of haplolethal and haplosterile loci at the molecular level, our data will directly benefit efforts to attain complete deletion coverage of the D. melanogaster genome. PMID:17927810

Phase-field model for isothermal phase transitions in binary alloys

NASA Technical Reports Server (NTRS)

Wheeler, A. A.; Boettinger, W. J.; Mcfadden, G. B.

1992-01-01

A new phase field model is described which models isothermal phase transitions between ideal binary alloy solution phases. Equations are developed for the temporal and spatial variation of the phase field, which describes the identity of the phase, and of the composition. An asymptotic analysis, as the gradient energy coefficient of the phase field becomes small, was conducted. From the analysis, it is shown that the model recovers classical sharp interface models of this situation when the interfacial layers are thin, and they show how to relate the parameters appearing in the phase field model to material and growth parameters in real systems. Further, three stages of temporal evolution are identified: the first corresponding to interfacial genesis which occurs very rapidly; the second to interfacial motion controlled by the local energy difference across the interface and diffusion; the last taking place on a long time scale in which curvature effects are important and which correspond to Ostwald ripening. The results of the numerical calculations are presented.

Alcohol and cannabis consumption in the French Army: determination of consumer profiles to focus on prevention and care.

PubMed

Rigod, Violaine; Pilard, Michel; Paul, Frédéric; Deparis, Xavier; Marimoutou, Catherine

2011-07-01

To ascertain the different profiles of alcohol and cannabis consumers in the French Army to improve prevention measures. A representative sample of 990 French Army staff filled in self-questionnaires in 2006. A multiple correspondence analysis identified associations between consumption and consumer profiles. The multiple correspondence analysis found three main consumer profiles: non-consumers (women and officers), moderate consumers (non-commissioned officers > 30-years old, single parents with children), and occasional multi-consumers (18-25-years-old enlisted males, who occasionally consumed cannabis and high levels of alcohol, also tobacco-addicts). Two minor profiles emerged: daily alcohol drinkers (men, > or = 30 years) and regular dependent cannabis users (identical profile to multi-consumers). Our results favor targeting the youngest to prevent the risks of high alcohol intake and cannabis consumption and addiction linked to repeated binge drinking. Systematic questionnaires on consumption habits and addiction self-evaluations during medical consultations could lead to early care.

A Survey of Correspondence Course Training.

ERIC Educational Resources Information Center

Rocklyn, Eugene H.

Correspondence course training (CCT) systems, primarily in the military and government sectors, were surveyed to identify their critical problems. Other study objectives were to formulate the basic design of a CCT system to solve these problems and identify course completion factors and trends in systems operations. Seventeen CCT organizations…

Investigation of cell wall composition related to stem lodging resistance in wheat (Triticum aestivum L.) by FTIR spectroscopy.

PubMed

Wang, Jian; Zhu, Jinmao; Huang, RuZhu; Yang, YuSheng

2012-07-01

We explored the rapid qualitative analysis of wheat cultivars with good lodging resistances by Fourier transform infrared resonance (FTIR) spectroscopy and multivariate statistical analysis. FTIR imaging showing that wheat stem cell walls were mainly composed of cellulose, pectin, protein, and lignin. Principal components analysis (PCA) was used to eliminate multicollinearity among multiple peak absorptions. PCA revealed the developmental internodes of wheat stems could be distributed from low to high along the load of the second principal component, which was consistent with the corresponding bands of cellulose in the FTIR spectra of the cell walls. Furthermore, four distinct stem populations could also be identified by spectral features related to their corresponding mechanical properties via PCA and cluster analysis. Histochemical staining of four types of wheat stems with various abilities to resist lodging revealed that cellulose contributed more than lignin to the ability to resist lodging. These results strongly suggested that the main cell wall component responsible for these differences was cellulose. Therefore, the combination of multivariate analysis and FTIR could rapidly screen wheat cultivars with good lodging resistance. Furthermore, the application of these methods to a much wider range of cultivars of unknown mechanical properties promises to be of interest.

Symbolic universes between present and future of Europe. First results of the map of European societies' cultural milieu

PubMed Central

Fini, Viviana; Mannarini, Terri; Veltri, Giuseppe Alessandro; Avdi, Evrinomi; Battaglia, Fiorella; Castro-Tejerina, Jorge; Ciavolino, Enrico; Cremaschi, Marco; Kadianaki, Irini; Kharlamov, Nikita A.; Krasteva, Anna; Kullasepp, Katrin; Matsopoulos, Anastassios; Meschiari, Claudia; Mossi, Piergiorgio; Psinas, Polivios; Redd, Rozlyn; Rochira, Alessia; Santarpia, Alfonso; Sammut, Gordon; Valsiner, Jaan; Valmorbida, Antonella

2018-01-01

This paper reports the framework, method and main findings of an analysis of cultural milieus in 4 European countries (Estonia, Greece, Italy, and UK). The analysis is based on a questionnaire applied to a sample built through a two-step procedure of post-hoc random selection from a broader dataset based on an online survey. Responses to the questionnaire were subjected to multidimensional analysis–a combination of Multiple Correspondence Analysis and Cluster Analysis. We identified 5 symbolic universes, that correspond to basic, embodied, affect-laden, generalized worldviews. People in this study see the world as either a) an ordered universe; b) a matter of interpersonal bond; c) a caring society; d) consisting of a niche of belongingness; e) a hostile place (others’ world). These symbolic universes were also interpreted as semiotic capital: they reflect the capacity of a place to foster social and civic development. Moreover, the distribution of the symbolic universes, and therefore social and civic engagement, is demonstrated to be variable across the 4 countries in the analysis. Finally, we develop a retrospective reconstruction of the distribution of symbolic universes as well as the interplay between their current state and past, present and future socio-institutional scenarios. PMID:29298349

minepath.org: a free interactive pathway analysis web server.

PubMed

Koumakis, Lefteris; Roussos, Panos; Potamias, George

2017-07-03

( www.minepath.org ) is a web-based platform that elaborates on, and radically extends the identification of differentially expressed sub-paths in molecular pathways. Besides the network topology, the underlying MinePath algorithmic processes exploit exact gene-gene molecular relationships (e.g. activation, inhibition) and are able to identify differentially expressed pathway parts. Each pathway is decomposed into all its constituent sub-paths, which in turn are matched with corresponding gene expression profiles. The highly ranked, and phenotype inclined sub-paths are kept. Apart from the pathway analysis algorithm, the fundamental innovation of the MinePath web-server concerns its advanced visualization and interactive capabilities. To our knowledge, this is the first pathway analysis server that introduces and offers visualization of the underlying and active pathway regulatory mechanisms instead of genes. Other features include live interaction, immediate visualization of functional sub-paths per phenotype and dynamic linked annotations for the engaged genes and molecular relations. The user can download not only the results but also the corresponding web viewer framework of the performed analysis. This feature provides the flexibility to immediately publish results without publishing source/expression data, and get all the functionality of a web based pathway analysis viewer. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Computational approaches for identification of conserved/unique binding pockets in the A chain of ricin

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

Ecale Zhou, C L; Zemla, A T; Roe, D

2005-01-29

Specific and sensitive ligand-based protein detection assays that employ antibodies or small molecules such as peptides, aptamers, or other small molecules require that the corresponding surface region of the protein be accessible and that there be minimal cross-reactivity with non-target proteins. To reduce the time and cost of laboratory screening efforts for diagnostic reagents, we developed new methods for evaluating and selecting protein surface regions for ligand targeting. We devised combined structure- and sequence-based methods for identifying 3D epitopes and binding pockets on the surface of the A chain of ricin that are conserved with respect to a set ofmore » ricin A chains and unique with respect to other proteins. We (1) used structure alignment software to detect structural deviations and extracted from this analysis the residue-residue correspondence, (2) devised a method to compare corresponding residues across sets of ricin structures and structures of closely related proteins, (3) devised a sequence-based approach to determine residue infrequency in local sequence context, and (4) modified a pocket-finding algorithm to identify surface crevices in close proximity to residues determined to be conserved/unique based on our structure- and sequence-based methods. In applying this combined informatics approach to ricin A we identified a conserved/unique pocket in close proximity (but not overlapping) the active site that is suitable for bi-dentate ligand development. These methods are generally applicable to identification of surface epitopes and binding pockets for development of diagnostic reagents, therapeutics, and vaccines.« less

Identification of Chinese plague foci from long-term epidemiological data

PubMed Central

Ben-Ari, Tamara; Neerinckx, Simon; Agier, Lydiane; Cazelles, Bernard; Xu, Lei; Zhang, Zhibin; Fang, Xiye; Wang, Shuchun; Liu, Qiyong; Stenseth, Nils C.

2012-01-01

Carrying out statistical analysis over an extensive dataset of human plague reports in Chinese villages from 1772 to 1964, we identified plague endemic territories in China (i.e., plague foci). Analyses rely on (i) a clustering method that groups time series based on their time-frequency resemblances and (ii) an ecological niche model that helps identify plague suitable territories characterized by value ranges for a set of predefined environmental variables. Results from both statistical tools indicate the existence of two disconnected plague territories corresponding to Northern and Southern China. Altogether, at least four well defined independent foci are identified. Their contours compare favorably with field observations. Potential and limitations of inferring plague foci and dynamics using epidemiological data is discussed. PMID:22570501

Taxicab Correspondence Analysis of Contingency Tables with One Heavyweight Column

ERIC Educational Resources Information Center

Choulakian, V.

2008-01-01

The aim of this paper is to study the analysis of contingency tables with one heavyweight column or one heavyweight entry by taxicab correspondence analysis (TCA). Given that the mathematics of TCA is simpler than the mathematics of correspondence analysis (CA), the influence of one heavyweight column on the outputs of TCA is studied explicitly…

Comparative analysis of the mating-type loci from Neurospora crassa and Sordaria macrospora: identification of novel transcribed ORFs.

PubMed

Pöggeler, S; Kück, U

2000-03-01

The mating-type locus controls mating and sexual development in filamentous ascomycetes. In the heterothallic ascomycete Neurospora crassa, the genes that confer mating behavior comprise dissimilar DNA sequences (idiomorphs) in the mat a and mat A mating partners. In the homothallic fungus Sordaria macrospora, sequences corresponding to both idiomorphs are located contiguously in the mating-type locus, which contains one chimeric gene, Smt A-3, that includes sequences which are similar to sequences found at the mat A and mat a mating-type idiomorphs in N. crassa. In this study, we describe the comparative transcriptional analysis of the chimeric mating-type region of S. macrospora and the corresponding region of the N. crassa mat a idiomorph. By means of RT-PCR experiments, we identified novel intervening sequences in the mating-type loci of both ascomycetes and, hence, concluded that an additional ORF, encoding a putative polypeptide of 79 amino acids, is present in the N. crassa mat a idiomorph. Furthermore, our analysis revealed co-transcription of the novel gene with the mat a-1 gene in N. crassa. The same mode of transcription was found in the corresponding mating-type region of S. macrospora, where the chimeric Smt A-3 gene is co-transcribed with the mat a-specific Smt a-1 gene. Analysis of a Smt A-3 cDNA revealed optional splicing of two introns. We believe that this is the first report of co-transcription of protein-encoding nuclear genes in filamentous fungi. Possible functions of the novel ORFs in regulating mating-type gene expression are discussed.

A novel Bayesian approach to acoustic emission data analysis.

PubMed

Agletdinov, E; Pomponi, E; Merson, D; Vinogradov, A

2016-12-01

Acoustic emission (AE) technique is a popular tool for materials characterization and non-destructive testing. Originating from the stochastic motion of defects in solids, AE is a random process by nature. The challenging problem arises whenever an attempt is made to identify specific points corresponding to the changes in the trends in the fluctuating AE time series. A general Bayesian framework is proposed for the analysis of AE time series, aiming at automated finding the breakpoints signaling a crossover in the dynamics of underlying AE sources. Copyright © 2016 Elsevier B.V. All rights reserved.

Large-Scale Analysis of Network Bistability for Human Cancers

PubMed Central

Shiraishi, Tetsuya; Matsuyama, Shinako; Kitano, Hiroaki

2010-01-01

Protein–protein interaction and gene regulatory networks are likely to be locked in a state corresponding to a disease by the behavior of one or more bistable circuits exhibiting switch-like behavior. Sets of genes could be over-expressed or repressed when anomalies due to disease appear, and the circuits responsible for this over- or under-expression might persist for as long as the disease state continues. This paper shows how a large-scale analysis of network bistability for various human cancers can identify genes that can potentially serve as drug targets or diagnosis biomarkers. PMID:20628618

Description of the supporting factors of final project in Mathematics and Natural Sciences Faculty of Syiah Kuala University with multiple correspondence analysis

NASA Astrophysics Data System (ADS)

Rusyana, Asep; Nurhasanah; Maulizasari

2018-05-01

Syiah Kuala University (Unsyiah) is hoped to have graduates who are qualified for working or creating a field of work. A final project course implementation process must be effective. This research uses data from the evaluation conducted by Mathematics and Natural Sciences Faculty (FMIPA) of Unsyiah. Some of the factors that support the completion of the final project are duration, guidance, the final project seminars, facility, public impact, and quality. This research aims to know the factors that have a relationship with the completion of the final project and identify similarities among variables. The factors that support the completion of the final project at every study program in FMIPA are (1) duration, (2) guidance and (3) facilities. These factors are examined for the correlations by chi-square test. After that, the variables are analyzed with multiple correspondence analysis. Based on the plot of correspondence, the activities of the guidance and facilities in Informatics Study Program are included in the fair category, while the guidance and facilities in the Chemistry are included in the best category. Besides that, students in Physics can finish the final project with the fastest completion duration, while students in Pharmacy finish for the longest time.

Visualizing weakly bound surface Fermi arcs and their correspondence to bulk Weyl fermions

PubMed Central

Batabyal, Rajib; Morali, Noam; Avraham, Nurit; Sun, Yan; Schmidt, Marcus; Felser, Claudia; Stern, Ady; Yan, Binghai; Beidenkopf, Haim

2016-01-01

Fermi arcs are the surface manifestation of the topological nature of Weyl semimetals, enforced by the bulk-boundary correspondence with the bulk Weyl nodes. The surface of tantalum arsenide, similar to that of other members of the Weyl semimetal class, hosts nontopological bands that obscure the exploration of this correspondence. We use the spatial structure of the Fermi arc wave function, probed by scanning tunneling microscopy, as a spectroscopic tool to distinguish and characterize the surface Fermi arc bands. We find that, as opposed to nontopological states, the Fermi arc wave function is weakly affected by the surface potential: it spreads rather uniformly within the unit cell and penetrates deeper into the bulk. Fermi arcs reside predominantly on tantalum sites, from which the topological bulk bands are derived. Furthermore, we identify a correspondence between the Fermi arc dispersion and the energy and momentum of the bulk Weyl nodes that classify this material as topological. We obtain these results by introducing an analysis based on the role the Bloch wave function has in shaping quantum electronic interference patterns. It thus carries broader applicability to the study of other electronic systems and other physical processes. PMID:27551687

Terahertz spectral unmixing based method for identifying gastric cancer

NASA Astrophysics Data System (ADS)

Cao, Yuqi; Huang, Pingjie; Li, Xian; Ge, Weiting; Hou, Dibo; Zhang, Guangxin

2018-02-01

At present, many researchers are exploring biological tissue inspection using terahertz time-domain spectroscopy (THz-TDS) techniques. In this study, based on a modified hard modeling factor analysis method, terahertz spectral unmixing was applied to investigate the relationships between the absorption spectra in THz-TDS and certain biomarkers of gastric cancer in order to systematically identify gastric cancer. A probability distribution and box plot were used to extract the distinctive peaks that indicate carcinogenesis, and the corresponding weight distributions were used to discriminate the tissue types. The results of this work indicate that terahertz techniques have the potential to detect different levels of cancer, including benign tumors and polyps.

Simultaneous Two-Way Clustering of Multiple Correspondence Analysis

ERIC Educational Resources Information Center

Hwang, Heungsun; Dillon, William R.

2010-01-01

A 2-way clustering approach to multiple correspondence analysis is proposed to account for cluster-level heterogeneity of both respondents and variable categories in multivariate categorical data. Specifically, in the proposed method, multiple correspondence analysis is combined with k-means in a unified framework in which "k"-means is…

Insights into MIS 3 and 4 climate in the Alps from the Baumkirchen paleo-lake site: Results of pollen analysis

NASA Astrophysics Data System (ADS)

Barrett, Samuel; Drescher-Schneider, Ruth; Starnberger, Reinhard; Spötl, Christoph

2016-04-01

The well-known Baumkirchen site of western Austria has recently been the focus of a renewed research effort. New drilling has greatly extended the length of the known lacustrine sequence to over 250 m. Luminescence dating has corroborated the late MIS 3 radiocarbon dates for the upper part of the sequence and revealed two lake phases: the upper extending from late MIS 3 back to mid MIS 3, and the lower covering late MIS 4 or early MIS 3 back possibly as far as MIS 5a. X-ray fluorescence core scanning analysis confirmed the presence of two phases which have different geochemical signals, and provided a chemistry-based stratigraphy in the visually monotonous sediments. In these uniform sediments, the only clear indication of climatic conditions from the sediments themselves is a short sequence of ice-rafted debris corresponding to the end of MIS 4. However, given their age and location within the Alps, these sediments provide an important archive of Alpine climate in the last glacial cycle. We present new results from pollen analysis and discuss them in the context of previously reported findings. Due to high sedimentation rates, pollen counts were very low. However, two stadials and two interstadials were identified. The entire lower lake phase corresponding to MIS 4 was identified as a stadial, being characterised by a very low total pollen concentrations, a dominance of herb over tree pollen and significant reworking of pre-Quaternary forms and wood fragments. The upper lake phase contains two interstadials split by an intervening stadial. The interstadials are characterised by higher total pollen concentrations and proportion of woody species including the sporadic presence of relatively warm climate species with the upper of the two appearing better developed with these indicators more strongly expressed. This upper interstadial corresponds to the location of well dated plant remains putting its age around 35 ka cal BP, strongly suggesting a correlation to Greenland interstadial 7, while the correspondence of the lower interstadial is uncertain. Overall, the vegetation of the central Inn Valley during MIS 3 and 4 was dominated by steppe-like open-vegetation (consistent with earlier work from the upper part of the sequence) with tree stands (but not forests) establishing themselves during the interstadials.

Do corresponding authors take responsibility for their work? A covert survey.

PubMed

Teunis, Teun; Nota, Sjoerd P F T; Schwab, Joseph H

2015-02-01

Publication of a manuscript does not end an author's responsibilities. Reasons to contact an author after publication include clarification, access to raw data, and collaboration. However, legitimate questions have been raised regarding whether these responsibilities generally are being met by corresponding authors of biomedical publications. This study aims to establish (1) what proportion of corresponding authors accept the responsibility of correspondence; (2) identify characteristics of responders; and (3) assess email address decay with time. We hypothesize that the response rate is unrelated to journal impact factor. We contacted 450 corresponding authors throughout various fields of biomedical research regarding the availability of additional data from their study, under the pretense of needing these data for a related review article. Authors were randomly selected from 45 journals whose impact factors ranged from 52 to 0; the source articles were published between May 2003 and May 2013. The proportion of corresponding authors who replied, along with author characteristics were recorded, as was the proportion of emails that were returned for inactive addresses; 446 authors were available for final analysis. Fifty-three percent (190/357) of the authors with working email addresses responded to our request. Clinical researchers were more likely to reply than basic/translational scientists (51% [114/225] versus 34% [76/221]; p<0.001). Impact factor and other author characteristics did not differ. Logistic regression analysis showed that the odds of replying decreased by 15% per year (odds ratio [OR], 0.85; 95% CI, 0.79-0.91; p<0.001), and showed a positive relationship between clinical research and response (OR, 2.0; 95% CI, 1.3-2.9; p=0.001). In 2013 all email addresses (45/45) were reachable, but within 10 years, 49% (21/43) had become invalid. Our results suggest that contacting corresponding authors is problematic throughout the field of biomedical research. Defining the responsibilities of corresponding authors by journals more explicitly-particularly after publication of their manuscript-may increase the response rate on data requests. Possible other ways to improve communication after research publication are: (1) listing more than one email address per corresponding author, eg, an institutional and personal address; (2) specifying all authors' email addresses; (3) when an author leaves an institution, send an automated reply offering alternative ways to get in touch; and (4) linking published manuscripts to research platforms.

Building a multidisciplinary team for burn treatment - Lessons learned from the Montreal tendon transfer experience.

PubMed

Karam, E; Lévesque, M C; Jacquemin, G; Delure, A; Robidoux, I; Laramée, M T; Odobescu, A; Harris, P G; Danino, A M

2014-03-31

Multidisciplinary teams (MDTs) represent a recognized component of care in the treatment of complex conditions such as burns. However, most institutions do not provide adequate support for the formation of these teams. Furthermore, the majority of specialists lack the managerial skills required to create a team and have difficulties finding the proper tools. Our objective is to provide an insight for health care professionals, who wish to form a MDT for burn treatment, on the challenges that are likely to be faced, and to identify key elements that may facilitate the establishment of such a project. The setting for this was a plastic surgery department and rehabilitation center at a national reference center. A qualitative analysis was performed on all correspondences related to our tetraplegia project, from 2006 to 2008. To guide our thematic analysis, we used a form of systems theory known as the complexity theory. The qualitative analysis was performed using the NVivo software (Version 8.0 QSR International Melbourne, Australia). Lastly, the data was organized in chronologic order. Three main themes emerged from the results: knowledge acquisition, project organizational setup and project steps design. These themes represented respectively 24%, 50% and 26% of all correspondences. Project steps design and knowledge acquisition correspondences increased significantly after the introduction of the mentor team to our network. We conclude that an early association with a mentor team is beneficial for the establishment of a MDT.

Experienced quality factors: qualitative evaluation approach to audiovisual quality

NASA Astrophysics Data System (ADS)

Jumisko-Pyykkö, Satu; Häkkinen, Jukka; Nyman, Göte

2007-02-01

Subjective evaluation is used to identify impairment factors of multimedia quality. The final quality is often formulated via quantitative experiments, but this approach has its constraints, as subject's quality interpretations, experiences and quality evaluation criteria are disregarded. To identify these quality evaluation factors, this study examined qualitatively the criteria participants used to evaluate audiovisual video quality. A semi-structured interview was conducted with 60 participants after a subjective audiovisual quality evaluation experiment. The assessment compared several, relatively low audio-video bitrate ratios with five different television contents on mobile device. In the analysis, methodological triangulation (grounded theory, Bayesian networks and correspondence analysis) was applied to approach the qualitative quality. The results showed that the most important evaluation criteria were the factors of visual quality, contents, factors of audio quality, usefulness - followability and audiovisual interaction. Several relations between the quality factors and the similarities between the contents were identified. As a research methodological recommendation, the focus on content and usage related factors need to be further examined to improve the quality evaluation experiments.

Characterising volcanic cycles at Soufriere Hills Volcano, Montserrat: Time series analysis of multi-parameter satellite data

NASA Astrophysics Data System (ADS)

Flower, Verity J. B.; Carn, Simon A.

2015-10-01

The identification of cyclic volcanic activity can elucidate underlying eruption dynamics and aid volcanic hazard mitigation. Whilst satellite datasets are often analysed individually, here we exploit the multi-platform NASA A-Train satellite constellation to cross-correlate cyclical signals identified using complementary measurement techniques at Soufriere Hills Volcano (SHV), Montserrat. In this paper we present a Multi-taper (MTM) Fast Fourier Transform (FFT) analysis of coincident SO2 and thermal infrared (TIR) satellite measurements at SHV facilitating the identification of cyclical volcanic behaviour. These measurements were collected by the Ozone Monitoring Instrument (OMI) and Moderate Resolution Imaging Spectroradiometer (MODIS) (respectively) in the A-Train. We identify a correlating cycle in both the OMI and MODIS data (54-58 days), with this multi-week feature attributable to episodes of dome growth. The 50 day cycles were also identified in ground-based SO2 data at SHV, confirming the validity of our analysis and further corroborating the presence of this cycle at the volcano. In addition a 12 day cycle was identified in the OMI data, previously attributed to variable lava effusion rates on shorter timescales. OMI data also display a one week (7-8 days) cycle attributable to cyclical variations in viewing angle resulting from the orbital characteristics of the Aura satellite. Longer period cycles possibly relating to magma intrusion were identified in the OMI record (102-, 121-, and 159 days); in addition to a 238-day cycle identified in the MODIS data corresponding to periodic destabilisation of the lava dome. Through the analysis of reconstructions generated from cycles identified in the OMI and MODIS data, periods of unrest were identified, including the major dome collapse of 20th May 2006 and significant explosive event of 3rd January 2009. Our analysis confirms the potential for identification of cyclical volcanic activity through combined analysis of satellite data, which would be of particular value at poorly monitored volcanic systems.

Spectrum of mucocutaneous manifestations in 277 patients with joint hypermobility syndrome/Ehlers-Danlos syndrome, hypermobility type.

PubMed

Castori, Marco; Dordoni, Chiara; Morlino, Silvia; Sperduti, Isabella; Ritelli, Marco; Valiante, Michele; Chiarelli, Nicola; Zanca, Arianna; Celletti, Claudia; Venturini, Marina; Camerota, Filippo; Calzavara-Pinton, Piergiacomo; Grammatico, Paola; Colombi, Marina

2015-03-01

Cutaneous manifestations are a diagnostic criterion of Ehlers-Danlos syndrome, hypermobility type (EDS-HT) and joint hypermobility syndrome (JHS). These two conditions, originally considered different disorders, are now accepted as clinically indistinguishable and often segregate as a single-familial trait. EDS-HT and JHS are still exclusion diagnoses not supported by any specific laboratory test. Accuracy of clinical diagnosis is, therefore, crucial for appropriate patients' classification and management, but it is actually hampered by the low consistency of many applied criteria including the cutaneous one. We report on mucocutaneous findings in 277 patients with JHS/EDS-HT with both sexes and various ages. Sixteen objective and five anamnestic items were selected and ascertained in two specialized outpatient clinics. Feature rates were compared by sex and age by a series of statistical tools. Data were also used for a multivariate correspondence analysis with the attempt to identify non-causal associations of features depicting recognizable phenotypic clusters. Our findings identified a few differences between sexes and thus indicated an attenuated sexual dimorphism for mucocutaneous features in JHS/EDS-HT. Ten features showed significantly distinct rates at different ages and this evidence corroborated the concept of an evolving phenotype in JHS/EDS-HT also affecting the skin. Multivariate correspondence analysis identified three relatively discrete phenotypic profiles, which may represent the cutaneous counterparts of the three disease phases previously proposed for JHS/EDS-HT. These findings could be used for revising the cutaneous criterion in a future consensus for the clinical diagnosis of JHS/EDS-HT. © 2015 Wiley Periodicals, Inc.

The two ∇6 R 4 type invariants and their higher order generalisation

NASA Astrophysics Data System (ADS)

Bossard, Guillaume; Verschinin, Valentin

2015-07-01

We show that there are two distinct classes of ∇6 R 4 type supersymmetry invariants in maximal supergravity. The second class includes a coupling in F 2∇4 R 4 that generalises to 1/8 BPS protected F 2 k ∇4 R 4 couplings. We work out the supersymmetry constraints on the corresponding threshold functions, and argue that the functions in the second class satisfy to homogeneous differential equations for arbitrary k ≥ 1, such that the corresponding exact threshold functions in type II string theory should be proportional to Eisenstein series, which we identify. This analysis explains in particular that the exact ∇6 R 4 threshold function is the sum of an Eisenstein function and a solution to an inhomogeneous Poisson equation in string theory.

Synchronized voltage contrast display analysis system

NASA Technical Reports Server (NTRS)

Johnston, M. F.; Shumka, A.; Miller, E.; Evans, K. C. (Inventor)

1982-01-01

An apparatus and method for comparing internal voltage potentials of first and second operating electronic components such as large scale integrated circuits (LSI's) in which voltage differentials are visually identified via an appropriate display means are described. More particularly, in a first embodiment of the invention a first and second scanning electron microscope (SEM) are configured to scan a first and second operating electronic component respectively. The scan pattern of the second SEM is synchronized to that of the first SEM so that both simultaneously scan corresponding portions of the two operating electronic components. Video signals from each SEM corresponding to secondary electron signals generated as a result of a primary electron beam intersecting each operating electronic component in accordance with a predetermined scan pattern are provided to a video mixer and color encoder.

Information analysis of hyperspectral images from the hyperion satellite

NASA Astrophysics Data System (ADS)

Puzachenko, Yu. G.; Sandlersky, R. B.; Krenke, A. N.; Puzachenko, M. Yu.

2017-07-01

A new method of estimating the outgoing radiation spectra data obtained from the Hyperion EO-1 satellite is considered. In theoretical terms, this method is based on the nonequilibrium thermodynamics concept with corresponding estimates of the entropy and the Kullbak information. The obtained information estimates make it possible to assess the effective work of the landscape cover both in general and for its various types and to identify the spectrum ranges primarily responsible for the information increment and, accordingly, for the effective work. The information is measured in the frequency band intervals corresponding to the peaks of solar radiation absorption by different pigments, mesophyll, and water to evaluate the system operation by their synthesis and moisture accumulation. This method is assumed to be effective in investigation of ecosystem functioning by hyperspectral remote sensing.

Vibrational spectral investigation and natural bond orbital analysis of pharmaceutical compound 7-Amino-2,4-dimethylquinolinium formate - DFT approach

NASA Astrophysics Data System (ADS)

Suresh, D. M.; Amalanathan, M.; Sebastian, S.; Sajan, D.; Hubert Joe, I.; Bena Jothy, V.; Nemec, Ivan

2013-11-01

The molecular geometry, the normal mode frequencies and corresponding vibrational assignments, natural bond orbital analysis and the HOMO-LUMO analysis of 7-Amino-2,4-dimethylquinolinium formate in the ground state were performed by B3LYP levels of theory using the 6-31G(d) basis set. The optimised bond lengths and bond angles are in good agreement with the X-ray data. The vibrational spectra of the title compound which is calculated by DFT method, reproduces vibrational wave numbers and intensities with an accuracy which allows reliable vibrational assignments. The possibility of N-H⋯O hydrogen bonding was identified using NBO analysis. Natural bond orbital analysis confirms the presence of intramolecular charge transfer and the hydrogen bonding interaction.

Use of multiple correspondence analysis (MCA) to identify interactive meteorological conditions affecting relative throughfall

NASA Astrophysics Data System (ADS)

Van Stan, John T.; Gay, Trent E.; Lewis, Elliott S.

2016-02-01

Forest canopies alter rainfall reaching the surface by redistributing it as throughfall. Throughfall supplies water and nutrients to a variety of ecohydrological components (soil microbial communities, stream water discharge/chemistry, and stormflow pathways) and is controlled by canopy structural interactions with meteorological conditions across temporal scales. This work introduces and applies multiple correspondence analyses (MCAs) to a range of meteorological thresholds (median intensity, median absolute deviation (MAD) of intensity, median wind-driven droplet inclination angle, and MAD of wind speed) for an example throughfall problem: identification of interacting storm conditions corresponding to temporal concentration in relative throughfall beyond the median observation (⩾73% of rain). MCA results from the example show that equalling or exceeding rain intensity thresholds (median and MAD) corresponded with temporal concentration of relative throughfall across all storms. Under these intensity conditions, two wind mechanisms produced significant correspondences: (1) high, steady wind-driven droplet inclination angles increased surface wetting; and (2) sporadic winds shook entrained droplets from surfaces. A discussion is provided showing that these example MCA findings agree well with previous work relying on more historically common methods (e.g., multiple regression and analytical models). Meteorological threshold correspondences to temporal concentration of relative throughfall at our site may be a function of heavy Tillandsia usneoides coverage. Applications of MCA within other forests may provide useful insights to how temporal throughfall dynamics are affected for drainage pathways dependent on different structures (leaves, twigs, branches, etc.).

ICSNPathway: identify candidate causal SNPs and pathways from genome-wide association study by one analytical framework.

PubMed

Zhang, Kunlin; Chang, Suhua; Cui, Sijia; Guo, Liyuan; Zhang, Liuyan; Wang, Jing

2011-07-01

Genome-wide association study (GWAS) is widely utilized to identify genes involved in human complex disease or some other trait. One key challenge for GWAS data interpretation is to identify causal SNPs and provide profound evidence on how they affect the trait. Currently, researches are focusing on identification of candidate causal variants from the most significant SNPs of GWAS, while there is lack of support on biological mechanisms as represented by pathways. Although pathway-based analysis (PBA) has been designed to identify disease-related pathways by analyzing the full list of SNPs from GWAS, it does not emphasize on interpreting causal SNPs. To our knowledge, so far there is no web server available to solve the challenge for GWAS data interpretation within one analytical framework. ICSNPathway is developed to identify candidate causal SNPs and their corresponding candidate causal pathways from GWAS by integrating linkage disequilibrium (LD) analysis, functional SNP annotation and PBA. ICSNPathway provides a feasible solution to bridge the gap between GWAS and disease mechanism study by generating hypothesis of SNP → gene → pathway(s). The ICSNPathway server is freely available at http://icsnpathway.psych.ac.cn/.

Validation of a robust proteomic analysis carried out on formalin-fixed paraffin-embedded tissues of the pancreas obtained from mouse and human.

PubMed

Kojima, Kyoko; Bowersock, Gregory J; Kojima, Chinatsu; Klug, Christopher A; Grizzle, William E; Mobley, James A

2012-11-01

A number of reports have recently emerged with focus on extraction of proteins from formalin-fixed paraffin-embedded (FFPE) tissues for MS analysis; however, reproducibility and robustness as compared to flash frozen controls is generally overlooked. The goal of this study was to identify and validate a practical and highly robust approach for the proteomics analysis of FFPE tissues. FFPE and matched frozen pancreatic tissues obtained from mice (n = 8) were analyzed using 1D-nanoLC-MS(MS)(2) following work up with commercially available kits. The chosen approach for FFPE tissues was found to be highly comparable to that of frozen. In addition, the total number of unique peptides identified between the two groups was highly similar, with 958 identified for FFPE and 1070 identified for frozen, with protein identifications that corresponded by approximately 80%. This approach was then applied to archived human FFPE pancreatic cancer specimens (n = 11) as compared to uninvolved tissues (n = 8), where 47 potential pancreatic ductal adenocarcinoma markers were identified as significantly increased, of which 28 were previously reported. Further, these proteins share strongly overlapping pathway associations to pancreatic cancer that include estrogen receptor α. Together, these data support the validation of an approach for the proteomic analysis of FFPE tissues that is straightforward and highly robust, which can also be effectively applied toward translational studies of disease. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The role of tectonic inheritance in the morphostructural evolution of the Galicia continental margin and adjacent abyssal plains from digital bathymetric model (DBM) analysis (NW Spain)

NASA Astrophysics Data System (ADS)

Maestro, A.; Jané, G.; Llave, E.; López-Martínez, J.; Bohoyo, F.; Druet, M.

2018-06-01

The identification of recent major tectonic structures in the Galicia continental margin and adjacent abyssal plains was carried out by means of a quantitative analysis of the linear structures having bathymetric expression on the seabed. It was possible to identify about 5800 lineaments throughout the entire study area, of approximately 271,500 km2. Most lineaments are located in the Charcot and Coruña highs, in the western sector of the Galicia Bank, in the area of the Marginal Platforms and in the northern sector of the margin. Analysis of the lineament orientations shows a predominant NE-SW direction and three relative maximum directions: NW-SE, E-W and N-S. The total length of the lineaments identified is over 44,000 km, with a mode around 5000 m and an average length of about 7800 m. In light of different tectonic studies undertaken in the northwestern margin of the Iberian Peninsula, we establish that the lineaments obtained from analysis of the digital bathymetric model of the Galicia continental margin and adjacent abyssal plains would correspond to fracture systems. In general, the orientation of lineaments corresponds to main faults, tectonic structures following the directions of ancient faults that resulted from late stages of the Variscan orogeny and Mesozoic extension phases related to Triassic rifting and Upper Jurassic to Early Cretaceous opening of the North Atlantic Ocean. The N-S convergence between Eurasian and African plates since Palaeogene times until the Miocene, and NW-SE convergence from Neogene to present, reactivated the Variscan and Mesozoic fault systems and related physiography.

Assessment of pedophilia using hemodynamic brain response to sexual stimuli.

PubMed

Ponseti, Jorge; Granert, Oliver; Jansen, Olav; Wolff, Stephan; Beier, Klaus; Neutze, Janina; Deuschl, Günther; Mehdorn, Hubertus; Siebner, Hartwig; Bosinski, Hartmut

2012-02-01

Accurately assessing sexual preference is important in the treatment of child sex offenders. Phallometry is the standard method to identify sexual preference; however, this measure has been criticized for its intrusiveness and limited reliability. To evaluate whether spatial response pattern to sexual stimuli as revealed by a change in the blood oxygen level-dependent signal facilitates the identification of pedophiles. During functional magnetic resonance imaging, pedophilic and nonpedophilic participants were briefly exposed to same- and opposite-sex images of nude children and adults. We calculated differences in blood oxygen level-dependent signals to child and adult sexual stimuli for each participant. The corresponding contrast images were entered into a group analysis to calculate whole-brain difference maps between groups. We calculated an expression value that corresponded to the group result for each participant. These expression values were submitted to 2 different classification algorithms: Fisher linear discriminant analysis and κ -nearest neighbor analysis. This classification procedure was cross-validated using the leave-one-out method. Section of Sexual Medicine, Medical School, Christian Albrechts University of Kiel, Kiel, Germany. We recruited 24 participants with pedophilia who were sexually attracted to either prepubescent girls (n = 11) or prepubescent boys (n = 13) and 32 healthy male controls who were sexually attracted to either adult women (n = 18) or adult men (n = 14). Sensitivity and specificity scores of the 2 classification algorithms. The highest classification accuracy was achieved by Fisher linear discriminant analysis, which showed a mean accuracy of 95% (100% specificity, 88% sensitivity). Functional brain response patterns to sexual stimuli contain sufficient information to identify pedophiles with high accuracy. The automatic classification of these patterns is a promising objective tool to clinically diagnose pedophilia.

Identification of Putative Genes Involved in Limonoids Biosynthesis in Citrus by Comparative Transcriptomic Analysis

PubMed Central

Wang, Fusheng; Wang, Mei; Liu, Xiaona; Xu, Yuanyuan; Zhu, Shiping; Shen, Wanxia; Zhao, Xiaochun

2017-01-01

Limonoids produced by citrus are a group of highly bioactive secondary metabolites which provide health benefits for humans. Currently there is a lack of information derived from research on the genetic mechanisms controlling the biosynthesis of limonoids, which has limited the improvement of citrus for high production of limonoids. In this study, the transcriptome sequences of leaves, phloems and seeds of pummelo (Citrus grandis (L.) Osbeck) at different development stages with variances in limonoids contents were used for digital gene expression profiling analysis in order to identify the genes corresponding to the biosynthesis of limonoids. Pair-wise comparison of transcriptional profiles between different tissues identified 924 differentially expressed genes commonly shared between them. Expression pattern analysis suggested that 382 genes from three conjunctive groups of K-means clustering could be possibly related to the biosynthesis of limonoids. Correlation analysis with the samples from different genotypes, and different developing tissues of the citrus revealed that the expression of 15 candidate genes were highly correlated with the contents of limonoids. Among them, the cytochrome P450s (CYP450s) and transcriptional factor MYB demonstrated significantly high correlation coefficients, which indicated the importance of those genes on the biosynthesis of limonoids. CiOSC gene encoding the critical enzyme oxidosqualene cyclase (OSC) for biosynthesis of the precursor of triterpene scaffolds was found positively corresponding to the accumulation of limonoids during the development of seeds. Suppressing the expression of CiOSC with VIGS (Virus-induced gene silencing) demonstrated that the level of gene silencing was significantly correlated to the reduction of limonoids contents. The results indicated that the CiOSC gene plays a pivotal role in biosynthesis of limonoids. PMID:28553308

Characteristics of cyclist crashes in Italy using latent class analysis and association rule mining

PubMed Central

De Angelis, Marco; Marín Puchades, Víctor; Fraboni, Federico; Pietrantoni, Luca

2017-01-01

The factors associated with severity of the bicycle crashes may differ across different bicycle crash patterns. Therefore, it is important to identify distinct bicycle crash patterns with homogeneous attributes. The current study aimed at identifying subgroups of bicycle crashes in Italy and analyzing separately the different bicycle crash types. The present study focused on bicycle crashes that occurred in Italy during the period between 2011 and 2013. We analyzed categorical indicators corresponding to the characteristics of infrastructure (road type, road signage, and location type), road user (i.e., opponent vehicle and cyclist’s maneuver, type of collision, age and gender of the cyclist), vehicle (type of opponent vehicle), and the environmental and time period variables (time of the day, day of the week, season, pavement condition, and weather). To identify homogenous subgroups of bicycle crashes, we used latent class analysis. Using latent class analysis, the bicycle crash data set was segmented into 19 classes, which represents 19 different bicycle crash types. Logistic regression analysis was used to identify the association between class membership and severity of the bicycle crashes. Finally, association rules were conducted for each of the latent classes to uncover the factors associated with an increased likelihood of severity. Association rules highlighted different crash characteristics associated with an increased likelihood of severity for each of the 19 bicycle crash types. PMID:28158296

Integrative analysis of the heat shock response in Aspergillus fumigatus

PubMed Central

2010-01-01

Background Aspergillus fumigatus is a thermotolerant human-pathogenic mold and the most common cause of invasive aspergillosis (IA) in immunocompromised patients. Its predominance is based on several factors most of which are still unknown. The thermotolerance of A. fumigatus is one of the traits which have been assigned to pathogenicity. It allows the fungus to grow at temperatures up to and above that of a fevered human host. To elucidate the mechanisms of heat resistance, we analyzed the change of the A. fumigatus proteome during a temperature shift from 30°C to 48°C by 2D-fluorescence difference gel electrophoresis (DIGE). To improve 2D gel image analysis results, protein spot quantitation was optimized by missing value imputation and normalization. Differentially regulated proteins were compared to previously published transcriptome data of A. fumigatus. The study was augmented by bioinformatical analysis of transcription factor binding sites (TFBSs) in the promoter region of genes whose corresponding proteins were differentially regulated upon heat shock. Results 91 differentially regulated protein spots, representing 64 different proteins, were identified by mass spectrometry (MS). They showed a continuous up-, down- or an oscillating regulation. Many of the identified proteins were involved in protein folding (chaperones), oxidative stress response, signal transduction, transcription, translation, carbohydrate and nitrogen metabolism. A correlation between alteration of transcript levels and corresponding proteins was detected for half of the differentially regulated proteins. Interestingly, some previously undescribed putative targets for the heat shock regulator Hsf1 were identified. This provides evidence for Hsf1-dependent regulation of mannitol biosynthesis, translation, cytoskeletal dynamics and cell division in A. fumigatus. Furthermore, computational analysis of promoters revealed putative binding sites for an AP-2alpha-like transcription factor upstream of some heat shock induced genes. Until now, this factor has only been found in vertebrates. Conclusions Our newly established DIGE data analysis workflow yields improved data quality and is widely applicable for other DIGE datasets. Our findings suggest that the heat shock response in A. fumigatus differs from already well-studied yeasts and other filamentous fungi. PMID:20074381

Nuclear States with Abnormally Large Radii (size Isomers)

NASA Astrophysics Data System (ADS)

Ogloblin, A. A.; Demyanova, A. S.; Danilov, A. N.; Belyaeva, T. L.; Goncharov, S. A.

2015-06-01

Application of the methods of measuring the radii of the short-lived excited states (Modified diffraction model MDM, Inelastic nuclear rainbow scattering method INRS, Asymptotic normalization coefficients method ANC) to the analysis of some nuclear reactions provide evidence of existing in 9Be, 11B, 12C, 13C the excited states whose radii exceed those of the corresponding ground states by ~ 30%. Two types of structure of these "size isomers" were identified: neutron halo an α-clusters.

Computational Analysis Identifies Putative Prognostic Biomarkers of Pathological Scarring in Skin Wounds

DTIC Science & Technology

2018-02-20

in/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Background Cutaneous hypertrophic scars (HTSs) are a common...of Open Access Journal of Translational Medicine *Correspondence: jaques.reifman.civ@mail.mil 1 Department of Defense Biotechnology High ...MCMR-TT, 504 Scott Street, Ft. Detrick, MD 21702, USA Full list of author information is available at the end of the article Page 2 of 13Nagaraja et al

Textural features for radar image analysis

NASA Technical Reports Server (NTRS)

Shanmugan, K. S.; Narayanan, V.; Frost, V. S.; Stiles, J. A.; Holtzman, J. C.

1981-01-01

Texture is seen as an important spatial feature useful for identifying objects or regions of interest in an image. While textural features have been widely used in analyzing a variety of photographic images, they have not been used in processing radar images. A procedure for extracting a set of textural features for characterizing small areas in radar images is presented, and it is shown that these features can be used in classifying segments of radar images corresponding to different geological formations.

Identification of Coffee Varieties Using Laser-Induced Breakdown Spectroscopy and Chemometrics.

PubMed

Zhang, Chu; Shen, Tingting; Liu, Fei; He, Yong

2017-12-31

We linked coffee quality to its different varieties. This is of interest because the identification of coffee varieties should help coffee trading and consumption. Laser-induced breakdown spectroscopy (LIBS) combined with chemometric methods was used to identify coffee varieties. Wavelet transform (WT) was used to reduce LIBS spectra noise. Partial least squares-discriminant analysis (PLS-DA), radial basis function neural network (RBFNN), and support vector machine (SVM) were used to build classification models. Loadings of principal component analysis (PCA) were used to select the spectral variables contributing most to the identification of coffee varieties. Twenty wavelength variables corresponding to C I, Mg I, Mg II, Al II, CN, H, Ca II, Fe I, K I, Na I, N I, and O I were selected. PLS-DA, RBFNN, and SVM models on selected wavelength variables showed acceptable results. SVM and RBFNN models performed better with a classification accuracy of over 80% in the prediction set, for both full spectra and the selected variables. The overall results indicated that it was feasible to use LIBS and chemometric methods to identify coffee varieties. For further studies, more samples are needed to produce robust classification models, research should be conducted on which methods to use to select spectral peaks that correspond to the elements contributing most to identification, and the methods for acquiring stable spectra should also be studied.

Buildings Change Detection Based on Shape Matching for Multi-Resolution Remote Sensing Imagery

NASA Astrophysics Data System (ADS)

Abdessetar, M.; Zhong, Y.

2017-09-01

Buildings change detection has the ability to quantify the temporal effect, on urban area, for urban evolution study or damage assessment in disaster cases. In this context, changes analysis might involve the utilization of the available satellite images with different resolutions for quick responses. In this paper, to avoid using traditional method with image resampling outcomes and salt-pepper effect, building change detection based on shape matching is proposed for multi-resolution remote sensing images. Since the object's shape can be extracted from remote sensing imagery and the shapes of corresponding objects in multi-scale images are similar, it is practical for detecting buildings changes in multi-scale imagery using shape analysis. Therefore, the proposed methodology can deal with different pixel size for identifying new and demolished buildings in urban area using geometric properties of objects of interest. After rectifying the desired multi-dates and multi-resolutions images, by image to image registration with optimal RMS value, objects based image classification is performed to extract buildings shape from the images. Next, Centroid-Coincident Matching is conducted, on the extracted building shapes, based on the Euclidean distance measurement between shapes centroid (from shape T0 to shape T1 and vice versa), in order to define corresponding building objects. Then, New and Demolished buildings are identified based on the obtained distances those are greater than RMS value (No match in the same location).

TEM in situ cube-corner indentation analysis using ViBe motion detection algorithm

NASA Astrophysics Data System (ADS)

Yano, K. H.; Thomas, S.; Swenson, M. J.; Lu, Y.; Wharry, J. P.

2018-04-01

Transmission electron microscopic (TEM) in situ mechanical testing is a promising method for understanding plasticity in shallow ion irradiated layers and other volume-limited materials. One of the simplest TEM in situ experiments is cube-corner indentation of a lamella, but the subsequent analysis and interpretation of the experiment is challenging, especially in engineering materials with complex microstructures. In this work, we: (a) develop MicroViBE, a motion detection and background subtraction-based post-processing approach, and (b) demonstrate the ability of MicroViBe, in combination with post-mortem TEM imaging, to carry out an unbiased qualitative interpretation of TEM indentation videos. We focus this work around a Fe-9%Cr oxide dispersion strengthened (ODS) alloy, irradiated with Fe2+ ions to 3 dpa at 500 °C. MicroViBe identifies changes in Laue contrast that are induced by the indentation; these changes accumulate throughout the mechanical loading to generate a "heatmap" of features in the original TEM video that change the most during the loading. Dislocation loops with b = ½ <111> identified by post-mortem scanning TEM (STEM) imaging correspond to hotspots on the heatmap, whereas positions of dislocation loops with b = <100> do not correspond to hotspots. Further, MicroViBe enables consistent, objective quantitative approximation of the b = ½ <111> dislocation loop number density.

Identification of Coffee Varieties Using Laser-Induced Breakdown Spectroscopy and Chemometrics

PubMed Central

Zhang, Chu; Shen, Tingting

2017-01-01

We linked coffee quality to its different varieties. This is of interest because the identification of coffee varieties should help coffee trading and consumption. Laser-induced breakdown spectroscopy (LIBS) combined with chemometric methods was used to identify coffee varieties. Wavelet transform (WT) was used to reduce LIBS spectra noise. Partial least squares-discriminant analysis (PLS-DA), radial basis function neural network (RBFNN), and support vector machine (SVM) were used to build classification models. Loadings of principal component analysis (PCA) were used to select the spectral variables contributing most to the identification of coffee varieties. Twenty wavelength variables corresponding to C I, Mg I, Mg II, Al II, CN, H, Ca II, Fe I, K I, Na I, N I, and O I were selected. PLS-DA, RBFNN, and SVM models on selected wavelength variables showed acceptable results. SVM and RBFNN models performed better with a classification accuracy of over 80% in the prediction set, for both full spectra and the selected variables. The overall results indicated that it was feasible to use LIBS and chemometric methods to identify coffee varieties. For further studies, more samples are needed to produce robust classification models, research should be conducted on which methods to use to select spectral peaks that correspond to the elements contributing most to identification, and the methods for acquiring stable spectra should also be studied. PMID:29301228

Sequential pattern data mining and visualization

DOEpatents

Wong, Pak Chung [Richland, WA; Jurrus, Elizabeth R [Kennewick, WA; Cowley, Wendy E [Benton City, WA; Foote, Harlan P [Richland, WA; Thomas, James J [Richland, WA

2011-12-06

One or more processors (22) are operated to extract a number of different event identifiers therefrom. These processors (22) are further operable to determine a number a display locations each representative of one of the different identifiers and a corresponding time. The display locations are grouped into sets each corresponding to a different one of several event sequences (330a, 330b, 330c. 330d, 330e). An output is generated corresponding to a visualization (320) of the event sequences (330a, 330b, 330c, 330d, 330e).

Sequential pattern data mining and visualization

DOEpatents

Wong, Pak Chung [Richland, WA; Jurrus, Elizabeth R [Kennewick, WA; Cowley, Wendy E [Benton City, WA; Foote, Harlan P [Richland, WA; Thomas, James J [Richland, WA

2009-05-26

One or more processors (22) are operated to extract a number of different event identifiers therefrom. These processors (22) are further operable to determine a number a display locations each representative of one of the different identifiers and a corresponding time. The display locations are grouped into sets each corresponding to a different one of several event sequences (330a, 330b, 330c. 330d, 330e). An output is generated corresponding to a visualization (320) of the event sequences (330a, 330b, 330c, 330d, 330e).

Characterisation of lab in typical Salento Pecorino cheese.

PubMed

Cappello, M S; Laddomada, B; Poltronieri, P; Zacheo, G

2001-01-01

Twenty-nine strains of Lactic Acid Bacteria isolated from the typical Pecorino cheese of the Salento area of Italy, were identified and grouped according to their genetic similarity. A preliminary characterisation of the strains was conducted by means of morphological and biochemical analysis, but molecular approaches were necessary for the clear identification of the species. For the species detection, the amplification and sequencing of the 16S rDNA gene was employed In addition, restriction analysis of amplified rDNA (ARDRA) and PCR and AFLP fingerprinting enabled inter- and intra-specific variation to be estimated UPGMA cluster analysis was used to divide the strains into distinct clusters which corresponded with the species delineation obtained by molecular identification. The data obtained show that the community of lactobacilli responsible for the fermentation and aging of Pecorino cheese is composed of a limited number of species. The main identified strains were Lactobacillus brevis, L. plantarum, L. casei, L. sakei, L. pentosus, L. farciminis and Leuconostoc mesenteroides.

Solar wind conditions leading to efficient radiation belt electron acceleration: A superposed epoch analysis

DOE PAGES

Li, W.; Thorne, R. M.; Bortnik, J.; ...

2015-09-07

In this study by determining preferential solar wind conditions leading to efficient radiation belt electron acceleration is crucial for predicting radiation belt electron dynamics. Using Van Allen Probes electron observations (>1 MeV) from 2012 to 2015, we identify a number of efficient and inefficient acceleration events separately to perform a superposed epoch analysis of the corresponding solar wind parameters and geomagnetic indices. By directly comparing efficient and inefficient acceleration events, we clearly show that prolonged southward Bz, high solar wind speed, and low dynamic pressure are critical for electron acceleration to >1 MeV energies in the heart of the outermore » radiation belt. We also evaluate chorus wave evolution using the superposed epoch analysis for the identified efficient and inefficient acceleration events and find that chorus wave intensity is much stronger and lasts longer during efficient electron acceleration events, supporting the scenario that chorus waves play a key role in MeV electron acceleration.« less

Novel seminal fluid proteins in the seed beetle Callosobruchus maculatus identified by a proteomic and transcriptomic approach.

PubMed

Bayram, H; Sayadi, A; Goenaga, J; Immonen, E; Arnqvist, G

2017-02-01

The seed beetle Callosobruchus maculatus is a significant agricultural pest and increasingly studied model of sexual conflict. Males possess genital spines that increase the transfer of seminal fluid proteins (SFPs) into the female body. As SFPs alter female behaviour and physiology, they are likely to modulate reproduction and sexual conflict in this species. Here, we identified SFPs using proteomics combined with a de novo transcriptome. A prior 2D-sodium dodecyl sulphate polyacrylamide gel electrophoresis analysis identified male accessory gland protein spots that were probably transferred to the female at mating. Proteomic analysis of these spots identified 98 proteins, a majority of which were also present within ejaculates collected from females. Standard annotation workflows revealed common functional groups for SFPs, including proteases and metabolic proteins. Transcriptomic analysis found 84 transcripts differentially expressed between the sexes. Notably, genes encoding 15 proteins were highly expressed in male abdomens and only negligibly expressed within females. Most of these sequences corresponded to 'unknown' proteins (nine of 15) and may represent rapidly evolving SFPs novel to seed beetles. Our combined analyses highlight 44 proteins for which there is strong evidence that they are SFPs. These results can inform further investigation, to better understand the molecular mechanisms of sexual conflict in seed beetles. © 2016 The Royal Entomological Society.

Evolutionary lineages of marine snails identified using molecular phylogenetics and geometric morphometric analysis of shells.

PubMed

Vaux, Felix; Trewick, Steven A; Crampton, James S; Marshall, Bruce A; Beu, Alan G; Hills, Simon F K; Morgan-Richards, Mary

2018-06-15

The relationship between morphology and inheritance is of perennial interest in evolutionary biology and palaeontology. Using three marine snail genera Penion, Antarctoneptunea and Kelletia, we investigate whether systematics based on shell morphology accurately reflect evolutionary lineages indicated by molecular phylogenetics. Members of these gastropod genera have been a taxonomic challenge due to substantial variation in shell morphology, conservative radular and soft tissue morphology, few known ecological differences, and geographical overlap between numerous species. Sampling all sixteen putative taxa identified across the three genera, we infer mitochondrial and nuclear ribosomal DNA phylogenetic relationships within the group, and compare this to variation in adult shell shape and size. Results of phylogenetic analysis indicate that each genus is monophyletic, although the status of some phylogenetically derived and likely more recently evolved taxa within Penion is uncertain. The recently described species P. lineatus is supported by genetic evidence. Morphology, captured using geometric morphometric analysis, distinguishes the genera and matches the molecular phylogeny, although using the same dataset, species and phylogenetic subclades are not identified with high accuracy. Overall, despite abundant variation, we find that shell morphology accurately reflects genus-level classification and the corresponding deep phylogenetic splits identified in this group of marine snails. Copyright © 2018 Elsevier Inc. All rights reserved.

Classification of alloys using laser induced breakdown spectroscopy with principle component analysis

NASA Astrophysics Data System (ADS)

Syuhada Mangsor, Aneez; Haider Rizvi, Zuhaib; Chaudhary, Kashif; Safwan Aziz, Muhammad

2018-05-01

The study of atomic spectroscopy has contributed to a wide range of scientific applications. In principle, laser induced breakdown spectroscopy (LIBS) method has been used to analyse various types of matter regardless of its physical state, either it is solid, liquid or gas because all elements emit light of characteristic frequencies when it is excited to sufficiently high energy. The aim of this work was to analyse the signature spectrums of each element contained in three different types of samples. Metal alloys of Aluminium, Titanium and Brass with the purities of 75%, 80%, 85%, 90% and 95% were used as the manipulated variable and their LIBS spectra were recorded. The characteristic emission lines of main elements were identified from the spectra as well as its corresponding contents. Principal component analysis (PCA) was carried out using the data from LIBS spectra. Three obvious clusters were observed in 3-dimensional PCA plot which corresponding to the different group of alloys. Findings from this study showed that LIBS technology with the help of principle component analysis could conduct the variety discrimination of alloys demonstrating the capability of LIBS-PCA method in field of spectro-analysis. Thus, LIBS-PCA method is believed to be an effective method for classifying alloys with different percentage of purifications, which was high-cost and time-consuming before.

Anthropogenic Enrichment of Heavy Metals in Urban Dust and Possible Corresponding Sources

NASA Astrophysics Data System (ADS)

van Laaten, Neele; Merten, Dirk; Pirrung, Michael

2017-04-01

Atmospheric dust (particulate matter, PM) is regarded as a crucial factor for human health and a major environmental problem in densely populated areas. Due to anthropogenic processes like traffic, waste incineration and industry increased amounts of PM can be detected in those areas. To reduce the amounts detailed knowledge on both the composition of PM and the source contribution in a target area is needed. The latter has, to our knowledge, rarely been regarded in central Europe. Within this study, spider webs from various locations in the city of Jena (Germany), that act as natural trappers of PM, were analyzed for the contents of 27 trace elements using aqua regia digestion followed by ICP-OES and ICP-MS determinations. Aerosol-crust enrichment factors were calculated for selected elements and both a cluster analysis and a factor analysis were executed to identify sources of PM. High values for the enrichment factors clearly show an anthropogenic influence. In addition, the cluster analysis leads to a grouping of the sampling points mainly depending on the kind and volume of traffic at the corresponding locations. Five different possible sources of PM can be found by the factor analysis: Soil erosion (41% of variance), abrasion of rails (16%), tyre and break wear (16%), charcoal combustion (8%) and oil combustion (7%).

Dominance and leadership in research activities: Collaboration between countries of differing human development is reflected through authorship order and designation as corresponding authors in scientific publications

PubMed Central

Park, Jinseo; Huamaní, Charles; Ramos, José M.

2017-01-01

Introduction Scientific collaboration is an important mechanism that enables the integration of the least developed countries into research activities. In the present study, we use the order of author signatures and addresses for correspondence in scientific publications as variables to analyze the interactions between countries of very high (VHHD), high (HHD), medium (MHD), and low human development (LHD). Methodology We identified all documents published between 2011 and 2015 in journals included in the Science Citation Index-Expanded categories’ of Tropical Medicine, Infectious Diseases, Parasitology, and Pediatrics. We then classified the countries participating in the publications according to their Human Development Index (HDI), analyzing the international collaboration; positioning and influence of some countries over others in cooperative networks; their leadership; and the impact of the work based on the HDI and the type of collaboration. Results We observed a high degree of international collaboration in all the areas analyzed, in the case of both LHD and MHD countries. We identified numerous cooperative links between VHHD countries and MHD/LHD countries, reflecting the fact that cooperative links are an important mechanism for integrating research activities into the latter. The countries with large emerging economies, such as Brazil and China stand out due to the dominance they exert in the collaborations established with the United States, the UK, and other European countries. The analysis of the leadership role of the countries, measured by the frequency of lead authorships, shows limited participation by MHD/LHD countries. This reduced participation among less developed countries is further accentuated by their limited presence in the addresses for correspondence. We observed significant statistical differences in the degree of citation according to the HDI of the participating countries. Conclusions The order of signatures and the address for correspondence in scientific publications are bibliographic characteristics that facilitate a precise, in-depth analysis of cooperative practices and their associations with concepts like dominance or leadership. This is useful to monitor the existing balance in research participation in health research publications. PMID:28792519

Role of CFTR mutation analysis in the diagnostic algorithm for cystic fibrosis.

PubMed

Ratkiewicz, Michelle; Pastore, Matthew; McCoy, Karen Sharrock; Thompson, Rohan; Hayes, Don; Sheikh, Shahid Ijaz

2017-04-01

The cystic fibrosis transmembrane conductance regulator (CFTR) gene mutation identification is being used with increased frequency to aid in the diagnosis of cystic fibrosis (CF) in those suspected with CF. Aim of this study was to identify diagnostic outcomes when CFTR mutational analysis was used in CF diagnosis. CFTR mutational analysis results were also compared with sweat chloride results. This study was done on all patients at our institution who had CFTR mutation analysis over a sevenyear period since August 2006. A total of 315 patients underwent CFTR mutational analysis. Fifty-one (16.2%) patients had two mutations identified. Among them 32 had positive sweat chloride levels (≥60 mmol/L), while seven had borderline sweat chloride levels (40-59 mmol/L). An additional 70 patients (22.3%) had only one mutation identified. Among them eight had positive sweat chloride levels, and 17 had borderline sweat chloride levels. Fifty-five patients (17.5%) without CFTR mutations had either borderline (n=45) or positive (n=10) sweat chloride results. Three patients with a CF phenotype had negative CFTR analysis but elevated sweat chloride levels. In eighty-three patients (26.4%) CFTR mutational analysis was done without corresponding sweat chloride testing. Although CFTR mutation analysis has improved the diagnostic capability for CF, its use either as the first step or the only test to diagnose CFTR dysfunction should be discouraged and CF diagnostic guidelines need to be followed.

Parental identification of rapists and pedophiles.

PubMed

Levant, M D; Bass, B A

1991-10-01

It is well documented that sex offenders experience a higher incidence of sexual abuse and are more likely to have been reared in dysfunctional families than are individuals in most comparison groups. It is unclear, however, whether growing up in an abusive or dysfunctional family affects the extent to which the potential sex offender would subsequently identify with his parents. Sixteen rapists, 18 pedophiles, 9 general offenders, and 11 college students completed the Parental Identification Scale to assess their parental identification. It was predicted that the rapists and pedophiles would identify less with their parents than would college students or general offenders. Analysis indicated a strong and significant correlation between group membership and parental identification. Rapists and pedophiles identified less with their mothers and fathers than did members of corresponding control groups.

Benthic foraminifera as indicators of habitat in a Mediterranean delta: implications for ecological and palaeoenvironmental studies

NASA Astrophysics Data System (ADS)

Benito, Xavier; Trobajo, Rosa; Cearreta, Alejandro; Ibáñez, Carles

2016-10-01

The ecology and modern distribution of benthic foraminiferal assemblages were analysed in the Ebro Delta (NW Mediterranean Sea). Foraminiferal distributions were from 191 sediment surface samples covering a wide range of deltaic habitats and adjacent open sea areas. According to similarity in species composition, cluster analysis identified four habitat types: (1) offshore habitat, (2) nearshore and outer bays, (3) salt and brackish marshes and (4) coastal lagoons and inner bays. Canonical Correspondence Analysis identified water depth, salinity and sand content as the main environmental factors structuring living foraminiferal assemblages. Partial Canonical Correspondence Analysis revealed water depth as the most statistically significant associated with the distribution of modern foraminifera in the Ebro Delta. Thus, a transfer function for water depth using Weighted Average Partial Least Squares regression was successfully developed. Although depth per se is unlikely to affect the foraminifera directly but will exert its effects via various environmental variables that co-vary with depth in the deltaic habitats (e.g. hydrodynamics, oxygen, food availability, etc), the resulting model (r2 = 0.89; RMSEP = 0.32 log10 m) suggested a strong correlation between observed and foraminifera-predicted water depths, and therefore provided a potentially useful tool for water-depth reconstructions in the Ebro Delta. This work indicated the potential role of modern foraminifera as quantitative indicators of water depth and habitat types in the Ebro Delta. This complementary approach (transfer function and indicator species) will allow reconstruction of the palaeoenvironmental changes that have occurred in the Ebro Delta based on the benthic foraminiferal record.

EvoDB: a database of evolutionary rate profiles, associated protein domains and phylogenetic trees for PFAM-A

PubMed Central

Ndhlovu, Andrew; Durand, Pierre M.; Hazelhurst, Scott

2015-01-01

The evolutionary rate at codon sites across protein-coding nucleotide sequences represents a valuable tier of information for aligning sequences, inferring homology and constructing phylogenetic profiles. However, a comprehensive resource for cataloguing the evolutionary rate at codon sites and their corresponding nucleotide and protein domain sequence alignments has not been developed. To address this gap in knowledge, EvoDB (an Evolutionary rates DataBase) was compiled. Nucleotide sequences and their corresponding protein domain data including the associated seed alignments from the PFAM-A (protein family) database were used to estimate evolutionary rate (ω = dN/dS) profiles at codon sites for each entry. EvoDB contains 98.83% of the gapped nucleotide sequence alignments and 97.1% of the evolutionary rate profiles for the corresponding information in PFAM-A. As the identification of codon sites under positive selection and their position in a sequence profile is usually the most sought after information for molecular evolutionary biologists, evolutionary rate profiles were determined under the M2a model using the CODEML algorithm in the PAML (Phylogenetic Analysis by Maximum Likelihood) suite of software. Validation of nucleotide sequences against amino acid data was implemented to ensure high data quality. EvoDB is a catalogue of the evolutionary rate profiles and provides the corresponding phylogenetic trees, PFAM-A alignments and annotated accession identifier data. In addition, the database can be explored and queried using known evolutionary rate profiles to identify domains under similar evolutionary constraints and pressures. EvoDB is a resource for evolutionary, phylogenetic studies and presents a tier of information untapped by current databases. Database URL: http://www.bioinf.wits.ac.za/software/fire/evodb PMID:26140928

EvoDB: a database of evolutionary rate profiles, associated protein domains and phylogenetic trees for PFAM-A.

PubMed

Ndhlovu, Andrew; Durand, Pierre M; Hazelhurst, Scott

2015-01-01

The evolutionary rate at codon sites across protein-coding nucleotide sequences represents a valuable tier of information for aligning sequences, inferring homology and constructing phylogenetic profiles. However, a comprehensive resource for cataloguing the evolutionary rate at codon sites and their corresponding nucleotide and protein domain sequence alignments has not been developed. To address this gap in knowledge, EvoDB (an Evolutionary rates DataBase) was compiled. Nucleotide sequences and their corresponding protein domain data including the associated seed alignments from the PFAM-A (protein family) database were used to estimate evolutionary rate (ω = dN/dS) profiles at codon sites for each entry. EvoDB contains 98.83% of the gapped nucleotide sequence alignments and 97.1% of the evolutionary rate profiles for the corresponding information in PFAM-A. As the identification of codon sites under positive selection and their position in a sequence profile is usually the most sought after information for molecular evolutionary biologists, evolutionary rate profiles were determined under the M2a model using the CODEML algorithm in the PAML (Phylogenetic Analysis by Maximum Likelihood) suite of software. Validation of nucleotide sequences against amino acid data was implemented to ensure high data quality. EvoDB is a catalogue of the evolutionary rate profiles and provides the corresponding phylogenetic trees, PFAM-A alignments and annotated accession identifier data. In addition, the database can be explored and queried using known evolutionary rate profiles to identify domains under similar evolutionary constraints and pressures. EvoDB is a resource for evolutionary, phylogenetic studies and presents a tier of information untapped by current databases. © The Author(s) 2015. Published by Oxford University Press.

Genetic Architecture of Aluminum Tolerance in Rice (Oryza sativa) Determined through Genome-Wide Association Analysis and QTL Mapping

PubMed Central

Famoso, Adam N.; Zhao, Keyan; Clark, Randy T.; Tung, Chih-Wei; Wright, Mark H.; Bustamante, Carlos; Kochian, Leon V.; McCouch, Susan R.

2011-01-01

Aluminum (Al) toxicity is a primary limitation to crop productivity on acid soils, and rice has been demonstrated to be significantly more Al tolerant than other cereal crops. However, the mechanisms of rice Al tolerance are largely unknown, and no genes underlying natural variation have been reported. We screened 383 diverse rice accessions, conducted a genome-wide association (GWA) study, and conducted QTL mapping in two bi-parental populations using three estimates of Al tolerance based on root growth. Subpopulation structure explained 57% of the phenotypic variation, and the mean Al tolerance in Japonica was twice that of Indica. Forty-eight regions associated with Al tolerance were identified by GWA analysis, most of which were subpopulation-specific. Four of these regions co-localized with a priori candidate genes, and two highly significant regions co-localized with previously identified QTLs. Three regions corresponding to induced Al-sensitive rice mutants (ART1, STAR2, Nrat1) were identified through bi-parental QTL mapping or GWA to be involved in natural variation for Al tolerance. Haplotype analysis around the Nrat1 gene identified susceptible and tolerant haplotypes explaining 40% of the Al tolerance variation within the aus subpopulation, and sequence analysis of Nrat1 identified a trio of non-synonymous mutations predictive of Al sensitivity in our diversity panel. GWA analysis discovered more phenotype–genotype associations and provided higher resolution, but QTL mapping identified critical rare and/or subpopulation-specific alleles not detected by GWA analysis. Mapping using Indica/Japonica populations identified QTLs associated with transgressive variation where alleles from a susceptible aus or indica parent enhanced Al tolerance in a tolerant Japonica background. This work supports the hypothesis that selectively introgressing alleles across subpopulations is an efficient approach for trait enhancement in plant breeding programs and demonstrates the fundamental importance of subpopulation in interpreting and manipulating the genetics of complex traits in rice. PMID:21829395

Recurrent R-spondin fusions in colon cancer.

PubMed

Seshagiri, Somasekar; Stawiski, Eric W; Durinck, Steffen; Modrusan, Zora; Storm, Elaine E; Conboy, Caitlin B; Chaudhuri, Subhra; Guan, Yinghui; Janakiraman, Vasantharajan; Jaiswal, Bijay S; Guillory, Joseph; Ha, Connie; Dijkgraaf, Gerrit J P; Stinson, Jeremy; Gnad, Florian; Huntley, Melanie A; Degenhardt, Jeremiah D; Haverty, Peter M; Bourgon, Richard; Wang, Weiru; Koeppen, Hartmut; Gentleman, Robert; Starr, Timothy K; Zhang, Zemin; Largaespada, David A; Wu, Thomas D; de Sauvage, Frederic J

2012-08-30

Identifying and understanding changes in cancer genomes is essential for the development of targeted therapeutics. Here we analyse systematically more than 70 pairs of primary human colon tumours by applying next-generation sequencing to characterize their exomes, transcriptomes and copy-number alterations. We have identified 36,303 protein-altering somatic changes that include several new recurrent mutations in the Wnt pathway gene TCF7L2, chromatin-remodelling genes such as TET2 and TET3 and receptor tyrosine kinases including ERBB3. Our analysis for significantly mutated cancer genes identified 23 candidates, including the cell cycle checkpoint kinase ATM. Copy-number and RNA-seq data analysis identified amplifications and corresponding overexpression of IGF2 in a subset of colon tumours. Furthermore, using RNA-seq data we identified multiple fusion transcripts including recurrent gene fusions involving R-spondin family members RSPO2 and RSPO3 that together occur in 10% of colon tumours. The RSPO fusions were mutually exclusive with APC mutations, indicating that they probably have a role in the activation of Wnt signalling and tumorigenesis. Consistent with this we show that the RSPO fusion proteins were capable of potentiating Wnt signalling. The R-spondin gene fusions and several other gene mutations identified in this study provide new potential opportunities for therapeutic intervention in colon cancer.

Recurrent R-spondin fusions in colon cancer

PubMed Central

Seshagiri, Somasekar; Stawiski, Eric W.; Durinck, Steffen; Modrusan, Zora; Storm, Elaine E.; Conboy, Caitlin B.; Chaudhuri, Subhra; Guan, Yinghui; Janakiraman, Vasantharajan; Jaiswal, Bijay S.; Guillory, Joseph; Ha, Connie; Dijkgraaf, Gerrit J. P.; Stinson, Jeremy; Gnad, Florian; Huntley, Melanie A.; Degenhardt, Jeremiah D.; Haverty, Peter M.; Bourgon, Richard; Wang, Weiru; Koeppen, Hartmut; Gentleman, Robert; Starr, Timothy K.; Zhang, Zemin; Largaespada, David A.; Wu, Thomas D.; de Sauvage, Frederic J

2013-01-01

Identifying and understanding changes in cancer genomes is essential for the development of targeted therapeutics1. Here we analyse systematically more than 70 pairs of primary human colon tumours by applying next-generation sequencing to characterize their exomes, transcriptomes and copy-number alterations. We have identified 36,303 protein-altering somatic changes that include several new recurrent mutations in the Wnt pathway gene TCF7L2, chromatin-remodelling genes such as TET2 and TET3 and receptor tyrosine kinases including ERBB3. Our analysis for significantly mutated cancer genes identified 23 candidates, including the cell cycle checkpoint kinase ATM. Copy-number and RNA-seq data analysis identified amplifications and corresponding overexpression of IGF2 in a subset of colon tumours. Furthermore, using RNA-seq data we identified multiple fusion transcripts including recurrent gene fusions involving R-spondin family members RSPO2 and RSPO3 that together occur in 10% of colon tumours. The RSPO fusions were mutually exclusive with APC mutations, indicating that they probably have a role in the activation of Wnt signalling and tumorigenesis. Consistent with this we show that the RSPO fusion proteins were capable of potentiating Wnt signalling. The R-spondin gene fusions and several other gene mutations identified in this study provide new potential opportunities for therapeutic intervention in colon cancer. PMID:22895193

Holder and Topic Based Analysis of Emotions on Blog Texts: A Case Study for Bengali

NASA Astrophysics Data System (ADS)

Das, Dipankar; Bandyopadhyay, Sivaji

The paper presents an extended approach of analyzing emotions of the blog users on different topics. The rule based techniques to identify emotion holders and topics with respect to their corresponding emotional expressions helps to develop the baseline system. On the other hand, the Support Vector Machine (SVM) based supervised framework identifies the holders, topics and emotional expressions from the blog sentences by outperforming the baseline system. The existence of many to many relations between the holders and the topics with respect to Ekman's six different emotion classes has been examined using two way evaluation techniques, one is with respect to holder and other is from the perspective of topic. The results of the system were found satisfactory in comparison with the agreement of the subjective annotation. The error analysis shows that the topic of a blog at document level is not always conveyed at the sentence level. Moreover, the difficulty in identifying topic from a blog document is due to the problem of identifying some features like bigrams, Named Entities and sentiment. Thus, we employed a semantic clustering approach along with these features to identify the similarity between document level topic and sentential topic as well as to improve the results of identifying the document level topic.

Spatial patterns of large natural fires in Sierra Nevada wilderness areas

USGS Publications Warehouse

Collins, B.M.; Kelly, M.; van Wagtendonk, J.W.; Stephens, S.L.

2007-01-01

The effects of fire on vegetation vary based on the properties and amount of existing biomass (or fuel) in a forest stand, weather conditions, and topography. Identifying controls over the spatial patterning of fire-induced vegetation change, or fire severity, is critical in understanding fire as a landscape scale process. We use gridded estimates of fire severity, derived from Landsat ETM+ imagery, to identify the biotic and abiotic factors contributing to the observed spatial patterns of fire severity in two large natural fires. Regression tree analysis indicates the importance of weather, topography, and vegetation variables in explaining fire severity patterns between the two fires. Relative humidity explained the highest proportion of total sum of squares throughout the Hoover fire (Yosemite National Park, 2001). The lowest fire severity corresponded with increased relative humidity. For the Williams fire (Sequoia/Kings Canyon National Parks, 2003) dominant vegetation type explains the highest proportion of sum of squares. Dominant vegetation was also important in determining fire severity throughout the Hoover fire. In both fires, forest stands that were dominated by lodgepole pine (Pinus contorta) burned at highest severity, while red fir (Abies magnifica) stands corresponded with the lowest fire severities. There was evidence in both fires that lower wind speed corresponded with higher fire severity, although the highest fire severity in the Williams fire occurred during increased wind speed. Additionally, in the vegetation types that were associated with lower severity, burn severity was lowest when the time since last fire was fewer than 11 and 17 years for the Williams and Hoover fires, respectively. Based on the factors and patterns identified, managers can anticipate the effects of management ignited and naturally ignited fires at the forest stand and the landscape levels. ?? 2007 Springer Science+Business Media, Inc.

Online coupled camera pose estimation and dense reconstruction from video

DOEpatents

Medioni, Gerard; Kang, Zhuoliang

2016-11-01

A product may receive each image in a stream of video image of a scene, and before processing the next image, generate information indicative of the position and orientation of an image capture device that captured the image at the time of capturing the image. The product may do so by identifying distinguishable image feature points in the image; determining a coordinate for each identified image feature point; and for each identified image feature point, attempting to identify one or more distinguishable model feature points in a three dimensional (3D) model of at least a portion of the scene that appears likely to correspond to the identified image feature point. Thereafter, the product may find each of the following that, in combination, produce a consistent projection transformation of the 3D model onto the image: a subset of the identified image feature points for which one or more corresponding model feature points were identified; and, for each image feature point that has multiple likely corresponding model feature points, one of the corresponding model feature points. The product may update a 3D model of at least a portion of the scene following the receipt of each video image and before processing the next video image base on the generated information indicative of the position and orientation of the image capture device at the time of capturing the received image. The product may display the updated 3D model after each update to the model.

Independent component analysis-based algorithm for automatic identification of Raman spectra applied to artistic pigments and pigment mixtures.

PubMed

González-Vidal, Juan José; Pérez-Pueyo, Rosanna; Soneira, María José; Ruiz-Moreno, Sergio

2015-03-01

A new method has been developed to automatically identify Raman spectra, whether they correspond to single- or multicomponent spectra. The method requires no user input or judgment. There are thus no parameters to be tweaked. Furthermore, it provides a reliability factor on the resulting identification, with the aim of becoming a useful support tool for the analyst in the decision-making process. The method relies on the multivariate techniques of principal component analysis (PCA) and independent component analysis (ICA), and on some metrics. It has been developed for the application of automated spectral analysis, where the analyzed spectrum is provided by a spectrometer that has no previous knowledge of the analyzed sample, meaning that the number of components in the sample is unknown. We describe the details of this method and demonstrate its efficiency by identifying both simulated spectra and real spectra. The method has been applied to artistic pigment identification. The reliable and consistent results that were obtained make the methodology a helpful tool suitable for the identification of pigments in artwork or in paint in general.

Can natural proteins designed with 'inverted' peptide sequences adopt native-like protein folds?

PubMed

Sridhar, Settu; Guruprasad, Kunchur

2014-01-01

We have carried out a systematic computational analysis on a representative dataset of proteins of known three-dimensional structure, in order to evaluate whether it would possible to 'swap' certain short peptide sequences in naturally occurring proteins with their corresponding 'inverted' peptides and generate 'artificial' proteins that are predicted to retain native-like protein fold. The analysis of 3,967 representative proteins from the Protein Data Bank revealed 102,677 unique identical inverted peptide sequence pairs that vary in sequence length between 5-12 and 18 amino acid residues. Our analysis illustrates with examples that such 'artificial' proteins may be generated by identifying peptides with 'similar structural environment' and by using comparative protein modeling and validation studies. Our analysis suggests that natural proteins may be tolerant to accommodating such peptides.

Digital transcriptome analysis of putative sex-determination genes in papaya (Carica papaya).

PubMed

Urasaki, Naoya; Tarora, Kazuhiko; Shudo, Ayano; Ueno, Hiroki; Tamaki, Moritoshi; Miyagi, Norimichi; Adaniya, Shinichi; Matsumura, Hideo

2012-01-01

Papaya (Carica papaya) is a trioecious plant species that has male, female and hermaphrodite flowers on different plants. The primitive sex chromosomes genetically determine the sex of the papaya. Although draft sequences of the papaya genome are already available, the genes for sex determination have not been identified, likely due to the complicated structure of its sex-chromosome sequences. To identify the candidate genes for sex determination, we conducted a transcriptome analysis of flower samples from male, female and hermaphrodite plants using high-throughput SuperSAGE for digital gene expression analysis. Among the short sequence tags obtained from the transcripts, 312 unique tags were specifically mapped to the primitive sex chromosome (X or Y(h)) sequences. An annotation analysis revealed that retroelements are the most abundant sequences observed in the genes corresponding to these tags. The majority of tags on the sex chromosomes were located on the X chromosome, and only 30 tags were commonly mapped to both the X and Y(h) chromosome, implying a loss of many genes on the Y(h) chromosome. Nevertheless, candidate Y(h) chromosome-specific female determination genes, including a MADS-box gene, were identified. Information on these sex chromosome-specific expressed genes will help elucidating sex determination in the papaya.

Tissue phosphoproteomics with PolyMAC identifies potential therapeutic targets in a transgenic mouse model of HER2 positive breast cancer

PubMed Central

Searleman, Adam C.; Iliuk, Anton B.; Collier, Timothy S.; Chodosh, Lewis A.; Tao, W. Andy; Bose, Ron

2014-01-01

Altered protein phosphorylation is a feature of many human cancers that can be targeted therapeutically. Phosphopeptide enrichment is a critical step for maximizing the depth of phosphoproteome coverage by MS, but remains challenging for tissue specimens because of their high complexity. We describe the first analysis of a tissue phosphoproteome using polymer-based metal ion affinity capture (PolyMAC), a nanopolymer that has excellent yield and specificity for phosphopeptide enrichment, on a transgenic mouse model of HER2-driven breast cancer. By combining phosphotyrosine immunoprecipitation with PolyMAC, 411 unique peptides with 139 phosphotyrosine, 45 phosphoserine, and 29 phosphothreonine sites were identified from five LC-MS/MS runs. Combining reverse phase liquid chromatography fractionation at pH 8.0 with PolyMAC identified 1571 unique peptides with 1279 phosphoserine, 213 phosphothreonine, and 21 phosphotyrosine sites from eight LC-MS/MS runs. Linear motif analysis indicated that many of the phosphosites correspond to well-known phosphorylation motifs. Analysis of the tyrosine phosphoproteome with the Drug Gene Interaction database uncovered a network of potential therapeutic targets centered on Src family kinases with inhibitors that are either FDA-approved or in clinical development. These results demonstrate that PolyMAC is well suited for phosphoproteomic analysis of tissue specimens. PMID:24723360

Digital Transcriptome Analysis of Putative Sex-Determination Genes in Papaya (Carica papaya)

PubMed Central

Urasaki, Naoya; Tarora, Kazuhiko; Shudo, Ayano; Ueno, Hiroki; Tamaki, Moritoshi; Miyagi, Norimichi; Adaniya, Shinichi; Matsumura, Hideo

2012-01-01

Papaya (Carica papaya) is a trioecious plant species that has male, female and hermaphrodite flowers on different plants. The primitive sex chromosomes genetically determine the sex of the papaya. Although draft sequences of the papaya genome are already available, the genes for sex determination have not been identified, likely due to the complicated structure of its sex-chromosome sequences. To identify the candidate genes for sex determination, we conducted a transcriptome analysis of flower samples from male, female and hermaphrodite plants using high-throughput SuperSAGE for digital gene expression analysis. Among the short sequence tags obtained from the transcripts, 312 unique tags were specifically mapped to the primitive sex chromosome (X or Yh) sequences. An annotation analysis revealed that retroelements are the most abundant sequences observed in the genes corresponding to these tags. The majority of tags on the sex chromosomes were located on the X chromosome, and only 30 tags were commonly mapped to both the X and Yh chromosome, implying a loss of many genes on the Yh chromosome. Nevertheless, candidate Yh chromosome-specific female determination genes, including a MADS-box gene, were identified. Information on these sex chromosome-specific expressed genes will help elucidating sex determination in the papaya. PMID:22815863

Identification of a 'Candidatus Phytoplasma hispanicum'-related strain, associated with yellows-type diseases, in smoke-tree sharpshooter (Homalodisca liturata Ball).

PubMed

Servín-Villegas, Rosalía; Caamal-Chan, Maria Goretty; Chavez-Medina, Alicia; Loera-Muro, Abraham; Barraza, Aarón; Medina-Hernández, Diana; Holguín-Peña, Ramón Jaime

2018-04-11

The 16SrXIII group from phytoplasma bacteria were identified in salivary glands from Homalodisca liturata, which were collected in El Comitán on the Baja California peninsula in Mexico. We were able to positively identify 15 16S rRNA gene sequences with the corresponding signature sequence of 'CandidatusPhytoplasma' (CAAGAYBATKATGTKTAGCYGGDCT) and in silico restriction fragment length polymorphism (RFLP) profiles (F value estimations) coupled with a phylogenetic analysis to confirm their relatedness to 'CandidatusPhytoplasma hispanicum', which in turn belongs to the 16SrXIII group. A restriction analysis was carried out with AluI and EcoRI to confirm that the five sequences belongs to subgroup D. The rest of the sequences did not exhibit any known RFLP profile related to a subgroup reported in the 16SrXIII group.

Sequence determination and analysis of S-adenosyl-L-homocysteine hydrolase from yellow lupine (Lupinus luteus).

PubMed

Brzeziński, K; Janowski, R; Podkowiński, J; Jaskólski, M

2001-01-01

The coding sequences of two S-adenosyl-L-homocysteine hydrolases (SAHases) were identified in yellow lupine by screenig of a cDNA library. One of them, corresponding to the complete protein, was sequenced and compared with 52 other SAHase sequences. Phylogenetic analysis of these proteins identified three groups of the enzymes. Group A comprises only bacterial sequences. Group B is subdivided into two subgroups, one of which (B1) is formed by animal sequences. Subgroup B2 consist of two distinct clusters, B2a and B2b. Cluster B2b comprises all known plant sequences, including the yellow lupine enzyme, which are distinguished by a 50-residue insert. Group C is heterogeneous and contains SAHases from Archaea as well as a new class of animal enzymes, distinctly different from those in group B1.

Embedded sparse representation of fMRI data via group-wise dictionary optimization

NASA Astrophysics Data System (ADS)

Zhu, Dajiang; Lin, Binbin; Faskowitz, Joshua; Ye, Jieping; Thompson, Paul M.

2016-03-01

Sparse learning enables dimension reduction and efficient modeling of high dimensional signals and images, but it may need to be tailored to best suit specific applications and datasets. Here we used sparse learning to efficiently represent functional magnetic resonance imaging (fMRI) data from the human brain. We propose a novel embedded sparse representation (ESR), to identify the most consistent dictionary atoms across different brain datasets via an iterative group-wise dictionary optimization procedure. In this framework, we introduced additional criteria to make the learned dictionary atoms more consistent across different subjects. We successfully identified four common dictionary atoms that follow the external task stimuli with very high accuracy. After projecting the corresponding coefficient vectors back into the 3-D brain volume space, the spatial patterns are also consistent with traditional fMRI analysis results. Our framework reveals common features of brain activation in a population, as a new, efficient fMRI analysis method.

Mitochondria localize to injured axons to support regeneration

PubMed Central

Han, Sung Min; Baig, Huma S.; Hammarlund, Marc

2016-01-01

SUMMARY Axon regeneration is essential to restore the nervous system after axon injury. However, the neuronal cell biology that underlies axon regeneration is incompletely understood. Here we use in vivo single-neuron analysis to investigate the relationship between nerve injury, mitochondrial localization, and axon regeneration. Mitochondria translocate into injured axons, so that average mitochondria density increases after injury. Moreover, single-neuron analysis reveals that axons that fail to increase mitochondria have poor regeneration. Experimental alterations to axonal mitochondrial distribution or mitochondrial respiratory chain function result in corresponding changes to regeneration outcomes. Axonal mitochondria are specifically required for growth cone migration, identifying a key energy challenge for injured neurons. Finally, mitochondrial localization to the axon after injury is regulated in part by dual-leucine zipper kinase-1 (DLK-1), a conserved regulator of axon regeneration. These data identify regulation of axonal mitochondria as a new cell biological mechanism that helps determine the regenerative response of injured neurons. PMID:28009276

Eating patterns in the Brazilian Longitudinal Study of Adult Health (ELSA-Brasil): an exploratory analysis.

PubMed

Cardoso, Letícia de Oliveira; Carvalho, Marilia Sá; Cruz, Oswaldo Gonçalves; Melere, Cristiane; Luft, Vivian Cristine; Molina, Maria Del Carmen Bisi; Faria, Carolina Perim de; Benseñor, Isabela M; Matos, Sheila Maria Alvim; Fonseca, Maria de Jesus Mendes da; Griep, Rosane Harter; Chor, Dóra

2016-01-01

The food consumption of 15,071 public employees was analyzed in six Brazilian cities participating in the baseline for Brazilian Longitudinal Study of Adult Health (ELSA-Brasil, 2008-2010) with the aim of identifying eating patterns and their relationship to socio-demographic variables. Multiple correspondence and cluster analysis were applied. Four patterns were identified, with their respective frequencies: "traditional" (48%); "fruits and vegetables" (25%); "pastry shop" (24%); and "diet/light" (5%) The "traditional" and "pastry shop" patterns were more frequent among men, younger individuals, and those with less schooling. "Fruits and vegetables" and "diet/light" were more frequent in women, older individuals, and those with more schooling. Our findings show the inclusion of new items in the "traditional" pattern and the appearance of the "low sugar/low fat" pattern among the eating habits of Brazilian workers, and signal socio-demographic and regional differences.

Selection of sourdough lactobacilli with antifungal activity for use as biopreservatives in bakery products.

PubMed

Garofalo, Cristiana; Zannini, Emanuele; Aquilanti, Lucia; Silvestri, Gloria; Fierro, Olga; Picariello, Gianluca; Clementi, Francesca

2012-08-08

Two hundred and sixteen LAB cultures from sourdoughs and dough for bread and panettone production were screened for in vitro antifungal properties against three indicator cultures ascribed to Aspergillus japonicus , Eurotium repens , and Penicillium roseopurpureum , isolated from bakery environment and moldy panettone. Nineteen preselected isolates were subjected to minimum inhibitory concentration determination against the indicator cultures. Sourdoughs prepared with the two most promising strains, identified as Lactobacillus rossiae LD108 and Lactobacillus paralimentarius PB127, were characterized. The sourdough extracts were subjected to HPLC analysis coupled with a microtiter plate bioassay against A. japonicus to identify the active fractions. MALDI-TOF MS analysis revealed the occurrence of a series of peptides corresponding to wheat α-gliadin proteolysis fragments in the active fraction from L. rossiae LD108 sourdough. The ability to prevent mold growth on bread was demonstrated for both strains, whereas L. rossiae LD108 also inhibited mold growth on panettone.

Identifying protein domains by global analysis of soluble fragment data.

PubMed

Bulloch, Esther M M; Kingston, Richard L

2014-11-15

The production and analysis of individual structural domains is a common strategy for studying large or complex proteins, which may be experimentally intractable in their full-length form. However, identifying domain boundaries is challenging if there is little structural information concerning the protein target. One experimental procedure for mapping domains is to screen a library of random protein fragments for solubility, since truncation of a domain will typically expose hydrophobic groups, leading to poor fragment solubility. We have coupled fragment solubility screening with global data analysis to develop an effective method for identifying structural domains within a protein. A gene fragment library is generated using mechanical shearing, or by uracil doping of the gene and a uracil-specific enzymatic digest. A split green fluorescent protein (GFP) assay is used to screen the corresponding protein fragments for solubility when expressed in Escherichia coli. The soluble fragment data are then analyzed using two complementary approaches. Fragmentation "hotspots" indicate possible interdomain regions. Clustering algorithms are used to group related fragments, and concomitantly predict domain location. The effectiveness of this Domain Seeking procedure is demonstrated by application to the well-characterized human protein p85α. Copyright © 2014 Elsevier Inc. All rights reserved.

Two splice variants of the bovine lactoferrin gene identified in Staphylococcus aureus isolated from mastitis in dairy cattle.

PubMed

Huang, J M; Wang, Z Y; Ju, Z H; Wang, C F; Li, Q L; Sun, T; Hou, Q L; Hang, S Q; Hou, M H; Zhong, J F

2011-12-21

Bovine lactoferrin (bLF) is a member of the transferrin family; it plays an important role in the innate immune response. We identified novel splice variants of the bLF gene in mastitis-infected and healthy cows. Reverse transcription-polymerase chain reaction (RT-PCR) and clone sequencing analysis were used to screen the splice variants of the bLF gene in the mammary gland, spleen and liver tissues. One main transcript corresponding to the bLF reference sequence was found in three tissues in both healthy and mastitis-infected cows. Quantitative real-time PCR analysis showed that the expression levels of the LF gene's main transcript were not significantly different in tissues from healthy versus mastitis-infected cows. However, the new splice variant, LF-AS2, which has the exon-skipping alternative splicing pattern, was only identified in mammary glands infected with Staphylococcus aureus. Sequencing analysis showed that the new splice variant was 251 bp in length, including exon 1, part of exon 2, part of exon 16, and exon 17. We conclude that bLF may play a role in resistance to mastitis through alternative splicing mechanisms.

An In Planta-Expressed Polyketide Synthase Produces (R)-Mellein in the Wheat Pathogen Parastagonospora nodorum

PubMed Central

Krill, Christian; Barrow, Russell A.; Chen, Shasha; Trengove, Robert; Oliver, Richard P.; Solomon, Peter S.

2014-01-01

Parastagonospora nodorum is a pathogen of wheat that affects yields globally. Previous transcriptional analysis identified a partially reducing polyketide synthase (PR-PKS) gene, SNOG_00477 (SN477), in P. nodorum that is highly upregulated during infection of wheat leaves. Disruption of the corresponding SN477 gene resulted in the loss of production of two compounds, which we identified as (R)-mellein and (R)-O-methylmellein. Using a Saccharomyces cerevisiae yeast heterologous expression system, we successfully demonstrated that SN477 is the only enzyme required for the production of (R)-mellein. This is the first identification of a fungal PKS that is responsible for the synthesis of (R)-mellein. The P. nodorum ΔSN477 mutant did not show any significant difference from the wild-type strain in its virulence against wheat. However, (R)-mellein at 200 μg/ml inhibited the germination of wheat (Triticum aestivum) and barrel medic (Medicago truncatula) seeds. Comparative sequence analysis identified the presence of mellein synthase (MLNS) homologues in several Dothideomycetes and two sodariomycete genera. Phylogenetic analysis suggests that the MLNSs in fungi and bacteria evolved convergently from fungal and bacterial 6-methylsalicylic acid synthases. PMID:25326302

Extending existing structural identifiability analysis methods to mixed-effects models.

PubMed

Janzén, David L I; Jirstrand, Mats; Chappell, Michael J; Evans, Neil D

2018-01-01

The concept of structural identifiability for state-space models is expanded to cover mixed-effects state-space models. Two methods applicable for the analytical study of the structural identifiability of mixed-effects models are presented. The two methods are based on previously established techniques for non-mixed-effects models; namely the Taylor series expansion and the input-output form approach. By generating an exhaustive summary, and by assuming an infinite number of subjects, functions of random variables can be derived which in turn determine the distribution of the system's observation function(s). By considering the uniqueness of the analytical statistical moments of the derived functions of the random variables, the structural identifiability of the corresponding mixed-effects model can be determined. The two methods are applied to a set of examples of mixed-effects models to illustrate how they work in practice. Copyright © 2017 Elsevier Inc. All rights reserved.

Gene signatures of postoperative atrial fibrillation in atrial tissue after coronary artery bypass grafting surgery in patients receiving β-blockers.

PubMed

Kertai, Miklos D; Qi, Wenjing; Li, Yi-Ju; Lombard, Frederick W; Liu, Yutao; Smith, Michael P; Stafford-Smith, Mark; Newman, Mark F; Milano, Carmelo A; Mathew, Joseph P; Podgoreanu, Mihai V

2016-03-01

Atrial tissue gene expression profiling may help to determine how differentially expressed genes in the human atrium before cardiopulmonary bypass (CPB) are related to subsequent biologic pathway activation patterns, and whether specific expression profiles are associated with an increased risk for postoperative atrial fibrillation (AF) or altered response to β-blocker (BB) therapy after coronary artery bypass grafting (CABG) surgery. Right atrial appendage (RAA) samples were collected from 45 patients who were receiving perioperative BB treatment, and underwent CABG surgery. The isolated RNA samples were used for microarray gene expression analysis, to identify probes that were expressed differently in patients with and without postoperative AF. Gene expression analysis was performed to identify probes that were expressed differently in patients with and without postoperative AF. Gene set enrichment analysis (GSEA) was performed to determine how sets of genes might be systematically altered in patients with postoperative AF. Of the 45 patients studied, genomic DNA from 42 patients was used for target sequencing of 66 candidate genes potentially associated with AF, and 2,144 single-nucleotide polymorphisms (SNPs) were identified. We then performed expression quantitative trait loci (eQTL) analysis to determine the correlation between SNPs identified in the genotyped patients, and RAA expression. Probes that met a false discovery rate<0.25 were selected for eQTL analysis. Of the 17,678 gene expression probes analyzed, 2 probes met our prespecified significance threshold of false discovery rate<0.25. The most significant probe corresponded to vesicular overexpressed in cancer - prosurvival protein 1 gene (VOPP1; 1.83 fold change; P=3.47×10(-7)), and was up-regulated in patients with postoperative AF, whereas the second most significant probe, which corresponded to the LOC389286 gene (0.49 fold change; P=1.54×10(-5)), was down-regulated in patients with postoperative AF. GSEA highlighted the role of VOPP1 in pathways with biologic relevance to myocardial homeostasis, and oxidative stress and redox modulation. Candidate gene eQTL showed a trans-acting association between variants of G protein-coupled receptor kinase 5 gene, previously linked to altered BB response, and high expression of VOPP1. In patients undergoing CABG surgery, RAA gene expression profiling, and pathway and eQTL analysis suggested that VOPP1 plays a novel etiological role in postoperative AF despite perioperative BB therapy. Copyright © 2016. Published by Elsevier Ltd.

The challenges of neural mind-reading paradigms.

PubMed

Vilarroya, Oscar

2013-01-01

Neural mind-reading studies, based on multivariate pattern analysis (MVPA) methods, are providing exciting new studies. Some of the results obtained with these paradigms have raised high expectations, such as the possibility of creating brain reading devices. However, such hopes are based on the assumptions that: (a) the BOLD signal is a marker of neural activity; (b) the BOLD pattern identified by a MVPA is a neurally sound pattern; (c) the MVPA's feature space is a good mapping of the neural representation of a stimulus, and (d) the pattern identified by a MVPA corresponds to a representation. I examine here the challenges that still have to be met before fully accepting such assumptions.

Social space, social class and Bourdieu: health inequalities in British Columbia, Canada.

PubMed

Veenstra, Gerry

2007-03-01

This article adopts Pierre Bourdieu's cultural-structuralist approach to conceptualizing and identifying social classes in social space and seeks to identify health effects of class in one Canadian province. Utilizing data from an original questionnaire survey of randomly selected adults from 25 communities in British Columbia, social (class) groupings defined by cultural tastes and dispositions, lifestyle practices, social background, educational capital, economic capital, social capital and occupational categories are presented in visual mappings of social space constructed by use of exploratory multiple correspondence analysis techniques. Indicators of physical and mental health are then situated within this social space, enabling speculations pertaining to health effects of social class in British Columbia.

Geospatial-temporal semantic graph representations of trajectories from remote sensing and geolocation data

DOEpatents

Perkins, David Nikolaus; Brost, Randolph; Ray, Lawrence P.

2017-08-08

Various technologies for facilitating analysis of large remote sensing and geolocation datasets to identify features of interest are described herein. A search query can be submitted to a computing system that executes searches over a geospatial temporal semantic (GTS) graph to identify features of interest. The GTS graph comprises nodes corresponding to objects described in the remote sensing and geolocation datasets, and edges that indicate geospatial or temporal relationships between pairs of nodes in the nodes. Trajectory information is encoded in the GTS graph by the inclusion of movable nodes to facilitate searches for features of interest in the datasets relative to moving objects such as vehicles.

A novel principal component analysis for spatially misaligned multivariate air pollution data.

PubMed

Jandarov, Roman A; Sheppard, Lianne A; Sampson, Paul D; Szpiro, Adam A

2017-01-01

We propose novel methods for predictive (sparse) PCA with spatially misaligned data. These methods identify principal component loading vectors that explain as much variability in the observed data as possible, while also ensuring the corresponding principal component scores can be predicted accurately by means of spatial statistics at locations where air pollution measurements are not available. This will make it possible to identify important mixtures of air pollutants and to quantify their health effects in cohort studies, where currently available methods cannot be used. We demonstrate the utility of predictive (sparse) PCA in simulated data and apply the approach to annual averages of particulate matter speciation data from national Environmental Protection Agency (EPA) regulatory monitors.

ANTECEDENT VERSUS CONSEQUENT EVENTS AS PREDICTORS OF PROBLEM BEHAVIOR

PubMed Central

Camp, Erin M; Iwata, Brian A; Hammond, Jennifer L; Bloom, Sarah E

2009-01-01

Comparisons of results from descriptive and functional analyses of problem behavior generally have shown poor correspondence. Most descriptive analyses have focused on relations between consequent events and behavior, and it has been noted that attention is a common consequence for problem behavior even though it may not be a functional reinforcer. Because attention may be prescribed simply as a means of stopping serious problem behavior, it is possible that naturally occurring antecedent events (establishing operations) might be better predictors of problem behavior than consequences. We conducted descriptive and functional analyses of the problem behaviors of 7 participants. Conditional probabilities based on combined antecedent and consequent events showed correspondence with the functional analysis data for 4 of the 7 participants, but antecedent events were no better than consequent events in identifying the function of problem behavior. PMID:19949538

Very highly excited vibrational states of LiCN using a discrete variable representation

NASA Astrophysics Data System (ADS)

Henderson, James R.; Tennyson, Jonathan

Calculations are presented for the lowest 900 vibrational (J = 0) states of the LiCN floppy system for a two dimensional potential energy surface (rCN frozen). Most of these states lie well above the barrier separating the two linear isomers of the molecule and the point where the classical dynamics of the system becomes chaotic. Analysis of the wavefunctions of individual states in the high energy region shows that while most have an irregular nodal structure, a significant number of states appear regular - corresponding to solutions of standard, 'mode localized' hamiltonians. Motions corresponding in zero-order to Li-CN and Li-NC normal modes as well as free rotor states are identified. The distribution of level spacings is also studied and yields results in good agreement with those obtained by analysing nodal structures.

How weak values emerge in joint measurements on cloned quantum systems.

PubMed

Hofmann, Holger F

2012-07-13

A statistical analysis of optimal universal cloning shows that it is possible to identify an ideal (but nonpositive) copying process that faithfully maps all properties of the original Hilbert space onto two separate quantum systems, resulting in perfect correlations for all observables. The joint probabilities for noncommuting measurements on separate clones then correspond to the real parts of the complex joint probabilities observed in weak measurements on a single system, where the measurements on the two clones replace the corresponding sequence of weak measurement and postselection. The imaginary parts of weak measurement statics can be obtained by replacing the cloning process with a partial swap operation. A controlled-swap operation combines both processes, making the complete weak measurement statistics accessible as a well-defined contribution to the joint probabilities of fully resolved projective measurements on the two output systems.

Identifying U.S. Marine Corps Recruit Characteristics That Correspond to Success in Specific Occupational Fields

DTIC Science & Technology

2016-06-01

Reserve Affairs MAGTF Marine Air Ground Task Force MC Mechanical Comprehension MCMAP Marine Corps Martial Arts Program MCO Marine Corps Order MCRC... Martial Arts Program (MCMAP) belt level. Setting the MCMCAP belt level to “NOT TRAINED” is required to maintain the MCMAP records for future analysis...BELT MARTIAL ARTS INSTRUCTOR 60 MMG BROWN BELT MARTIAL ARTS INSTRUCTOR 70 MMJ BLACK BELT, 1ST DEGREE MARTIAL ARTS INSTRUCTOR 80 MMK BLACK BELT, 1ST

Report for 2012 from the Bordeaux IVS Analysis Center

NASA Technical Reports Server (NTRS)

Charlot, Patrick; Bellanger, Antoine; Bouffet, Romuald; Bourda, Geraldine; Collioud, Arnaud; Baudry, Alain

2013-01-01

This report summarizes the activities of the Bordeaux IVS Analysis Center during the year 2012. The work focused on (i) regular analysis of the IVS-R1 and IVS-R4 sessions with the GINS software package; (ii) systematic VLBI imaging of the RDV sessions and calculation of the corresponding source structure index and compactness values; (iii) investigation of the correlation between astrometric position instabilities and source structure variations; and (iv) continuation of our VLBI observational program to identify optically-bright radio sources suitable for the link with the future Gaia frame. Also of importance is the 11th European VLBI Network Symposium, which we organized last October in Bordeaux and which drew much attention from the European and International VLBI communities.

The application of complex network time series analysis in turbulent heated jets

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

Charakopoulos, A. K.; Karakasidis, T. E., E-mail: thkarak@uth.gr; Liakopoulos, A.

In the present study, we applied the methodology of the complex network-based time series analysis to experimental temperature time series from a vertical turbulent heated jet. More specifically, we approach the hydrodynamic problem of discriminating time series corresponding to various regions relative to the jet axis, i.e., time series corresponding to regions that are close to the jet axis from time series originating at regions with a different dynamical regime based on the constructed network properties. Applying the transformation phase space method (k nearest neighbors) and also the visibility algorithm, we transformed time series into networks and evaluated the topologicalmore » properties of the networks such as degree distribution, average path length, diameter, modularity, and clustering coefficient. The results show that the complex network approach allows distinguishing, identifying, and exploring in detail various dynamical regions of the jet flow, and associate it to the corresponding physical behavior. In addition, in order to reject the hypothesis that the studied networks originate from a stochastic process, we generated random network and we compared their statistical properties with that originating from the experimental data. As far as the efficiency of the two methods for network construction is concerned, we conclude that both methodologies lead to network properties that present almost the same qualitative behavior and allow us to reveal the underlying system dynamics.« less

The application of complex network time series analysis in turbulent heated jets

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

Charakopoulos, A. K.; Karakasidis, T. E., E-mail: thkarak@uth.gr; Liakopoulos, A.

2014-06-15

In the present study, we applied the methodology of the complex network-based time series analysis to experimental temperature time series from a vertical turbulent heated jet. More specifically, we approach the hydrodynamic problem of discriminating time series corresponding to various regions relative to the jet axis, i.e., time series corresponding to regions that are close to the jet axis from time series originating at regions with a different dynamical regime based on the constructed network properties. Applying the transformation phase space method (k nearest neighbors) and also the visibility algorithm, we transformed time series into networks and evaluated the topologicalmore » properties of the networks such as degree distribution, average path length, diameter, modularity, and clustering coefficient. The results show that the complex network approach allows distinguishing, identifying, and exploring in detail various dynamical regions of the jet flow, and associate it to the corresponding physical behavior. In addition, in order to reject the hypothesis that the studied networks originate from a stochastic process, we generated random network and we compared their statistical properties with that originating from the experimental data. As far as the efficiency of the two methods for network construction is concerned, we conclude that both methodologies lead to network properties that present almost the same qualitative behavior and allow us to reveal the underlying system dynamics.« less

Proteomic analysis of tardigrades: towards a better understanding of molecular mechanisms by anhydrobiotic organisms.

PubMed

Schokraie, Elham; Hotz-Wagenblatt, Agnes; Warnken, Uwe; Mali, Brahim; Frohme, Marcus; Förster, Frank; Dandekar, Thomas; Hengherr, Steffen; Schill, Ralph O; Schnölzer, Martina

2010-03-03

Tardigrades are small, multicellular invertebrates which are able to survive times of unfavourable environmental conditions using their well-known capability to undergo cryptobiosis at any stage of their life cycle. Milnesium tardigradum has become a powerful model system for the analysis of cryptobiosis. While some genetic information is already available for Milnesium tardigradum the proteome is still to be discovered. Here we present to the best of our knowledge the first comprehensive study of Milnesium tardigradum on the protein level. To establish a proteome reference map we developed optimized protocols for protein extraction from tardigrades in the active state and for separation of proteins by high resolution two-dimensional gel electrophoresis. Since only limited sequence information of M. tardigradum on the genome and gene expression level is available to date in public databases we initiated in parallel a tardigrade EST sequencing project to allow for protein identification by electrospray ionization tandem mass spectrometry. 271 out of 606 analyzed protein spots could be identified by searching against the publicly available NCBInr database as well as our newly established tardigrade protein database corresponding to 144 unique proteins. Another 150 spots could be identified in the tardigrade clustered EST database corresponding to 36 unique contigs and ESTs. Proteins with annotated function were further categorized in more detail by their molecular function, biological process and cellular component. For the proteins of unknown function more information could be obtained by performing a protein domain annotation analysis. Our results include proteins like protein member of different heat shock protein families and LEA group 3, which might play important roles in surviving extreme conditions. The proteome reference map of Milnesium tardigradum provides the basis for further studies in order to identify and characterize the biochemical mechanisms of tolerance to extreme desiccation. The optimized proteomics workflow will enable application of sensitive quantification techniques to detect differences in protein expression, which are characteristic of the active and anhydrobiotic states of tardigrades.

Proteomic Analysis of Tardigrades: Towards a Better Understanding of Molecular Mechanisms by Anhydrobiotic Organisms

PubMed Central

Schokraie, Elham; Hotz-Wagenblatt, Agnes; Warnken, Uwe; Mali, Brahim; Frohme, Marcus; Förster, Frank; Dandekar, Thomas; Hengherr, Steffen; Schill, Ralph O.; Schnölzer, Martina

2010-01-01

Background Tardigrades are small, multicellular invertebrates which are able to survive times of unfavourable environmental conditions using their well-known capability to undergo cryptobiosis at any stage of their life cycle. Milnesium tardigradum has become a powerful model system for the analysis of cryptobiosis. While some genetic information is already available for Milnesium tardigradum the proteome is still to be discovered. Principal Findings Here we present to the best of our knowledge the first comprehensive study of Milnesium tardigradum on the protein level. To establish a proteome reference map we developed optimized protocols for protein extraction from tardigrades in the active state and for separation of proteins by high resolution two-dimensional gel electrophoresis. Since only limited sequence information of M. tardigradum on the genome and gene expression level is available to date in public databases we initiated in parallel a tardigrade EST sequencing project to allow for protein identification by electrospray ionization tandem mass spectrometry. 271 out of 606 analyzed protein spots could be identified by searching against the publicly available NCBInr database as well as our newly established tardigrade protein database corresponding to 144 unique proteins. Another 150 spots could be identified in the tardigrade clustered EST database corresponding to 36 unique contigs and ESTs. Proteins with annotated function were further categorized in more detail by their molecular function, biological process and cellular component. For the proteins of unknown function more information could be obtained by performing a protein domain annotation analysis. Our results include proteins like protein member of different heat shock protein families and LEA group 3, which might play important roles in surviving extreme conditions. Conclusions The proteome reference map of Milnesium tardigradum provides the basis for further studies in order to identify and characterize the biochemical mechanisms of tolerance to extreme desiccation. The optimized proteomics workflow will enable application of sensitive quantification techniques to detect differences in protein expression, which are characteristic of the active and anhydrobiotic states of tardigrades. PMID:20224743

Genomic Organization, Phylogenetic Comparison and Differential Expression of the SBP-Box Family Genes in Grape

PubMed Central

Hou, Hongmin; Li, Jun; Gao, Min; Singer, Stacy D.; Wang, Hao; Mao, Linyong; Fei, Zhangjun; Wang, Xiping

2013-01-01

Background The SBP-box gene family is specific to plants and encodes a class of zinc finger-containing transcription factors with a broad range of functions. Although SBP-box genes have been identified in numerous plants including green algae, moss, silver birch, snapdragon, Arabidopsis, rice and maize, there is little information concerning SBP-box genes, or the corresponding miR156/157, function in grapevine. Methodology/Principal Findings Eighteen SBP-box gene family members were identified in Vitis vinifera, twelve of which bore sequences that were complementary to miRNA156/157. Phylogenetic reconstruction demonstrated that plant SBP-domain proteins could be classified into seven subgroups, with the V. vinifera SBP-domain proteins being more closely related to SBP-domain proteins from dicotyledonous angiosperms than those from monocotyledonous angiosperms. In addition, synteny analysis between grape and Arabidopsis demonstrated that homologs of several grape SBP genes were found in corresponding syntenic blocks of Arabidopsis. Expression analysis of the grape SBP-box genes in various organs and at different stages of fruit development in V. quinquangularis ‘Shang-24’ revealed distinct spatiotemporal patterns. While the majority of the grape SBP-box genes lacking a miR156/157 target site were expressed ubiquitously and constitutively, most genes bearing a miR156/157 target site exhibited distinct expression patterns, possibly due to the inhibitory role of the microRNA. Furthermore, microarray data mining and quantitative real-time RT-PCR analysis identified several grape SBP-box genes that are potentially involved in the defense against biotic and abiotic stresses. Conclusion The results presented here provide a further understanding of SBP-box gene function in plants, and yields additional insights into the mechanism of stress management in grape, which may have important implications for the future success of this crop. PMID:23527172

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

Ogami, Koichi; Cho, Rihe; Hoshino, Shin-ichi, E-mail: hoshino@phar.nagoya-cu.ac.jp

Highlights: ► So far, only an enzymatically inactive isoform of PAPD7 was reported. ► The novel isoform: PAPD7 l shows robust nucleotidyl transferase activity. ► The newly identified amino terminal region is required for the activity. ► PAPD7 l localizes to the nucleoplasm. ► The N terminal region identified is also required for the nuclear localization. - Abstract: Non-canonical poly(A) polymerases (ncPAPs) catalyze the addition of poly(A) tail to the 3′ end of RNA to play pivotal roles in the regulation of gene expression and also in quality control. Here we identified a novel isoform of the 7th member ofmore » ncPAPs: PAPD7 (PAPD7 l), which contains 230 extra amino acids at the amino terminus of the previously identified PAPD7 (PAPD7 s). In sharp contrast to the inactive PAPD7 s, PAPD7 l showed robust nucleotidyl transferase activity when tethered to an RNA. A region required for the activity was localized to 187–219 aa, and this region was also required for the nuclear retention of PAPD7 l. Western blot analysis revealed that 94 kDa band (corresponding to PAPD7 l) but not 62 kDa band (corresponding to PAPD7 s) detected by PAPD7 antibody was specifically depleted by treatment with PAPD7 siRNA in both HeLa and U2OS cells. These results suggest that PAPD7 l is the major and active isoform of PAPD7 expressed in cells.« less

Identifying constituent spectra sources in multispectral images to quantify and locate cervical neoplasia

NASA Astrophysics Data System (ADS)

Baker, Kevin C.; Bambot, Shabbir

2011-02-01

Optical spectroscopy has been shown to be an effective method for detecting neoplasia. Guided Therapeutics has developed LightTouch, a non invasive device that uses a combination of reflectance and fluorescence spectroscopy for identifying early cancer of the human cervix. The combination of the multispectral information from the two spectroscopic modalities has been shown to be an effective method to screen for cervical cancer. There has however been a relative paucity of work in identifying the individual spectral components that contribute to the measured fluorescence and reflectance spectra. This work aims to identify the constituent source spectra and their concentrations. We used non-negative matrix factorization (NNMF) numerical methods to decompose the mixed multispectral data into the constituent spectra and their corresponding concentrations. NNMF is an iterative approach that factorizes the measured data into non-negative factors. The factors are chosen to minimize the root-mean-squared residual error. NNMF has shown promise for feature extraction and identification in the fields of text mining and spectral data analysis. Since both the constituent source spectra and their corresponding concentrations are assumed to be non-negative by nature NNMF is a reasonable approach to deconvolve the measured multispectral data. Supervised learning methods were then used to determine which of the constituent spectra sources best predict the amount of neoplasia. The constituent spectra sources found to best predict neoplasia were then compared with spectra of known biological chromophores.

Theoretical research and experimental validation of quasi-static load spectra on bogie frame structures of high-speed trains

NASA Astrophysics Data System (ADS)

Zhu, Ning; Sun, Shou-Guang; Li, Qiang; Zou, Hua

2014-12-01

One of the major problems in structural fatigue life analysis is establishing structural load spectra under actual operating conditions. This study conducts theoretical research and experimental validation of quasi-static load spectra on bogie frame structures of high-speed trains. The quasistatic load series that corresponds to quasi-static deformation modes are identified according to the structural form and bearing conditions of high-speed train bogie frames. Moreover, a force-measuring frame is designed and manufactured based on the quasi-static load series. The load decoupling model of the quasi-static load series is then established via calibration tests. Quasi-static load-time histories, together with online tests and decoupling analysis, are obtained for the intermediate range of the Beijing—Shanghai dedicated passenger line. The damage consistency calibration of the quasi-static discrete load spectra is performed according to a damage consistency criterion and a genetic algorithm. The calibrated damage that corresponds with the quasi-static discrete load spectra satisfies the safety requirements of bogie frames.

Volume 42, Issue5 (May 2005)Articles in the Current Issue:Developmental growth in students' concept of energy: Analysis of selected items from the TIMSS database

NASA Astrophysics Data System (ADS)

Liu, Xiufeng; McKeough, Anne

2005-05-01

The aim of this study was to develop a model of students' energy concept development. Applying Case's (1985, 1992) structural theory of cognitive development, we hypothesized that students' concept of energy undergoes a series of transitions, corresponding to systematic increases in working memory capacity. The US national sample from the Third International Mathematics and Science Study (TIMSS) database was used to test our hypothesis. Items relevant to the energy concept in the TIMSS test booklets for three populations were identified. Item difficulty from Rasch modeling was used to test the hypothesized developmental sequence, and percentage of students' correct responses was used to test the correspondence between students' age/grade level and level of the energy concepts. The analysis supported our hypothesized sequence of energy concept development and suggested mixed effects of maturation and schooling on energy concept development. Further, the results suggest that curriculum and instruction design take into consideration the developmental progression of students' concept of energy.

Identifying the principal driving factors of water ecosystem dependence and the corresponding indicator species in a pilot City, China

NASA Astrophysics Data System (ADS)

Zhao, C. S.; Shao, N. F.; Yang, S. T.; Xiang, H.; Lou, H. Z.; Sun, Y.; Yang, Z. Y.; Zhang, Y.; Yu, X. Y.; Zhang, C. B.; Yu, Q.

2018-01-01

The world's aquatic ecosystems yield numerous vital services, which are essential to human existence but have deteriorated seriously in recent years. By studying the mechanisms of interaction between ecosystems and habitat processes, the constraining factors can be identified, and this knowledge can be used to improve the success rate of ecological restoration initiatives. At present, there is insufficient data on the link between hydrological, water quality factors and the changes in the structure of aquatic communities to allow any meaningful study of driving factors of aquatic ecosystems. In this study, the typical monitoring stations were selected by fuzzy clustering analysis based on the spatial and temporal distribution characteristics of water ecology in Jinan City, the first pilot city for the construction of civilized aquatic ecosystems in China. The dominant species identification model was used to identify the dominant species of the aquatic community. The driving effect of hydrological and water quality factors on dominant species was analyzed by Canonical Correspondence Analysis. Then, the principal factors of aquatic ecosystem dependence were selected. The results showed that there were 10 typical monitoring stations out of 59 monitoring sites, which were representative of aquatic ecosystems, 9 dominant fish species, and 20 dominant invertebrate species. The selection of factors for aquatic ecosystem dependence in Jinan were highly influenced by its regional conditions. Chemical environmental parameters influence the temporal and spatial variation of invertebrate much more than that of fish in Jinan City. However, the methodologies coupling typical monitoring stations selection, dominant species determination and driving factors identification were certified to be a cost-effective way, which can provide in-deep theoretical and technical directions for the restoration of aquatic ecosystems elsewhere.

A Set of Functional Brain Networks for the Comprehensive Evaluation of Human Characteristics.

PubMed

Sung, Yul-Wan; Kawachi, Yousuke; Choi, Uk-Su; Kang, Daehun; Abe, Chihiro; Otomo, Yuki; Ogawa, Seiji

2018-01-01

Many human characteristics must be evaluated to comprehensively understand an individual, and measurements of the corresponding cognition/behavior are required. Brain imaging by functional MRI (fMRI) has been widely used to examine brain function related to human cognition/behavior. However, few aspects of cognition/behavior of individuals or experimental groups can be examined through task-based fMRI. Recently, resting state fMRI (rs-fMRI) signals have been shown to represent functional infrastructure in the brain that is highly involved in processing information related to cognition/behavior. Using rs-fMRI may allow diverse information about the brain through a single MRI scan to be obtained, as rs-fMRI does not require stimulus tasks. In this study, we attempted to identify a set of functional networks representing cognition/behavior that are related to a wide variety of human characteristics and to evaluate these characteristics using rs-fMRI data. If possible, these findings would support the potential of rs-fMRI to provide diverse information about the brain. We used resting-state fMRI and a set of 130 psychometric parameters that cover most human characteristics, including those related to intelligence and emotional quotients and social ability/skill. We identified 163 brain regions by VBM analysis using regression analysis with 130 psychometric parameters. Next, using a 163 × 163 correlation matrix, we identified functional networks related to 111 of the 130 psychometric parameters. Finally, we made an 8-class support vector machine classifiers corresponding to these 111 functional networks. Our results demonstrate that rs-fMRI signals contain intrinsic information about brain function related to cognition/behaviors and that this set of 111 networks/classifiers can be used to comprehensively evaluate human characteristics.

Tropical cloud and precipitation regimes as seen from near-simultaneous TRMM, CloudSat, and CALIPSO observations and comparison with ISCCP

NASA Astrophysics Data System (ADS)

Luo, Zhengzhao Johnny; Anderson, Ricardo C.; Rossow, William B.; Takahashi, Hanii

2017-06-01

Although Tropical Rainfall Measuring Mission (TRMM) and CloudSat/CALIPSO fly in different orbits, they frequently cross each other so that for the period between 2006 and 2010, a total of 15,986 intersect lines occurred within 20 min of each other from 30°S to 30°N, providing a rare opportunity to study tropical cloud and precipitation regimes and their internal vertical structure from near-simultaneous measurements by these active sensors. A k-means cluster analysis of TRMM and CloudSat matchups identifies three tropical cloud and precipitation regimes: the first two regimes correspond to, respectively, organized deep convection with heavy rain and cirrus anvils with moderate rain; the third regime is a convectively suppressed regime that can be further divided into three subregimes, which correspond to, respectively, stratocumulus clouds with drizzle, cirrus overlying low clouds, and nonprecipitating cumulus. Inclusion of CALIPSO data adds to the dynamic range of cloud properties and identifies one more cluster; subcluster analysis further identifies a thin, midlevel cloud regime associated with tropical mountain ranges. The radar-lidar cloud regimes are compared with the International Satellite Cloud Climatology Project (ISCCP) weather states (WSs) for the extended tropics. Focus is placed on the four convectively active WSs, namely, WS1-WS4. ISCCP WS1 and WS2 are found to be counterparts of Regime 1 and Regime 2 in radar-lidar observations, respectively. ISCCP WS3 and WS4, which are mainly isolated convection and broken, detached cirrus, do not have a strong association with any individual radar and lidar regimes, a likely effect of the different sampling strategies between ISCCP and active sensors and patchy cloudiness of these WSs.

Diffeomorphic functional brain surface alignment: Functional demons.

PubMed

Nenning, Karl-Heinz; Liu, Hesheng; Ghosh, Satrajit S; Sabuncu, Mert R; Schwartz, Ernst; Langs, Georg

2017-08-01

Aligning brain structures across individuals is a central prerequisite for comparative neuroimaging studies. Typically, registration approaches assume a strong association between the features used for alignment, such as macro-anatomy, and the variable observed, such as functional activation or connectivity. Here, we propose to use the structure of intrinsic resting state fMRI signal correlation patterns as a basis for alignment of the cortex in functional studies. Rather than assuming the spatial correspondence of functional structures between subjects, we have identified locations with similar connectivity profiles across subjects. We mapped functional connectivity relationships within the brain into an embedding space, and aligned the resulting maps of multiple subjects. We then performed a diffeomorphic alignment of the cortical surfaces, driven by the corresponding features in the joint embedding space. Results show that functional alignment based on resting state fMRI identifies functionally homologous regions across individuals with higher accuracy than alignment based on the spatial correspondence of anatomy. Further, functional alignment enables measurement of the strength of the anatomo-functional link across the cortex, and reveals the uneven distribution of this link. Stronger anatomo-functional dissociation was found in higher association areas compared to primary sensory- and motor areas. Functional alignment based on resting state features improves group analysis of task based functional MRI data, increasing statistical power and improving the delineation of task-specific core regions. Finally, a comparison of the anatomo-functional dissociation between cohorts is demonstrated with a group of left and right handed subjects. Copyright © 2017 Elsevier Inc. All rights reserved.

Managing Complexity in Evidence Analysis: A Worked Example in Pediatric Weight Management.

PubMed

Parrott, James Scott; Henry, Beverly; Thompson, Kyle L; Ziegler, Jane; Handu, Deepa

2018-05-02

Nutrition interventions are often complex and multicomponent. Typical approaches to meta-analyses that focus on individual causal relationships to provide guideline recommendations are not sufficient to capture this complexity. The objective of this study is to describe the method of meta-analysis used for the Pediatric Weight Management (PWM) Guidelines update and provide a worked example that can be applied in other areas of dietetics practice. The effects of PWM interventions were examined for body mass index (BMI), body mass index z-score (BMIZ), and waist circumference at four different time periods. For intervention-level effects, intervention types were identified empirically using multiple correspondence analysis paired with cluster analysis. Pooled effects of identified types were examined using random effects meta-analysis models. Differences in effects among types were examined using meta-regression. Context-level effects are examined using qualitative comparative analysis. Three distinct types (or families) of PWM interventions were identified: medical nutrition, behavioral, and missing components. Medical nutrition and behavioral types showed statistically significant improvements in BMIZ across all time points. Results were less consistent for BMI and waist circumference, although four distinct patterns of weight status change were identified. These varied by intervention type as well as outcome measure. Meta-regression indicated statistically significant differences between the medical nutrition and behavioral types vs the missing component type for both BMIZ and BMI, although the pattern varied by time period and intervention type. Qualitative comparative analysis identified distinct configurations of context characteristics at each time point that were consistent with positive outcomes among the intervention types. Although analysis of individual causal relationships is invaluable, this approach is inadequate to capture the complexity of dietetics practice. An alternative approach that integrates intervention-level with context-level meta-analyses may provide deeper understanding in the development of practice guidelines. Copyright © 2018 Academy of Nutrition and Dietetics. Published by Elsevier Inc. All rights reserved.

Quantitative descriptive analysis and principal component analysis for sensory characterization of Indian milk product cham-cham.

PubMed

Puri, Ritika; Khamrui, Kaushik; Khetra, Yogesh; Malhotra, Ravinder; Devraja, H C

2016-02-01

Promising development and expansion in the market of cham-cham, a traditional Indian dairy product is expected in the coming future with the organized production of this milk product by some large dairies. The objective of this study was to document the extent of variation in sensory properties of market samples of cham-cham collected from four different locations known for their excellence in cham-cham production and to find out the attributes that govern much of variation in sensory scores of this product using quantitative descriptive analysis (QDA) and principal component analysis (PCA). QDA revealed significant (p < 0.05) difference in sensory attributes of cham-cham among the market samples. PCA identified four significant principal components that accounted for 72.4 % of the variation in the sensory data. Factor scores of each of the four principal components which primarily correspond to sweetness/shape/dryness of interior, surface appearance/surface dryness, rancid and firmness attributes specify the location of each market sample along each of the axes in 3-D graphs. These findings demonstrate the utility of quantitative descriptive analysis for identifying and measuring attributes of cham-cham that contribute most to its sensory acceptability.

A systems biology approach to detect key pathways and interaction networks in gastric cancer on the basis of microarray analysis.

PubMed

Guo, Leilei; Song, Chunhua; Wang, Peng; Dai, Liping; Zhang, Jianying; Wang, Kaijuan

2015-11-01

The aim of the present study was to explore key molecular pathways contributing to gastric cancer (GC) and to construct an interaction network between significant pathways and potential biomarkers. Publicly available gene expression profiles of GSE29272 for GC, and data for the corresponding normal tissue, were downloaded from Gene Expression Omnibus. Pre‑processing and differential analysis were performed with R statistical software packages, and a number of differentially expressed genes (DEGs) were obtained. A functional enrichment analysis was performed for all the DEGs with a BiNGO plug‑in in Cytoscape. Their correlation was analyzed in order to construct a network. The modularity analysis and pathway identification operations were used to identify graph clusters and associated pathways. The underlying molecular mechanisms involving these DEGs were also assessed by data mining. A total of 249 DEGs, which were markedly upregulated and downregulated, were identified. The extracellular region contained the most significantly over‑represented functional terms, with respect to upregulated and downregulated genes, and the closest topological matches were identified for taste transduction and regulation of autophagy. In addition, extracellular matrix‑receptor interactions were identified as the most relevant pathway associated with the progression of GC. The genes for fibronectin 1, secreted phosphoprotein 1, collagen type 4 variant α‑1/2 and thrombospondin 1, which are involved in the pathways, may be considered as potential therapeutic targets for GC. A series of associations between candidate genes and key pathways were also identified for GC, and their correlation may provide novel insights into the pathogenesis of GC.

Phosphoproteomic analysis of chromoplasts from sweet orange during fruit ripening.

PubMed

Zeng, Yunliu; Pan, Zhiyong; Wang, Lun; Ding, Yuduan; Xu, Qiang; Xiao, Shunyuan; Deng, Xiuxin

2014-02-01

Like other types of plastids, chromoplasts have essential biosynthetic and metabolic activities which may be regulated via post-translational modifications, such as phosphorylation, of their resident proteins. We here report a proteome-wide mapping of in vivo phosphorylation sites in chromoplast-enriched samples prepared from sweet orange [Citrus sinensis (L.) Osbeck] at different ripening stages by titanium dioxide-based affinity chromatography for phosphoprotein enrichment with LC-MS/MS. A total of 109 plastid-localized phosphoprotein candidates were identified that correspond to 179 unique phosphorylation sites in 135 phosphopeptides. On the basis of Motif-X analysis, two distinct types of phosphorylation sites, one as proline-directed phosphorylation motif and the other as casein kinase II motif, can be generalized from these identified phosphopeptides. While most identified phosphoproteins show high homology to those already identified in plastids, approximately 22% of them are novel based on BLAST search using the public databases PhosPhAt and P(3) DB. A close comparative analysis showed that approximately 50% of the phosphoproteins identified in citrus chromoplasts find obvious counterparts in the chloroplast phosphoproteome, suggesting a rather high-level of conservation in basic metabolic activities in these two types of plastids. Not surprisingly, the phosphoproteome of citrus chromoplasts is also characterized by the lack of phosphoproteins involved in photosynthesis and by the presence of more phosphoproteins implicated in stress/redox responses. This study presents the first comprehensive phosphoproteomic analysis of chromoplasts and may help to understand how phosphorylation regulates differentiation of citrus chromoplasts during fruit ripening. © 2013 Scandinavian Plant Physiology Society.

Subpathway-GM: identification of metabolic subpathways via joint power of interesting genes and metabolites and their topologies within pathways.

PubMed

Li, Chunquan; Han, Junwei; Yao, Qianlan; Zou, Chendan; Xu, Yanjun; Zhang, Chunlong; Shang, Desi; Zhou, Lingyun; Zou, Chaoxia; Sun, Zeguo; Li, Jing; Zhang, Yunpeng; Yang, Haixiu; Gao, Xu; Li, Xia

2013-05-01

Various 'omics' technologies, including microarrays and gas chromatography mass spectrometry, can be used to identify hundreds of interesting genes, proteins and metabolites, such as differential genes, proteins and metabolites associated with diseases. Identifying metabolic pathways has become an invaluable aid to understanding the genes and metabolites associated with studying conditions. However, the classical methods used to identify pathways fail to accurately consider joint power of interesting gene/metabolite and the key regions impacted by them within metabolic pathways. In this study, we propose a powerful analytical method referred to as Subpathway-GM for the identification of metabolic subpathways. This provides a more accurate level of pathway analysis by integrating information from genes and metabolites, and their positions and cascade regions within the given pathway. We analyzed two colorectal cancer and one metastatic prostate cancer data sets and demonstrated that Subpathway-GM was able to identify disease-relevant subpathways whose corresponding entire pathways might be ignored using classical entire pathway identification methods. Further analysis indicated that the power of a joint genes/metabolites and subpathway strategy based on their topologies may play a key role in reliably recalling disease-relevant subpathways and finding novel subpathways.

Risk-based damage potential and loss estimation of extreme flooding scenarios in the Austrian Federal Province of Tyrol

NASA Astrophysics Data System (ADS)

Huttenlau, M.; Stötter, J.; Stiefelmeyer, H.

2010-12-01

Within the last decades serious flooding events occurred in many parts of Europe and especially in 2005 the Austrian Federal Province of Tyrol was serious affected. These events in general and particularly the 2005 event have sensitised decision makers and the public. Beside discussions pertaining to protection goals and lessons learnt, the issue concerning potential consequences of extreme and severe flooding events has been raised. Additionally to the general interest of the public, decision makers of the insurance industry, public authorities, and responsible politicians are especially confronted with the question of possible consequences of extreme events. Answers thereof are necessary for the implementation of preventive appropriate risk management strategies. Thereby, property and liability losses reflect a large proportion of the direct tangible losses. These are of great interest for the insurance sector and can be understood as main indicators to interpret the severity of potential events. The natural scientific-technical risk analysis concept provides a predefined and structured framework to analyse the quantities of affected elements at risk, their corresponding damage potentials, and the potential losses. Generally, this risk concept framework follows the process steps hazard analysis, exposition analysis, and consequence analysis. Additionally to the conventional hazard analysis, the potential amount of endangered elements and their corresponding damage potentials were analysed and, thereupon, concrete losses were estimated. These took the specific vulnerability of the various individual elements at risk into consideration. The present flood risk analysis estimates firstly the general exposures of the risk indicators in the study area and secondly analyses the specific exposures and consequences of five extreme event scenarios. In order to precisely identify, localize, and characterize the relevant risk indicators of buildings, dwellings and inventory, vehicles, and individuals, a detailed geodatabase of the existing stock of elements and values was established on a single object level. Therefore, the localized and functional differentiated stock of elements was assessed monetarily on the basis of derived representative mean insurance values. Thus, well known difference factors between the analysis of the stock of elements and values on local and on regional scale could be reduced considerably. The spatial join of the results of the hazard analysis with the stock of elements and values enables the identification and quantification of the elements at risk and their corresponding damage potential. Thereupon, Extreme Scenario Losses (ESL) were analysed under consideration of different vulnerability approaches which describe the individual element's specific susceptibility. This results in scenario-specific ranges of ESL rather than in single values. The exposure analysis of the general endangerment in Tyrol identifies (i) 105 330 individuals, (ii) 20 272 buildings and 50 157 dwellings with a corresponding damage potential of approx. EUR 20 bn. and (iii) 62 494 vehicles with a corresponding damage potential of EUR 1 bn. Depending on the individual extreme event scenarios, the ESL solely to buildings and inventory vary between EUR 0.9-1.3 bn. for the scenario with the least ESL and EUR 2.2-2.5 bn. for the most serious scenarios. The correlation of the private property losses to buildings and inventory with further direct tangible loss categories on the basis of investigation after the event in 2005, results in potential direct tangible ESL of up to EUR 7.6 bn. Apart from the specific study results a general finding shows that beside the further development of modelling capabilities and scenario concepts, the key to considerably decrease uncertainties of integral flood risk analyses is the development and implementation of more precise methods. These are to determine the stock of elements and values and to evaluate the vulnerability or susceptibility of affected structures to certain flood characteristics more differentiated.

Profiles of Reactivity in Cocaine-Exposed Children

PubMed Central

Schuetze, Pamela; Molnar, Danielle S.; Eiden, Rina D.

2012-01-01

This study explored the possibility that specific, theoretically consistent profiles of reactivity could be identified in a sample of cocaine-exposed infants and whether these profiles were associated with a range of infant and/or maternal characteristics. Cluster analysis was used to identify distinct groups of infants based on physiological, behavioral and maternal reported measures of reactivity. Five replicable clusters were identified which corresponded to 1) Dysregulated/High Maternal Report Reactors, 2) Low Behavioral Reactors, 3) High Reactors, 4) Optimal Reactors and 5) Dysregulated/Low Maternal Report Reactors. These clusters were associated with differences in prenatal cocaine exposure status, birthweight, maternal depressive symptoms, and maternal negative affect during mother-infant interactions. These results support the presence of distinct reactivity profiles among high risk infants recruited on the basis of prenatal cocaine exposure and demographically similar control group infants not exposed to cocaine. PMID:23204615

Identifying Emotions on the Basis of Neural Activation

PubMed Central

Kassam, Karim S.; Markey, Amanda R.; Cherkassky, Vladimir L.; Loewenstein, George; Just, Marcel Adam

2013-01-01

We attempt to determine the discriminability and organization of neural activation corresponding to the experience of specific emotions. Method actors were asked to self-induce nine emotional states (anger, disgust, envy, fear, happiness, lust, pride, sadness, and shame) while in an fMRI scanner. Using a Gaussian Naïve Bayes pooled variance classifier, we demonstrate the ability to identify specific emotions experienced by an individual at well over chance accuracy on the basis of: 1) neural activation of the same individual in other trials, 2) neural activation of other individuals who experienced similar trials, and 3) neural activation of the same individual to a qualitatively different type of emotion induction. Factor analysis identified valence, arousal, sociality, and lust as dimensions underlying the activation patterns. These results suggest a structure for neural representations of emotion and inform theories of emotional processing. PMID:23840392

Identifying Emotions on the Basis of Neural Activation.

PubMed

Kassam, Karim S; Markey, Amanda R; Cherkassky, Vladimir L; Loewenstein, George; Just, Marcel Adam

2013-01-01

We attempt to determine the discriminability and organization of neural activation corresponding to the experience of specific emotions. Method actors were asked to self-induce nine emotional states (anger, disgust, envy, fear, happiness, lust, pride, sadness, and shame) while in an fMRI scanner. Using a Gaussian Naïve Bayes pooled variance classifier, we demonstrate the ability to identify specific emotions experienced by an individual at well over chance accuracy on the basis of: 1) neural activation of the same individual in other trials, 2) neural activation of other individuals who experienced similar trials, and 3) neural activation of the same individual to a qualitatively different type of emotion induction. Factor analysis identified valence, arousal, sociality, and lust as dimensions underlying the activation patterns. These results suggest a structure for neural representations of emotion and inform theories of emotional processing.

Proteomic Analysis of Sauvignon Blanc Grape Skin, Pulp and Seed and Relative Quantification of Pathogenesis-Related Proteins.

PubMed

Tian, Bin; Harrison, Roland; Morton, James; Deb-Choudhury, Santanu

2015-01-01

Thaumatin-like proteins (TLPs) and chitinases are the main constituents of so-called protein hazes which can form in finished white wine and which is a great concern of winemakers. These soluble pathogenesis-related (PR) proteins are extracted from grape berries. However, their distribution in different grape tissues is not well documented. In this study, proteins were first separately extracted from the skin, pulp and seed of Sauvignon Blanc grapes, followed by trypsin digestion and analysis by liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS). Proteins identified included 75 proteins from Sauvignon Blanc grape skin, 63 from grape pulp and 35 from grape seed, mostly functionally classified as associated with metabolism and energy. Some were present exclusively in specific grape tissues; for example, proteins involved in photosynthesis were only detected in grape skin and proteins found in alcoholic fermentation were only detected in grape pulp. Moreover, proteins identified in grape seed were less diverse than those identified in grape skin and pulp. TLPs and chitinases were identified in both Sauvignon Blanc grape skin and pulp, but not in the seed. To relatively quantify the PR proteins, the protein extracts of grape tissues were seperated by HPLC first and then analysed by SDS-PAGE. The results showed that the protein fractions eluted at 9.3 min and 19.2 min under the chromatographic conditions of this study confirmed that these corresponded to TLPs and chitinases seperately. Thus, the relative quantification of TLPs and chitinases in protein extracts was carried out by comparing the area of corresponding peaks against the area of a thamautin standard. The results presented in this study clearly demonstrated the distribution of haze-forming PR proteins in grape berries, and the relative quantification of TLPs and chitinases could be applied in fast tracking of changes in PR proteins during grape growth and determination of PR proteins in berries at harvest.

Proteomic Analysis of Sauvignon Blanc Grape Skin, Pulp and Seed and Relative Quantification of Pathogenesis-Related Proteins

PubMed Central

Tian, Bin; Harrison, Roland; Morton, James; Deb-Choudhury, Santanu

2015-01-01

Thaumatin-like proteins (TLPs) and chitinases are the main constituents of so-called protein hazes which can form in finished white wine and which is a great concern of winemakers. These soluble pathogenesis-related (PR) proteins are extracted from grape berries. However, their distribution in different grape tissues is not well documented. In this study, proteins were first separately extracted from the skin, pulp and seed of Sauvignon Blanc grapes, followed by trypsin digestion and analysis by liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS). Proteins identified included 75 proteins from Sauvignon Blanc grape skin, 63 from grape pulp and 35 from grape seed, mostly functionally classified as associated with metabolism and energy. Some were present exclusively in specific grape tissues; for example, proteins involved in photosynthesis were only detected in grape skin and proteins found in alcoholic fermentation were only detected in grape pulp. Moreover, proteins identified in grape seed were less diverse than those identified in grape skin and pulp. TLPs and chitinases were identified in both Sauvignon Blanc grape skin and pulp, but not in the seed. To relatively quantify the PR proteins, the protein extracts of grape tissues were seperated by HPLC first and then analysed by SDS-PAGE. The results showed that the protein fractions eluted at 9.3 min and 19.2 min under the chromatographic conditions of this study confirmed that these corresponded to TLPs and chitinases seperately. Thus, the relative quantification of TLPs and chitinases in protein extracts was carried out by comparing the area of corresponding peaks against the area of a thamautin standard. The results presented in this study clearly demonstrated the distribution of haze-forming PR proteins in grape berries, and the relative quantification of TLPs and chitinases could be applied in fast tracking of changes in PR proteins during grape growth and determination of PR proteins in berries at harvest. PMID:26076362

Correspondence analysis

USDA-ARS?s Scientific Manuscript database

Correspondence analysis is a powerful exploratory multivariate technique for categorical variables with many levels. It is a data analysis tool that characterizes associations between levels of 2 or more categorical variables using graphical representations of the information in a contingency table...

Model-free fMRI group analysis using FENICA.

PubMed

Schöpf, V; Windischberger, C; Robinson, S; Kasess, C H; Fischmeister, F PhS; Lanzenberger, R; Albrecht, J; Kleemann, A M; Kopietz, R; Wiesmann, M; Moser, E

2011-03-01

Exploratory analysis of functional MRI data allows activation to be detected even if the time course differs from that which is expected. Independent Component Analysis (ICA) has emerged as a powerful approach, but current extensions to the analysis of group studies suffer from a number of drawbacks: they can be computationally demanding, results are dominated by technical and motion artefacts, and some methods require that time courses be the same for all subjects or that templates be defined to identify common components. We have developed a group ICA (gICA) method which is based on single-subject ICA decompositions and the assumption that the spatial distribution of signal changes in components which reflect activation is similar between subjects. This approach, which we have called Fully Exploratory Network Independent Component Analysis (FENICA), identifies group activation in two stages. ICA is performed on the single-subject level, then consistent components are identified via spatial correlation. Group activation maps are generated in a second-level GLM analysis. FENICA is applied to data from three studies employing a wide range of stimulus and presentation designs. These are an event-related motor task, a block-design cognition task and an event-related chemosensory experiment. In all cases, the group maps identified by FENICA as being the most consistent over subjects correspond to task activation. There is good agreement between FENICA results and regions identified in prior GLM-based studies. In the chemosensory task, additional regions are identified by FENICA and temporal concatenation ICA that we show is related to the stimulus, but exhibit a delayed response. FENICA is a fully exploratory method that allows activation to be identified without assumptions about temporal evolution, and isolates activation from other sources of signal fluctuation in fMRI. It has the advantage over other gICA methods that it is computationally undemanding, spotlights components relating to activation rather than artefacts, allows the use of familiar statistical thresholding through deployment of a higher level GLM analysis and can be applied to studies where the paradigm is different for all subjects. Copyright © 2010 Elsevier Inc. All rights reserved.

Identification and Analysis of a Novel Gene Cluster Involves in Fe2+ Oxidation in Acidithiobacillus ferrooxidans ATCC 23270, a Typical Biomining Acidophile.

PubMed

Ai, Chenbing; Liang, Yuting; Miao, Bo; Chen, Miao; Zeng, Weimin; Qiu, Guanzhou

2018-07-01

Iron-oxidizing Acidithiobacillus spp. are applied worldwide in biomining industry to extract metals from sulfide minerals. They derive energy for survival through Fe 2+ oxidation and generate Fe 3+ for the dissolution of sulfide minerals. However, molecular mechanisms of their iron oxidation still remain elusive. A novel two-cytochrome-encoding gene cluster (named tce gene cluster) encoding a high-molecular-weight cytochrome c (AFE_1428) and a c 4 -type cytochrome c 552 (AFE_1429) in A. ferrooxidans ATCC 23270 was first identified in this study. Bioinformatic analysis together with transcriptional study showed that AFE_1428 and AFE_1429 were the corresponding paralog of Cyc2 (AFE_3153) and Cyc1 (AFE_3152) which were encoded by the extensively studied rus operon and had been proven involving in ferrous iron oxidation. Both AFE_1428 and AFE_1429 contained signal peptide and the classic heme-binding motif(s) as their corresponding paralog. The modeled structure of AFE_1429 showed high resemblance to Cyc1. AFE_1428 and AFE_1429 were preferentially transcribed as their corresponding paralogs in the presence of ferrous iron as sole energy source as compared with sulfur. The tce gene cluster is highly conserved in the genomes of four phylogenetic-related A. ferrooxidans strains that were originally isolated from different sites separated with huge geographical distance, which further implies the importance of this gene cluster. Collectively, AFE_1428 and AFE_1429 involve in Fe 2+ oxidation like their corresponding paralog by integrating with the metalloproteins encoded by rus operon. This study provides novel insights into the Fe 2+ oxidation mechanism in Fe 2+ -oxidizing A. ferrooxidans ssp.

Rapid identification of herbal compounds derived metabolites using zebrafish larvae as the biotransformation system.

PubMed

Wang, Chen; Yin, Ying-Hao; Wei, Ying-Jie; Shi, Zi-Qi; Liu, Jian-Qun; Liu, Li-Fang; Xin, Gui-Zhong

2017-09-15

Metabolites derived from herbal compounds are becoming promising sources for discovering new drugs. However, the rapid identification of metabolites from biological matrixes is limited by massive endogenous interference and low abundance of metabolites. Thus, by using zebrafish larvae as the biotransformation system, we herein proposed and validated an integrated strategy for rapid identification of metabolites derived from herbal compounds. Two pivotal steps involved in this strategy are to differentiate metabolites from herbal compounds and match metabolites with their parent compounds. The differentiation step was achieved by cross orthogonal partial least-squares discriminant analysis. Automatic matching analysis was performed on R Project based on a self-developed program, of which the number of matched ionic clusters and its corresponding percentage between metabolite and parent compound were taken into account to assess their similarity. Using this strategy, 46 metabolites screened from incubation water samples of zebrafish treated with total Epimedium flavonoids (EFs) could be matched with their corresponding parent compounds, 37 of them were identified and validated by the known metabolic pathways and fragmentation patterns. Finally, 75% of the identified EFs metabolites were successfully detected in urine samples of rats treated with EFs. These experimental results indicate that the proposed strategy using zebrafish larvae as the biotransformation system will facilitate the rapid identification of metabolites derived from herbal compounds, which shows promising perspectives in providing additional resources for pharmaceutical developments from natural products. Copyright © 2017 Elsevier B.V. All rights reserved.

Quantitative computed tomography for the prediction of pulmonary function after lung cancer surgery: a simple method using simulation software.

PubMed

Ueda, Kazuhiro; Tanaka, Toshiki; Li, Tao-Sheng; Tanaka, Nobuyuki; Hamano, Kimikazu

2009-03-01

The prediction of pulmonary functional reserve is mandatory in therapeutic decision-making for patients with resectable lung cancer, especially those with underlying lung disease. Volumetric analysis in combination with densitometric analysis of the affected lung lobe or segment with quantitative computed tomography (CT) helps to identify residual pulmonary function, although the utility of this modality needs investigation. The subjects of this prospective study were 30 patients with resectable lung cancer. A three-dimensional CT lung model was created with voxels representing normal lung attenuation (-600 to -910 Hounsfield units). Residual pulmonary function was predicted by drawing a boundary line between the lung to be preserved and that to be resected, directly on the lung model. The predicted values were correlated with the postoperative measured values. The predicted and measured values corresponded well (r=0.89, p<0.001). Although the predicted values corresponded with values predicted by simple calculation using a segment-counting method (r=0.98), there were two outliers whose pulmonary functional reserves were predicted more accurately by CT than by segment counting. The measured pulmonary functional reserves were significantly higher than the predicted values in patients with extensive emphysematous areas (<-910 Hounsfield units), but not in patients with chronic obstructive pulmonary disease. Quantitative CT yielded accurate prediction of functional reserve after lung cancer surgery and helped to identify patients whose functional reserves are likely to be underestimated. Hence, this modality should be utilized for patients with marginal pulmonary function.

Rapid qualitative review of ethical issues surrounding healthcare for pregnant women or women of reproductive age in epidemic outbreaks

PubMed Central

2018-01-01

This article describes, categorizes, and discusses the results of a rapid literature review aiming to provide an overview of the ethical issues and corresponding solutions surrounding pregnancies in epidemic outbreaks. The review was commissioned by the World Health Organization to inform responses to the Zika outbreak that began in 2015. Due to the urgency of the response efforts that needed to be informed by the literature search, a rapid qualitative review of the literature published in PubMed was conducted. The search and analysis were based on the operationalization of 3 key concepts: ethics, pregnancy, and epidemic outbreak. Ethical issues and solutions were interpreted within a principlist framework. The data were analyzed using qualitative content analysis. The search identified 259 publications, of which the full text of 23 papers was read. Of those, 20 papers contained a substantive part devoted to the topic of interest and were therefore analyzed further. We clustered the ethical issues and solutions around 4 themes: uncertainty, harms, autonomy/liberty, and effectiveness. Recognition of the identified ethical issues and corresponding solutions can inform and improve response efforts, public health planning, policies, and decision-making, as well as the activities of medical staff and counselors who practice before, during, or after an epidemic outbreak that affects pregnant women or those of reproductive age. The rapid review format proved to be useful despite its limited data basis and expedited review process. PMID:29370682

A Map of Clinical Dermatology Research Centers in Spain: Results of the MaIND Study.

PubMed

Molina-Leyva, A; Descalzo, M A; García-Doval, I

2017-11-01

Bibliometric indicators and analyses of clinical research articles can help to quantify the scientific production of hospitals and institutions and identify their main areas of research. The aim of this study was to draw up a bibliometric map of clinical research in dermatology by Spanish hospitals and institutions through an analysis of quantitative, qualitative, and topic-based variables. Bibliometric study of clinical research articles that met the inclusion criteria and had a definitive publication date between 2005 and 2014 in PubMed or Embase in which the corresponding author's affiliation was a Spanish dermatology department or institution. Barcelona and Madrid were the provinces with the highest number of articles and citations. The centers with the most articles and citations were Hospital Clínic and Instituto Valenciano de Oncología. Those 2 hospitals also produced the highest number of articles on the most common research topic identified: melanoma. Because the articles were selected on the basis of the affiliation of the corresponding author to a Spanish dermatology center, this analysis does not include collaborative studies or clinical research studies led by nondermatology centers. We have created a bibliometric map of clinical dermatology research in Spain that shows the distribution of scientific production and the main areas of research by province and hospital/institution. This map could be useful for education and research purposes. Copyright © 2017 AEDV. Publicado por Elsevier España, S.L.U. All rights reserved.

Rapid qualitative review of ethical issues surrounding healthcare for pregnant women or women of reproductive age in epidemic outbreaks.

PubMed

Hummel, Patrik; Saxena, Abha; Klingler, Corinna

2018-01-01

This article describes, categorizes, and discusses the results of a rapid literature review aiming to provide an overview of the ethical issues and corresponding solutions surrounding pregnancies in epidemic outbreaks. The review was commissioned by the World Health Organization to inform responses to the Zika outbreak that began in 2015. Due to the urgency of the response efforts that needed to be informed by the literature search, a rapid qualitative review of the literature published in PubMed was conducted. The search and analysis were based on the operationalization of 3 key concepts: ethics, pregnancy, and epidemic outbreak. Ethical issues and solutions were interpreted within a principlist framework. The data were analyzed using qualitative content analysis. The search identified 259 publications, of which the full text of 23 papers was read. Of those, 20 papers contained a substantive part devoted to the topic of interest and were therefore analyzed further. We clustered the ethical issues and solutions around 4 themes: uncertainty, harms, autonomy/liberty, and effectiveness. Recognition of the identified ethical issues and corresponding solutions can inform and improve response efforts, public health planning, policies, and decision-making, as well as the activities of medical staff and counselors who practice before, during, or after an epidemic outbreak that affects pregnant women or those of reproductive age. The rapid review format proved to be useful despite its limited data basis and expedited review process.

HOXB2 as a novel prognostic indicator for stage I lung adenocarcinomas.

PubMed

Inamura, Kentauro; Togashi, Yuki; Okui, Michiyo; Ninomiya, Hironori; Hiramatsu, Miyako; Satoh, Yukitoshi; Okumura, Sakae; Nakagawa, Ken; Shimoji, Takashi; Noda, Tetsuo; Ishikawa, Yuichi

2007-09-01

Outcomes of patients with lung adenocarcinomas can be predicted to some extent from the pathologic stage (p-stage). Although all attempts are made to fully remove cancer lesions, still a number of p-stage I patients without metastatic disease at the time of surgery develop recurrences and die of cancer. It is thus very important to identify p-stage I patients who are at risk of recurrence. Previously, using microdissected samples, we identified metastasis-related genes. Using real-time reverse-transcriptase polymerase chain reaction analysis, we investigated the transcriptional levels of the top metastasis-related genes using 96 independent test lung adenocarcinoma samples and investigated their correlations with the prognosis. We document evidence that p-stage I patients with HOXB2 up-regulation have a worse prognosis than those with HOXB2 down-regulation (p = 0.0065), whereas the HOXB2 status has no prognostic significance for p-stage II-IV patients. Comparing tumors and corresponding normal lung tissue, we confirmed HOXB2 up-regulated lesions to have much higher HOXB2 expression than the corresponding normal tissue. Confirmation with a larger number of samples is needed, with further research to clarify the molecular functions of HOXB2.

Identifying the Factors Affecting Papers' Citability in the Field of Medicine: an Evidence-based Approach Using 200 Highly and Lowly-cited Papers.

PubMed

Yaminfirooz, Mousa; Ardali, Farzaneh Raeesi

2018-01-01

Nowadays, publishing highly-cited papers is important for researchers and editors. In this evidence-based study, the factors influencing the citability of published papers in the field of medicine have been identified. 200 papers indexed in Scopus (in two groups: highly-cited and lowly-cited) with 100 papers in each were studied. Needed data were manually collected with a researcher-made checklist. Data analysis was done in SPSS using descriptive and inferential statistics. Variables such as journal IF, journal rank, journal subject quartile, the first/corresponding author's h-index, the number of documents produced by the first/corresponding author, SJR and SNIP had significantly positive correlation with paper citability (p< .05). Other variables, including among others, paper age, paper type, the number of references, the number of authors, indexing institute and journal kind had not any relationship with paper citability (p> .05). the factors affecting the citability are among indicators relating to authors, publishing journals and published papers. Determining the extent to which these factors influence the citability of a paper needs further large-scaled research. Authors and editors searching for high-citedness should consider these factors when authoring and publishing papers.

Synthesis, characterization and toxicity studies of pyridinecarboxaldehydes and L-tryptophan derived Schiff bases and corresponding copper (II) complexes.

PubMed

Malakyan, Margarita; Babayan, Nelly; Grigoryan, Ruzanna; Sarkisyan, Natalya; Tonoyan, Vahan; Tadevosyan, Davit; Matosyan, Vladimir; Aroutiounian, Rouben; Arakelyan, Arsen

2016-01-01

Schiff bases and their metal-complexes are versatile compounds exhibiting a broad range of biological activities and thus actively used in the drug development process. The aim of the present study was the synthesis and characterization of new Schiff bases and their copper (II) complexes, derived from L-tryptophan and isomeric (2-; 3-; 4-) pyridinecarboxaldehydes, as well as the assessment of their toxicity in vitro . The optimal conditions of the Schiff base synthesis resulting in up to 75-85% yield of target products were identified. The structure-activity relationship analysis indicated that the location of the carboxaldehyde group at 2-, 3- or 4-position with regard to nitrogen of the pyridine ring in aldehyde component of the L-tryptophan derivative Schiff bases and corresponding copper complexes essentially change the biological activity of the compounds. The carboxaldehyde group at 2- and 4-positions leads to the higher cytotoxic activity, than that of at 3-position, and the presence of the copper in the complexes increases the cytotoxicity. Based on toxicity classification data, the compounds with non-toxic profile were identified, which can be used as new entities in the drug development process using Schiff base scaffold.

Synthesis, characterization and toxicity studies of pyridinecarboxaldehydes and L-tryptophan derived Schiff bases and corresponding copper (II) complexes

PubMed Central

Malakyan, Margarita; Babayan, Nelly; Grigoryan, Ruzanna; Sarkisyan, Natalya; Tonoyan, Vahan; Tadevosyan, Davit; Matosyan, Vladimir; Aroutiounian, Rouben; Arakelyan, Arsen

2016-01-01

Schiff bases and their metal-complexes are versatile compounds exhibiting a broad range of biological activities and thus actively used in the drug development process. The aim of the present study was the synthesis and characterization of new Schiff bases and their copper (II) complexes, derived from L-tryptophan and isomeric (2-; 3-; 4-) pyridinecarboxaldehydes, as well as the assessment of their toxicity in vitro. The optimal conditions of the Schiff base synthesis resulting in up to 75-85% yield of target products were identified. The structure-activity relationship analysis indicated that the location of the carboxaldehyde group at 2-, 3- or 4-position with regard to nitrogen of the pyridine ring in aldehyde component of the L-tryptophan derivative Schiff bases and corresponding copper complexes essentially change the biological activity of the compounds. The carboxaldehyde group at 2- and 4-positions leads to the higher cytotoxic activity, than that of at 3-position, and the presence of the copper in the complexes increases the cytotoxicity. Based on toxicity classification data, the compounds with non-toxic profile were identified, which can be used as new entities in the drug development process using Schiff base scaffold. PMID:28344771

Genome-wide association study of handedness excludes simple genetic models

PubMed Central

Armour, J AL; Davison, A; McManus, I C

2014-01-01

Handedness is a human behavioural phenotype that appears to be congenital, and is often assumed to be inherited, but for which the developmental origin and underlying causation(s) have been elusive. Models of the genetic basis of variation in handedness have been proposed that fit different features of the observed resemblance between relatives, but none has been decisively tested or a corresponding causative locus identified. In this study, we applied data from well-characterised individuals studied at the London Twin Research Unit. Analysis of genome-wide SNP data from 3940 twins failed to identify any locus associated with handedness at a genome-wide level of significance. The most straightforward interpretation of our analyses is that they exclude the simplest formulations of the ‘right-shift' model of Annett and the ‘dextral/chance' model of McManus, although more complex modifications of those models are still compatible with our observations. For polygenic effects, our study is inadequately powered to reliably detect alleles with effect sizes corresponding to an odds ratio of 1.2, but should have good power to detect effects at an odds ratio of 2 or more. PMID:24065183

Model Transformation for a System of Systems Dependability Safety Case

NASA Technical Reports Server (NTRS)

Murphy, Judy; Driskell, Stephen B.

2010-01-01

Software plays an increasingly larger role in all aspects of NASA's science missions. This has been extended to the identification, management and control of faults which affect safety-critical functions and by default, the overall success of the mission. Traditionally, the analysis of fault identification, management and control are hardware based. Due to the increasing complexity of system, there has been a corresponding increase in the complexity in fault management software. The NASA Independent Validation & Verification (IV&V) program is creating processes and procedures to identify, and incorporate safety-critical software requirements along with corresponding software faults so that potential hazards may be mitigated. This Specific to Generic ... A Case for Reuse paper describes the phases of a dependability and safety study which identifies a new, process to create a foundation for reusable assets. These assets support the identification and management of specific software faults and, their transformation from specific to generic software faults. This approach also has applications to other systems outside of the NASA environment. This paper addresses how a mission specific dependability and safety case is being transformed to a generic dependability and safety case which can be reused for any type of space mission with an emphasis on software fault conditions.

Evolution of temperature of a droplet of liquid composite fuel interacting with heated airflow

NASA Astrophysics Data System (ADS)

Glushkov, D. O.; Zakharevich, A. V.; Strizhak, P. A.; Syrodoy, S. V.

2016-11-01

The macroscopic patterns of a temperature change at the center of a droplet of three-component (coal, water, petroleum) composite liquid fuel (CLF) were studied using a low-inertia thermoelectric converter and system of high-speed (up to 105 frames per second) video recording during the induction period at different heating intensity by the air flow with variable parameters: temperature of 670-870 K and motion velocity of 1-4 m/s. The studies were carried out for two groups of CLF compositions: fuel based on brown coal and coal cleaning rejects (filter cake). To assess the effect of liquid combustible component of CLF on characteristics of the ignition process, the corresponding composition of two-component coal-water fuel (CWF) was studied. The stages of inert heating of CLF and CWF droplets with characteristic size corresponding to radius of 0.75-1.5 mm, evaporation of moisture and liquid oil (for CLF), thermal decomposition of the organic part of coal, gas mixture ignition, and carbon burnout were identified. Regularities of changes in the temperature of CLF and CWF droplets at each of identified stages were identified for the cooccurrence of phase transitions and chemical reactions. Comparative analysis of the times of ignition delay and complete combustion of the droplets of examined fuel compositions was performed with varying droplet dimensions, temperatures, and oxidant flow velocity.

Pore Structure Characterization of Sodium Hydroxide Activated Slag Using Mercury Intrusion Porosimetry, Nitrogen Adsorption, and Image Analysis.

PubMed

Zuo, Yibing; Ye, Guang

2018-06-19

The pore structure of alkali-activated slag has a significant influence on its performance. However, the literature shows insufficient studies regarding the suitability of different techniques for characterizing the pore structure and the influences of Na₂O and curing age on pore structure development. In pursuit of a better understanding, the pore structure of sodium hydroxide activated slag paste was characterized by multiple techniques, e.g., mercury intrusion porosimetry (MIP), nitrogen (N₂) adsorption, and scanning electron microscopy (SEM) image analysis. The sodium hydroxide activated slag pastes were prepared with three different contents of Na₂O (Na₂O/slag = 4, 6, and 8%) and cured for different times up to 360 days. The microstructure observation reveals that outer C⁻(N⁻)A⁻S⁻H and inner C⁻(N⁻)A⁻S⁻H grow successively around the reacting slag grains, along with crystalline reaction products which are formed in the empty coarse pore space. The increase of Na₂O content and curing age lead to a finer pore structure. The MIP measurements show that the total porosity drops about 70% within the first day, and that one peak at most, corresponding to gel pores, was identified in the differential curves of all the investigated samples from 1 to 360 days. On the contrary, only one peak, corresponding to capillary pores, was identified by SEM-image analysis. The differential curves derived from N₂ adsorption generally reveal two peaks, and the trend that the pore diameters of those two peaks vary with curing age depends on the content of Na₂O. Compared to Portland cement, sodium hydroxide activated slag has a higher pore space filling capacity ( χ , V products / V slag-reacted ), while the capacity decreases with increasing Na₂O content and curing age.

RNAseq versus genome-predicted transcriptomes: a large population of novel transcripts identified in an Illumina-454 Hydra transcriptome.

PubMed

Wenger, Yvan; Galliot, Brigitte

2013-03-25

Evolutionary studies benefit from deep sequencing technologies that generate genomic and transcriptomic sequences from a variety of organisms. Genome sequencing and RNAseq have complementary strengths. In this study, we present the assembly of the most complete Hydra transcriptome to date along with a comparative analysis of the specific features of RNAseq and genome-predicted transcriptomes currently available in the freshwater hydrozoan Hydra vulgaris. To produce an accurate and extensive Hydra transcriptome, we combined Illumina and 454 Titanium reads, giving the primacy to Illumina over 454 reads to correct homopolymer errors. This strategy yielded an RNAseq transcriptome that contains 48'909 unique sequences including splice variants, representing approximately 24'450 distinct genes. Comparative analysis to the available genome-predicted transcriptomes identified 10'597 novel Hydra transcripts that encode 529 evolutionarily-conserved proteins. The annotation of 170 human orthologs points to critical functions in protein biosynthesis, FGF and TOR signaling, vesicle transport, immunity, cell cycle regulation, cell death, mitochondrial metabolism, transcription and chromatin regulation. However, a majority of these novel transcripts encodes short ORFs, at least 767 of them corresponding to pseudogenes. This RNAseq transcriptome also lacks 11'270 predicted transcripts that correspond either to silent genes or to genes expressed below the detection level of this study. We established a simple and powerful strategy to combine Illumina and 454 reads and we produced, with genome assistance, an extensive and accurate Hydra transcriptome. The comparative analysis of the RNAseq transcriptome with genome-predicted transcriptomes lead to the identification of large populations of novel as well as missing transcripts that might reflect Hydra-specific evolutionary events.

RNAseq versus genome-predicted transcriptomes: a large population of novel transcripts identified in an Illumina-454 Hydra transcriptome

PubMed Central

2013-01-01

Background Evolutionary studies benefit from deep sequencing technologies that generate genomic and transcriptomic sequences from a variety of organisms. Genome sequencing and RNAseq have complementary strengths. In this study, we present the assembly of the most complete Hydra transcriptome to date along with a comparative analysis of the specific features of RNAseq and genome-predicted transcriptomes currently available in the freshwater hydrozoan Hydra vulgaris. Results To produce an accurate and extensive Hydra transcriptome, we combined Illumina and 454 Titanium reads, giving the primacy to Illumina over 454 reads to correct homopolymer errors. This strategy yielded an RNAseq transcriptome that contains 48’909 unique sequences including splice variants, representing approximately 24’450 distinct genes. Comparative analysis to the available genome-predicted transcriptomes identified 10’597 novel Hydra transcripts that encode 529 evolutionarily-conserved proteins. The annotation of 170 human orthologs points to critical functions in protein biosynthesis, FGF and TOR signaling, vesicle transport, immunity, cell cycle regulation, cell death, mitochondrial metabolism, transcription and chromatin regulation. However, a majority of these novel transcripts encodes short ORFs, at least 767 of them corresponding to pseudogenes. This RNAseq transcriptome also lacks 11’270 predicted transcripts that correspond either to silent genes or to genes expressed below the detection level of this study. Conclusions We established a simple and powerful strategy to combine Illumina and 454 reads and we produced, with genome assistance, an extensive and accurate Hydra transcriptome. The comparative analysis of the RNAseq transcriptome with genome-predicted transcriptomes lead to the identification of large populations of novel as well as missing transcripts that might reflect Hydra-specific evolutionary events. PMID:23530871

ANALYSIS OF SURGICAL SITE INFECTIONS IN PEDIATRIC PATIENTS AFTER ORTHOPEDIC SURGERY: A CASE-CONTROL STUDY

PubMed Central

Chagas, Mariana de Queiroz Leite; Costa, Ana Maria Magalhães; Mendes, Pedro Henrique Barros; Gomes, Saint Clair

2017-01-01

ABSTRACT Objectives: To describe the rate of surgical site infections in children undergoing orthopedic surgery in centers of excellence and analyze the patients’ profiles. Methods: Medical records of pediatric patients undergoing orthopedic surgery in the Jamil Haddad National Institute of Traumatology and Orthopedics from January 2012 to December 2013 were analyzed and monitored for one year. Patients diagnosed with surgical site infection were matched with patients without infection by age, date of admission, field of orthopedic surgery and type of surgical procedure. Patient, surgical and follow-up variables were examined. Descriptive, bivariate and correspondence analyses were performed to evaluate the patients’ profiles. Results: 347 surgeries and 10 surgical site infections (2.88%) were identified. There was association of infections with age - odds ratio (OR) 11.5 (confidence interval - 95%CI 1.41-94.9) -, implant - OR 7.3 (95%CI 1.46-36.3) -, preoperative period - OR 9.8 (95%CI 1.83-53.0), and length of hospitalization - OR 20.6 (95%CI 3.7-114.2). The correspondence analysis correlated the infection and preoperative period, weight, weight Z-score, age, implant, type of surgical procedure, and length of hospitalization. Average time to diagnosis of infection occurred 26.5±111.46 days after surgery. Conclusions: The rate of surgical site infection was 2.88%, while higher in children over 24 months of age who underwent surgical implant procedures and had longer preoperative periods and lengths of hospitalization. This study identified variables for the epidemiological surveillance of these events in children. Available databases and appropriate analysis methods are essential to monitor and improve the quality of care offered to the pediatric population. PMID:28977312

Vibrational spectral investigation and natural bond orbital analysis of pharmaceutical compound 7-Amino-2,4-dimethylquinolinium formate - DFT approach.

PubMed

Suresh, D M; Amalanathan, M; Sebastian, S; Sajan, D; Hubert Joe, I; Bena Jothy, V; Nemec, Ivan

2013-11-01

The molecular geometry, the normal mode frequencies and corresponding vibrational assignments, natural bond orbital analysis and the HOMO-LUMO analysis of 7-Amino-2,4-dimethylquinolinium formate in the ground state were performed by B3LYP levels of theory using the 6-31G(d) basis set. The optimised bond lengths and bond angles are in good agreement with the X-ray data. The vibrational spectra of the title compound which is calculated by DFT method, reproduces vibrational wave numbers and intensities with an accuracy which allows reliable vibrational assignments. The possibility of N-H⋯O hydrogen bonding was identified using NBO analysis. Natural bond orbital analysis confirms the presence of intramolecular charge transfer and the hydrogen bonding interaction. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

Texture-Based Correspondence Display

NASA Technical Reports Server (NTRS)

Gerald-Yamasaki, Michael

2004-01-01

Texture-based correspondence display is a methodology to display corresponding data elements in visual representations of complex multidimensional, multivariate data. Texture is utilized as a persistent medium to contain a visual representation model and as a means to create multiple renditions of data where color is used to identify correspondence. Corresponding data elements are displayed over a variety of visual metaphors in a normal rendering process without adding extraneous linking metadata creation and maintenance. The effectiveness of visual representation for understanding data is extended to the expression of the visual representation model in texture.

The Immersive Virtual Reality Experience: A Typology of Users Revealed Through Multiple Correspondence Analysis Combined with Cluster Analysis Technique.

PubMed

Rosa, Pedro J; Morais, Diogo; Gamito, Pedro; Oliveira, Jorge; Saraiva, Tomaz

2016-03-01

Immersive virtual reality is thought to be advantageous by leading to higher levels of presence. However, and despite users getting actively involved in immersive three-dimensional virtual environments that incorporate sound and motion, there are individual factors, such as age, video game knowledge, and the predisposition to immersion, that may be associated with the quality of virtual reality experience. Moreover, one particular concern for users engaged in immersive virtual reality environments (VREs) is the possibility of side effects, such as cybersickness. The literature suggests that at least 60% of virtual reality users report having felt symptoms of cybersickness, which reduces the quality of the virtual reality experience. The aim of this study was thus to profile the right user to be involved in a VRE through head-mounted display. To examine which user characteristics are associated with the most effective virtual reality experience (lower cybersickness), a multiple correspondence analysis combined with cluster analysis technique was performed. Results revealed three distinct profiles, showing that the PC gamer profile is more associated with higher levels of virtual reality effectiveness, that is, higher predisposition to be immersed and reduced cybersickness symptoms in the VRE than console gamer and nongamer. These findings can be a useful orientation in clinical practice and future research as they help identify which users are more predisposed to benefit from immersive VREs.

Geographic atrophy phenotype identification by cluster analysis.

PubMed

Monés, Jordi; Biarnés, Marc

2018-03-01

To identify ocular phenotypes in patients with geographic atrophy secondary to age-related macular degeneration (GA) using a data-driven cluster analysis. This was a retrospective analysis of data from a prospective, natural history study of patients with GA who were followed for ≥6 months. Cluster analysis was used to identify subgroups within the population based on the presence of several phenotypic features: soft drusen, reticular pseudodrusen (RPD), primary foveal atrophy, increased fundus autofluorescence (FAF), greyish FAF appearance and subfoveal choroidal thickness (SFCT). A comparison of features between the subgroups was conducted, and a qualitative description of the new phenotypes was proposed. The atrophy growth rate between phenotypes was then compared. Data were analysed from 77 eyes of 77 patients with GA. Cluster analysis identified three groups: phenotype 1 was characterised by high soft drusen load, foveal atrophy and slow growth; phenotype 3 showed high RPD load, extrafoveal and greyish FAF appearance and thin SFCT; the characteristics of phenotype 2 were midway between phenotypes 1 and 3. Phenotypes differed in all measured features (p≤0.013), with decreases in the presence of soft drusen, foveal atrophy and SFCT seen from phenotypes 1 to 3 and corresponding increases in high RPD load, high FAF and greyish FAF appearance. Atrophy growth rate differed between phenotypes 1, 2 and 3 (0.63, 1.91 and 1.73 mm 2 /year, respectively, p=0.0005). Cluster analysis identified three distinct phenotypes in GA. One of them showed a particularly slow growth pattern. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Diagnostic fragment-ion-based and extension strategy coupled to DFIs intensity analysis for identification of chlorogenic acids isomers in Flos Lonicerae Japonicae by HPLC-ESI-MS(n).

PubMed

Zhang, Jia-Yu; Zhang, Qian; Li, Ning; Wang, Zi-Jian; Lu, Jian-Qiu; Qiao, Yan-Jiang

2013-01-30

A method of modified diagnostic fragment-ion-based extension strategy (DFIBES) coupled to DFIs (diagnostic fragmentation ions) intensity analysis was successfully established to simultaneously screen and identify the chlorogenic acids (CGAs) in Flos Lonicerae Japonicae (FLJ) by HPLC-ESI-MS(n). DFIs, such as m/z 191 [quinic acid-H](-), m/z 179 [caffeic acid-H](-) and m/z 173 [quinic acid-H-H2O](-) were determined or proposed from the fragmentation patterns analysis of corresponding reference substances for every chemical family of CGAs. A "structure extension" method was then proposed based on the well-demonstrated fragmentation patterns and was successively applied into the rapid screening of CGAs in FLJ. Considering that substitution isomerism is a common phenomenon, a full ESI-MS(n) fragmentation analysis according to the intensity of DFIs has been performed to identify the CGA isomers. Based on the DFIs and intensity analysis, 41 peaks attributed to CGAs including 4 caffeoylquinic acids (CQA), 7 CQA glycosides, 6 dicaffeoylquinic acids (DiCQA), 10 DiCQA glycosides, 1 tricaffeoylquinic acids (TriCQA), 4p-coumaroylquinic acids (pCoQA), 3 feruloylquinic acids (FQA) and 6 caffeoylferuloylquinic acids (CFQA) were identified preliminarily in a 65-min chromatographic run. It was the first time to systematically report the presence of CGAs in FLJ, especially for CQA glycosides, DiCQA glycosides, TriCQA, pCoQA and CFQA. All the results indicated that the method of developed DFIBES coupled to DFIs analysis was feasible, reliable and universal for screening and identifying the constituents with the same carbon skeletons especially the isomeric compounds from the complex extract of TCMs. Copyright © 2012 Elsevier B.V. All rights reserved.

Quantum-classical correspondence in the vicinity of periodic orbits

NASA Astrophysics Data System (ADS)

Kumari, Meenu; Ghose, Shohini

2018-05-01

Quantum-classical correspondence in chaotic systems is a long-standing problem. We describe a method to quantify Bohr's correspondence principle and calculate the size of quantum numbers for which we can expect to observe quantum-classical correspondence near periodic orbits of Floquet systems. Our method shows how the stability of classical periodic orbits affects quantum dynamics. We demonstrate our method by analyzing quantum-classical correspondence in the quantum kicked top (QKT), which exhibits both regular and chaotic behavior. We use our correspondence conditions to identify signatures of classical bifurcations even in a deep quantum regime. Our method can be used to explain the breakdown of quantum-classical correspondence in chaotic systems.

System and method employing a self-organizing map load feature database to identify electric load types of different electric loads

DOEpatents

Lu, Bin; Harley, Ronald G.; Du, Liang; Yang, Yi; Sharma, Santosh K.; Zambare, Prachi; Madane, Mayura A.

2014-06-17

A method identifies electric load types of a plurality of different electric loads. The method includes providing a self-organizing map load feature database of a plurality of different electric load types and a plurality of neurons, each of the load types corresponding to a number of the neurons; employing a weight vector for each of the neurons; sensing a voltage signal and a current signal for each of the loads; determining a load feature vector including at least four different load features from the sensed voltage signal and the sensed current signal for a corresponding one of the loads; and identifying by a processor one of the load types by relating the load feature vector to the neurons of the database by identifying the weight vector of one of the neurons corresponding to the one of the load types that is a minimal distance to the load feature vector.

Detection of Significant Pneumococcal Meningitis Biomarkers by Ego Network.

PubMed

Wang, Qian; Lou, Zhifeng; Zhai, Liansuo; Zhao, Haibin

2017-06-01

To identify significant biomarkers for detection of pneumococcal meningitis based on ego network. Based on the gene expression data of pneumococcal meningitis and global protein-protein interactions (PPIs) data recruited from open access databases, the authors constructed a differential co-expression network (DCN) to identify pneumococcal meningitis biomarkers in a network view. Here EgoNet algorithm was employed to screen the significant ego networks that could accurately distinguish pneumococcal meningitis from healthy controls, by sequentially seeking ego genes, searching candidate ego networks, refinement of candidate ego networks and significance analysis to identify ego networks. Finally, the functional inference of the ego networks was performed to identify significant pathways for pneumococcal meningitis. By differential co-expression analysis, the authors constructed the DCN that covered 1809 genes and 3689 interactions. From the DCN, a total of 90 ego genes were identified. Starting from these ego genes, three significant ego networks (Module 19, Module 70 and Module 71) that could predict clinical outcomes for pneumococcal meningitis were identified by EgoNet algorithm, and the corresponding ego genes were GMNN, MAD2L1 and TPX2, respectively. Pathway analysis showed that these three ego networks were related to CDT1 association with the CDC6:ORC:origin complex, inactivation of APC/C via direct inhibition of the APC/C complex pathway, and DNA strand elongation, respectively. The authors successfully screened three significant ego modules which could accurately predict the clinical outcomes for pneumococcal meningitis and might play important roles in host response to pathogen infection in pneumococcal meningitis.

Near ground level sensing for spatial analysis of vegetation

NASA Technical Reports Server (NTRS)

Sauer, Tom; Rasure, John; Gage, Charlie

1991-01-01

Measured changes in vegetation indicate the dynamics of ecological processes and can identify the impacts from disturbances. Traditional methods of vegetation analysis tend to be slow because they are labor intensive; as a result, these methods are often confined to small local area measurements. Scientists need new algorithms and instruments that will allow them to efficiently study environmental dynamics across a range of different spatial scales. A new methodology that addresses this problem is presented. This methodology includes the acquisition, processing, and presentation of near ground level image data and its corresponding spatial characteristics. The systematic approach taken encompasses a feature extraction process, a supervised and unsupervised classification process, and a region labeling process yielding spatial information.

Study of dynamics of two-phase flow through a minichannel by means of recurrences

NASA Astrophysics Data System (ADS)

Litak, Grzegorz; Górski, Grzegorz; Mosdorf, Romuald; Rysak, Andrzej

2017-05-01

By changing air and water flow rates in the two-phase (air-water) flow through a minichannel, we observed the evolution of air bubbles and slugs patterns. This spatiotemporal behaviour was identified qualitatively by using a digital camera. Simultaneously, we provided a detailed analysis of these phenomena by using the corresponding sequences of light transmission time series recorded with a laser-phototransistor sensor. To distinguish particular patterns, we used recurrence plots and recurrence quantification analysis. Finally, we showed that the maxima of various recurrence quantificators obtained from the laser time series could follow the bubble and slugs patterns in studied ranges of air and water flows.

The LaueUtil toolkit for Laue photocrystallography. II. Spot finding and integration

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

Kalinowski, Jaroslaw A.; Fournier, Bertrand; Makal, Anna

2015-10-15

A spot-integration method is described which does not require prior indexing of the reflections. It is based on statistical analysis of the values from each of the pixels on successive frames, followed for each frame by morphological analysis to identify clusters of high value pixels which form an appropriate mask corresponding to a reflection peak. The method does not require prior assumptions such as fitting of a profile or definition of an integration box. The results are compared with those of the seed-skewness method which is based on minimizing the skewness of the intensity distribution within a peak's integration box.more » Applications in Laue photocrystallography are presented.« less

The impact of industrial anthropization on mosquito (Diptera, Culicidae) communities in mangrove areas of Guanabara Bay (Rio de Janeiro, Brazil).

PubMed

de Souza, A S; Couri, M S; Florindo, L

2012-02-01

The effects of industrial anthropization on species composition and community diversity of Culicidae (Diptera) were studied in a mangrove area impacted by industrial activities as compared to a preserved area, both around Guanabara Bay in the state of Rio de Janeiro, Brazil. Diversity, equitability, and species richness in Culicidae community differed between the studied areas. Indicator species analysis and correspondence analysis were carried out and indicated that the Sabethini, especially Wyeomyia (Phoniomyia) theobaldi Lane, Wyeomyia (Phoniomyia) fuscipes (Edwards), and a non-identified species of Wyeomyia sp. were associated to the preserved area, whereas Aedes taeniorhynchus Wiedemann and Aedes scapularis (Rondani) to the impacted area.

Formation of fivefold axes in the FCC-metal nanoclusters

NASA Astrophysics Data System (ADS)

Myasnichenko, Vladimir S.; Starostenkov, Mikhail D.

2012-11-01

Formation of atomistic structures of metallic Cu, Au, Ag clusters and bimetallic Cu-Au clusters was studied with the help of molecular dynamics using the many-body tight-binding interatomic potential. The simulation of the crystallization process of clusters with the number of atoms ranging from 300 to 1092 was carried out. The most stable configurations of atoms in the system, corresponding to the minimum of potential energy, was found during super-fast cooling from 1000 K. Atoms corresponding to fcc, hcp, and Ih phases were identified by the method of common neighbor analysis. Incomplete icosahedral core can be discovered at the intersection of one of the Ih axes with the surface of monometallic cluster. The decahedron-shaped structure of bimetallic Cu-Au cluster with seven completed icosahedral cores was obtained. The principles of the construction of small bimetallic clusters with icosahedral symmetry and increased fractal dimensionality were offered.

Correspondence of the brain's functional architecture during activation and rest.

PubMed

Smith, Stephen M; Fox, Peter T; Miller, Karla L; Glahn, David C; Fox, P Mickle; Mackay, Clare E; Filippini, Nicola; Watkins, Kate E; Toro, Roberto; Laird, Angela R; Beckmann, Christian F

2009-08-04

Neural connections, providing the substrate for functional networks, exist whether or not they are functionally active at any given moment. However, it is not known to what extent brain regions are continuously interacting when the brain is "at rest." In this work, we identify the major explicit activation networks by carrying out an image-based activation network analysis of thousands of separate activation maps derived from the BrainMap database of functional imaging studies, involving nearly 30,000 human subjects. Independently, we extract the major covarying networks in the resting brain, as imaged with functional magnetic resonance imaging in 36 subjects at rest. The sets of major brain networks, and their decompositions into subnetworks, show close correspondence between the independent analyses of resting and activation brain dynamics. We conclude that the full repertoire of functional networks utilized by the brain in action is continuously and dynamically "active" even when at "rest."

Instability, finite amplitude pulsation and mass-loss in models of massive OB-type stars

NASA Astrophysics Data System (ADS)

Yadav, Abhay Pratap; Glatzel, Wolfgang

2017-11-01

Variability and mass-loss are common phenomena in massive OB-type stars. It is argued that they are caused by violent strange mode instabilities identified in corresponding stellar models. We present a systematic linear stability analysis with respect to radial perturbations of massive OB-type stars with solar chemical composition and masses between 23 and 100 M⊙. For selected unstable stellar models, we perform non-linear simulations of the evolution of the instabilities into the non-linear regime. Finite amplitude pulsations with periods in the range between hours and 100 d are found to be the final result of the instabilities. The pulsations are associated with a mean acoustic luminosity which can be the origin of a pulsationally driven wind. Corresponding mass-loss rates lie in the range between 10-9 and 10-4 M⊙ yr-1 and may thus affect the evolution of massive stars.

Cytomorphology of Circulating Colorectal Tumor Cells:A Small Case Series

PubMed Central

Marrinucci, Dena; Bethel, Kelly; Lazar, Daniel; Fisher, Jennifer; Huynh, Edward; Clark, Peter; Bruce, Richard; Nieva, Jorge; Kuhn, Peter

2010-01-01

Several methodologies exist to enumerate circulating tumor cells (CTCs) from the blood of cancer patients; however, most methodologies lack high-resolution imaging, and thus, little is known about the cytomorphologic features of these cells. In this study of metastatic colorectal cancer patients, we used immunofluorescent staining with fiber-optic array scanning technology to identify CTCs, with subsequent Wright-Giemsa and Papanicolau staining. The CTCs were compared to the corresponding primary and metastatic tumors. The colorectal CTCs showed marked intrapatient pleomorphism. In comparison to the corresponding tissue biopsies, cells from all sites showed similar pleomorphism, demonstrating that colorectal CTCs retain the pleomorphism present in regions of solid growth. They also often retain particular cytomorphologic features present in the patient's primary and/or metastatic tumor tissue. This study provides an initial analysis of the cytomorphologic features of circulating colon cancer cells, providing a foundation for further investigation into the significance and metastatic potential of CTCs. PMID:20111743

Analysis of protein chromatographic profiles joint to partial least squares to detect adulterations in milk mixtures and cheeses.

PubMed

Rodríguez, N; Ortiz, M C; Sarabia, L; Gredilla, E

2010-04-15

To prevent possible frauds and give more protection to companies and consumers it is necessary to control that the types of milk used in the elaboration of dairy products correspond to those appearing in their label. Therefore, it is greatly interesting to have efficient, quick and cheap methods of analysis to identify them. In the present work, the multivariate data are the protein chromatographic profiles of cheese and milk extracts, obtained by high-performance liquid chromatography with diode-array detection (HPLC-DAD). These data correspond to pure samples of bovine, ovine and caprine milk, and also to binary and ternary mixtures. The structure of the data is studied through principal component analysis (PCA), whereas the percentage of each kind of milk has been determined by a partial least squares (PLS) calibration model. In cheese elaborated with mixtures of milk, the procedure employed allows one to detect 3.92, 2.81 and 1.47% of ovine, caprine and bovine milk, respectively, when the probability of false non-compliance is fixed at 0.05. These percentages reach 7.72, 5.52 and 2.89%, respectively, when both the probability of false non-compliance and false compliance are fixed at 0.05. (c) 2009 Elsevier B.V. All rights reserved.

Quantitative Tissue Proteomics Analysis Reveals Versican as Potential Biomarker for Early-Stage Hepatocellular Carcinoma.

PubMed

Naboulsi, Wael; Megger, Dominik A; Bracht, Thilo; Kohl, Michael; Turewicz, Michael; Eisenacher, Martin; Voss, Don Marvin; Schlaak, Jörg F; Hoffmann, Andreas-Claudius; Weber, Frank; Baba, Hideo A; Meyer, Helmut E; Sitek, Barbara

2016-01-04

Hepatocellular carcinoma (HCC) is one of the most aggressive tumors, and the treatment outcome of this disease is improved when the cancer is diagnosed at an early stage. This requires biomarkers allowing an accurate and early tumor diagnosis. To identify potential markers for such applications, we analyzed a patient cohort consisting of 50 patients (50 HCC and 50 adjacent nontumorous tissue samples as controls) using two independent proteomics approaches. We performed label-free discovery analysis on 19 HCC and corresponding tissue samples. The data were analyzed considering events known to take place in early events of HCC development, such as abnormal regulation of Wnt/b-catenin and activation of receptor tyrosine kinases (RTKs). 31 proteins were selected for verification experiments. For this analysis, the second set of the patient cohort (31 HCC and corresponding tissue samples) was analyzed using selected (multiple) reaction monitoring (SRM/MRM). We present the overexpression of ATP-dependent RNA helicase (DDX39), Fibulin-5 (FBLN5), myristoylated alanine-rich C-kinase substrate (MARCKS), and Serpin H1 (SERPINH1) in HCC for the first time. We demonstrate Versican core protein (VCAN) to be significantly associated with well differentiated and low-stage HCC. We revealed for the first time the evidence of VCAN as a potential biomarker for early-HCC diagnosis.

Identification of interactive gene networks: a novel approach in gene array profiling of myometrial events during guinea pig pregnancy.

PubMed

Mason, Clifford W; Swaan, Peter W; Weiner, Carl P

2006-06-01

The transition from myometrial quiescence to activation is poorly understood, and the analysis of array data is limited by the available data mining tools. We applied functional analysis and logical operations along regulatory gene networks to identify molecular processes and pathways underlying quiescence and activation. We analyzed some 18,400 transcripts and variants in guinea pig myometrium at stages corresponding to quiescence and activation, and compared them to the nonpregnant (control) counterpart using a functional mapping tool, MetaCore (GeneGo, St Joseph, MI) to identify novel gene networks composed of biological pathways during mid (MP) and late (LP) pregnancy. Genes altered during quiescence and or activation were identified following gene specific comparisons with myometrium from nonpregnant animals, and then linked to curated pathways and formulated networks. The MP and LP networks were subtracted from each other to identify unique genomic events during those periods. For example, changes 2-fold or greater in genes mediating protein biosynthesis, programmed cell death, microtubule polymerization, and microtubule based movement were noted during the transition to LP. We describe a novel approach combining microarrays and genetic data to identify networks associated with normal myometrial events. The resulting insights help identify potential biomarkers and permit future targeted investigations of these pathways or networks to confirm or refute their importance.

Violence in public transportation: an approach based on spatial analysis.

PubMed

Sousa, Daiane Castro Bittencourt de; Pitombo, Cira Souza; Rocha, Samille Santos; Salgueiro, Ana Rita; Delgado, Juan Pedro Moreno

2017-12-11

To carry out a spatial analysis of the occurrence of acts of violence (specifically robberies) in public transportation, identifying the regions of greater incidence, using geostatistics, and possible causes with the aid of a multicriteria analysis in the Geographic Information System. The unit of analysis is the traffic analysis zone of the survey named Origem-Destino, carried out in Salvador, state of Bahia, in 2013. The robberies recorded by the Department of Public Security of Bahia in 2013 were located and made compatible with the limits of the traffic analysis zones and, later, associated with the respective centroids. After determining the regions with the highest probability of robbery, we carried out a geographic analysis of the possible causes in the region with the highest robbery potential, considering the factors analyzed using a multicriteria analysis in a Geographic Information System environment. The execution of the two steps of this study allowed us to identify areas corresponding to the greater probability of occurrence of robberies in public transportation. In addition, the three most vulnerable road sections (Estrada da Liberdade, Rua Pero Vaz, and Avenida General San Martin) were identified in these areas. In these sections, the factors that most contribute with the potential for robbery in buses are: F1 - proximity to places that facilitate escape, F3 - great movement of persons, and F2 - absence of policing, respectively. Indicator Kriging (geostatistical estimation) can be used to construct a spatial probability surface, which can be a useful tool for the implementation of public policies. The multicriteria analysis in the Geographic Information System environment allowed us to understand the spatial factors related to the phenomenon under analysis.

Violence in public transportation: an approach based on spatial analysis

PubMed Central

de Sousa, Daiane Castro Bittencourt; Pitombo, Cira Souza; Rocha, Samille Santos; Salgueiro, Ana Rita; Delgado, Juan Pedro Moreno

2017-01-01

ABSTRACT OBJECTIVE To carry out a spatial analysis of the occurrence of acts of violence (specifically robberies) in public transportation, identifying the regions of greater incidence, using geostatistics, and possible causes with the aid of a multicriteria analysis in the Geographic Information System. METHODS The unit of analysis is the traffic analysis zone of the survey named Origem-Destino, carried out in Salvador, state of Bahia, in 2013. The robberies recorded by the Department of Public Security of Bahia in 2013 were located and made compatible with the limits of the traffic analysis zones and, later, associated with the respective centroids. After determining the regions with the highest probability of robbery, we carried out a geographic analysis of the possible causes in the region with the highest robbery potential, considering the factors analyzed using a multicriteria analysis in a Geographic Information System environment. RESULTS The execution of the two steps of this study allowed us to identify areas corresponding to the greater probability of occurrence of robberies in public transportation. In addition, the three most vulnerable road sections (Estrada da Liberdade, Rua Pero Vaz, and Avenida General San Martin) were identified in these areas. In these sections, the factors that most contribute with the potential for robbery in buses are: F1 - proximity to places that facilitate escape, F3 - great movement of persons, and F2 - absence of policing, respectively. CONCLUSIONS Indicator Kriging (geostatistical estimation) can be used to construct a spatial probability surface, which can be a useful tool for the implementation of public policies. The multicriteria analysis in the Geographic Information System environment allowed us to understand the spatial factors related to the phenomenon under analysis. PMID:29236883

Comparative sequence analysis of Sordaria macrospora and Neurospora crassa as a means to improve genome annotation.

PubMed

Nowrousian, Minou; Würtz, Christian; Pöggeler, Stefanie; Kück, Ulrich

2004-03-01

One of the most challenging parts of large scale sequencing projects is the identification of functional elements encoded in a genome. Recently, studies of genomes of up to six different Saccharomyces species have demonstrated that a comparative analysis of genome sequences from closely related species is a powerful approach to identify open reading frames and other functional regions within genomes [Science 301 (2003) 71, Nature 423 (2003) 241]. Here, we present a comparison of selected sequences from Sordaria macrospora to their corresponding Neurospora crassa orthologous regions. Our analysis indicates that due to the high degree of sequence similarity and conservation of overall genomic organization, S. macrospora sequence information can be used to simplify the annotation of the N. crassa genome.

Report for 2011 from the Bordeaux IVS Analysis Center

NASA Technical Reports Server (NTRS)

Charlot, Patrick; Bellanger, Antoine; Bourda, Geraldine; Collioud, Arnaud; Baudry, Alain

2012-01-01

This report summarizes the activities of the Bordeaux IVS Analysis Center during the year 2011. The work focused on (i) regular analysis of the IVS-R1 and IVS-R4 sessions with the GINS software package; (ii) systematic VLBI imaging of the RDV sessions and calculation of the corresponding source structure index and compactness values; (iii) imaging of the sources observed during the 2009 International Year of Astronomy IVS observing session; and (iv) continuation of our VLBI observational program to identify optically-bright radio sources suitable for the link with the future Gaia frame. Also of importance is the enhancement of the IVS LiveWeb site which now comprises all IVS sessions back to 2003, allowing one to search past observations for session-specific information (e.g. sources or stations).

Real-time detection method and system for identifying individual aerosol particles

DOEpatents

Gard, Eric E [San Francisco, CA; Coffee, Keith R [Patterson, CA; Frank, Matthias [Oakland, CA; Tobias, Herbert J [Kensington, CA; Fergenson, David P [Alamo, CA; Madden, Norm [Livermore, CA; Riot, Vincent J [Berkeley, CA; Steele, Paul T [Livermore, CA; Woods, Bruce W [Livermore, CA

2007-08-21

An improved method and system of identifying individual aerosol particles in real time. Sample aerosol particles are collimated, tracked, and screened to determine which ones qualify for mass spectrometric analysis based on predetermined qualification or selection criteria. Screening techniques include one or more of determining particle size, shape, symmetry, and fluorescence. Only qualifying particles passing all screening criteria are subject to desorption/ionization and single particle mass spectrometry to produce corresponding test spectra, which is used to determine the identities of each of the qualifying aerosol particles by comparing the test spectra against predetermined spectra for known particle types. In this manner, activation cycling of a particle ablation laser of a single particle mass spectrometer is reduced.

The identification of factors contributing to self-reported anomalies in civil aviation.

PubMed

Andrzejczak, Chris; Karwowski, Waldemar; Thompson, William

2014-01-01

The main objective of this study was to analyze anomalies voluntarily reported by pilots in civil aviation sector and identify factors leading to such anomalies. Experimental data were obtained from the NASA aviation safety reporting system (ASRS) database. These data contained a range of text records spanning 30 years of civilian aviation, both commercial (airline operations) and general aviation (private aircraft). Narrative data as well as categorical data were used. The associations between incident contributing factors and self-reported anomalies were investigated using data mining and correspondence analysis. The results revealed that a broadly defined human factors category and weather conditions were the main contributors to self-reported civil aviation anomalies. New associations between identified factors and reported anomaly conditions were also reported.

Dermoscopy for common skin problems in Chinese children using a novel Hong Kong-made dermoscope.

PubMed

Luk, David C K; Lam, Sam Y Y; Cheung, Patrick C H; Chan, Bill H B

2014-12-01

To evaluate the dermoscopic features of common skin problems in Chinese children. A case series with retrospective qualitative analysis of dermoscopic features of common skin problems in Chinese children. A regional hospital in Hong Kong. Dermoscopic image database, from 1 May 2013 to 31 October 2013, of 185 Chinese children (aged 0 to 18 years). Dermoscopic features of common paediatric skin problems in Chinese children were identified. These features corresponded with the known dermoscopic features reported in the western medical literature. New dermoscopic features were identified in café-au-lait macules. Dermoscopic features of common skin problems in Chinese children were consistent with those reported in western medical literature. Dermoscopy has a role in managing children with skin problems.

Molecular Predictors of 3D Morphogenesis by Breast Cancer Cell Lines in 3D Culture

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

Han, Ju; Chang, Hang; Giricz, Orsi

Correlative analysis of molecular markers with phenotypic signatures is the simplest model for hypothesis generation. In this paper, a panel of 24 breast cell lines was grown in 3D culture, their morphology was imaged through phase contrast microscopy, and computational methods were developed to segment and represent each colony at multiple dimensions. Subsequently, subpopulations from these morphological responses were identified through consensus clustering to reveal three clusters of round, grape-like, and stellate phenotypes. In some cases, cell lines with particular pathobiological phenotypes clustered together (e.g., ERBB2 amplified cell lines sharing the same morphometric properties as the grape-like phenotype). Next, associationsmore » with molecular features were realized through (i) differential analysis within each morphological cluster, and (ii) regression analysis across the entire panel of cell lines. In both cases, the dominant genes that are predictive of the morphological signatures were identified. Specifically, PPAR? has been associated with the invasive stellate morphological phenotype, which corresponds to triple-negative pathobiology. PPAR? has been validated through two supporting biological assays.« less

Genome-Wide Identification, Evolution and Expression Analysis of the Grape (Vitis vinifera L.) Zinc Finger-Homeodomain Gene Family

PubMed Central

Wang, Hao; Yin, Xiangjing; Li, Xiaoqin; Wang, Li; Zheng, Yi; Xu, Xiaozhao; Zhang, Yucheng; Wang, Xiping

2014-01-01

Plant zinc finger-homeodomain (ZHD) genes encode a family of transcription factors that have been demonstrated to play an important role in the regulation of plant growth and development. In this study, we identified a total of 13 ZHD genes (VvZHD) in the grape genome that were further classified into at least seven groups. Genome synteny analysis revealed that a number of VvZHD genes were present in the corresponding syntenic blocks of Arabidopsis, indicating that they arose before the divergence of these two species. Gene expression analysis showed that the identified VvZHD genes displayed distinct spatiotemporal expression patterns, and were differentially regulated under various stress conditions and hormone treatments, suggesting that the grape VvZHDs might be also involved in plant response to a variety of biotic and abiotic insults. Our work provides insightful information and knowledge about the ZHD genes in grape, which provides a framework for further characterization of their roles in regulation of stress tolerance as well as other aspects of grape productivity. PMID:24705465

Characterization of transformation related genes in oral cancer cells.

PubMed

Chang, D D; Park, N H; Denny, C T; Nelson, S F; Pe, M

1998-04-16

A cDNA representational difference analysis (cDNA-RDA) and an arrayed filter technique were used to characterize transformation-related genes in oral cancer. From an initial comparison of normal oral epithelial cells and a human papilloma virus (HPV)-immortalized oral epithelial cell line, we obtained 384 differentially expressed gene fragments and arrayed them on a filter. Two hundred and twelve redundant clones were identified by three rounds of back hybridization. Sequence analysis of the remaining clones revealed 99 unique clones corresponding to 69 genes. The expression of these transformation related gene fragments in three nontumorigenic HPV-immortalized oral epithelial cell lines and three oral cancer cell lines were simultaneously monitored using a cDNA array hybridization. Although there was a considerable cell line-to-cell line variability in the expression of these clones, a reliable prediction of their expression could be made from the cDNA array hybridization. Our study demonstrates the utility of combining cDNA-RDA and arrayed filters in high-throughput gene expression difference analysis. The differentially expressed genes identified in this study should be informative in studying oral epithelial cell carcinogenesis.

Identifying optimum performance trade-offs using a cognitively bounded rational analysis model of discretionary task interleaving.

PubMed

Janssen, Christian P; Brumby, Duncan P; Dowell, John; Chater, Nick; Howes, Andrew

2011-01-01

We report the results of a dual-task study in which participants performed a tracking and typing task under various experimental conditions. An objective payoff function was used to provide explicit feedback on how participants should trade off performance between the tasks. Results show that participants' dual-task interleaving strategy was sensitive to changes in the difficulty of the tracking task and resulted in differences in overall task performance. To test the hypothesis that people select strategies that maximize payoff, a Cognitively Bounded Rational Analysis model was developed. This analysis evaluated a variety of dual-task interleaving strategies to identify the optimal strategy for maximizing payoff in each condition. The model predicts that the region of optimum performance is different between experimental conditions. The correspondence between human data and the prediction of the optimal strategy is found to be remarkably high across a number of performance measures. This suggests that participants were honing their behavior to maximize payoff. Limitations are discussed. Copyright © 2011 Cognitive Science Society, Inc.

Localization of spontaneous magnetoencephalographic activity of neonates and fetuses using independent component and Hilbert phase analysis.

PubMed

Vairavan, Srinivasan; Eswaran, Hari; Preissl, Hubert; Wilson, James D; Haddad, Naim; Lowery, Curtis L; Govindan, Rathinaswamy B

2010-01-01

The fetal magnetoencephalogram (fMEG) is measured in the presence of large interference from maternal and fetal magnetocardiograms (mMCG and fMCG). These cardiac interferences can be attenuated by orthogonal projection (OP) technique of the corresponding spatial vectors. However, the OP technique redistributes the fMEG signal among the channels and also leaves some cardiac residuals (partially attenuated mMCG and fMCG) due to loss of stationarity in the signal. In this paper, we propose a novel way to extract and localize the neonatal and fetal spontaneous brain activity by using independent component analysis (ICA) technique. In this approach, we perform ICA on a small subset of sensors for 1-min duration. The independent components obtained are further investigated for the presence of discontinuous patterns as identified by the Hilbert phase analysis and are used as decision criteria for localizing the spontaneous brain activity. In order to locate the region of highest spontaneous brain activity content, this analysis is performed on the sensor subsets, which are traversed across the entire sensor space. The region of the spontaneous brain activity as identified by the proposed approach correlated well with the neonatal and fetal head location. In addition, the burst duration and the inter-burst interval computed for the identified discontinuous brain patterns are in agreement with the reported values.

Comparative proteomics analysis of oral cancer cell lines: identification of cancer associated proteins

PubMed Central

2014-01-01

Background A limiting factor in performing proteomics analysis on cancerous cells is the difficulty in obtaining sufficient amounts of starting material. Cell lines can be used as a simplified model system for studying changes that accompany tumorigenesis. This study used two-dimensional gel electrophoresis (2DE) to compare the whole cell proteome of oral cancer cell lines vs normal cells in an attempt to identify cancer associated proteins. Results Three primary cell cultures of normal cells with a limited lifespan without hTERT immortalization have been successfully established. 2DE was used to compare the whole cell proteome of these cells with that of three oral cancer cell lines. Twenty four protein spots were found to have changed in abundance. MALDI TOF/TOF was then used to determine the identity of these proteins. Identified proteins were classified into seven functional categories – structural proteins, enzymes, regulatory proteins, chaperones and others. IPA core analysis predicted that 18 proteins were related to cancer with involvements in hyperplasia, metastasis, invasion, growth and tumorigenesis. The mRNA expressions of two proteins – 14-3-3 protein sigma and Stress-induced-phosphoprotein 1 – were found to correlate with the corresponding proteins’ abundance. Conclusions The outcome of this analysis demonstrated that a comparative study of whole cell proteome of cancer versus normal cell lines can be used to identify cancer associated proteins. PMID:24422745

Determining the anaerobic threshold in postpolio syndrome: comparison with current guidelines for training intensity prescription.

PubMed

Voorn, Eric L; Gerrits, Karin H; Koopman, Fieke S; Nollet, Frans; Beelen, Anita

2014-05-01

To determine whether the anaerobic threshold (AT) can be identified in individuals with postpolio syndrome (PPS) using submaximal incremental exercise testing, and to compare current guidelines for intensity prescription in PPS with the AT. Cohort study. Research laboratory. Individuals with PPS (N=82). Not applicable. Power output, gas exchange variables, heart rate, and rating of perceived exertion (RPE) were measured in an incremental submaximal cycle ergometry test. Two independent observers identified the AT. Comparison of current guidelines for training intensity prescription in PPS (40%-60% heart rate reserve [HRR] or RPE of 12) with the AT was based on correlations between recommended heart rate and the heart rate at the AT. In addition, we determined the proportion of individuals that would have been recommended to train at an intensity corresponding to their AT. The AT was identified in 63 (77%) of the participants. Pearson correlation coefficients between the recommended heart rate and the heart rate at the AT were lower in cases of 40% HRR (r=.56) and 60% HRR (r=.50) than in cases of prescription based on the RPE (r=.86). Based on the RPE, 55% of the individuals would have been recommended to train at an intensity corresponding to their AT. This proportion was higher compared with 40% HRR (41%) or 60% HRR (18%) as criterion. The AT can be identified in most individuals with PPS offering an individualized target for aerobic training. If the AT cannot be identified (eg, because gas analysis equipment is not available), intensity prescription can best be based on the RPE. Copyright © 2014 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Does hospital accreditation impact bariatric surgery safety?

PubMed

Morton, John M; Garg, Trit; Nguyen, Ninh

2014-09-01

To evaluate the impact of hospital accreditation upon bariatric surgery outcomes. Since 2004, the American College of Surgeons and the American Society of Metabolic and Bariatric Surgery have accredited bariatric hospitals. Few studies have evaluated the impact of hospital accreditation on all bariatric surgery outcomes. Bariatric surgery hospitalizations were identified using International Classification of Diseases, Ninth Revision (ICD9) codes in the 2010 Nationwide Inpatient Sample (NIS). Hospital names and American Hospital Association (AHA) codes were used to identify accredited bariatric centers. Relevant ICD9 codes were used for identifying demographics, length of stay (LOS), total charges, mortality, complications, and failure to rescue (FTR) events. There were 117,478 weighted bariatric patient discharges corresponding to 235 unique hospitals in the 2010 NIS data set. A total of 72,615 (61.8%) weighted discharges, corresponding to 145 (61.7%) named or AHA-identifiable hospitals were included. Among the 145 hospitals, 66 (45.5%) were unaccredited and 79 (54.5%) accredited. Compared with accredited centers, unaccredited centers had a higher mean LOS (2.25 vs 1.99 days, P < 0.0001), as well as total charges ($51,189 vs $42,212, P < 0.0001). Incidence of any complication was higher at unaccredited centers than at accredited centers (12.3% vs 11.3%, P = 0.001), as was mortality (0.13% vs 0.07%, P = 0.019) and FTR (0.97% vs 0.55%, P = 0.046). Multivariable logistic regression analysis identified unaccredited status as a positive predictor of incidence of complication [odds ratio (OR) = 1.08, P < 0.0001], as well as mortality (OR = 2.13, P = 0.013). Hospital accreditation status is associated with safer outcomes, shorter LOS, and lower total charges after bariatric surgery.

Marketing Mix Formulation for Higher Education: An Integrated Analysis Employing Analytic Hierarchy Process, Cluster Analysis and Correspondence Analysis

ERIC Educational Resources Information Center

Ho, Hsuan-Fu; Hung, Chia-Chi

2008-01-01

Purpose: The purpose of this paper is to examine how a graduate institute at National Chiayi University (NCYU), by using a model that integrates analytic hierarchy process, cluster analysis and correspondence analysis, can develop effective marketing strategies. Design/methodology/approach: This is primarily a quantitative study aimed at…

A network analysis of the Chinese medicine Lianhua-Qingwen formula to identify its main effective components.

PubMed

Wang, Chun-Hua; Zhong, Yi; Zhang, Yan; Liu, Jin-Ping; Wang, Yue-Fei; Jia, Wei-Na; Wang, Guo-Cai; Li, Zheng; Zhu, Yan; Gao, Xiu-Mei

2016-02-01

Chinese medicine is known to treat complex diseases with multiple components and multiple targets. However, the main effective components and their related key targets and functions remain to be identified. Herein, a network analysis method was developed to identify the main effective components and key targets of a Chinese medicine, Lianhua-Qingwen Formula (LQF). The LQF is commonly used for the prevention and treatment of viral influenza in China. It is composed of 11 herbs, gypsum and menthol with 61 compounds being identified in our previous work. In this paper, these 61 candidate compounds were used to find their related targets and construct the predicted-target (PT) network. An influenza-related protein-protein interaction (PPI) network was constructed and integrated with the PT network. Then the compound-effective target (CET) network and compound-ineffective target network (CIT) were extracted, respectively. A novel approach was developed to identify effective components by comparing CET and CIT networks. As a result, 15 main effective components were identified along with 61 corresponding targets. 7 of these main effective components were further experimentally validated to have antivirus efficacy in vitro. The main effective component-target (MECT) network was further constructed with main effective components and their key targets. Gene Ontology (GO) analysis of the MECT network predicted key functions such as NO production being modulated by the LQF. Interestingly, five effective components were experimentally tested and exhibited inhibitory effects on NO production in the LPS induced RAW 264.7 cell. In summary, we have developed a novel approach to identify the main effective components in a Chinese medicine LQF and experimentally validated some of the predictions.

Do recognizable lifetime eating disorder phenotypes naturally occur in a culturally asian population? A combined latent profile and taxometric approach.

PubMed

Thomas, Jennifer J; Eddy, Kamryn T; Ruscio, John; Ng, King Lam; Casale, Kristen E; Becker, Anne E; Lee, Sing

2015-05-01

We examined whether empirically derived eating disorder (ED) categories in Hong Kong Chinese patients (N = 454) would be consistent with recognizable lifetime ED phenotypes derived from latent structure models of European and American samples. We performed latent profile analysis (LPA) using indicator variables from data collected during routine assessment, and then applied taxometric analysis to determine whether latent classes were qualitatively versus quantitatively distinct. Latent profile analysis identified four classes: (i) binge/purge (47%); (ii) non-fat-phobic low-weight (34%); (iii) fat-phobic low-weight (12%); and (iv) overweight disordered eating (6%). Taxometric analysis identified qualitative (categorical) distinctions between the binge/purge and non-fat-phobic low-weight classes, and also between the fat-phobic and non-fat-phobic low-weight classes. Distinctions between the fat-phobic low-weight and binge/purge classes were indeterminate. Empirically derived categories in Hong Kong showed recognizable correspondence with recognizable lifetime ED phenotypes. Although taxometric findings support two distinct classes of low weight EDs, LPA findings also support heterogeneity among non-fat-phobic individuals. Copyright © 2015 John Wiley & Sons, Ltd and Eating Disorders Association.

A general computation model based on inverse analysis principle used for rheological analysis of W/O rapeseed and soybean oil emulsions

NASA Astrophysics Data System (ADS)

Vintila, Iuliana; Gavrus, Adinel

2017-10-01

The present research paper proposes the validation of a rigorous computation model used as a numerical tool to identify rheological behavior of complex emulsions W/O. Considering a three-dimensional description of a general viscoplastic flow it is detailed the thermo-mechanical equations used to identify fluid or soft material's rheological laws starting from global experimental measurements. Analyses are conducted for complex emulsions W/O having generally a Bingham behavior using the shear stress - strain rate dependency based on a power law and using an improved analytical model. Experimental results are investigated in case of rheological behavior for crude and refined rapeseed/soybean oils and four types of corresponding W/O emulsions using different physical-chemical composition. The rheological behavior model was correlated with the thermo-mechanical analysis of a plane-plane rheometer, oil content, chemical composition, particle size and emulsifier's concentration. The parameters of rheological laws describing the industrial oils and the W/O concentrated emulsions behavior were computed from estimated shear stresses using a non-linear regression technique and from experimental torques using the inverse analysis tool designed by A. Gavrus (1992-2000).

Palaeomagnetism of the loess/palaeosol sequence in Viatovo (NE Bulgaria) in the Danube basin

NASA Astrophysics Data System (ADS)

Jordanova, Diana; Hus, Jozef; Evlogiev, Jordan; Geeraerts, Raoul

2008-03-01

The results of a palaeomagnetic investigation of a 27 m thick loess/palaeosol sequence in Viatovo (NE Bulgaria) are presented in this paper. The sequence consists of topsoil S 0, seven loess horizons (L 1-L 7) and six interbedded palaeosols (S 1-S 6) overlying a red clay (terra rossa) complex. Magnetic viscosity experiments, IRM acquisition, AMS analysis and NRM stepwise alternating and thermal demagnetisation experiments of pilot samples were implemented for precise determination of the characteristic remanence and construction of a reliable magnetostratigraphical scheme. Analysis of IRM acquisition curves using the expectation - maximization algorithm of Heslop et al. [Heslop, D., Dekkers, M., Kruiver, P., van Oorschot, H., 2002. Analysis of isothermal remanent magnetization acquisition curves using the expectation - maximization algorithm. Geophys. J. Int., 148, 58-64] suggests that the best fitting is obtained by three coercivity components. Component 1 corresponds to SD maghemite/magnetite, while component 2 is probably related to the presence of oxidised detrital magnetites. The third component shows varying coercivities depending on the degree of pedogenic alteration of the samples and probably reflects the presence of detrital magnetite grains oxidised at different degree. The relevance of the Viatovo section as a key representative sequence for the loess cover in the Danube basin is confirmed by the presence of geomagnetic polarity changes in the lower part of the sequence. The youngest one recorded in the seventh loess unit L 7 can be identified as corresponding to the Matuyama/Brunhes palaeomagnetic polarity transition. Two normal magnetozones were found in the red clay complex, probably corresponding to the Jaramillo and Olduvai subchronozones of the Matuyama chron.

A computational method for estimating the PCR duplication rate in DNA and RNA-seq experiments.

PubMed

Bansal, Vikas

2017-03-14

PCR amplification is an important step in the preparation of DNA sequencing libraries prior to high-throughput sequencing. PCR amplification introduces redundant reads in the sequence data and estimating the PCR duplication rate is important to assess the frequency of such reads. Existing computational methods do not distinguish PCR duplicates from "natural" read duplicates that represent independent DNA fragments and therefore, over-estimate the PCR duplication rate for DNA-seq and RNA-seq experiments. In this paper, we present a computational method to estimate the average PCR duplication rate of high-throughput sequence datasets that accounts for natural read duplicates by leveraging heterozygous variants in an individual genome. Analysis of simulated data and exome sequence data from the 1000 Genomes project demonstrated that our method can accurately estimate the PCR duplication rate on paired-end as well as single-end read datasets which contain a high proportion of natural read duplicates. Further, analysis of exome datasets prepared using the Nextera library preparation method indicated that 45-50% of read duplicates correspond to natural read duplicates likely due to fragmentation bias. Finally, analysis of RNA-seq datasets from individuals in the 1000 Genomes project demonstrated that 70-95% of read duplicates observed in such datasets correspond to natural duplicates sampled from genes with high expression and identified outlier samples with a 2-fold greater PCR duplication rate than other samples. The method described here is a useful tool for estimating the PCR duplication rate of high-throughput sequence datasets and for assessing the fraction of read duplicates that correspond to natural read duplicates. An implementation of the method is available at https://github.com/vibansal/PCRduplicates .

Investigation of the application of HCMM thermal data to snow hydrology. [Salt-Verde watershed, Arizona and Kings River Basin, California

NASA Technical Reports Server (NTRS)

Barnes, J. C. (Principal Investigator)

1980-01-01

The author has identified the following significant results. Analysis of HCMM digital thermal data for daytime passes over the Salt-Verde Watershed area on five dates show a gradual depletion of snow cover in the watershed (and in the Little Colorado Watershed to the north) from a maximum on February 9th to a nearly complete disappearance of the snow pack by April 15th. Temperature contours correspond closely with the snowline observed in the visible image.

Fourier analysis of surface plasmon waves launched from single nanohole and nanohole arrays: unraveling tip-induced effects.

PubMed

Chang, Y C; Chu, J Y; Wang, T J; Lin, M W; Yeh, J T; Wang, J K

2008-01-21

The authors report the investigation of surface plasmon waves (SPW) generated by single nanohole and nanohole arrays. Scattering-type scanning near-field microscopy is used to directly observe near-field distribution. The images after Fourier transformation display characteristic patterns that match with the derived analytic formula. The correspondence helps to identify the role of the scanning tip in generating SPW, making possible of the removal of this tip-induced effect. This study provides a means to perform in-depth investigation on surface plasmon polaritons.

Recognition of Potentially Novel Human Disease-Associated Pathogens by Implementation of Systematic 16S rRNA Gene Sequencing in the Diagnostic Laboratory▿ †

PubMed Central

Keller, Peter M.; Rampini, Silvana K.; Büchler, Andrea C.; Eich, Gerhard; Wanner, Roger M.; Speck, Roberto F.; Böttger, Erik C.; Bloemberg, Guido V.

2010-01-01

Clinical isolates that are difficult to identify by conventional means form a valuable source of novel human pathogens. We report on a 5-year study based on systematic 16S rRNA gene sequence analysis. We found 60 previously unknown 16S rRNA sequences corresponding to potentially novel bacterial taxa. For 30 of 60 isolates, clinical relevance was evaluated; 18 of the 30 isolates analyzed were considered to be associated with human disease. PMID:20631113

Factor structure of the Spanish version of the Object-Spatial Imagery and Verbal Questionnaire.

PubMed

Campos, Alfredo; Pérez-Fabello, María José

2011-04-01

The reliability and factor structure of the Spanish version of the Object-Spatial Imagery and Verbal Questionnaire (OSIVQ) were assessed in a sample of 213 Spanish university graduates. The questionnaire measures three types of processing preferences (verbal, object imagery, and spatial imagery). Principal components analysis with varimax rotation identified three factors, corresponding to the three scales proposed in the original version, explaining 33.1% of the overall variance. Cronbach's alphas were .72, .77, and .81 for the verbal, object imagery, and spatial imagery scales, respectively.

On the origin of a domesticated species: Identifying the parent population of Russian silver foxes (Vulpes vulpes)

PubMed Central

Statham, Mark J.; Trut, Lyudmila N.; Sacks, Ben N.; Kharlamova, Anastasiya V.; Oskina, Irina N.; Gulevich, Rimma G.; Johnson, Jennifer L.; Temnykh, Svetlana V.; Acland, Gregory M.; Kukekova, Anna V.

2011-01-01

The foxes at Novosibirsk, Russia, are the only population of domesticated foxes in the world. These domesticated foxes originated from farm-bred silver foxes (Vulpes vulpes), whose genetic source is unknown. In this study we examined the origin of the domesticated strain of foxes and two other farm-bred fox populations (aggressive and unselected) maintained in Novosibirsk. To identify the phylogenetic origin of these populations we sequenced two regions of mtDNA, cytochrome b and D-loop, from 24 Novosibirsk foxes (8 foxes from each population) and compared them with corresponding sequences of native red foxes from Europe, Asia, Alaska and Western Canada, Eastern Canada, and the Western Mountains of the USA. We identified seven cytochrome b - D-loop haplotypes in Novosibirsk populations, four of which were previously observed in Eastern North America. The three remaining haplotypes differed by one or two base change from the most common haplotype in Eastern Canada. ΦST analysis showed significant differentiation between Novosibirsk populations and red fox populations from all geographic regions except Eastern Canada. No haplotypes of Eurasian origin were identified in the Novosibirsk populations. These results are consistent with historical records indicating that the original breeding stock of farm-bred foxes originated from Prince Edward Island, Canada. Mitochondrial DNA data together with historical records indicate two stages in the selection of domesticated foxes: the first includes captive breeding for ~50 years with unconscious selection for behaviour; the second corresponds to over 50 further years of intensive selection for tame behaviour. PMID:21625363

Microbial communities related to volatile organic compound emission in automobile air conditioning units.

PubMed

Diekmann, Nina; Burghartz, Melanie; Remus, Lars; Kaufholz, Anna-Lena; Nawrath, Thorben; Rohde, Manfred; Schulz, Stefan; Roselius, Louisa; Schaper, Jörg; Mamber, Oliver; Jahn, Dieter; Jahn, Martina

2013-10-01

During operation of mobile air conditioning (MAC) systems in automobiles, malodours can occur. We studied the microbial communities found on contaminated heat exchanger fins of 45 evaporators from car MAC systems which were operated in seven different regions of the world and identified corresponding volatile organic compounds. Collected biofilms were examined by scanning electron microscopy and fluorescent in situ hybridization. The detected bacteria were loosely attached to the metal surface. Further analyses of the bacteria using PCR-based single-strand conformation polymorphism and sequencing of isolated 16S rRNA gene fragments identified highly divergent microbial communities with multiple members of the Alphaproteobacteriales, Methylobacteria were the prevalent bacteria. In addition, Sphingomonadales, Burkholderiales, Bacillales, Alcanivorax spp. and Stenotrophomonas spp. were found among many others depending on the location the evaporators were operated. Interestingly, typical pathogenic bacteria related to air conditioning systems including Legionella spp. were not found. In order to determine the nature of the chemical compounds produced by the bacteria, the volatile organic compounds were examined by closed loop stripping analysis and identified by combined gas chromatography/mass spectrometry. Sulphur compounds, i.e. di-, tri- and multiple sulphides, acetylthiazole, aromatic compounds and diverse substituted pyrazines were detected. Mathematical clustering of the determined microbial community structures against their origin identified a European/American/Arabic cluster versus two mainly tropical Asian clusters. Interestingly, clustering of the determined volatiles against the origin of the corresponding MAC revealed a highly similar pattern. A close relationship of microbial community structure and resulting malodours to the climate and air quality at the location of MAC operation was concluded.

A HOT FLUX ROPE OBSERVED BY SDO/AIA

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

Aparna, V.; Tripathi, Durgesh, E-mail: aparnav@iucaa.in

2016-03-01

A filament eruption was observed on 2010 October 31 in the images recorded by the Atmospheric Imaging Assembly (AIA) on board the Solar Dynamic Observatory (SDO) in its Extreme Ultra-Violet (EUV) channels. The filament showed a slow-rise phase followed by a fast rise and was classified to be an asymmetric eruption. In addition, multiple localized brightenings which were spatially and temporally associated with the slow-rise phase were identified, leading us to believe that the tether-cutting mechanism initiated the eruption. An associated flux rope was detected in high-temperature channels of AIA, namely 94 and 131 Å, corresponding to 7 and 11more » MK plasma respectively. In addition, these channels are also sensitive to cooler plasma corresponding to 1–2 MK. In this study, we have applied the algorithm devised by Warren et al. to remove cooler emission from the 94 Å channel to deduce only the high-temperature structure of the flux rope and to study its temporal evolution. We found that the flux rope was very clearly seen in the clean 94 Å channel image corresponding to Fe xviii emission, which corresponds to a plasma at a temperature of 7 MK. This temperature matched well with that obtained using Differential Emission Measure analysis. This study provides important constrains in the modeling of the thermodynamic structure of the flux ropes in coronal mass ejections.« less

Genome-Wide Screening of Genes Showing Altered Expression in Liver Metastases of Human Colorectal Cancers by cDNA Microarray1

PubMed Central

Yanagawa, Rempei; Furukawa, Yoichi; Tsunoda, Tatsuhiko; Kitahara, Osamu; Kameyama, Masao; Murata, Kohei; Ishikawa, Osamu; Nakamura, Yusuke

2001-01-01

Abstract In spite of intensive and increasingly successful attempts to determine the multiple steps involved in colorectal carcinogenesis, the mechanisms responsible for metastasis of colorectal tumors to the liver remain to be clarified. To identify genes that are candidates for involvement in the metastatic process, we analyzed genome-wide expression profiles of 10 primary colorectal cancers and their corresponding metastatic lesions by means of a cDNA microarray consisting of 9121 human genes. This analysis identified 40 genes whose expression was commonly upregulated in metastatic lesions, and 7 that were commonly downregulated. The upregulated genes encoded proteins involved in cell adhesion, or remodeling of the actin cytoskeleton. Investigation of the functions of more of the altered genes should improve our understanding of metastasis and may identify diagnostic markers and/or novel molecular targets for prevention or therapy of metastatic lesions. PMID:11687950

Signal analysis of the female singing voice: Features for perceptual singer identity

NASA Astrophysics Data System (ADS)

Mellody, Maureen

2001-07-01

Individual singing voices tend to be easy for a listener to identify, particularly when compared to the difficulty of identifying the performer of any other musical instrument. What cues does a listener use to identify a particular singing voice? This work seeks to identify a set of features with which one can synthesize notes with the vocal quality of a particular singer. Such analysis and synthesis influences computer music (in the creation of synthetic sounds with different timbre), vocal pedagogy (as a training tool to help singers understand properties of their own voice as well as different professional-quality voices), and vocal health (to identify improper behavior in vocal production). The problem of singer identification is approached in three phases: signal analysis, the development of low- order representations, and perceptual evaluation. To perform the signal analysis, a high-resolution time- frequency distribution is applied to vowel tokens from sopranos and mezzo-sopranos. From these results, low- order representations are created for each singer's notes, which are used to synthesize sounds with the timbral quality of that singer. Finally, these synthesized sounds, along with original recordings, are evaluated by trained listeners in a variety of perceptual experiments to determine the extent to which the vocal quality of the desired singer is captured. Results from the signal analysis show that amplitude and frequency estimates extracted from the time-frequency signal analysis can be used to re-create each signal with little degradation in quality and no loss of perceptual identity. Low-order representations derived from the signal analysis are used in clustering and classification, which successfully clusters signals with corresponding singer identity. Finally, perceptual results indicate that trained listeners are, surprisingly, only modestly successful at correctly identifying the singer of a recording, and find the task to be particularly difficult for certain voices and extremely easy for others. Listeners also indicate that the majority of sounds synthesized with the low-order representations sufficiently capture the desired vocal timbre. Again, the task is easy for certain voices and much more difficult when evaluating other singers, consistent with the results from the original recordings.

Classification and ordination of understory vegetation using multivariate techniques in the Pinus wallichiana forests of Swat Valley, northern Pakistan

NASA Astrophysics Data System (ADS)

Rahman, Inayat Ur; Khan, Nasrullah; Ali, Kishwar

2017-04-01

An understory vegetation survey of the Pinus wallichiana-dominated temperate forests of Swat District was carried out to inspect the structure, composition and ecological associations of the forest vegetation. A quadrat method of sampling was used to record the floristic and phytosociological data necessary for the analysis using 300 quadrats of 10 × 10 m each. Some vegetation parameters viz. frequency and density for trees (overstory vegetation) as well as for the understory vegetation were recorded. The results revealed that in total, 92 species belonging to 77 different genera and 45 families existed in the area. The largest families were Asteraceae, Rosaceae and Lamiaceae with 12, ten and nine species, respectively. Ward's agglomerative cluster analysis for tree species resulted in three floristically and ecologically distinct community types along different topographic and soil variables. Importance value indices (IVI) were also calculated for understory vegetation and were subjected to ordination techniques, i.e. canonical correspondence analysis (CCA) and detrended correspondence analysis (DCA). DCA bi-plots for stands show that most of the stands were scattered around the centre of the DCA bi-plot, identified by two slightly scattered clusters. DCA for species bi-plot clearly identified three clusters of species revealing three types of understory communities in the study area. Results of the CCA were somewhat different from the DCA showing the impact of environmental variables on the understory species. CCA results reveal that three environmental variables, i.e. altitude, slope and P (mg/kg), have a strong influence on distribution of stands and species. Impact of tree species on the understory vegetation was also tested by CCA which showed that four tree species, i.e. P. wallichiana A.B. Jackson, Juglans regia Linn., Quercus dilatata Lindl. ex Royle and Cedrus deodara (Roxb. ex Lamb.) G. Don, have strong influences on associated understory vegetation. It is therefore concluded that Swat District has various microclimatic zones with suitable environmental variables to support distinct flora.

Propagation of gaseous detonation waves in a spatially inhomogeneous reactive medium

NASA Astrophysics Data System (ADS)

Mi, XiaoCheng; Higgins, Andrew J.; Ng, Hoi Dick; Kiyanda, Charles B.; Nikiforakis, Nikolaos

2017-05-01

Detonation propagation in a compressible medium wherein the energy release has been made spatially inhomogeneous is examined via numerical simulation. The inhomogeneity is introduced via step functions in the reaction progress variable, with the local value of energy release correspondingly increased so as to maintain the same average energy density in the medium and thus a constant Chapman-Jouguet (CJ) detonation velocity. A one-step Arrhenius rate governs the rate of energy release in the reactive zones. The resulting dynamics of a detonation propagating in such systems with one-dimensional layers and two-dimensional squares are simulated using a Godunov-type finite-volume scheme. The resulting wave dynamics are analyzed by computing the average wave velocity and one-dimensional averaged wave structure. In the case of sufficiently inhomogeneous media wherein the spacing between reactive zones is greater than the inherent reaction zone length, average wave speeds significantly greater than the corresponding CJ speed of the homogenized medium are obtained. If the shock transit time between reactive zones is less than the reaction time scale, then the classical CJ detonation velocity is recovered. The spatiotemporal averaged structure of the waves in these systems is analyzed via a Favre-averaging technique, with terms associated with the thermal and mechanical fluctuations being explicitly computed. The analysis of the averaged wave structure identifies the super-CJ detonations as weak detonations owing to the existence of mechanical nonequilibrium at the effective sonic point embedded within the wave structure. The correspondence of the super-CJ behavior identified in this study with real detonation phenomena that may be observed in experiments is discussed.

Posttest analysis of the 1:6-scale reinforced concrete containment

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

Pfeiffer, P.A.; Kennedy, J.M.; Marchertas, A.H.

A prediction of the response of the Sandia National Laboratories 1:6- scale reinforced concrete containment model test was made by Argonne National Laboratory. ANL along with nine other organizations performed a detailed nonlinear response analysis of the 1:6-scale model containment subjected to overpressurization in the fall of 1986. The two-dimensional code TEMP-STRESS and the three-dimensional NEPTUNE code were utilized (1) to predict the global response of the structure, (2) to identify global failure sites and the corresponding failure pressures and (3) to identify some local failure sites and pressure levels. A series of axisymmetric models was studied with the two-dimensionalmore » computer program TEMP-STRESS. The comparison of these pretest computations with test data from the containment model has provided a test for the capability of the respective finite element codes to predict global failure modes, and hence serves as a validation of these codes. Only the two-dimensional analyses will be discussed in this paper. 3 refs., 10 figs.« less

Analysis of human immunodeficiency virus type 1 Vif gene sequences among men who have sex with men in Heilongjiang province of China.

PubMed

Shao, Bing; Li, Hang; Liu, Sheng-Yuan; Li, Wen-Jing; Huang, Chao-Qun; Lin, Yuan-Long; Wang, Fu-Xiang; Wang, Bin-You

2013-05-01

To identify the current prevalent subtypes and to study the genetic variation of HIV-1 strains in men who have sex with men (MSM) residing in Heilongjiang province, China. We analyzed the characteristics of the nucleotide sequences and the corresponding deduced protein of Vif of HIV-1 strains isolated from 17 drug-naive HIV-1-seropositive MSM. Subtypes B (7.65%) and B' (Thailand B) (11.76%), CRF07_BC (47.06%), and CRF01_AE (23.53%) were identified. Phylogenetic analysis showed that there was a close relationship between our strains and those from the same MSM population in Hebei province, which is geographically close to Heilongjiang. Most of the documented Vif functional motifs are well conserved in the majority of our analyzed sequences. Taken together, our results suggest that there might be multiple introductions of HIV in Heilongjiang MSM and frequent sexual communications with other geographically nearby MSM populations.

Identification of a putative protein profile associating with tamoxifen therapy resistance in breast cancer

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

Umar, Arzu; Kang, Hyuk; Timmermans, A. M.

2009-06-01

Tamoxifen-resistance is a major cause of death in patients with recurrent breast cancer. Current clinical factors can correctly predict therapy response in only half of the treated patients. Identification of proteins that associate with tamoxifen-resistance is a first step towards better response prediction and tailored treatment of patients. In the present study we intended to identify putative protein biomarkers indicative of tamoxifen therapy-resistance in breast cancer, using nanoLC coupled with FTICR MS. Comparative proteome analysis was performed on ~5,500 pooled tumor cells (corresponding to ~550 ng protein lysate/analysis) obtained through laser capture microdissection (LCM) from two independently processed data setsmore » (n=24 and n=27) containing both tamoxifen therapy-sensitive and therapy-resistant tumors. Peptides and proteins were identified by matching mass and elution time of newly acquired LC-MS features to information in previously generated accurate mass and time tag (AMT) reference databases.« less

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

PubMed

Raieta, Katia; Muccillo, Livio; Colantuoni, Vittorio

2015-04-01

Extra virgin olive oil production has a worldwide economic impact. The use of this brand, however, is of great concern to Institutions and private industries because of the increasing number of fraud and adulteration attempts to the market products. Here, we present a novel, reliable and not expensive method for extracting the DNA from commercial virgin and extra virgin olive oils. The DNA is stable overtime and amenable for molecular analyses; in fact, by carrying out simple sequence repeats (SSRs) markers analysis, we characterise the genetic profile of monovarietal olive oils. By comparing the oil-derived pattern with that of the corresponding tree, we can unambiguously identify four cultivars from Samnium, a region of Southern Italy, and distinguish them from reference and more widely used varieties. Through a parentage statistical analysis, we also identify the putative pollinators, establishing an unprecedented and powerful tool for olive oil traceability. Copyright © 2014 Elsevier Ltd. All rights reserved.

Experimental analysis of precursors to severe problem behavior.

PubMed

Fritz, Jennifer N; Iwata, Brian A; Hammond, Jennifer L; Bloom, Sarah E

2013-01-01

Some individuals engage in both mild and severe forms of problem behavior. Research has shown that when mild behaviors precede severe behaviors (i.e., the mild behaviors serve as precursors), they can (a) be maintained by the same source of reinforcement as severe behavior and (b) reduce rates of severe behavior observed during assessment. In Study 1, we developed an objective checklist to identify precursors via videotaped trials for 16 subjects who engaged in problem behavior and identified at least 1 precursor for every subject. In Study 2, we conducted separate functional analyses of precursor and severe problem behaviors for 8 subjects, and obtained correspondence between outcomes in 7 cases. In Study 3, we evaluated noncontingent reinforcement schedule thinning plus differential reinforcement of alternative behavior to reduce precursors, increase appropriate behavior, and maintain low rates of severe behavior during 3 treatment analyses for 2 subjects. Results showed that this treatment strategy was effective for behaviors maintained by positive and negative reinforcement. © Society for the Experimental Analysis of Behavior.

Acquisition of Malay word recognition skills: lessons from low-progress early readers.

PubMed

Lee, Lay Wah; Wheldall, Kevin

2011-02-01

Malay is a consistent alphabetic orthography with complex syllable structures. The focus of this research was to investigate word recognition performance in order to inform reading interventions for low-progress early readers. Forty-six Grade 1 students were sampled and 11 were identified as low-progress readers. The results indicated that both syllable awareness and phoneme blending were significant predictors of word recognition, suggesting that both syllable and phonemic grain-sizes are important in Malay word recognition. Item analysis revealed a hierarchical pattern of difficulty based on the syllable and the phonic structure of the words. Error analysis identified the sources of errors to be errors due to inefficient syllable segmentation, oversimplification of syllables, insufficient grapheme-phoneme knowledge and inefficient phonemic code assembly. Evidence also suggests that direct instruction in syllable segmentation, phonemic awareness and grapheme-phoneme correspondence is necessary for low-progress readers to acquire word recognition skills. Finally, a logical sequence to teach grapheme-phoneme decoding in Malay is suggested. Copyright © 2010 John Wiley & Sons, Ltd.

Introduction and Highlights of the Workshop

NASA Technical Reports Server (NTRS)

Noor, Ahmed K.; Venneri, Samuel L.

1997-01-01

Four generations of CAD/CAM systems can be identified, corresponding to changes in both modeling functionality and software architecture. The systems evolved from 2D and wireframes to solid modeling, to parametric/variational modelers to the current simulation-embedded systems. Recent developments have enabled design engineers to perform many of the complex analysis tasks, typically performed by analysis experts. Some of the characteristics of the current and emerging CAD/CAM/CAE systems are described in subsequent presentations. The focus of the workshop is on the potential of CAD/CAM/CAE systems for use in simulating the entire mission and life-cycle of future aerospace systems, and the needed development to realize this potential. First, the major features of the emerging computing, communication and networking environment are outlined; second, the characteristics and design drivers of future aerospace systems are identified; third, the concept of intelligent synthesis environment being planned by NASA, the UVA ACT Center and JPL is presented; and fourth, the objectives and format of the workshop are outlined.

Combating omission errors through task analysis and good reminders.

PubMed

Reason, J

2002-03-01

Leaving out necessary task steps is the single most common human error type. Certain task steps possess characteristics that are more likely to provoke omissions than others, and can be identified in advance. The paper reports two studies. The first, involving a simple photocopier, established that failing to remove the last page of the original is the commonest omission. This step possesses four distinct error-provoking features that combine their effects in an additive fashion. The second study examined the degree to which everyday memory aids satisfy five features of a good reminder: conspicuity, contiguity, content, context, and countability. A close correspondence was found between the percentage use of strategies and the degree to which they satisfied these five criteria. A three stage omission management programme was outlined: task analysis (identifying discrete task steps) of some safety critical activity; assessing the omission likelihood of each step; and the choice and application of a suitable reminder. Such a programme is applicable to a variety of healthcare procedures.

Voltage-induced switching of an antiferromagnetically ordered topological Dirac semimetal

NASA Astrophysics Data System (ADS)

Kim, Youngseok; Kang, Kisung; Schleife, André; Gilbert, Matthew J.

2018-04-01

An antiferromagnetic semimetal has been recently identified as a new member of topological semimetals that may host three-dimensional symmetry-protected Dirac fermions. A reorientation of the Néel vector may break the underlying symmetry and open a gap in the quasiparticle spectrum, inducing the (semi)metal-insulator transition. Here, we predict that such a transition may be controlled by manipulating the chemical potential location of the material. We perform both analytical and numerical analysis on the thermodynamic potential of the model Hamiltonian and find that the gapped spectrum is preferred when the chemical potential is located at the Dirac point. As the chemical potential deviates from the Dirac point, the system shows a possible transition from the gapped to the gapless phase and switches the corresponding Néel vector configuration. We perform density functional theory calculations to verify our analysis using a realistic material and discuss a two terminal transport measurement as a possible route to identify the voltage-induced switching of the Néel vector.

Ripening of salami: assessment of colour and aspect evolution using image analysis and multivariate image analysis.

PubMed

Fongaro, Lorenzo; Alamprese, Cristina; Casiraghi, Ernestina

2015-03-01

During ripening of salami, colour changes occur due to oxidation phenomena involving myoglobin. Moreover, shrinkage due to dehydration results in aspect modifications, mainly ascribable to fat aggregation. The aim of this work was the application of image analysis (IA) and multivariate image analysis (MIA) techniques to the study of colour and aspect changes occurring in salami during ripening. IA results showed that red, green, blue, and intensity parameters decreased due to the development of a global darker colour, while Heterogeneity increased due to fat aggregation. By applying MIA, different salami slice areas corresponding to fat and three different degrees of oxidised meat were identified and quantified. It was thus possible to study the trend of these different areas as a function of ripening, making objective an evaluation usually performed by subjective visual inspection. Copyright © 2014 Elsevier Ltd. All rights reserved.

Adult attachment interview, thematic analysis, and communicative style in families with substance use disorder.

PubMed

Anolli, Luigi; Balconi, Michela

2002-02-01

The paper examined the Adult Attachment Interview with special reference to thematic and semantic analysis in line with the discourse study (van Dijk, 1997). The hypothesis was that correspondence between the communicative organization of speech and the mental representations of the attachment experiences would be substantial. Eight Adult Attachment Interview transcripts of fathers with a heroin addicted young son were analyzed at two levels, (a) thematic analysis to individuate the topics of their talk applying the structural and semantic study of discourse and (b) enunciative analysis of speech to define their linguistic patterns utilizing a set of linguistic micro- and macro-units. Results showed nine main topics in the Adult Attachment Interview, each of which was characterized by a distinctive linguistic profile. In this perspective this device seems to be effective not only for discriminating attachment styles between subjects but also to identify differences within subjects belonging to the same attachment pattern.

Automatic Identification of Character Types from Film Dialogs

PubMed Central

Skowron, Marcin; Trapp, Martin; Payr, Sabine; Trappl, Robert

2016-01-01

ABSTRACT We study the detection of character types from fictional dialog texts such as screenplays. As approaches based on the analysis of utterances’ linguistic properties are not sufficient to identify all fictional character types, we develop an integrative approach that complements linguistic analysis with interactive and communication characteristics, and show that it can improve the identification performance. The interactive characteristics of fictional characters are captured by the descriptive analysis of semantic graphs weighted by linguistic markers of expressivity and social role. For this approach, we introduce a new data set of action movie character types with their corresponding sequences of dialogs. The evaluation results demonstrate that the integrated approach outperforms baseline approaches on the presented data set. Comparative in-depth analysis of a single screenplay leads on to the discussion of possible limitations of this approach and to directions for future research. PMID:29118463

A new technique for ordering asymmetrical three-dimensional data sets in ecology.

PubMed

Pavoine, Sandrine; Blondel, Jacques; Baguette, Michel; Chessel, Daniel

2007-02-01

The aim of this paper is to tackle the problem that arises from asymmetrical data cubes formed by two crossed factors fixed by the experimenter (factor A and factor B, e.g., sites and dates) and a factor which is not controlled for (the species). The entries of this cube are densities in species. We approach this kind of data by the comparison of patterns, that is to say by analyzing first the effect of factor B on the species-factor A pattern, and second the effect of factor A on the species-factor B pattern. The analysis of patterns instead of individual responses requires a correspondence analysis. We use a method we call Foucart's correspondence analysis to coordinate the correspondence analyses of several independent matrices of species x factor A (respectively B) type, corresponding to each modality of factor B (respectively A). Such coordination makes it possible to evaluate the effect of factor B (respectively A) on the species-factor A (respectively B) pattern. The results obtained by such a procedure are much more insightful than those resulting from a classical single correspondence analysis applied to the global matrix that is obtained by simply unrolling the data cube, juxtaposing for example the individual species x factor A matrices through modalities of factor B. This is because a single global correspondence analysis combines three effects of factors in a way that cannot be determined from factorial maps (factor A, factor B, and factor A x factor B interaction) whereas the applications of Foucart's correspondence analysis clearly discriminate two different issues. Using two data sets, we illustrate that this technique proves to be particularly powerful in the analyses of ecological convergence which include several distinct data sets and in the analyses of spatiotemporal variations of species distributions.

Comparing the Maryland Comprehensive Cancer Control Plan With Federal Cancer Prevention and Control Recommendations.

PubMed

Fowler, Stephanie L; Platz, Elizabeth A; Diener-West, Marie; Hokenmaier, Sarah; Truss, Meredith; Lewis, Courtney; Kanarek, Norma F

2015-10-01

Since the introduction of the Affordable Care Act (ACA) in 2012, 11 million more Americans now have access to preventive services via health care coverage. Several prevention-related recommendations issued by the US Preventive Services Task Force (USPSTF), Centers for Disease Control and Prevention (CDC), and Advisory Committee on Immunization Practices (ACIP) are covered under the ACA. State cancer plans often provide prevention strategies, but whether these strategies correspond to federal evidence-based recommendations is unclear. The objective of this article is to assess whether federal evidence-based recommendations, including those covered under the ACA, are included in the Maryland Comprehensive Cancer Control Plan (MCCCP). A total of 19 federal recommendations pertaining to cancer prevention and control were identified. Inclusion of federal cancer-related recommendations by USPSTF, CDC, and ACIP in the MCCCP's goals, objectives, and strategies was examined. Nine of the federal recommendations were issued after the MCCCP's publication. MCCCP recommendations corresponded completely with 4 federal recommendations and corresponded only partially with 3. Reasons for partial correspondence included specification of less restrictive at-risk populations or different intervention implementers. Three federal recommendations were not mentioned in the MCCCP's goals, objectives, and strategies. Many cancer-related federal recommendations were released after the MCCCP's publication and therefore do not appear in the most current version. We recommend that the results of this analysis be considered in the update of the MCCCP. Our findings underscore the need for a periodic scan for changes to federal recommendations and for adjusting state policies and programs to correspond with federal recommendations, as appropriate for Marylanders.

[Process management in the hospital pharmacy for the improvement of the patient safety].

PubMed

Govindarajan, R; Perelló-Juncá, A; Parès-Marimòn, R M; Serrais-Benavente, J; Ferrandez-Martí, D; Sala-Robinat, R; Camacho-Calvente, A; Campabanal-Prats, C; Solà-Anderiu, I; Sanchez-Caparrós, S; Gonzalez-Estrada, J; Martinez-Olalla, P; Colomer-Palomo, J; Perez-Mañosas, R; Rodríguez-Gallego, D

2013-01-01

To define a process management model for a hospital pharmacy in order to measure, analyse and make continuous improvements in patient safety and healthcare quality. In order to implement process management, Igualada Hospital was divided into different processes, one of which was the Hospital Pharmacy. A multidisciplinary management team was given responsibility for each process. For each sub-process one person was identified to be responsible, and a working group was formed under his/her leadership. With the help of each working group, a risk analysis using failure modes and effects analysis (FMEA) was performed, and the corresponding improvement actions were implemented. Sub-process indicators were also identified, and different process management mechanisms were introduced. The first risk analysis with FMEA produced more than thirty preventive actions to improve patient safety. Later, the weekly analysis of errors, as well as the monthly analysis of key process indicators, permitted us to monitor process results and, as each sub-process manager participated in these meetings, also to assume accountability and responsibility, thus consolidating the culture of excellence. The introduction of different process management mechanisms, with the participation of people responsible for each sub-process, introduces a participative management tool for the continuous improvement of patient safety and healthcare quality. Copyright © 2012 SECA. Published by Elsevier Espana. All rights reserved.

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

Caliandro, Rocco; Sibillano, Teresa; Belviso, B. Danilo

In this study, we have developed a general X-ray powder diffraction (XPD) methodology for the simultaneous structural and compositional characterization of inorganic nanomaterials. The approach is validated on colloidal tungsten oxide nanocrystals (WO 3-x NCs), as a model polymorphic nanoscale material system. Rod-shaped WO 3-x NCs with different crystal structure and stoichiometry are comparatively investigated under an inert atmosphere and after prolonged air exposure. An initial structural model for the as-synthesized NCs is preliminarily identified by means of Rietveld analysis against several reference crystal phases, followed by atomic pair distribution function (PDF) refinement of the best-matching candidates (static analysis). Subtlemore » stoichiometry deviations from the corresponding bulk standards are revealed. NCs exposed to air at room temperature are monitored by XPD measurements at scheduled time intervals. The static PDF analysis is complemented with an investigation into the evolution of the WO 3-x NC structure, performed by applying the modulation enhanced diffraction technique to the whole time series of XPD profiles (dynamical analysis). Prolonged contact with ambient air is found to cause an appreciable increase in the static disorder of the O atoms in the WO 3-x NC lattice, rather than a variation in stoichiometry. Finally, the time behavior of such structural change is identified on the basis of multivariate analysis.« less

Importation of exotic ticks and tick-borne spotted fever group rickettsiae into the United States by migrating songbirds.

PubMed

Mukherjee, Nabanita; Beati, Lorenza; Sellers, Michael; Burton, Laquita; Adamson, Steven; Robbins, Richard G; Moore, Frank; Karim, Shahid

2014-03-01

Birds are capable of carrying ticks and, consequently, tick-transmitted microorganisms over long distances and across geographical barriers such as oceans and deserts. Ticks are hosts for several species of spotted fever group rickettsiae (SFGR), which can be transmitted to vertebrates during blood meals. In this study, the prevalence of this group of rickettsiae was examined in ticks infesting migratory songbirds by using polymerase chain reaction (PCR). During the 2009 and 2010 spring migration season, 2064 northward-migrating passerine songbirds were examined for ticks at Johnson Bayou, Louisiana. A total of 91 ticks was removed from 35 individual songbirds for tick species identification and spotted fever group rickettsia detection. Ticks were identified as Haemaphysalis juxtakochi (n=38, 42%), Amblyomma longirostre (n=22, 24%), Amblyomma nodosum (n=17, 19%), Amblyomma calcaratum (n=11, 12%), Amblyomma maculatum (n=2, 2%), and Haemaphysalis leporispalustris (n=1, 1%) by comparing their 12S rDNA gene sequence to homologous sequences in GenBank. Most of the identified ticks were exotic species originating outside of the United States. The phylogenetic analysis of the 71 ompA gene sequences of the rickettsial strains detected in the ticks revealed the occurrence of 6 distinct rickettsial genotypes. Two genotypes (corresponding to a total of 28 samples) were included in the Candidatus Rickettsia amblyommii clade (less than 1% divergence), 2 of them (corresponding to a total of 14 samples) clustered with Rickettsia sp. "Argentina" with less than 0.2% sequence divergence, and 2 of them (corresponding to a total of 27 samples), although closely related to the R. parkeri-R. africae lineage (2.50-3.41% divergence), exhibited sufficient genetic divergence from its members to possibly constitute a new rickettsial genotype. Overall, there does not seem to be a specific relationship between exotic tick species, the rickettsiae they harbor, or the reservoir competence of the corresponding bird species. Copyright © 2013 Elsevier GmbH. All rights reserved.

Domain architecture of the p62 subunit from the human transcription/repair factor TFIIH deduced by limited proteolysis and mass spectrometry analysis.

PubMed

Jawhari, Anass; Boussert, Stéphanie; Lamour, Valérie; Atkinson, R Andrew; Kieffer, Bruno; Poch, Olivier; Potier, Noelle; van Dorsselaer, Alain; Moras, Dino; Poterszman, Arnaud

2004-11-16

TFIIH is a multiprotein complex that plays a central role in both transcription and DNA repair. The subunit p62 is a structural component of the TFIIH core that is known to interact with VP16, p53, Eralpha, and E2F1 in the context of activated transcription, as well as with the endonuclease XPG in DNA repair. We used limited proteolysis experiments coupled to mass spectrometry to define structural domains within the conserved N-terminal part of the molecule. The first domain identified resulted from spontaneous proteolysis and corresponds to residues 1-108. The second domain encompasses residues 186-240, and biophysical characterization by fluorescence studies and NMR analysis indicated that it is at least partially folded and thus may correspond to a structural entity. This module contains a region of high sequence conservation with an invariant FWxxPhiPhi motif (Phi representing either tyrosine or phenylalanine), which was also found in other protein families and could play a key role as a protein-protein recognition module within TFIIH. The approach used in this study is general and can be straightforwardly applied to other multidomain proteins and/or multiprotein assemblies.

Fermionic spin liquid analysis of the paramagnetic state in volborthite

NASA Astrophysics Data System (ADS)

Chern, Li Ern; Schaffer, Robert; Sorn, Sopheak; Kim, Yong Baek

2017-10-01

Recently, thermal Hall effect has been observed in the paramagnetic state of volborthite, which consists of distorted kagome layers with S =1 /2 local moments. Despite the appearance of magnetic order below 1 K , the response to external magnetic field and unusual properties of the paramagnetic state above 1 K suggest possible realization of exotic quantum phases. Motivated by these discoveries, we investigate possible spin liquid phases with fermionic spinon excitations in a nonsymmorphic version of the kagome lattice, which belongs to the two-dimensional crystallographic group p 2 g g . This nonsymmorphic structure is consistent with the spin model obtained in the density functional theory calculation. Using projective symmetry group analysis and fermionic parton mean field theory, we identify twelve distinct Z2 spin liquid states, four of which are found to have correspondence in the eight Schwinger boson spin liquid states we classified earlier. We focus on the four fermionic states with bosonic counterpart and find that the spectrum of their corresponding root U (1 ) states features spinon Fermi surface. The existence of spinon Fermi surface in candidate spin liquid states may offer a possible explanation of the finite thermal Hall conductivity observed in volborthite.

Autumn ichthyoplankton assemblage in the Yangtze Estuary shaped by environmental factors.

PubMed

Zhang, Hui; Xian, Weiwei; Liu, Shude

2016-01-01

This study investigated the response of the ichthyoplankton community to environmental changes in the Yangtze Estuary using canonical correspondence analysis. Ichthyoplankton community and environmental data were recorded during the autumns of 1998, 2000, 2002, 2003, 2004, 2007 and 2009. Among the ichthyoplankton, the dominant larval and juvenile families were the Engraulidae, Gobiidae and Salangidae, and the most common eggs were from Trichiurus lepturus. The ichthyoplankton was identified via canonical correspondence analysis to three assemblages: an estuary assemblage dominated by Chaeturichthys stigmatias, a coastal assemblage dominated by Engraulis japonicus and Stolephorus commersonii, and an offshore assemblage dominated by Trichiurus lepturus. Regarding environmental factors in the Yangtze Estuary, suspended matter and surface seawater salinity were the main factors influencing the distributions of the different assemblages, while sediment from the Yangtze River during the rainy season and chlorophyll a were the principle drivers of the annual variances in the distribution of ichthyoplankton assemblages. Our aims in this study were to provide detailed characterizations of the ichthyoplankton assemblage in the autumns of seven years, examine the long-term dynamics of autumn ichthyoplankton assemblages, and evaluate the influence of environmental factors on the spatial distribution and inter-annual variations of ichthyoplankton assemblages associated with the Yangtze Estuary.

Autumn ichthyoplankton assemblage in the Yangtze Estuary shaped by environmental factors

PubMed Central

Liu, Shude

2016-01-01

This study investigated the response of the ichthyoplankton community to environmental changes in the Yangtze Estuary using canonical correspondence analysis. Ichthyoplankton community and environmental data were recorded during the autumns of 1998, 2000, 2002, 2003, 2004, 2007 and 2009. Among the ichthyoplankton, the dominant larval and juvenile families were the Engraulidae, Gobiidae and Salangidae, and the most common eggs were from Trichiurus lepturus. The ichthyoplankton was identified via canonical correspondence analysis to three assemblages: an estuary assemblage dominated by Chaeturichthys stigmatias, a coastal assemblage dominated by Engraulis japonicus and Stolephorus commersonii, and an offshore assemblage dominated by Trichiurus lepturus. Regarding environmental factors in the Yangtze Estuary, suspended matter and surface seawater salinity were the main factors influencing the distributions of the different assemblages, while sediment from the Yangtze River during the rainy season and chlorophyll a were the principle drivers of the annual variances in the distribution of ichthyoplankton assemblages. Our aims in this study were to provide detailed characterizations of the ichthyoplankton assemblage in the autumns of seven years, examine the long-term dynamics of autumn ichthyoplankton assemblages, and evaluate the influence of environmental factors on the spatial distribution and inter-annual variations of ichthyoplankton assemblages associated with the Yangtze Estuary. PMID:27114877

Epigenetic transgenerational inheritance of somatic transcriptomes and epigenetic control regions

PubMed Central

2012-01-01

Background Environmentally induced epigenetic transgenerational inheritance of adult onset disease involves a variety of phenotypic changes, suggesting a general alteration in genome activity. Results Investigation of different tissue transcriptomes in male and female F3 generation vinclozolin versus control lineage rats demonstrated all tissues examined had transgenerational transcriptomes. The microarrays from 11 different tissues were compared with a gene bionetwork analysis. Although each tissue transgenerational transcriptome was unique, common cellular pathways and processes were identified between the tissues. A cluster analysis identified gene modules with coordinated gene expression and each had unique gene networks regulating tissue-specific gene expression and function. A large number of statistically significant over-represented clusters of genes were identified in the genome for both males and females. These gene clusters ranged from 2-5 megabases in size, and a number of them corresponded to the epimutations previously identified in sperm that transmit the epigenetic transgenerational inheritance of disease phenotypes. Conclusions Combined observations demonstrate that all tissues derived from the epigenetically altered germ line develop transgenerational transcriptomes unique to the tissue, but common epigenetic control regions in the genome may coordinately regulate these tissue-specific transcriptomes. This systems biology approach provides insight into the molecular mechanisms involved in the epigenetic transgenerational inheritance of a variety of adult onset disease phenotypes. PMID:23034163

Molecular identification and cluster analysis of homofermentative thermophilic lactobacilli isolated from dairy products.

PubMed

Andrighetto, C; De Dea, P; Lombardi, A; Neviani, E; Rossetti, L; Giraffa, G

1998-10-01

Twenty-five strains of thermophilic lactobacilli isolated from yoghurt and from semi-hard and hard cheeses (in parallel with nine type or reference strains) were identified and grouped according to their genetic relatedness. Strains were identified by sugar fermentation patterns using the "API 50 CHL" galleries, by species-specific DNA probes in dot-blot hybridization experiments, by amplification and restriction analysis of the 16S rRNA gene (ARDRA) and by polymerase chain reaction (PCR) using species-specific oligonucleotide primers. Strains were classified as Lactobacillus delbrueckii subsp. lactis and subsp. bulgaricus, L. helveticus, and L. acidophilus. Strains which were atypical by sugar fermentation patterns were also identified. Most of the strains could not be grouped using carbohydrate fermentation profiles. PCR fingerprinting was used to identify DNA profiles for the 25 lactobacilli. Experimentally obtained PCR profiles enabled discrimination of all strains, which were grouped according to the similarities in their combined patterns. In general, the clustering of the strains corresponded well with species delineation obtained by molecular identification. The dendrogram of genetic relatedness enabled the unambiguous identification of most of the strains which were shown to be atypical by the sugar fermentation profile, except for a discrepancy in one L. delbrueckii subsp. lactis strain and one atypical Lactobacillus sp. strain.

Clustering analysis of water distribution systems: identifying critical components and community impacts.

PubMed

Diao, K; Farmani, R; Fu, G; Astaraie-Imani, M; Ward, S; Butler, D

2014-01-01

Large water distribution systems (WDSs) are networks with both topological and behavioural complexity. Thereby, it is usually difficult to identify the key features of the properties of the system, and subsequently all the critical components within the system for a given purpose of design or control. One way is, however, to more explicitly visualize the network structure and interactions between components by dividing a WDS into a number of clusters (subsystems). Accordingly, this paper introduces a clustering strategy that decomposes WDSs into clusters with stronger internal connections than external connections. The detected cluster layout is very similar to the community structure of the served urban area. As WDSs may expand along with urban development in a community-by-community manner, the correspondingly formed distribution clusters may reveal some crucial configurations of WDSs. For verification, the method is applied to identify all the critical links during firefighting for the vulnerability analysis of a real-world WDS. Moreover, both the most critical pipes and clusters are addressed, given the consequences of pipe failure. Compared with the enumeration method, the method used in this study identifies the same group of the most critical components, and provides similar criticality prioritizations of them in a more computationally efficient time.

Subpathway-GM: identification of metabolic subpathways via joint power of interesting genes and metabolites and their topologies within pathways

PubMed Central

Li, Chunquan; Han, Junwei; Yao, Qianlan; Zou, Chendan; Xu, Yanjun; Zhang, Chunlong; Shang, Desi; Zhou, Lingyun; Zou, Chaoxia; Sun, Zeguo; Li, Jing; Zhang, Yunpeng; Yang, Haixiu; Gao, Xu; Li, Xia

2013-01-01

Various ‘omics’ technologies, including microarrays and gas chromatography mass spectrometry, can be used to identify hundreds of interesting genes, proteins and metabolites, such as differential genes, proteins and metabolites associated with diseases. Identifying metabolic pathways has become an invaluable aid to understanding the genes and metabolites associated with studying conditions. However, the classical methods used to identify pathways fail to accurately consider joint power of interesting gene/metabolite and the key regions impacted by them within metabolic pathways. In this study, we propose a powerful analytical method referred to as Subpathway-GM for the identification of metabolic subpathways. This provides a more accurate level of pathway analysis by integrating information from genes and metabolites, and their positions and cascade regions within the given pathway. We analyzed two colorectal cancer and one metastatic prostate cancer data sets and demonstrated that Subpathway-GM was able to identify disease-relevant subpathways whose corresponding entire pathways might be ignored using classical entire pathway identification methods. Further analysis indicated that the power of a joint genes/metabolites and subpathway strategy based on their topologies may play a key role in reliably recalling disease-relevant subpathways and finding novel subpathways. PMID:23482392

Investigation of Tectonic Boundaries in Taiwan Obtained with a Hierarchical Clustering of Dense GNSS Data

NASA Astrophysics Data System (ADS)

Takahashi, A.; Hashimoto, M.; Hu, J. C.; Fukahata, Y.

2017-12-01

Taiwan Island is composed of many geological structures. The main tectonic feature is the collision of the Luzon volcanic arc with the Eurasian continent, which propagates westward and generates complicated crustal deformation. One way to model crustal deformation is to divide Taiwan island into man rigid blocks that moves relatively each other along the boundaries (deformation zones) of the blocks. Since earthquakes tend to occur in the deformation zones, identification of such tectonic boundaries is important. So far, many tectonic boundaries have been proposed on the basis of geology, geomorphology, seismology and geodesy. However, which is the most significant boundary depends on disciplines and there is no way to objectively classify them. Here, we introduce an objective method to identify significant tectonic boundaries with a hierarchical representation proposed by Simpson et al. [2012].We apply a hierarchical agglomerative clustering algorithm to dense GNSS horizontal velocity data in Taiwan. One of the significant merits of the hierarchical representation of the clustering results is that we can consistently explore crustal structures from larger to smaller scales. This is because a higher hierarchy corresponds to a larger crustal structure, and a lower hierarchy corresponds to a smaller crustal structure. Relative motion between clusters can be obtained from this analysis.The first major boundary is identified along the eastern margin of the Longitudinal Valley, which corresponds to the separation of the Philippine Sea plate and the Eurasian continental margin. The second major boundary appears along the Chaochou fault and the Chishan fault in southwestern Taiwan. The third major boundary appears along the eastern margin of the coastal plane. The identified major clusters can be divided into several smaller blocks without losing consistency with geological boundaries. For example, the Fengshun fault, concealed beneath thick sediment layers, is identified. Furthermore, obtained relative motion between clusters demands a reverse fault or a left lateral fault in the off shore of the coastal range.Our clustering based block modeling is consistent with tectonics of Taiwan, implying that observed crustal deformation in Taiwan can be attributed to motion or deformation of shallow structures.

Integrated analysis of DNA methylation, immunohistochemistry and mRNA expression, data identifies a Methylation Expression Index (MEI) robustly associated with survival of ER-positive breast cancer patients

PubMed Central

Garcia-Closas, Montserrat; Davis, Sean; Meltzer, Paul; Lissowska, Jolanta; Horne, Hisani N.; Sherman, Mark E.; Lee, Maxwell

2015-01-01

Identification of prognostic gene expression signatures may enable improved decisions about management of breast cancer. To identify a prognostic signature for breast cancer, we performed DNA methylation profiling and identified methylation markers that were associated with expression of ER, PR, HER2, CK5/6 and EGFR proteins. Methylation markers that were correlated with corresponding mRNA expression levels were identified using 208 invasive tumors from a population-based case-control study conducted in Poland. Using this approach, we defined the Methylation Expression Index (MEI) signature that was based on a weighted sum of mRNA levels of 57 genes. Classification of cases as low or high MEI scores were related to survival using Cox regression models. In the Polish study, women with ER-positive low MEI cancers had reduced survival at a median of 5.20 years of follow-up, HR=2.85 95%CI=1.25-6.47. Low MEI was also related to decreased survival in four independent datasets totaling over 2500 ER-positive breast cancers. These results suggest that integrated analysis of tumor expression markers, DNA methylation, and mRNA data can be an important approach for identifying breast cancer prognostic signatures. Prospective assessment of MEI along with other prognostic signatures should be evaluated in future studies. PMID:25773928

How to select equivalent and complimentary reversed phase liquid chromatography columns from column characterization databases.

PubMed

Borges, Endler M

2014-01-07

Three RP-LC column characterization protocols [Tanaka et al. (1989), Snyder et al. (PQRI, 2002), and NIST SRM 870 (2000)] were evaluated using both Euclidian distance and Principal Components Analysis to evaluate effectiveness at identifying equivalent columns. These databases utilize specific chromatographic properties such as hydrophobicity, hydrogen bonding, shape/steric selectivity, and ion exchange capacity of stationary phases. The chromatographic parameters of each test were shown to be uncorrelated. Despite this, the three protocols were equally successful in identifying similar and/or dissimilar stationary phases. The veracity of the results has been supported by some real life pharmaceutical separations. The use of Principal Component Analysis to identify similar/dissimilar phases appears to have some limitations in terms of loss of information. In contrast, the use of Euclidian distances is a much more convenient and reliable approach. The use of auto scaled data is favoured over the use of weighted factors as the former data transformation is less affected by the addition or removal of columns from the database. The use of these free databases and their corresponding software tools shown to be valid for identifying similar columns with equivalent chromatographic selectivity and retention as a "backup column". In addition, dissimilar columns with complimentary chromatographic selectivity can be identified for method development screening strategies. Copyright © 2013 Elsevier B.V. All rights reserved.

StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase

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

Zemla, A; Lang, D; Kostova, T

2010-11-29

Most of the currently used methods for protein function prediction rely on sequence-based comparisons between a query protein and those for which a functional annotation is provided. A serious limitation of sequence similarity-based approaches for identifying residue conservation among proteins is the low confidence in assigning residue-residue correspondences among proteins when the level of sequence identity between the compared proteins is poor. Multiple sequence alignment methods are more satisfactory - still, they cannot provide reliable results at low levels of sequence identity. Our goal in the current work was to develop an algorithm that could overcome these difficulties and facilitatemore » the identification of structurally (and possibly functionally) relevant residue-residue correspondences between compared protein structures. Here we present StralSV, a new algorithm for detecting closely related structure fragments and quantifying residue frequency from tight local structure alignments. We apply StralSV in a study of the RNA-dependent RNA polymerase of poliovirus and demonstrate that the algorithm can be used to determine regions of the protein that are relatively unique or that shared structural similarity with structures that are distantly related. By quantifying residue frequencies among many residue-residue pairs extracted from local alignments, one can infer potential structural or functional importance of specific residues that are determined to be highly conserved or that deviate from a consensus. We further demonstrate that considerable detailed structural and phylogenetic information can be derived from StralSV analyses. StralSV is a new structure-based algorithm for identifying and aligning structure fragments that have similarity to a reference protein. StralSV analysis can be used to quantify residue-residue correspondences and identify residues that may be of particular structural or functional importance, as well as unusual or unexpected residues at a given sequence position.« less

SU-F-303-11: Implementation and Applications of Rapid, SIFT-Based Cine MR Image Binning and Region Tracking

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

Mazur, T; Wang, Y; Fischer-Valuck, B

2015-06-15

Purpose: To develop a novel and rapid, SIFT-based algorithm for assessing feature motion on cine MR images acquired during MRI-guided radiotherapy treatments. In particular, we apply SIFT descriptors toward both partitioning cine images into respiratory states and tracking regions across frames. Methods: Among a training set of images acquired during a fraction, we densely assign SIFT descriptors to pixels within the images. We cluster these descriptors across all frames in order to produce a dictionary of trackable features. Associating the best-matching descriptors at every frame among the training images to these features, we construct motion traces for the features. Wemore » use these traces to define respiratory bins for sorting images in order to facilitate robust pixel-by-pixel tracking. Instead of applying conventional methods for identifying pixel correspondences across frames we utilize a recently-developed algorithm that derives correspondences via a matching objective for SIFT descriptors. Results: We apply these methods to a collection of lung, abdominal, and breast patients. We evaluate the procedure for respiratory binning using target sites exhibiting high-amplitude motion among 20 lung and abdominal patients. In particular, we investigate whether these methods yield minimal variation between images within a bin by perturbing the resulting image distributions among bins. Moreover, we compare the motion between averaged images across respiratory states to 4DCT data for these patients. We evaluate the algorithm for obtaining pixel correspondences between frames by tracking contours among a set of breast patients. As an initial case, we track easily-identifiable edges of lumpectomy cavities that show minimal motion over treatment. Conclusions: These SIFT-based methods reliably extract motion information from cine MR images acquired during patient treatments. While we performed our analysis retrospectively, the algorithm lends itself to prospective motion assessment. Applications of these methods include motion assessment, identifying treatment windows for gating, and determining optimal margins for treatment.« less

StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase.

PubMed

Zemla, Adam T; Lang, Dorothy M; Kostova, Tanya; Andino, Raul; Ecale Zhou, Carol L

2011-06-02

Most of the currently used methods for protein function prediction rely on sequence-based comparisons between a query protein and those for which a functional annotation is provided. A serious limitation of sequence similarity-based approaches for identifying residue conservation among proteins is the low confidence in assigning residue-residue correspondences among proteins when the level of sequence identity between the compared proteins is poor. Multiple sequence alignment methods are more satisfactory--still, they cannot provide reliable results at low levels of sequence identity. Our goal in the current work was to develop an algorithm that could help overcome these difficulties by facilitating the identification of structurally (and possibly functionally) relevant residue-residue correspondences between compared protein structures. Here we present StralSV (structure-alignment sequence variability), a new algorithm for detecting closely related structure fragments and quantifying residue frequency from tight local structure alignments. We apply StralSV in a study of the RNA-dependent RNA polymerase of poliovirus, and we demonstrate that the algorithm can be used to determine regions of the protein that are relatively unique, or that share structural similarity with proteins that would be considered distantly related. By quantifying residue frequencies among many residue-residue pairs extracted from local structural alignments, one can infer potential structural or functional importance of specific residues that are determined to be highly conserved or that deviate from a consensus. We further demonstrate that considerable detailed structural and phylogenetic information can be derived from StralSV analyses. StralSV is a new structure-based algorithm for identifying and aligning structure fragments that have similarity to a reference protein. StralSV analysis can be used to quantify residue-residue correspondences and identify residues that may be of particular structural or functional importance, as well as unusual or unexpected residues at a given sequence position. StralSV is provided as a web service at http://proteinmodel.org/AS2TS/STRALSV/.

A novel comparative pattern count analysis reveals a chronic ethanol-induced dynamic shift in immediate early NF-κB genome-wide promoter binding during liver regeneration.

PubMed

Kuttippurathu, Lakshmi; Patra, Biswanath; Hoek, Jan B; Vadigepalli, Rajanikanth

2016-03-01

Liver regeneration after partial hepatectomy is a clinically important process that is impaired by adaptation to chronic alcohol intake. We focused on the initial time points following partial hepatectomy (PHx) to analyze the genome-wide binding activity of NF-κB, a key immediate early regulator. We investigated the effect of chronic alcohol intake on immediate early NF-κB genome-wide localization, in the adapted state as well as in response to partial hepatectomy, using chromatin immunoprecipitation followed by promoter microarray analysis. We found many ethanol-specific NF-κB binding target promoters in the ethanol-adapted state, corresponding to the regulation of biosynthetic processes, oxidation-reduction and apoptosis. Partial hepatectomy induced a diet-independent shift in NF-κB binding loci relative to the transcription start sites. We employed a novel pattern count analysis to exhaustively enumerate and compare the number of promoters corresponding to the temporal binding patterns in ethanol and pair-fed control groups. The highest pattern count corresponded to promoters with NF-κB binding exclusively in the ethanol group at 1 h post PHx. This set was associated with the regulation of cell death, response to oxidative stress, histone modification, mitochondrial function, and metabolic processes. Integration with the global gene expression profiles to identify putative transcriptional consequences of NF-κB binding patterns revealed that several of ethanol-specific 1 h binding targets showed ethanol-specific differential expression through 6 h post PHx. Motif analysis yielded co-incident binding loci for STAT3, AP-1, CREB, C/EBP-β, PPAR-γ and C/EBP-α, likely participating in co-regulatory modules with NF-κB in shaping the immediate early response to PHx. We conclude that adaptation to chronic ethanol intake disrupts the NF-κB promoter binding landscape with consequences for the immediate early gene regulatory response to the acute challenge of PHx.

Identifying Repetitive Institutional Review Board Stipulations by Natural Language Processing and Network Analysis.

PubMed

Kury, Fabrício S P; Cimino, James J

2015-01-01

The corrections ("stipulations") to a proposed research study protocol produced by an institutional review board (IRB) can often be repetitive across many studies; however, there is no standard set of stipulations that could be used, for example, by researchers wishing to anticipate and correct problems in their research proposals prior to submitting to an IRB. The objective of the research was to computationally identify the most repetitive types of stipulations generated in the course of IRB deliberations. The text of each stipulation was normalized using the natural language processing techniques. An undirected weighted network was constructed in which each stipulation was represented by a node, and each link, if present, had weight corresponding to the TF-IDF Cosine Similarity of the stipulations. Network analysis software was then used to identify clusters in the network representing similar stipulations. The final results were correlated with additional data to produce further insights about the IRB workflow. From a corpus of 18,582 stipulations we identified 31 types of repetitive stipulations. Those types accounted for 3,870 stipulations (20.8% of the corpus) produced for 697 (88.7%) of all protocols in 392 (also 88.7%) of all the CNS IRB meetings with stipulations entered in our data source. A notable peroportion of the corrections produced by the IRB can be considered highly repetitive. Our shareable method relied on a minimal manual analysis and provides an intuitive exploration with theoretically unbounded granularity. Finer granularity allowed for the insight that is anticipated to prevent the need for identifying the IRB panel expertise or any human supervision.

Population fragmentation and inter-ecosystem movements of grizzly bears in Western Canada and the Northern United States

USGS Publications Warehouse

Proctor, M.F.; Paetkau, David; McLellan, B.N.; Stenhouse, G.B.; Kendall, K.C.; Mace, R.D.; Kasworm, W.F.; Servheen, C.; Lausen, C.L.; Gibeau, M.L.; Wakkinen, W.L.; Haroldson, M.A.; Mowat, G.; Apps, C.D.; Ciarniello, L.M.; Barclay, R.M.R.; Boyce, M.S.; Schwartz, C.C.; Strobeck, C.

2012-01-01

Population fragmentation compromises population viability, reduces a species ability to respond to climate change, and ultimately may reduce biodiversity. We studied the current state and potential causes of fragmentation in grizzly bears over approximately 1,000,000 km 2 of western Canada, the northern United States (US), and southeast Alaska. We compiled much of our data from projects undertaken with a variety of research objectives including population estimation and trend, landscape fragmentation, habitat selection, vital rates, and response to human development. Our primary analytical techniques stemmed from genetic analysis of 3,134 bears, supplemented with radiotelemetry data from 792 bears. We used 15 locus microsatellite data coupled withmeasures of genetic distance, isolation-by-distance (IBD) analysis, analysis of covariance (ANCOVA), linear multiple regression, multi-factorial correspondence analysis (to identify population divisions or fractures with no a priori assumption of group membership), and population-assignment methods to detect individual migrants between immediately adjacent areas. These data corroborated observations of inter-area movements from our telemetry database. In northern areas, we found a spatial genetic pattern of IBD, although there was evidence of natural fragmentation from the rugged heavily glaciated coast mountains of British Columbia (BC) and the Yukon. These results contrasted with the spatial pattern of fragmentation in more southern parts of their distribution. Near the Canada-US border area, we found extensive fragmentation that corresponded to settled mountain valleys andmajor highways. Genetic distances across developed valleys were elevated relative to those across undeveloped valleys in central and northern BC. In disturbed areas, most inter-area movements detected were made by male bears, with few female migrants identified. North-south movements within mountain ranges (Mts) and across BC Highway 3 were more common than east-west movements across settled mountain valleys separating Mts. Our results suggest that relatively distinct subpopulations exist in this region, including the Cabinet, Selkirk South, and the decadesisolated Yellowstone populations. Current movement rates do not appear sufficient to consider the subpopulations we identify along the Canada-US border as 1 inter-breeding unit. Although we detected enough male movement to mediate gene flow, the current low rate of female movement detected among areas is insufficient to provide a demographic rescue effect between areas in the immediate future (0-15 yr). In Alberta, we found fragmentation corresponded to major east-west highways (Highways 3, 11, 16, and 43) and most inter-area movements were made by males. Gene flow and movement rates between Alberta and BC were highest across the Continental Divide south of Highway 1 and north of Highway 16. In the central region between Highways 1 and 11, we found evidence of natural fragmentation associated with the extensive glaciers and icefields along the Continental Divide. The discontinuities that we identified would form appropriate boundaries formanagement units. We related sex-specific movement rates between adjacent areas to several metrics of human use (highway traffic, settlement, and humancaused mortality) to understand the causes of fragmentation. This analysis used data from 1,508 bears sampled over a 161,500-km 2 area in southeastern BC, western Alberta, northern Idaho, and northern Montana during 1979-2007. This area was bisected by numerous human transportation and settlement corridors of varying intensity and complexity. We used multiple linear regression and ANCOVA to document the responses of female and male bears to disturbance. Males and females both demonstrated reduced movement rates with increasing settlement and traffic. However, females reduced their movement rates dramatically when settlement increased to >20% of the fracture zone. At this same

Deriving phenological metrics from NDVI through an open source tool developed in QGIS

NASA Astrophysics Data System (ADS)

Duarte, Lia; Teodoro, A. C.; Gonçalves, Hernãni

2014-10-01

Vegetation indices have been commonly used over the past 30 years for studying vegetation characteristics using images collected by remote sensing satellites. One of the most commonly used is the Normalized Difference Vegetation Index (NDVI). The various stages that green vegetation undergoes during a complete growing season can be summarized through time-series analysis of NDVI data. The analysis of such time-series allow for extracting key phenological variables or metrics of a particular season. These characteristics may not necessarily correspond directly to conventional, ground-based phenological events, but do provide indications of ecosystem dynamics. A complete list of the phenological metrics that can be extracted from smoothed, time-series NDVI data is available in the USGS online resources (http://phenology.cr.usgs.gov/methods_deriving.php).This work aims to develop an open source application to automatically extract these phenological metrics from a set of satellite input data. The main advantage of QGIS for this specific application relies on the easiness and quickness in developing new plug-ins, using Python language, based on the experience of the research group in other related works. QGIS has its own application programming interface (API) with functionalities and programs to develop new features. The toolbar developed for this application was implemented using the plug-in NDVIToolbar.py. The user introduces the raster files as input and obtains a plot and a report with the metrics. The report includes the following eight metrics: SOST (Start Of Season - Time) corresponding to the day of the year identified as having a consistent upward trend in the NDVI time series; SOSN (Start Of Season - NDVI) corresponding to the NDVI value associated with SOST; EOST (End of Season - Time) which corresponds to the day of year identified at the end of a consistent downward trend in the NDVI time series; EOSN (End of Season - NDVI) corresponding to the NDVI value associated with EOST; MAXN (Maximum NDVI) which corresponds to the maximum NDVI value; MAXT (Time of Maximum) which is the day associated with MAXN; DUR (Duration) defined as the number of days between SOST and EOST; and AMP (Amplitude) which is the difference between MAXN and SOSN. This application provides all these metrics in a single step. Initially, the data points are interpolated using a moving average graphic with five and three points. The eight metrics previously described are then obtained from the spline using numpy functions. In the present work, the developed toolbar was applied to MODerate resolution Imaging Spectroradiometer (MODIS) data covering a particular region of Portugal, which can be generally applied to other satellite data and study area. The code is open and can be modified according to the user requirements. Other advantage in publishing the plug-ins and the application code is the possibility of other users to improve this application.

Toxicogenomic analysis of N-nitrosomorpholine induced changes in rat liver: Comparison of genomic and proteomic responses and anchoring to histopathological parameters

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

Oberemm, A., E-mail: axel.oberemm@bfr.bund.d; Ahr, H.-J.; Bannasch, P.

2009-12-01

A common animal model of chemical hepatocarcinogenesis was used to examine the utility of transcriptomic and proteomic data to identify early biomarkers related to chemically induced carcinogenesis. N-nitrosomorpholine, a frequently used genotoxic model carcinogen, was applied via drinking water at 120 mg/L to male Wistar rats for 7 weeks followed by an exposure-free period of 43 weeks. Seven specimens of each treatment group (untreated control and 120 mg/L N-nitrosomorpholine in drinking water) were sacrificed at nine time points during and after N-nitrosomorpholine treatment. Individual samples from the liver were prepared for histological and toxicogenomic analyses. For histological detection of preneoplasticmore » and neoplastic tissue areas, sections were stained using antibodies against the placental form of glutathione-S-transferase (GST-P). Gene and protein expression profiles of liver tissue homogenates were analyzed using RG-U34A Affymetrix rat gene chips and two-dimensional gel electrophoresis-based proteomics, respectively. In order to compare results obtained by histopathology, transcriptomics and proteomics, GST-P-stained liver sections were evaluated morphometrically, which revealed a parallel time course of the area fraction of preneoplastic lesions and gene plus protein expression patterns. On the transcriptional level, an increase of hepatic GST-P expression was detectable as early as 3 weeks after study onset. Comparing deregulated genes and proteins, eight species were identified which showed a corresponding expression profile on both expression levels. Functional analysis suggests that these genes and corresponding proteins may be useful as biomarkers of early hepatocarcinogenesis.« less

Dynamic decomposition of spatiotemporal neural signals

PubMed Central

2017-01-01

Neural signals are characterized by rich temporal and spatiotemporal dynamics that reflect the organization of cortical networks. Theoretical research has shown how neural networks can operate at different dynamic ranges that correspond to specific types of information processing. Here we present a data analysis framework that uses a linearized model of these dynamic states in order to decompose the measured neural signal into a series of components that capture both rhythmic and non-rhythmic neural activity. The method is based on stochastic differential equations and Gaussian process regression. Through computer simulations and analysis of magnetoencephalographic data, we demonstrate the efficacy of the method in identifying meaningful modulations of oscillatory signals corrupted by structured temporal and spatiotemporal noise. These results suggest that the method is particularly suitable for the analysis and interpretation of complex temporal and spatiotemporal neural signals. PMID:28558039

Qualitative and Quantitative Phytochemical Analysis of Different Extracts from Thymus algeriensis Aerial Parts.

PubMed

Boutaoui, Nassima; Zaiter, Lahcene; Benayache, Fadila; Benayache, Samir; Carradori, Simone; Cesa, Stefania; Giusti, Anna Maria; Campestre, Cristina; Menghini, Luigi; Innosa, Denise; Locatelli, Marcello

2018-02-20

This study was performed to evaluate the metabolite recovery from different extraction methods applied to Thymus algeriensis aerial parts. A high-performance liquid chromatographic method using photodiode array detector with gradient elution has been developed and validated for the simultaneous estimation of different phenolic compounds in the extracts and in their corresponding purified fractions. The experimental results show that microwave-assisted aqueous extraction for 15 min at 100 °C gave the most phenolics-enriched extract, reducing extraction time without degradation effects on bioactives. Sixteen compounds were identified in this extract, 11 phenolic compounds and five flavonoids, all known for their biological activities. Color analysis and determination of chlorophylls and carotenoids implemented the knowledge of the chemical profile of this plant.

Market inefficiency identified by both single and multiple currency trends

NASA Astrophysics Data System (ADS)

Tokár, T.; Horváth, D.

2012-11-01

Many studies have shown that there are good reasons to claim very low predictability of currency returns; nevertheless, the deviations from true randomness exist which have potential predictive and prognostic power [J. James, Simple trend-following strategies in currency trading, Quantitative finance 3 (2003) C75-C77]. We analyze the local trends which are of the main focus of the technical analysis. In this article we introduced various statistical quantities examining role of single temporal discretized trend or multitude of grouped trends corresponding to different time delays. Our specific analysis based predominantly on Euro-dollar currency pair data at the one minute frequency suggests the importance of cumulative nonrandom effect of trends on the potential forecasting performance.

A new Microbacterium species isolated from the blood of a patient with fever: Microbacterium pyrexiae sp. nov.

PubMed

Ko, Kwan Soo; Oh, Won Sup; Lee, Mi Young; Peck, Kyong Ran; Lee, Nam Yong; Song, Jae-Hoon

2007-04-01

A Gram-positive bacterium, SMC-A8265(T), which was isolated from the blood of a patient with fever but could not be identified by a conventional microbiologic method, was finally characterized by performing phenotypic and genotypic analyses. 16S rRNA gene sequence analysis revealed that the strain SMC-A8265(T) belonged to the genus Microbacterium, but it did not correspond to any of the previously described Microbacterium spp. Biochemical tests and cellular fatty acid composition analysis also confirmed that this bacterium is distinct from other Microbacterium spp. Based on the phenotypic and genotypic characteristics, we propose that the strain SMC-A8265(T) should be classified as a new species, namely, Microbacterium pyrexiae sp. nov.

M.S.L.A.P. Modular Spectral Line Analysis Program documentation

NASA Technical Reports Server (NTRS)

Joseph, Charles L.; Jenkins, Edward B.

1991-01-01

MSLAP is a software for analyzing spectra, providing the basic structure to identify spectral features, to make quantitative measurements of this features, and to store the measurements for convenient access. MSLAP can be used to measure not only the zeroth moment (equivalent width) of a profile, but also the first and second moments. Optical depths and the corresponding column densities across the profile can be measured as well for sufficiently high resolution data. The software was developed for an interactive, graphical analysis where the computer carries most of the computational and data organizational burden and the investigator is responsible only for all judgement decisions. It employs sophisticated statistical techniques for determining the best polynomial fit to the continuum and for calculating the uncertainties.

Reservoir sequence analysis: A new technology for the 90`s and its application to oil and gas fields

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

Wornardt, W.W.

1996-08-01

Reservoir Sequence Analysis when applied to existing fields can increase the production, life of the field and extend the field with a minimum of cost. In this technology we identify reservoir sands in a standard-of-reference well, to establish a seismic sequence stratigraphic well-tie for the entire field. Age date the Maximum Flooding Surfaces and Sequence Boundaries above and below reservoir sands on a well-log and seismic pro- file and/or workstation using High Resolution Biostratigraphic Analysis, species abundance and diversity histograms and their patterns, and paleoenvironmental paleobathymetric changes. Identify the systems tracts and their corresponding reservoir sands in between age datedmore » Maximum Flooding Surfaces. Interpret the reservoir sands as to type, i.e. IVF, point bar, coastal belt, forced regression, falling stage, bottom-set (shingled) turbidites, slope fan channel, channel overbank, and basin floor fans. Identify and correlate the same individual sands in different wells, and note new sands in a well and sands that shale-out in a well. Correlate the Maximum Flooding Surfaces above and below the reservoir section in additional wells to see which part of the reservoir section and sands have been penetrated. Identify systems tracts in additional wells and construct isopach, sand percent maps of individual systems tract interval in each well. Correlate sand packages, with a high degree of confidence, from upthrown to downthrown fault blocks, around salt domes, and updip with downdip.« less

Expression quantitative trait loci (eQTL) mapping in Puerto Rican children.

PubMed

Chen, Wei; Brehm, John M; Lin, Jerome; Wang, Ting; Forno, Erick; Acosta-Pérez, Edna; Boutaoui, Nadia; Canino, Glorisa; Celedón, Juan C

2015-01-01

Expression quantitative trait loci (eQTL) have been identified using tissue or cell samples from diverse human populations, thus enhancing our understanding of regulation of gene expression. However, few studies have attempted to identify eQTL in racially admixed populations such as Hispanics. We performed a systematic eQTL study to identify regulatory variants of gene expression in whole blood from 121 Puerto Rican children with (n = 63) and without (n = 58) asthma. Genome-wide genotyping was conducted using the Illumina Omni2.5M Bead Chip, and gene expression was assessed using the Illumina HT-12 microarray. After completing quality control, we performed a pair-wise genome analysis of ~15 K transcripts and ~1.3 M SNPs for both local and distal effects. This analysis was conducted under a regression framework adjusting for age, gender and principal components derived from both genotypic and mRNA data. We used a false discovery rate (FDR) approach to identify significant eQTL signals, which were next compared to top eQTL signals from existing eQTL databases. We then performed a pathway analysis for our top genes. We identified 36,720 local pairs in 3,391 unique genes and 1,851 distal pairs in 446 unique genes at FDR <0.05, corresponding to unadjusted P values lower than 1.5x10-4 and 4.5x10-9, respectively. A significant proportion of genes identified in our study overlapped with those identified in previous studies. We also found an enrichment of disease-related genes in our eQTL list. We present results from the first eQTL study in Puerto Rican children, who are members of a unique Hispanic cohort disproportionately affected with asthma, prematurity, obesity and other common diseases. Our study confirmed eQTL signals identified in other ethnic groups, while also detecting additional eQTLs unique to our study population. The identified eQTLs will help prioritize findings from future genome-wide association studies in Puerto Ricans.

SITEHOUND-web: a server for ligand binding site identification in protein structures.

PubMed

Hernandez, Marylens; Ghersi, Dario; Sanchez, Roberto

2009-07-01

SITEHOUND-web (http://sitehound.sanchezlab.org) is a binding-site identification server powered by the SITEHOUND program. Given a protein structure in PDB format SITEHOUND-web will identify regions of the protein characterized by favorable interactions with a probe molecule. These regions correspond to putative ligand binding sites. Depending on the probe used in the calculation, sites with preference for different ligands will be identified. Currently, a carbon probe for identification of binding sites for drug-like molecules, and a phosphate probe for phosphorylated ligands (ATP, phoshopeptides, etc.) have been implemented. SITEHOUND-web will display the results in HTML pages including an interactive 3D representation of the protein structure and the putative sites using the Jmol java applet. Various downloadable data files are also provided for offline data analysis.

Stratification and mobility in contemporary Egypt.

PubMed

Nagi, Saad Z; Nagi, Omar

2011-01-01

The objectives in this statement are to characterize and explain the patterns of change in stratification and mobility in Egypt, over the last half century, by placing them within conceptual, explanatory, and historical contexts. First, literature relevant to the primary concepts of "class" and "status", is reviewed. Second, four institutions whose influence is fundamental in shaping these patterns are identified to form an explanatory context: family, polity, economy, and education. And third, an historical account is presented to demonstrate the interplay of these institutions and their consequences for stratification and mobility. For this, four periods are identified that are marked by change in the dominance of institutions and their corresponding influence on stratification and mobility. In addition to data available in relevant literature, this analysis utilizes primary data generated through a national probability household survey.

An overview of the web-based Google Earth coincident imaging tool

USGS Publications Warehouse

Chander, Gyanesh; Kilough, B.; Gowda, S.

2010-01-01

The Committee on Earth Observing Satellites (CEOS) Visualization Environment (COVE) tool is a browser-based application that leverages Google Earth web to display satellite sensor coverage areas. The analysis tool can also be used to identify near simultaneous surface observation locations for two or more satellites. The National Aeronautics and Space Administration (NASA) CEOS System Engineering Office (SEO) worked with the CEOS Working Group on Calibration and Validation (WGCV) to develop the COVE tool. The CEOS member organizations are currently operating and planning hundreds of Earth Observation (EO) satellites. Standard cross-comparison exercises between multiple sensors to compare near-simultaneous surface observations and to identify corresponding image pairs are time-consuming and labor-intensive. COVE is a suite of tools that have been developed to make such tasks easier.

Lie integrable cases of the simplified multistrain/two-stream model for tuberculosis and dengue fever

NASA Astrophysics Data System (ADS)

Nucci, M. C.; Leach, P. G. L.

2007-09-01

We apply the techniques of Lie's symmetry analysis to a caricature of the simplified multistrain model of Castillo-Chavez and Feng [C. Castillo-Chavez, Z. Feng, To treat or not to treat: The case of tuberculosis, J. Math. Biol. 35 (1997) 629-656] for the transmission of tuberculosis and the coupled two-stream vector-based model of Feng and Velasco-Hernandez [Z. Feng, J.X. Velasco-Hernandez, Competitive exclusion in a vector-host model for the dengue fever, J. Math. Biol. 35 (1997) 523-544] to identify the combinations of parameters which lead to the existence of nontrivial symmetries. In particular we identify those combinations which lead to the possibility of the linearization of the system and provide the corresponding solutions. Many instances of additional symmetry are analyzed.

Characterization of a proposed dichorhavirus associated with the citrus leprosis disease and analysis of the host response.

PubMed

Cruz-Jaramillo, José Luis; Ruiz-Medrano, Roberto; Rojas-Morales, Lourdes; López-Buenfil, José Abel; Morales-Galván, Oscar; Chavarín-Palacio, Claudio; Ramírez-Pool, José Abrahán; Xoconostle-Cázares, Beatriz

2014-07-07

The causal agents of Citrus leprosis are viruses; however, extant diagnostic methods to identify them have failed to detect known viruses in orange, mandarin, lime and bitter orange trees with severe leprosis symptoms in Mexico, an important citrus producer. Using high throughput sequencing, a virus associated with citrus leprosis was identified, belonging to the proposed Dichorhavirus genus. The virus was termed Citrus Necrotic Spot Virus (CNSV) and contains two negative-strand RNA components; virions accumulate in the cytoplasm and are associated with plasmodesmata-channels interconnecting neighboring cells-suggesting a mode of spread within the plant. The present study provides insights into the nature of this pathogen and the corresponding plant response, which is likely similar to other pathogens that do not spread systemically in plants.

Anthocyanins in the bracts of Curcuma species and relationship of the species based on anthocyanin composition.

PubMed

Koshioka, Masaji; Umegaki, Naoko; Boontiang, Kriangsuk; Pornchuti, Witayaporn; Thammasiri, Kanchit; Yamaguchi, Satoshi; Tatsuzawa, Fumi; Nakayama, Masayoshi; Tateishi, Akira; Kubota, Satoshi

2015-03-01

Five anthocyanins, delphinidin 3-O-rutinoside, cyanidin 3-O-rutinoside, petunidin 3-O-rutinoside, malvidin 3-O-glucoside and malvidin 3-O-rutinoside, were identified. Three anthocyanins, delphinidin 3-O-glucoside, cyanidin 3-O-glucoside and pelargonidin 3-O-rutinoside, were putatively identified based on C18 HPLC retention time, absorption spectrum, including λmax, and comparisons with those of corresponding standard anthocyanins, as the compounds responsible for the pink to purple-red pigmentation of the bracts of Curcuma alismatifolia and five related species. Cluster analysis based on four major anthocyanins formed two clusters. One consisted of only one species, C. alismatifolia, and the other consisted of five. Each cluster further formed sub-clusters depending on either species or habitats.

Matching biomedical ontologies based on formal concept analysis.

PubMed

Zhao, Mengyi; Zhang, Songmao; Li, Weizhuo; Chen, Guowei

2018-03-19

The goal of ontology matching is to identify correspondences between entities from different yet overlapping ontologies so as to facilitate semantic integration, reuse and interoperability. As a well developed mathematical model for analyzing individuals and structuring concepts, Formal Concept Analysis (FCA) has been applied to ontology matching (OM) tasks since the beginning of OM research, whereas ontological knowledge exploited in FCA-based methods is limited. This motivates the study in this paper, i.e., to empower FCA with as much as ontological knowledge as possible for identifying mappings across ontologies. We propose a method based on Formal Concept Analysis to identify and validate mappings across ontologies, including one-to-one mappings, complex mappings and correspondences between object properties. Our method, called FCA-Map, incrementally generates a total of five types of formal contexts and extracts mappings from the lattices derived. First, the token-based formal context describes how class names, labels and synonyms share lexical tokens, leading to lexical mappings (anchors) across ontologies. Second, the relation-based formal context describes how classes are in taxonomic, partonomic and disjoint relationships with the anchors, leading to positive and negative structural evidence for validating the lexical matching. Third, the positive relation-based context can be used to discover structural mappings. Afterwards, the property-based formal context describes how object properties are used in axioms to connect anchor classes across ontologies, leading to property mappings. Last, the restriction-based formal context describes co-occurrence of classes across ontologies in anonymous ancestors of anchors, from which extended structural mappings and complex mappings can be identified. Evaluation on the Anatomy, the Large Biomedical Ontologies, and the Disease and Phenotype track of the 2016 Ontology Alignment Evaluation Initiative campaign demonstrates the effectiveness of FCA-Map and its competitiveness with the top-ranked systems. FCA-Map can achieve a better balance between precision and recall for large-scale domain ontologies through constructing multiple FCA structures, whereas it performs unsatisfactorily for smaller-sized ontologies with less lexical and semantic expressions. Compared with other FCA-based OM systems, the study in this paper is more comprehensive as an attempt to push the envelope of the Formal Concept Analysis formalism in ontology matching tasks. Five types of formal contexts are constructed incrementally, and their derived concept lattices are used to cluster the commonalities among classes at lexical and structural level, respectively. Experiments on large, real-world domain ontologies show promising results and reveal the power of FCA.

Identification of Load Categories in Rotor System Based on Vibration Analysis

PubMed Central

Yang, Zhaojian

2017-01-01

Rotating machinery is often subjected to variable loads during operation. Thus, monitoring and identifying different load types is important. Here, five typical load types have been qualitatively studied for a rotor system. A novel load category identification method for rotor system based on vibration signals is proposed. This method is a combination of ensemble empirical mode decomposition (EEMD), energy feature extraction, and back propagation (BP) neural network. A dedicated load identification test bench for rotor system was developed. According to loads characteristics and test conditions, an experimental plan was formulated, and loading tests for five loads were conducted. Corresponding vibration signals of the rotor system were collected for each load condition via eddy current displacement sensor. Signals were reconstructed using EEMD, and then features were extracted followed by energy calculations. Finally, characteristics were input to the BP neural network, to identify different load types. Comparison and analysis of identifying data and test data revealed a general identification rate of 94.54%, achieving high identification accuracy and good robustness. This shows that the proposed method is feasible. Due to reliable and experimentally validated theoretical results, this method can be applied to load identification and fault diagnosis for rotor equipment used in engineering applications. PMID:28726754

Preparation of hydrophilic monolithic capillary column by in situ photo-polymerization of N-vinyl-2-pyrrolidinone and acrylamide for highly selective and sensitive enrichment of N-linked glycopeptides.

PubMed

Jiang, Hao; Yuan, Huiming; Qu, Yanyan; Liang, Yu; Jiang, Bo; Wu, Qi; Deng, Nan; Liang, Zhen; Zhang, Lihua; Zhang, Yukui

2016-01-01

In this study, a novel kind of amide functionalized hydrophilic monolith was synthesized by the in situ photo-polymerization of N-vinyl-2-pyrrolidinone (NVP), acrylamide (AM), and N, N'-methylenebisacrylamide (MBA) in a UV transparent capillary, and successfully applied for hydrophilic interaction chromatography (HILIC) based enrichment of N-linked glycopeptides. With 2 μg of the tryptic digests of IgG as the sample, after enrichment, 18 glycopeptides could be identified by MALDI-TOF/TOF MS analysis. Furthermore, with the mixture of BSA and IgG digests (10,000:1, m/m) as the sample, 6 N-linked glycopeptides were unambiguously identified after enrichment, indicating the high selectivity and good specificity of such material. Moreover, such a monolithic capillary column was also applied for the N-glycosylation sites profiling of 6 μg protein digests from HeLa cells and 1 μL human serum. In total, 530 and 262 unique N-glycosylated peptides were identified, respectively, corresponding to 282 and 124N-glycoproteins, demonstrating its great potential for the large scale glycoproteomics analysis. Copyright © 2015 Elsevier B.V. All rights reserved.

Prostate: techniques, results, and potential applications of color Doppler US scanning.

PubMed

Rifkin, M D; Sudakoff, G S; Alexander, A A

1993-02-01

Color Doppler ultrasound (US) scanning and conventional endorectal gray-scale US of the prostate were performed in 619 patients. Pathologic correlation was available in all cases after US-guided transrectal biopsy. There were 132 cancers in 121 men, 13 foci of atypia in 10 men, 33 foci of inflammation in 31 men, and 469 benign lesions in 457 men. Two hundred seventy patients with abnormal areas of flow identified at color Doppler scanning also underwent spectral waveform analysis of the area of potential concern. No statistical difference in the mean resistive indexes was identified in any patient (P = .25; Scheffe F test, analysis of variance). All malignant lesions had abnormalities demonstrated at gray-scale US and/or focal or diffuse abnormal flow demonstrated at color Doppler scanning. Of the 132 cancers, 123 (93%) had corresponding gray-scale abnormalities and 114 (86%) demonstrated abnormal flow at color Doppler imaging. Nine of the 132 cancers (7%) had no obviously identifiable abnormality at gray-scale scanning but had distinctly abnormal flow at color Doppler scanning. Abnormal findings at color scanning without abnormal findings at gray-scale scanning occurred in eight of the 33 cases of inflammatory foci (24%) and in 24 of the 469 (5%) benign lesions.

Microvessel prediction in H&E Stained Pathology Images using fully convolutional neural networks.

PubMed

Yi, Faliu; Yang, Lin; Wang, Shidan; Guo, Lei; Huang, Chenglong; Xie, Yang; Xiao, Guanghua

2018-02-27

Pathological angiogenesis has been identified in many malignancies as a potential prognostic factor and target for therapy. In most cases, angiogenic analysis is based on the measurement of microvessel density (MVD) detected by immunostaining of CD31 or CD34. However, most retrievable public data is generally composed of Hematoxylin and Eosin (H&E)-stained pathology images, for which is difficult to get the corresponding immunohistochemistry images. The role of microvessels in H&E stained images has not been widely studied due to their complexity and heterogeneity. Furthermore, identifying microvessels manually for study is a labor-intensive task for pathologists, with high inter- and intra-observer variation. Therefore, it is important to develop automated microvessel-detection algorithms in H&E stained pathology images for clinical association analysis. In this paper, we propose a microvessel prediction method using fully convolutional neural networks. The feasibility of our proposed algorithm is demonstrated through experimental results on H&E stained images. Furthermore, the identified microvessel features were significantly associated with the patient clinical outcomes. This is the first study to develop an algorithm for automated microvessel detection in H&E stained pathology images.

A transcriptional dynamic network during Arabidopsis thaliana pollen development.

PubMed

Wang, Jigang; Qiu, Xiaojie; Li, Yuhua; Deng, Youping; Shi, Tieliu

2011-01-01

To understand transcriptional regulatory networks (TRNs), especially the coordinated dynamic regulation between transcription factors (TFs) and their corresponding target genes during development, computational approaches would represent significant advances in the genome-wide expression analysis. The major challenges for the experiments include monitoring the time-specific TFs' activities and identifying the dynamic regulatory relationships between TFs and their target genes, both of which are currently not yet available at the large scale. However, various methods have been proposed to computationally estimate those activities and regulations. During the past decade, significant progresses have been made towards understanding pollen development at each development stage under the molecular level, yet the regulatory mechanisms that control the dynamic pollen development processes remain largely unknown. Here, we adopt Networks Component Analysis (NCA) to identify TF activities over time course, and infer their regulatory relationships based on the coexpression of TFs and their target genes during pollen development. We carried out meta-analysis by integrating several sets of gene expression data related to Arabidopsis thaliana pollen development (stages range from UNM, BCP, TCP, HP to 0.5 hr pollen tube and 4 hr pollen tube). We constructed a regulatory network, including 19 TFs, 101 target genes and 319 regulatory interactions. The computationally estimated TF activities were well correlated to their coordinated genes' expressions during the development process. We clustered the expression of their target genes in the context of regulatory influences, and inferred new regulatory relationships between those TFs and their target genes, such as transcription factor WRKY34, which was identified that specifically expressed in pollen, and regulated several new target genes. Our finding facilitates the interpretation of the expression patterns with more biological relevancy, since the clusters corresponding to the activity of specific TF or the combination of TFs suggest the coordinated regulation of TFs to their target genes. Through integrating different resources, we constructed a dynamic regulatory network of Arabidopsis thaliana during pollen development with gene coexpression and NCA. The network illustrated the relationships between the TFs' activities and their target genes' expression, as well as the interactions between TFs, which provide new insight into the molecular mechanisms that control the pollen development.

Eukaryotic Protein Kinases (ePKs) of the Helminth Parasite Schistosoma mansoni

PubMed Central

2011-01-01

Background Schistosomiasis remains an important parasitic disease and a major economic problem in many countries. The Schistosoma mansoni genome and predicted proteome sequences were recently published providing the opportunity to identify new drug candidates. Eukaryotic protein kinases (ePKs) play a central role in mediating signal transduction through complex networks and are considered druggable targets from the medical and chemical viewpoints. Our work aimed at analyzing the S. mansoni predicted proteome in order to identify and classify all ePKs of this parasite through combined computational approaches. Functional annotation was performed mainly to yield insights into the parasite signaling processes relevant to its complex lifestyle and to select some ePKs as potential drug targets. Results We have identified 252 ePKs, which corresponds to 1.9% of the S. mansoni predicted proteome, through sequence similarity searches using HMMs (Hidden Markov Models). Amino acid sequences corresponding to the conserved catalytic domain of ePKs were aligned by MAFFT and further used in distance-based phylogenetic analysis as implemented in PHYLIP. Our analysis also included the ePK homologs from six other eukaryotes. The results show that S. mansoni has proteins in all ePK groups. Most of them are clearly clustered with known ePKs in other eukaryotes according to the phylogenetic analysis. None of the ePKs are exclusively found in S. mansoni or belong to an expanded family in this parasite. Only 16 S. mansoni ePKs were experimentally studied, 12 proteins are predicted to be catalytically inactive and approximately 2% of the parasite ePKs remain unclassified. Some proteins were mentioned as good target for drug development since they have a predicted essential function for the parasite. Conclusions Our approach has improved the functional annotation of 40% of S. mansoni ePKs through combined similarity and phylogenetic-based approaches. As we continue this work, we will highlight the biochemical and physiological adaptations of S. mansoni in response to diverse environments during the parasite development, vector interaction, and host infection. PMID:21548963

Effect of B Vitamin (Folate, B6, and B12) Supplementation on Osteoporotic Fracture and Bone Turnover Markers: A Meta-Analysis

PubMed Central

Ruan, Jianwei; Gong, Xiaokang; Kong, Jinsong; Wang, Haibao; Zheng, Xin; Chen, Tao

2015-01-01

Background B vitamins (including folate, B6, and B12) supplementation can effectively and easily modify high plasma homocysteine (Hcy). However, the role of Hcy in the pathogenesis of osteoporotic fracture and bone turnover is still controversial. This meta-analysis aimed to assess the impact of B vitamin supplementation on occurrence of any osteoporotic fracture and bone turnover by pooling the results of previous studies. Material/Methods Relevant randomized controlled trials (RCTs) were searched in databases. Data integration and analysis were done by using Review Manager 5.3 (the Cochrane Collaboration). The risk ratio (RR) and corresponding 95% confidence intervals (CI) of fracture (intervention vs. control) were estimated. Changes in bone turnover indicators (continuous data), weighted mean difference (WMD), and corresponding 95% (CI) were pooled for estimation. Results Based on the results of 4 RCTs, this meta-analysis failed to identify a risk-reducing effect of daily supplementation of B vitamins on osteoporotic fracture in patients with vascular disease and with relatively normal plasma Hcy. In addition, we also did not find any positive effects of B vitamin supplementation on bone turnover. Conclusions B vitamin supplementation might not be effective in preventing fracture and improving bone turnover. However, the possible benefits in selective populations, such as populations with very high plasma Hcy and from regions without B vitamin fortification should be explored in the future. PMID:25805360

A comparative study of three tissue-cultured Dendrobium species and their wild correspondences by headspace gas chromatography-mass spectrometry combined with chemometric methods.

PubMed

Chen, Nai-Dong; You, Tao; Li, Jun; Bai, Li-Tao; Hao, Jing-Wen; Xu, Xiao-Yuan

2016-10-01

Plant tissue culture technique is widely used in the conservation and utilization of rare and endangered medicinal plants and it is crucial for tissue culture stocks to obtain the ability to produce similar bioactive components as their wild correspondences. In this paper, a headspace gas chromatography-mass spectrometry method combined with chemometric methods was applied to analyze and evaluate the volatile compounds in tissue-cultured and wild Dendrobium huoshanense Cheng and Tang, Dendrobium officinale Kimura et Migo and Dendrobium moniliforme (Linn.) Sw. In total, 63 volatile compounds were separated, with 53 being identified from the three Dendrobium spp. Different provenances of Dendrobiums had characteristic chemicals and showed remarkable quantity discrepancy of common compositions. The similarity evaluation disclosed that the accumulation of volatile compounds in Dendrobium samples might be affected by their provenance. Principal component analysis showed that the first three components explained 85.9% of data variance, demonstrating a good discrimination between samples. Gas chromatography-mass spectrometry techniques, combined with chemometrics, might be an effective strategy for identifying the species and their provenance, especially in the assessment of tissue-cultured Dendrobium quality for use in raw herbal medicines. Copyright © 2016. Published by Elsevier B.V.

Identifying the Factors Affecting Papers’ Citability in the Field of Medicine: an Evidence-based Approach Using 200 Highly and Lowly-cited Papers

PubMed Central

Yaminfirooz, Mousa; Ardali, Farzaneh Raeesi

2018-01-01

Introduction: Nowadays, publishing highly-cited papers is important for researchers and editors. In this evidence-based study, the factors influencing the citability of published papers in the field of medicine have been identified. Material and Methods: 200 papers indexed in Scopus (in two groups: highly-cited and lowly-cited) with 100 papers in each were studied. Needed data were manually collected with a researcher-made checklist. Data analysis was done in SPSS using descriptive and inferential statistics. Results: Variables such as journal IF, journal rank, journal subject quartile, the first/corresponding author’s h-index, the number of documents produced by the first/corresponding author, SJR and SNIP had significantly positive correlation with paper citability (p< .05). Other variables, including among others, paper age, paper type, the number of references, the number of authors, indexing institute and journal kind had not any relationship with paper citability (p> .05). Conclusion: the factors affecting the citability are among indicators relating to authors, publishing journals and published papers. Determining the extent to which these factors influence the citability of a paper needs further large-scaled research. Authors and editors searching for high-citedness should consider these factors when authoring and publishing papers. PMID:29719306

Molecular identification of black-pigmented bacteria from subgingival samples of cats suffering from periodontal disease.

PubMed

Pérez-Salcedo, L; Laguna, E; Sánchez, M C; Marín, M J; O'Connor, A; González, I; Sanz, M; Herrera, D

2015-04-01

To characterise the black-pigmented bacterial species found in the subgingival samples of cats with periodontal disease using molecular-based microbiological techniques. Sixty-five subgingival samples obtained from 50 cats with periodontal disease were analysed by polymerase chain reaction amplified ribosomal DNA restriction analysis and cloning and sequencing of the 16S rRNA genes. Among the 65 subgingival samples, eight phylogenetic profiles were obtained, of which the most prevalent species were: Porphyromonas gulae (40%), P. gingivalis/P. gulae (36 · 9%), P. gulae/Porphyromonas sp. UQD 406 (9 · 2%), Odoribacter denticanis (6 · 2%), P. gulae/Porphyromonas sp. UQD 348 (1 · 5%) and P. circumdentaria (1 · 5%). When compared with the species resulting from biochemical diagnosis, the identification of P. gulae was congruent in 70% of the cases, while colonies identified as P. intermedia-like corresponded in 80% of cases to P. gulae. The use of molecular-based microbiological diagnostic techniques resulted in a predominance of Porphyromonas spp. in the subgingival plaque of cats suffering from periodontal disease. Further characterisation of these bacteria identified P. gulae, O. denticanis and P. circumdentaria. The more frequently detected phylogenetic profiles corresponded to P. gingivalis and P. gulae. © 2015 British Small Animal Veterinary Association.

Systems and Methods for Imaging of Falling Objects

NASA Technical Reports Server (NTRS)

Fallgatter, Cale (Inventor); Garrett, Tim (Inventor)

2014-01-01

Imaging of falling objects is described. Multiple images of a falling object can be captured substantially simultaneously using multiple cameras located at multiple angles around the falling object. An epipolar geometry of the captured images can be determined. The images can be rectified to parallelize epipolar lines of the epipolar geometry. Correspondence points between the images can be identified. At least a portion of the falling object can be digitally reconstructed using the identified correspondence points to create a digital reconstruction.

Mine safety assessment using gray relational analysis and bow tie model

PubMed Central

2018-01-01

Mine safety assessment is a precondition for ensuring orderly and safety in production. The main purpose of this study was to prevent mine accidents more effectively by proposing a composite risk analysis model. First, the weights of the assessment indicators were determined by the revised integrated weight method, in which the objective weights were determined by a variation coefficient method and the subjective weights determined by the Delphi method. A new formula was then adopted to calculate the integrated weights based on the subjective and objective weights. Second, after the assessment indicator weights were determined, gray relational analysis was used to evaluate the safety of mine enterprises. Mine enterprise safety was ranked according to the gray relational degree, and weak links of mine safety practices identified based on gray relational analysis. Third, to validate the revised integrated weight method adopted in the process of gray relational analysis, the fuzzy evaluation method was used to the safety assessment of mine enterprises. Fourth, for first time, bow tie model was adopted to identify the causes and consequences of weak links and allow corresponding safety measures to be taken to guarantee the mine’s safe production. A case study of mine safety assessment was presented to demonstrate the effectiveness and rationality of the proposed composite risk analysis model, which can be applied to other related industries for safety evaluation. PMID:29561875

Altered Pathway Analyzer: A gene expression dataset analysis tool for identification and prioritization of differentially regulated and network rewired pathways

PubMed Central

Kaushik, Abhinav; Ali, Shakir; Gupta, Dinesh

2017-01-01

Gene connection rewiring is an essential feature of gene network dynamics. Apart from its normal functional role, it may also lead to dysregulated functional states by disturbing pathway homeostasis. Very few computational tools measure rewiring within gene co-expression and its corresponding regulatory networks in order to identify and prioritize altered pathways which may or may not be differentially regulated. We have developed Altered Pathway Analyzer (APA), a microarray dataset analysis tool for identification and prioritization of altered pathways, including those which are differentially regulated by TFs, by quantifying rewired sub-network topology. Moreover, APA also helps in re-prioritization of APA shortlisted altered pathways enriched with context-specific genes. We performed APA analysis of simulated datasets and p53 status NCI-60 cell line microarray data to demonstrate potential of APA for identification of several case-specific altered pathways. APA analysis reveals several altered pathways not detected by other tools evaluated by us. APA analysis of unrelated prostate cancer datasets identifies sample-specific as well as conserved altered biological processes, mainly associated with lipid metabolism, cellular differentiation and proliferation. APA is designed as a cross platform tool which may be transparently customized to perform pathway analysis in different gene expression datasets. APA is freely available at http://bioinfo.icgeb.res.in/APA. PMID:28084397

A Correspondence Analysis of Child-Care Students' and Medical Students' Knowledge about Teaching and Learning

ERIC Educational Resources Information Center

Askell-Williams, Helen; Lawson, Michael J.

2004-01-01

This paper describes the application of correspondence analysis to transcripts gathered from focussed interviews about teaching and learning held with a small sample of child-care students, medical students and the students' teachers. Seven dimensions emerged from the analysis, suggesting that the knowledge that underlies students' learning…

Social significance of community structure: Statistical view

NASA Astrophysics Data System (ADS)

Li, Hui-Jia; Daniels, Jasmine J.

2015-01-01

Community structure analysis is a powerful tool for social networks that can simplify their topological and functional analysis considerably. However, since community detection methods have random factors and real social networks obtained from complex systems always contain error edges, evaluating the significance of a partitioned community structure is an urgent and important question. In this paper, integrating the specific characteristics of real society, we present a framework to analyze the significance of a social community. The dynamics of social interactions are modeled by identifying social leaders and corresponding hierarchical structures. Instead of a direct comparison with the average outcome of a random model, we compute the similarity of a given node with the leader by the number of common neighbors. To determine the membership vector, an efficient community detection algorithm is proposed based on the position of the nodes and their corresponding leaders. Then, using a log-likelihood score, the tightness of the community can be derived. Based on the distribution of community tightness, we establish a connection between p -value theory and network analysis, and then we obtain a significance measure of statistical form . Finally, the framework is applied to both benchmark networks and real social networks. Experimental results show that our work can be used in many fields, such as determining the optimal number of communities, analyzing the social significance of a given community, comparing the performance among various algorithms, etc.

Quantitative Analysis of the Human Milk Whey Proteome Reveals Developing Milk and Mammary-Gland Functions across the First Year of Lactation

PubMed Central

Zhang, Qiang; Cundiff, Judy K.; Maria, Sarah D.; McMahon, Robert J.; Woo, Jessica G.; Davidson, Barbara S.; Morrow, Ardythe L.

2013-01-01

In-depth understanding of the changing functions of human milk (HM) proteins and the corresponding physiological adaptions of the lactating mammary gland has been inhibited by incomplete knowledge of the HM proteome. We analyzed the HM whey proteome (n = 10 women with samples at 1 week and 1, 3, 6, 9 and 12 months) using a quantitative proteomic approach. One thousand three hundred and thirty three proteins were identified with 615 being quantified. Principal component analysis revealed a transition in the HM whey proteome-throughout the first year of lactation. Abundance changes in IgG, sIgA and sIgM display distinct features during the first year. Complement components and other acute-phase proteins are generally at higher levels in early lactation. Proteomic analysis further suggests that the sources of milk fatty acids (FA) shift from more direct blood influx to more de novo mammary synthesis over lactation. The abundances of the majority of glycoproteins decline over lactation, which is consistent with increased enzyme expression in glycoprotein degradation and decreased enzyme expression in glycoprotein synthesis. Cellular detoxification machinery may be transformed as well, thereby accommodating increased metabolic activities in late lactation. The multiple developing functions of HM proteins and the corresponding mammary adaption become more apparent from this study. PMID:28250401

Empirical OPC rule inference for rapid RET application

NASA Astrophysics Data System (ADS)

Kulkarni, Anand P.

2006-10-01

A given technological node (45 nm, 65 nm) can be expected to process thousands of individual designs. Iterative methods applied at the node consume valuable days in determining proper placement of OPC features, and manufacturing and testing mask correspondence to wafer patterns in a trial-and-error fashion for each design. Repeating this fabrication process for each individual design is a time-consuming and expensive process. We present a novel technique which sidesteps the requirement to iterate through the model-based OPC analysis and pattern verification cycle on subsequent designs at the same node. Our approach relies on the inference of rules from a correct pattern at the wafer surface it relates to the OPC and pre-OPC pattern layout files. We begin with an offline phase where we obtain a "gold standard" design file that has been fab-tested at the node with a prepared, post-OPC layout file that corresponds to the intended on-wafer pattern. We then run an offline analysis to infer rules to be used in this method. During the analysis, our method implicitly identifies contextual OPC strategies for optimal placement of RET features on any design at that node. Using these strategies, we can apply OPC to subsequent designs at the same node with accuracy comparable to the original design file but significantly smaller expected runtimes. The technique promises to offer a rapid and accurate complement to existing RET application strategies.

Single-cell genetic analysis validates cytopathological identification of circulating cancer cells in patients with clear cell renal cell carcinoma.

PubMed

Broncy, Lucile; Njima, Basma Ben; Méjean, Arnaud; Béroud, Christophe; Romdhane, Khaled Ben; Ilie, Marius; Hofman, Veronique; Muret, Jane; Hofman, Paul; Bouhamed, Habiba Chaabouni; Paterlini-Bréchot, And Patrizia

2018-04-13

Circulating Rare Cells (CRC) are non-haematological cells circulating in blood. They include Circulating Cancer Cells (CCC) and cells with uncertain malignant features (CRC-UMF) according to cytomorphology. Clear cell renal cell carcinomas frequently bear a mutated Von Hippel-Lindau (VHL) gene. To match blind genetic analysis of CRC and tumor samples with CRC cytopathological diagnosis. 29/30 patients harboured CRC (20 harboured CCC, 29 CRC-UMF) and 25/29 patients carried VHL mutations in their tumour. 205 single CRC (64 CCC, 141 CRC-UMF) provided genetic data. 57/57 CCC and 104/125 CRC-UMF from the 25 patients with VHL-mutated tumor carried the same VHL mutation detected in the tumor. Seven CCC and 16 CRC-UMF did not carry VHL mutations but were found in patients with wild-type VHL tumor tissue. All the CCC and 83,2% (104/125) of the CRC-UMF were found to carry the same VHL mutation identified in the corresponding tumorous tissue, validating cytopathological identification of CCC in patients with clear cell renal cell carcinoma. The blood of 30 patients with clear cell renal cell carcinoma was treated by ISET ® for CRC isolation, cytopathology and single-cell VHL mutations analysis, performed blindly and compared to VHL mutations of corresponding tumor tissues and leukocytes.

Prognostic impact of a compartment-specific angiogenic marker profile in patients with pancreatic cancer.

PubMed

Kahlert, Christoph; Fiala, Maria; Musso, Gabriel; Halama, Niels; Keim, Sophia; Mazzone, Massimiliano; Lasitschka, Felix; Pecqueux, Mathieu; Klupp, Fee; Schmidt, Thomas; Rahbari, Nuh; Schölch, Sebastian; Pilarsky, Christian; Ulrich, Alexis; Schneider, Martin; Weitz, Juergen; Koch, Moritz

2014-12-30

Pancreatic cancer consists of a heterogenous bulk of tumor cells and stroma cells which contribute to tumor progression by releasing angiogenic factors. Those factors can be detected as circulating serum factors. We performed a compartment-specific analysis of tumor-derived and stroma-derived angiogenic factors to identify biomarkers and molecular targets for the treatment of pancreatic cancer. Kryo-frozen tissue from primary ductal adenocarcinomas (n = 51) was laser-microdissected to isolate tumor and stroma tissue. Expression of 17 angiogenic factors (angiopoietin-2, follistatin, GCSF, HGF, interleukin-8, leptin, PDGF-BB, PECAM-1, VEGF, matrix metalloproteinase -1, -2, -3, -7, -9, -10, -12, and -13) was analyzed using a multiplex elisa assay for tissue-derived proteins and corresponding serum. Our study reveals a compartment-specific expression profile for several angiogenic factors and matrix metalloproteinases. ROC analysis of corresponding serum samples reveals MMP-7 and MMP-12 as strong classifiers for the diagnosis of patients with pancreatic cancer vs. healthy control donors. High expression of tumor-derived PDGF-BB and MMP-1 correlates with prolonged survival in univariate and multivariate analysis. In conclusion, a distinct expression patterns for angiogenic cytokines and MMPs in pancreatic cancer and surrounding stroma may implicate them as novel targets for cancer treatment. Tumor-derived PDGF-BB and MMP-1 are significant and independent prognostic markers for poor survival.

38 CFR 21.4279 - Combination correspondence-residence program.

Code of Federal Regulations, 2010 CFR

2010-07-01

... VETERANS AFFAIRS (CONTINUED) VOCATIONAL REHABILITATION AND EDUCATION Administration of Educational.... (a) Requirements for pursuit. A program of education may be pursued partly in residence and partly by correspondence for the attainment of a predetermined and identified objective under the following conditions: (1...

Co-expression analysis identifies CRC and AP1 the regulator of Arabidopsis fatty acid biosynthesis.

PubMed

Han, Xinxin; Yin, Linlin; Xue, Hongwei

2012-07-01

Fatty acids (FAs) play crucial rules in signal transduction and plant development, however, the regulation of FA metabolism is still poorly understood. To study the relevant regulatory network, fifty-eight FA biosynthesis genes including de novo synthases, desaturases and elongases were selected as "guide genes" to construct the co-expression network. Calculation of the correlation between all Arabidopsis thaliana (L.) genes with each guide gene by Arabidopsis co-expression dating mining tools (ACT) identifies 797 candidate FA-correlated genes. Gene ontology (GO) analysis of these co-expressed genes showed they are tightly correlated to photosynthesis and carbohydrate metabolism, and function in many processes. Interestingly, 63 transcription factors (TFs) were identified as candidate FA biosynthesis regulators and 8 TF families are enriched. Two TF genes, CRC and AP1, both correlating with 8 FA guide genes, were further characterized. Analyses of the ap1 and crc mutant showed the altered total FA composition of mature seeds. The contents of palmitoleic acid, stearic acid, arachidic acid and eicosadienoic acid are decreased, whereas that of oleic acid is increased in ap1 and crc seeds, which is consistent with the qRT-PCR analysis revealing the suppressed expression of the corresponding guide genes. In addition, yeast one-hybrid analysis and electrophoretic mobility shift assay (EMSA) revealed that CRC can bind to the promoter regions of KCS7 and KCS15, indicating that CRC may directly regulate FA biosynthesis. © 2012 Institute of Botany, Chinese Academy of Sciences.

Extraction of Intraseasonal Phases of the East Asia Summer Monsoon using Self Organizing Maps and their ENSO effects

NASA Astrophysics Data System (ADS)

Chu, J.; Ha, K.; Hameed, S. N.

2011-12-01

We advance the hypothesis that regional characteristics of the East Asian Summer Monsoon (EASM) result from the presence of non-linear coupled features that modulate the seasonal circulation and rainfall at the intraseasonal timescale. To examine this hypothesis, we undertake the analysis of daily EASM variability using a non-linear multivariate data classifying algorithm known as Self Organizing Maps (SOM). SOM is used to locate archetypal circulation states present in a circulation state vector composed of important indices representing subtropical high pressure regions, the lower and upper level wind vectors and vertical and horizontal shear. These so-called nodes on the SOM identify prominent modes of temporal variations across the region Based on an analysis of the various SOM nodes, we identify 4 major intraseasonal phases of the EASM that are located at the far corners of the SOM. The first node describes a circulation state corresponding to weak tropical and subtropical pressure systems, weakened monsoonal winds, and cyclonic upper level vorticity. This mode that is related with large rainfall anomalies in South East China and Southern Japan occurs a few weeks prior to the onset of Changma rains in Korea. Based on its various characteristics, we identify it is as the Meiyu-Baiu phase. At the diagonally opposite corner from the node representing the Meiyu-Baiu phase, the circulation vector is its mirror image. Copious rains occur over Korea during this phase, which we term the post-Changma phase. The third node selected for this analysis represents the Changma-proper over Korea and occurs with a distinct circulation state corresponding to strengthened subtropical high, monsoonal winds and anticyclonic upper level vorticity to the southeast of Korea. The fourth node is diagonally opposite to this one and features a mirror image of the circulation vector. As Korea experiences a dry-spell associated with this SOM node, we refer to it as the dry-spell phase. We further demonstrate that a strong modulation of the Changma and dry-spell phases on the interannual timescales occurs during El Nino and La Nina years. Our results imply that the key to the predictability of the EASM on interannual timescales may lie with the analysis and exploitation of its non-linear characteristics.

[Correlation between body fat percentage and general obesity indexes in middle aged and old people in Guangzhou].

PubMed

Hu, Q; Jiang, C Q; Zhang, W S; Cheng, J J; Xu, L; Jin, Y L; Rao, S L; Zheng, H Q; Lam, D Q

2016-10-10

Objective: To examine the correlation between body fat percentage (BFP) and general obesity indexes, including body mass index (BMI), waist circumference (WC) and waist to hip ratio (WHR) and calculate the corresponding BFP cutoff values in the middle aged and old people in Guangzhou. The corresponding cut-point of optimal body fat percentage for Guangzhou older population. Methods: Based on the Guangzhou Biobank Cohort Study (GBCS), 3 490 relatively healthy Guangzhou residents aged ≥50 years were selected and were randomly divided into 2 groups. The equations between BFP and BMI, WC, WHR were set up with Curve fitting analysis in one group. The multiple regression analysis was undertaken to establish predictive equations between BFP and BMI, WC, WHR with stepwise model for adding gender, age, physical activity, drinking and smoking. Then, the optimal cut-points of BFP corresponding to BMI, WC and WHR to reflect the degree of obesity were calculated. The equations were then validated with another group. Results: BFP increased with the increase of WHR, WC and BMI. BMI was a better predictor of body fat percentage than WC and WHR. The final regression equation was BFP=(-23.47 -8.87×sex) +2.94× (BMI) - 0.024 × (BMI) 2 ,the coefficient of determination was 0.805. Based on the equation, the BFP corresponding to overweight/obesity (24 kg/m 2 ≤BMI<28 kg/m 2 ) were 24.3 % ≤BFP<31.1 % in men and 33.2 % ≤BFP<40.0 % in women, respectively. BMI had a better consistency with BFP in identify obesity compared with WC and WHR, obtained the area of ROC 0.909 in men and 0.919 in women respectively. The sensitivity and specificity were 70.3 % and 85.5 % in men; and 75.2 % and 93.0 % in women respectively. Conclusion: BFP has a better correlation with BMI. The study results indicated that BFP for middle aged and old males and females in Guangzhou corresponding to overweight/obesity (BMI≥24 kg/m 2 ) were <24.0 % and <33.0 % respectively.

Improving fMRI reliability in presurgical mapping for brain tumours.

PubMed

Stevens, M Tynan R; Clarke, David B; Stroink, Gerhard; Beyea, Steven D; D'Arcy, Ryan Cn

2016-03-01

Functional MRI (fMRI) is becoming increasingly integrated into clinical practice for presurgical mapping. Current efforts are focused on validating data quality, with reliability being a major factor. In this paper, we demonstrate the utility of a recently developed approach that uses receiver operating characteristic-reliability (ROC-r) to: (1) identify reliable versus unreliable data sets; (2) automatically select processing options to enhance data quality; and (3) automatically select individualised thresholds for activation maps. Presurgical fMRI was conducted in 16 patients undergoing surgical treatment for brain tumours. Within-session test-retest fMRI was conducted, and ROC-reliability of the patient group was compared to a previous healthy control cohort. Individually optimised preprocessing pipelines were determined to improve reliability. Spatial correspondence was assessed by comparing the fMRI results to intraoperative cortical stimulation mapping, in terms of the distance to the nearest active fMRI voxel. The average ROC-r reliability for the patients was 0.58±0.03, as compared to 0.72±0.02 in healthy controls. For the patient group, this increased significantly to 0.65±0.02 by adopting optimised preprocessing pipelines. Co-localisation of the fMRI maps with cortical stimulation was significantly better for more reliable versus less reliable data sets (8.3±0.9 vs 29±3 mm, respectively). We demonstrated ROC-r analysis for identifying reliable fMRI data sets, choosing optimal postprocessing pipelines, and selecting patient-specific thresholds. Data sets with higher reliability also showed closer spatial correspondence to cortical stimulation. ROC-r can thus identify poor fMRI data at time of scanning, allowing for repeat scans when necessary. ROC-r analysis provides optimised and automated fMRI processing for improved presurgical mapping. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Preliminary identification of unicellular algal genus by using combined confocal resonance Raman spectroscopy with PCA and DPLS analysis

NASA Astrophysics Data System (ADS)

He, Shixuan; Xie, Wanyi; Zhang, Ping; Fang, Shaoxi; Li, Zhe; Tang, Peng; Gao, Xia; Guo, Jinsong; Tlili, Chaker; Wang, Deqiang

2018-02-01

The analysis of algae and dominant alga plays important roles in ecological and environmental fields since it can be used to forecast water bloom and control its potential deleterious effects. Herein, we combine in vivo confocal resonance Raman spectroscopy with multivariate analysis methods to preliminary identify the three algal genera in water blooms at unicellular scale. Statistical analysis of characteristic Raman peaks demonstrates that certain shifts and different normalized intensities, resulting from composition of different carotenoids, exist in Raman spectra of three algal cells. Principal component analysis (PCA) scores and corresponding loading weights show some differences from Raman spectral characteristics which are caused by vibrations of carotenoids in unicellular algae. Then, discriminant partial least squares (DPLS) classification method is used to verify the effectiveness of algal identification with confocal resonance Raman spectroscopy. Our results show that confocal resonance Raman spectroscopy combined with PCA and DPLS could handle the preliminary identification of dominant alga for forecasting and controlling of water blooms.

A comparison of analysis methods to estimate contingency strength.

PubMed

Lloyd, Blair P; Staubitz, Johanna L; Tapp, Jon T

2018-05-09

To date, several data analysis methods have been used to estimate contingency strength, yet few studies have compared these methods directly. To compare the relative precision and sensitivity of four analysis methods (i.e., exhaustive event-based, nonexhaustive event-based, concurrent interval, concurrent+lag interval), we applied all methods to a simulated data set in which several response-dependent and response-independent schedules of reinforcement were programmed. We evaluated the degree to which contingency strength estimates produced from each method (a) corresponded with expected values for response-dependent schedules and (b) showed sensitivity to parametric manipulations of response-independent reinforcement. Results indicated both event-based methods produced contingency strength estimates that aligned with expected values for response-dependent schedules, but differed in sensitivity to response-independent reinforcement. The precision of interval-based methods varied by analysis method (concurrent vs. concurrent+lag) and schedule type (continuous vs. partial), and showed similar sensitivities to response-independent reinforcement. Recommendations and considerations for measuring contingencies are identified. © 2018 Society for the Experimental Analysis of Behavior.

Changes in functional brain networks following sports-related concussion in adolescents.

PubMed

Virji-Babul, Naznin; Hilderman, Courtney G E; Makan, Nadia; Liu, Aiping; Smith-Forrester, Jenna; Franks, Chris; Wang, Z J

2014-12-01

Sports-related concussion is a major public health issue; however, little is known about the underlying changes in functional brain networks in adolescents following injury. Our aim was to use the tools from graph theory to evaluate the changes in brain network properties following concussion in adolescent athletes. We recorded resting state electroencephalography (EEG) in 33 healthy adolescent athletes and 9 adolescent athletes with a clinical diagnosis of subacute concussion. Graph theory analysis was applied to these data to evaluate changes in brain networks. Global and local metrics of the structural properties of the graph were calculated for each group and correlated with Immediate Post-Concussion Assessment and Cognitive Testing (ImPACT) scores. Brain networks of both groups showed small-world topology with no statistically significant differences in the global metrics; however, significant differences were found in the local metrics. Specifically, in the concussed group, we noted: 1) increased values of betweenness and degree in frontal electrode sites corresponding to the (R) dorsolateral prefrontal cortex and the (R) inferior frontal gyrus and 2) decreased values of degree in the region corresponding to the (R) frontopolar prefrontal cortex. In addition, there was significant negative correlation between degree and hub value, with total symptom score at the electrode site corresponding to the (R) prefrontal cortex. This preliminary report in adolescent athletes shows for the first time that resting-state EEG combined with graph theoretical analysis may provide an objective method of evaluating changes in brain networks following concussion. This approach may be useful in identifying individuals at risk for future injury.

Using air/water/sediment temperature contrasts to identify groundwater seepage locations in small streams

NASA Astrophysics Data System (ADS)

Karan, S.; Sebok, E.; Engesgaard, P. K.

2016-12-01

For identifying groundwater seepage locations in small streams within a headwater catchment, we present a method expanding on the linear regression of air and stream temperatures. Thus, by measuring the temperatures in dual-depth; in the stream column and at the streambed-water interface (SWI), we apply metrics from linear regression analysis of temperatures between air/stream and air/SWI (linear regression slope, intercept and coefficient of determination), and the daily mean temperatures (temperature variance and the average difference between the minimum and maximum daily temperatures). Our study show that using metrics from single-depth stream temperature measurements only are not sufficient to identify substantial groundwater seepage locations within a headwater stream. Conversely, comparing the metrics from dual-depth temperatures show significant differences so that at groundwater seepage locations, temperatures at the SWI, merely explain 43-75 % of the variation opposed to ≥91 % at the corresponding stream column temperatures. The figure showing a box-plot of the variation in daily mean temperature depict that at several locations there is great variation in the range the upper and lower loggers due to groundwater seepage. In general, the linear regression show that at these locations at the SWI, the slopes (<0.25) and intercepts (>6.5oC) are substantially lower and higher, while the mean diel amplitudes (<0.98oC) are decreased compared to remaining locations. The dual-depth approach was applied in a post-glacial fluvial setting, where metrics analyses overall corresponded to field measurements of groundwater fluxes deduced from vertical streambed temperatures and stream flow accretions. Thus, we propose a method reliably identifying groundwater seepage locations along streambed in such settings.

Hunter-gatherer dental pathology: Do historic accounts of Aboriginal Australians correspond to the archeological record of dental disease?

PubMed

Littleton, Judith

2018-03-01

Studies of hunter-gatherer oral pathology, particularly in Australia, often focus upon dental wear and caries or assume that historic studies of Aboriginal people reflect the precontact past. Consequently the range of population variation has been underestimated. In this paper dental pathology from human remains from Roonka are compared with a model of dental pathology derived from historic studies. The aim is to identify aspects of dental pathology indicative of regional or intra-population diversity. Adult dentitions (n = 115) dating from the mid to late Holocene were recorded for the following conditions: dental wear, caries, periapical voids, calculus, periodontal disease and antemortem tooth loss. Statistical analysis was used to identify patterns of dental pathology and to identify causal relationships between conditions. Dental wear is marked while dental caries rates are extremely low. Other indications of dental pathology are uncommon (<7% of teeth affected). Temporal heterogeneity is apparent: there are 3 young adults with caries who died in the postcontact period. There is also a small group of middle age to old adults with disproportionate abscessing and pulp exposure who may represent temporal variation or heterogeneity in individual frailty. The results confirm dental wear as the major cause of dental pathology in this group and that, at a general level, historic accounts do correspond with this archeological sample. However, intra-sample heterogeneity is apparent while 2 dental conditions, calculus and periodontal disease, along with the pattern of sex differences deviate from expectation, demonstrating that to identify regional variation attention needs to be paid to the dentoalveolar complex as a whole. © 2017 Wiley Periodicals, Inc.

Identification of a New Mullet Species Complex Based on an Integrative Molecular and Cytogenetic Investigation of Mugil hospes (Mugilidae: Mugiliformes).

PubMed

Nirchio, Mauro; Paim, Fabilene G; Milana, Valentina; Rossi, Anna R; Oliveira, Claudio

2018-01-01

Mullets are very common fishes included in the family Mugilidae, (Mugiliformes), which are characterized by both a remarkably uniform external morphology and internal anatomy. Recently, within this family, different species complexes were molecularly identified within Mugil , a genus which is characterized by lineages that sometimes show very different karyotypes. Here we report the results of cytogenetic and molecular analyses conducted on Mugil hospes , commonly known as the hospe mullet, from Ecuador. The study aims to verify whether the original described species from the Pacific Ocean corresponds to that identified in the Atlantic Ocean, and to identify species-specific chromosome markers that can add new comparative data about Mugilidae karyotype evolution. The karyotype of M. hospes from Ecuador is composed of 48 acrocentric chromosomes and shows two active nucleolar organizer regions (NORs). In situ hybridization, using different types of repetitive sequences (rDNAs, U1 snDNA, telomeric repeats) as probes, identified species-specific chromosome markers that have been compared with those of other species of the genus Mugil . Cytochrome c oxidase subunit I (COI) sequence analysis shows only 92-93% similarity with sequences previously deposited under this species name in GenBank, all of which were from the Atlantic Ocean. Phylogenetic reconstructions indicate the presence of three well-supported hospe mullet lineages whose molecular divergence is compatible with the presence of distinct species. Indeed, the first lineage includes samples from Ecuador, whereas the other two lineages include the Atlantic samples and correspond to M. brevirostris from Brazil and Mugil sp. R from Belize/Venezuela. Results here provided reiterate the pivotal importance of an integrative molecular and cytogenetic approach in the reconstruction of the relationships within Mugilidae.

Identification of a New Mullet Species Complex Based on an Integrative Molecular and Cytogenetic Investigation of Mugil hospes (Mugilidae: Mugiliformes)

PubMed Central

Nirchio, Mauro; Paim, Fabilene G.; Milana, Valentina; Rossi, Anna R.; Oliveira, Claudio

2018-01-01

Mullets are very common fishes included in the family Mugilidae, (Mugiliformes), which are characterized by both a remarkably uniform external morphology and internal anatomy. Recently, within this family, different species complexes were molecularly identified within Mugil, a genus which is characterized by lineages that sometimes show very different karyotypes. Here we report the results of cytogenetic and molecular analyses conducted on Mugil hospes, commonly known as the hospe mullet, from Ecuador. The study aims to verify whether the original described species from the Pacific Ocean corresponds to that identified in the Atlantic Ocean, and to identify species-specific chromosome markers that can add new comparative data about Mugilidae karyotype evolution. The karyotype of M. hospes from Ecuador is composed of 48 acrocentric chromosomes and shows two active nucleolar organizer regions (NORs). In situ hybridization, using different types of repetitive sequences (rDNAs, U1 snDNA, telomeric repeats) as probes, identified species-specific chromosome markers that have been compared with those of other species of the genus Mugil. Cytochrome c oxidase subunit I (COI) sequence analysis shows only 92–93% similarity with sequences previously deposited under this species name in GenBank, all of which were from the Atlantic Ocean. Phylogenetic reconstructions indicate the presence of three well-supported hospe mullet lineages whose molecular divergence is compatible with the presence of distinct species. Indeed, the first lineage includes samples from Ecuador, whereas the other two lineages include the Atlantic samples and correspond to M. brevirostris from Brazil and Mugil sp. R from Belize/Venezuela. Results here provided reiterate the pivotal importance of an integrative molecular and cytogenetic approach in the reconstruction of the relationships within Mugilidae. PMID:29459882

Microbial Contaminants of Cord Blood Units Identified by 16S rRNA Sequencing and by API Test System, and Antibiotic Sensitivity Profiling

PubMed Central

França, Luís; Simões, Catarina; Taborda, Marco; Diogo, Catarina; da Costa, Milton S.

2015-01-01

Over a period of ten months a total of 5618 cord blood units (CBU) were screened for microbial contamination under routine conditions. The antibiotic resistance profile for all isolates was also examined using ATB strips. The detection rate for culture positive units was 7.5%, corresponding to 422 samples.16S rRNA sequence analysis and identification with API test system were used to identify the culturable aerobic, microaerophilic and anaerobic bacteria from CBUs. From these samples we recovered 485 isolates (84 operational taxonomic units, OTUs) assigned to the classes Bacteroidia, Actinobacteria, Clostridia, Bacilli, Betaproteobacteria and primarily to the Gammaproteobacteria. Sixty-nine OTUs, corresponding to 447 isolates, showed 16S rRNA sequence similarities above 99.0% with known cultured bacteria. However, 14 OTUs had 16S rRNA sequence similarities between 95 and 99% in support of genus level identification and one OTU with 16S rRNA sequence similarity of 90.3% supporting a family level identification only. The phenotypic identification formed 29 OTUs that could be identified to the species level and 9 OTUs that could be identified to the genus level by API test system. We failed to obtain identification for 14 OTUs, while 32 OTUs comprised organisms producing mixed identifications. Forty-two OTUs covered species not included in the API system databases. The API test system Rapid ID 32 Strep and Rapid ID 32 E showed the highest proportion of identifications to the species level, the lowest ratio of unidentified results and the highest agreement to the results of 16S rRNA assignments. Isolates affiliated to the Bacilli and Bacteroidia showed the highest antibiotic multi-resistance indices and microorganisms of the Clostridia displayed the most antibiotic sensitive phenotypes. PMID:26512991

Microbial Contaminants of Cord Blood Units Identified by 16S rRNA Sequencing and by API Test System, and Antibiotic Sensitivity Profiling.

PubMed

França, Luís; Simões, Catarina; Taborda, Marco; Diogo, Catarina; da Costa, Milton S

2015-01-01

Over a period of ten months a total of 5618 cord blood units (CBU) were screened for microbial contamination under routine conditions. The antibiotic resistance profile for all isolates was also examined using ATB strips. The detection rate for culture positive units was 7.5%, corresponding to 422 samples.16S rRNA sequence analysis and identification with API test system were used to identify the culturable aerobic, microaerophilic and anaerobic bacteria from CBUs. From these samples we recovered 485 isolates (84 operational taxonomic units, OTUs) assigned to the classes Bacteroidia, Actinobacteria, Clostridia, Bacilli, Betaproteobacteria and primarily to the Gammaproteobacteria. Sixty-nine OTUs, corresponding to 447 isolates, showed 16S rRNA sequence similarities above 99.0% with known cultured bacteria. However, 14 OTUs had 16S rRNA sequence similarities between 95 and 99% in support of genus level identification and one OTU with 16S rRNA sequence similarity of 90.3% supporting a family level identification only. The phenotypic identification formed 29 OTUs that could be identified to the species level and 9 OTUs that could be identified to the genus level by API test system. We failed to obtain identification for 14 OTUs, while 32 OTUs comprised organisms producing mixed identifications. Forty-two OTUs covered species not included in the API system databases. The API test system Rapid ID 32 Strep and Rapid ID 32 E showed the highest proportion of identifications to the species level, the lowest ratio of unidentified results and the highest agreement to the results of 16S rRNA assignments. Isolates affiliated to the Bacilli and Bacteroidia showed the highest antibiotic multi-resistance indices and microorganisms of the Clostridia displayed the most antibiotic sensitive phenotypes.

The Comprehensive Evaluation Method of Supervision Risk in Electricity Transaction Based on Unascertained Rational Number

NASA Astrophysics Data System (ADS)

Haining, Wang; Lei, Wang; Qian, Zhang; Zongqiang, Zheng; Hongyu, Zhou; Chuncheng, Gao

2018-03-01

For the uncertain problems in the comprehensive evaluation of supervision risk in electricity transaction, this paper uses the unidentified rational numbers to evaluation the supervision risk, to obtain the possible result and corresponding credibility of evaluation and realize the quantification of risk indexes. The model can draw the risk degree of various indexes, which makes it easier for the electricity transaction supervisors to identify the transaction risk and determine the risk level, assisting the decision-making and realizing the effective supervision of the risk. The results of the case analysis verify the effectiveness of the model.

Usage of noncontact human body measurements for development of Army Work Wear Trousers

NASA Astrophysics Data System (ADS)

Dabolina, Inga; Lapkovska, Eva; Vilumsone, Ausma

2017-10-01

The paper is based on issues related to imperfections of clothing fit, garment construction solutions and control measurement systems of finished products, which were identified in the research process analysing army soldier work wear trousers. The aim is to obtain target group body measurements using noncontact anthropometrical data acquisition method (3D scanning) for selection and analysis of scanned data suitable for trouser design. Tasks include comparison of scanned data with manually taken body measurements and different corresponding human body measurement standard data for establishing potential advantages of noncontact method usage in solving different trouser design issues.

Statistical indicators of collective behavior and functional clusters in gene networks of yeast

NASA Astrophysics Data System (ADS)

Živković, J.; Tadić, B.; Wick, N.; Thurner, S.

2006-03-01

We analyze gene expression time-series data of yeast (S. cerevisiae) measured along two full cell-cycles. We quantify these data by using q-exponentials, gene expression ranking and a temporal mean-variance analysis. We construct gene interaction networks based on correlation coefficients and study the formation of the corresponding giant components and minimum spanning trees. By coloring genes according to their cell function we find functional clusters in the correlation networks and functional branches in the associated trees. Our results suggest that a percolation point of functional clusters can be identified on these gene expression correlation networks.

Overview of BioCreative II gene mention recognition.

PubMed

Smith, Larry; Tanabe, Lorraine K; Ando, Rie Johnson nee; Kuo, Cheng-Ju; Chung, I-Fang; Hsu, Chun-Nan; Lin, Yu-Shi; Klinger, Roman; Friedrich, Christoph M; Ganchev, Kuzman; Torii, Manabu; Liu, Hongfang; Haddow, Barry; Struble, Craig A; Povinelli, Richard J; Vlachos, Andreas; Baumgartner, William A; Hunter, Lawrence; Carpenter, Bob; Tsai, Richard Tzong-Han; Dai, Hong-Jie; Liu, Feng; Chen, Yifei; Sun, Chengjie; Katrenko, Sophia; Adriaans, Pieter; Blaschke, Christian; Torres, Rafael; Neves, Mariana; Nakov, Preslav; Divoli, Anna; Maña-López, Manuel; Mata, Jacinto; Wilbur, W John

2008-01-01

Nineteen teams presented results for the Gene Mention Task at the BioCreative II Workshop. In this task participants designed systems to identify substrings in sentences corresponding to gene name mentions. A variety of different methods were used and the results varied with a highest achieved F1 score of 0.8721. Here we present brief descriptions of all the methods used and a statistical analysis of the results. We also demonstrate that, by combining the results from all submissions, an F score of 0.9066 is feasible, and furthermore that the best result makes use of the lowest scoring submissions.

The non-radiating component of the field generated by a finite monochromatic scalar source distribution

NASA Astrophysics Data System (ADS)

Hoenders, Bernhard J.; Ferwerda, Hedzer A.

1998-09-01

We separate the field generated by a spherically symmetric bounded scalar monochromatic source into a radiative and non-radiative part. The non-radiative part is obtained by projecting the total field on the space spanned by the non-radiating inhomogeneous modes, i.e. the modes which satisfy the inhomogeneous wave equation. Using residue techniques, introduced by Cauchy, we obtain an explicit analytical expression for the non-radiating component. We also identify the part of the source distribution which corresponds to this non-radiating part. The analysis is based on the scalar wave equation.

Mueller matrix imaging and analysis of cancerous cells

NASA Astrophysics Data System (ADS)

Fernández, A.; Fernández-Luna, J. L.; Moreno, F.; Saiz, J. M.

2017-08-01

Imaging polarimetry is a focus of increasing interest in diagnostic medicine because of its non-invasive nature and its potential for recognizing abnormal tissues. However, handling polarimetric images is not an easy task, and different intermediate steps have been proposed to introduce physical parameters that may be helpful to interpret results. In this work, transmission Mueller matrices (MM) corresponding to cancer cell samples have been experimentally obtained, and three different transformations have been applied: MM-Polar Decomposition, MM-Transformation and MM-Differential Decomposition. Special attention has been paid to diattenuation as a sensitive parameter to identify apoptosis processes induced by cisplatin and etoposide.

Overview of BioCreative II gene mention recognition

PubMed Central

Smith, Larry; Tanabe, Lorraine K; Ando, Rie Johnson nee; Kuo, Cheng-Ju; Chung, I-Fang; Hsu, Chun-Nan; Lin, Yu-Shi; Klinger, Roman; Friedrich, Christoph M; Ganchev, Kuzman; Torii, Manabu; Liu, Hongfang; Haddow, Barry; Struble, Craig A; Povinelli, Richard J; Vlachos, Andreas; Baumgartner, William A; Hunter, Lawrence; Carpenter, Bob; Tsai, Richard Tzong-Han; Dai, Hong-Jie; Liu, Feng; Chen, Yifei; Sun, Chengjie; Katrenko, Sophia; Adriaans, Pieter; Blaschke, Christian; Torres, Rafael; Neves, Mariana; Nakov, Preslav; Divoli, Anna; Maña-López, Manuel; Mata, Jacinto; Wilbur, W John

2008-01-01

Nineteen teams presented results for the Gene Mention Task at the BioCreative II Workshop. In this task participants designed systems to identify substrings in sentences corresponding to gene name mentions. A variety of different methods were used and the results varied with a highest achieved F1 score of 0.8721. Here we present brief descriptions of all the methods used and a statistical analysis of the results. We also demonstrate that, by combining the results from all submissions, an F score of 0.9066 is feasible, and furthermore that the best result makes use of the lowest scoring submissions. PMID:18834493

Models of Pilot Behavior and Their Use to Evaluate the State of Pilot Training

NASA Astrophysics Data System (ADS)

Jirgl, Miroslav; Jalovecky, Rudolf; Bradac, Zdenek

2016-07-01

This article discusses the possibilities of obtaining new information related to human behavior, namely the changes or progressive development of pilots' abilities during training. The main assumption is that a pilot's ability can be evaluated based on a corresponding behavioral model whose parameters are estimated using mathematical identification procedures. The mean values of the identified parameters are obtained via statistical methods. These parameters are then monitored and their changes evaluated. In this context, the paper introduces and examines relevant mathematical models of human (pilot) behavior, the pilot-aircraft interaction, and an example of the mathematical analysis.

Optimal Reflectance, Transmittance, and Absorptance Wavebands and Band Ratios for the Estimation of Leaf Chlorophyll Concentration

NASA Technical Reports Server (NTRS)

Carter, Gregory A.; Spiering, Bruce A.

2000-01-01

The present study utilized regression analysis to identify: wavebands and band ratios within the 400-850 nm range that could be used to estimate total chlorophyll concentration with minimal error; and simple regression models that were most effective in estimating chlorophyll concentrations were measured for two broadleaved species, a broadleaved vine, a needle-leaved conifer, and a representative of the grass family.Overall, reflectance, transmittance, and absorptance corresponded most precisely with chlorophyll concentration at wavelengths near 700 nm, although regressions were strong as well in the 550-625 nm range.

Heterogeneity of link weight and the evolution of cooperation

NASA Astrophysics Data System (ADS)

Iwata, Manabu; Akiyama, Eizo

2016-04-01

In this paper, we investigate the effect of heterogeneity of link weight, heterogeneity of the frequency or amount of interactions among individuals, on the evolution of cooperation. Based on an analysis of the evolutionary prisoner's dilemma game on a weighted one-dimensional lattice network with intra-individual heterogeneity, we confirm that moderate level of link-weight heterogeneity can facilitate cooperation. Furthermore, we identify two key mechanisms by which link-weight heterogeneity promotes the evolution of cooperation: mechanisms for spread and maintenance of cooperation. We also derive the corresponding conditions under which the mechanisms can work through evolutionary dynamics.

Surface-enhanced Raman spectroscopy studies of yellow organic dyestuffs and lake pigments in oil paint.

PubMed

Mayhew, Hannah E; Fabian, David M; Svoboda, Shelley A; Wustholz, Kristin L

2013-08-21

Identifying natural, organic dyes and pigments is important for the conservation, preservation, and historical interpretation of works of art. Although previous SERS studies have demonstrated high sensitivity and selectivity for red lake pigments using various pretreatment conditions, corresponding investigations of yellow lake pigments and paints are relatively sparse. Here, surface-enhanced Raman scattering (SERS) spectroscopy is used to identify a variety of yellow organic dyestuffs and lake pigments in oil paint. High-quality SERS spectra of yellow dyestuffs (i.e., turmeric, old fustic, Buckthorn berries) and corresponding paints could be obtained with or without sample pretreatment using microliter quantities of HCl and methanol at room temperature. However, the SERS spectra of yellow lake pigments (i.e., Stil de Grain, Reseda lake) and their corresponding oil paints were only observed upon sample pretreatment. Ultimately, we demonstrate a reliable sample treatment protocol for SERS-based identification of turmeric, old fustic, Buckthorn berries, Stil de Grain, and Reseda lake as well as for microscopic samples of the corresponding oil paints.

Method and system employing finite state machine modeling to identify one of a plurality of different electric load types

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

Du, Liang; Yang, Yi; Harley, Ronald Gordon

A system is for a plurality of different electric load types. The system includes a plurality of sensors structured to sense a voltage signal and a current signal for each of the different electric loads; and a processor. The processor acquires a voltage and current waveform from the sensors for a corresponding one of the different electric load types; calculates a power or current RMS profile of the waveform; quantizes the power or current RMS profile into a set of quantized state-values; evaluates a state-duration for each of the quantized state-values; evaluates a plurality of state-types based on the powermore » or current RMS profile and the quantized state-values; generates a state-sequence that describes a corresponding finite state machine model of a generalized load start-up or transient profile for the corresponding electric load type; and identifies the corresponding electric load type.« less

Method and system employing graphical electric load categorization to identify one of a plurality of different electric load types

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

Yang, Yi; Du, Liang

A system for different electric loads includes sensors structured to sense voltage and current signals for each of the different electric loads; a hierarchical load feature database having a plurality of layers, with one of the layers including a plurality of different load categories; and a processor. The processor acquires voltage and current waveforms from the sensors for a corresponding one of the different electric loads; maps a voltage-current trajectory to a grid including a plurality of cells, each of which is assigned a binary value of zero or one; extracts a plurality of different features from the mapped gridmore » of cells as a graphical signature of the corresponding one of the different electric loads; derives a category of the corresponding one of the different electric loads from the database; and identifies one of a plurality of different electric load types for the corresponding one of the different electric loads.« less

Public Health Surveillance of Fatal Child Maltreatment: Analysis of 3 State Programs

PubMed Central

Schnitzer, Patricia G.; Covington, Theresa M.; Wirtz, Stephen J.; Verhoek-Oftedahl, Wendy; Palusci, Vincent J.

2008-01-01

Objectives. We sought to describe approaches to surveillance of fatal child maltreatment and to identify options for improving case ascertainment. Methods. Three states—California, Michigan, and Rhode Island—used multiple data sources for surveillance. Potential cases were identified, operational definitions were applied, and the number of maltreatment deaths was determined. Results. These programs identified 258 maltreatment deaths in California, 192 in Michigan, and 60 in Rhode Island. Corresponding maltreatment fatality rates ranged from 2.5 per 100000 population in Michigan to 8.8 in Rhode Island. Most deaths were identified by child death review teams in Rhode Island (98%), Uniform Crime Reports in California (56%), and child welfare agency data in Michigan (44%). Compared with the total number of cases identified, child welfare agency (the official source for maltreatment reports) and death certificate data underascertain child maltreatment deaths by 55% to 76% and 80% to 90%, respectively. In all 3 states, more than 90% of cases ascertained could be identified by combining 2 data sources. Conclusions. No single data source was adequate for thorough surveillance of fatal child maltreatment, but combining just 2 sources substantially increased case ascertainment. The child death review team process may be the most promising surveillance approach. PMID:17538060

Public health surveillance of fatal child maltreatment: analysis of 3 state programs.

PubMed

Schnitzer, Patricia G; Covington, Theresa M; Wirtz, Stephen J; Verhoek-Oftedahl, Wendy; Palusci, Vincent J

2008-02-01

We sought to describe approaches to surveillance of fatal child maltreatment and to identify options for improving case ascertainment. Three states--California, Michigan, and Rhode Island--used multiple data sources for surveillance. Potential cases were identified, operational definitions were applied, and the number of maltreatment deaths was determined. These programs identified 258 maltreatment deaths in California, 192 in Michigan, and 60 in Rhode Island. Corresponding maltreatment fatality rates ranged from 2.5 per 100,000 population in Michigan to 8.8 in Rhode Island. Most deaths were identified by child death review teams in Rhode Island (98%), Uniform Crime Reports in California (56%), and child welfare agency data in Michigan (44%). Compared with the total number of cases identified, child welfare agency (the official source for maltreatment reports) and death certificate data underascertain child maltreatment deaths by 55% to 76% and 80% to 90%, respectively. In all 3 states, more than 90% of cases ascertained could be identified by combining 2 data sources. No single data source was adequate for thorough surveillance of fatal child maltreatment, but combining just 2 sources substantially increased case ascertainment. The child death review team process may be the most promising surveillance approach.

Amygdala activity at encoding corresponds with memory vividness and with memory for select episodic details.

PubMed

Kensinger, Elizabeth A; Addis, Donna Rose; Atapattu, Ranga K

2011-03-01

It is well known that amygdala activity during encoding corresponds with subsequent memory for emotional information. It is less clear how amygdala activity relates to the subjective and objective qualities of a memory. In the present study, participants viewed emotional and neutral objects while undergoing a functional magnetic resonance imaging scan. Participants then took a memory test, identifying which verbal labels named a studied object and indicating the vividness of their memory for that object. They then retrieved episodic details associated with each object's presentation, selecting which object exemplar had been studied and indicating in which screen quadrant, study list, and with which encoding question the exemplar had been studied. Parametric analysis of the encoding data allowed examination of the processes that tracked with increasing memory vividness or with an increase in the diversity of episodic details remembered. Dissociable networks tracked these two increases, and amygdala activity corresponded with the former but not the latter. Subsequent-memory analyses revealed that amygdala activity corresponded with memory for exemplar type but not for other episodic features. These results emphasize that amygdala activity does not ensure accurate encoding of all types of episodic detail, yet it does support encoding of some item-specific details and leads to the retention of a memory that will feel subjectively vivid. The types of episodic details tied to amygdala engagement may be those that are most important for creating a subjectively vivid memory. Copyright © 2011 Elsevier Ltd. All rights reserved.

Amygdala Activity at Encoding Corresponds with Memory Vividness and with Memory for Select Episodic Details

PubMed Central

Kensinger, Elizabeth A.; Addis, Donna Rose; Atapattu, Ranga K.

2011-01-01

It is well known that amygdala activity during encoding corresponds with subsequent memory for emotional information. It is less clear how amygdala activity relates to the subjective and objective qualities of a memory. In the present study, participants viewed emotional and neutral objects while undergoing a functional magnetic resonance imaging scan. Participants then took a memory test, identifying which verbal labels named a studied object and indicating the vividness of their memory for that object. They then retrieved episodic details associated with each object’s presentation, selecting which object exemplar had been studied and indicating in which screen quadrant, study list, and with which encoding question the exemplar had been studied. Parametric analysis of the encoding data allowed examination of the processes that tracked with increasing memory vividness or with an increase in the diversity of episodic details remembered. Dissociable networks tracked these two increases, and amygdala activity corresponded with the former but not the latter. Subsequent-memory analyses revealed that amygdala activity corresponded with memory for exemplar type but not for other episodic features. These results emphasize that amygdala activity does not ensure accurate encoding of all types of episodic detail, yet it does support encoding of some item-specific details and leads to the retention of a memory that will feel subjectively vivid. The types of episodic details tied to amygdala engagement may be those that are most important for creating a subjectively vivid memory. PMID:21262244

Extensive cross-talk and global regulators identified from an analysis of the integrated transcriptional and signaling network in Escherichia coli.

PubMed

Antiqueira, Lucas; Janga, Sarath Chandra; Costa, Luciano da Fontoura

2012-11-01

To understand the regulatory dynamics of transcription factors (TFs) and their interplay with other cellular components we have integrated transcriptional, protein-protein and the allosteric or equivalent interactions which mediate the physiological activity of TFs in Escherichia coli. To study this integrated network we computed a set of network measurements followed by principal component analysis (PCA), investigated the correlations between network structure and dynamics, and carried out a procedure for motif detection. In particular, we show that outliers identified in the integrated network based on their network properties correspond to previously characterized global transcriptional regulators. Furthermore, outliers are highly and widely expressed across conditions, thus supporting their global nature in controlling many genes in the cell. Motifs revealed that TFs not only interact physically with each other but also obtain feedback from signals delivered by signaling proteins supporting the extensive cross-talk between different types of networks. Our analysis can lead to the development of a general framework for detecting and understanding global regulatory factors in regulatory networks and reinforces the importance of integrating multiple types of interactions in underpinning the interrelationships between them.

Identification of microRNAs differentially expressed involved in male flower development.

PubMed

Wang, Zhengjia; Huang, Jianqin; Sun, Zhichao; Zheng, Bingsong

2015-03-01

Hickory (Carya cathayensis Sarg.) is one of the most economically important woody trees in eastern China, but its long flowering phase delays yield. Our understanding of the regulatory roles of microRNAs (miRNAs) in male flower development in hickory remains poor. Using high-throughput sequencing technology, we have pyrosequenced two small RNA libraries from two male flower differentiation stages in hickory. Analysis of the sequencing data identified 114 conserved miRNAs that belonged to 23 miRNA families, five novel miRNAs including their corresponding miRNA*s, and 22 plausible miRNA candidates. Differential expression analysis revealed 12 miRNA sequences that were upregulated in the later (reproductive) stage of male flower development. Quantitative real-time PCR showed similar expression trends as that of the deep sequencing. Novel miRNAs and plausible miRNA candidates were predicted using bioinformatic analysis methods. The miRNAs newly identified in this study have increased the number of known miRNAs in hickory, and the identification of differentially expressed miRNAs will provide new avenues for studies into miRNAs involved in the process of male flower development in hickory and other related trees.

Syntax-directed content analysis of videotext: application to a map detection recognition system

NASA Astrophysics Data System (ADS)

Aradhye, Hrishikesh; Herson, James A.; Myers, Gregory

2003-01-01

Video is an increasingly important and ever-growing source of information to the intelligence and homeland defense analyst. A capability to automatically identify the contents of video imagery would enable the analyst to index relevant foreign and domestic news videos in a convenient and meaningful way. To this end, the proposed system aims to help determine the geographic focus of a news story directly from video imagery by detecting and geographically localizing political maps from news broadcasts, using the results of videotext recognition in lieu of a computationally expensive, scale-independent shape recognizer. Our novel method for the geographic localization of a map is based on the premise that the relative placement of text superimposed on a map roughly corresponds to the geographic coordinates of the locations the text represents. Our scheme extracts and recognizes videotext, and iteratively identifies the geographic area, while allowing for OCR errors and artistic freedom. The fast and reliable recognition of such maps by our system may provide valuable context and supporting evidence for other sources, such as speech recognition transcripts. The concepts of syntax-directed content analysis of videotext presented here can be extended to other content analysis systems.

Estimated Flood Discharges and Map of Flood-Inundated Areas for Omaha Creek, near Homer, Nebraska, 2005

USGS Publications Warehouse

Dietsch, Benjamin J.; Wilson, Richard C.; Strauch, Kellan R.

2008-01-01

Repeated flooding of Omaha Creek has caused damage in the Village of Homer. Long-term degradation and bridge scouring have changed substantially the channel characteristics of Omaha Creek. Flood-plain managers, planners, homeowners, and others rely on maps to identify areas at risk of being inundated. To identify areas at risk for inundation by a flood having a 1-percent annual probability, maps were created using topographic data and water-surface elevations resulting from hydrologic and hydraulic analyses. The hydrologic analysis for the Omaha Creek study area was performed using historical peak flows obtained from the U.S. Geological Survey streamflow gage (station number 06601000). Flood frequency and magnitude were estimated using the PEAKFQ Log-Pearson Type III analysis software. The U.S. Army Corps of Engineers' Hydrologic Engineering Center River Analysis System, version 3.1.3, software was used to simulate the water-surface elevation for flood events. The calibrated model was used to compute streamflow-gage stages and inundation elevations for the discharges corresponding to floods of selected probabilities. Results of the hydrologic and hydraulic analyses indicated that flood inundation elevations are substantially lower than from a previous study.

Brain tumor classification using AFM in combination with data mining techniques.

PubMed

Huml, Marlene; Silye, René; Zauner, Gerald; Hutterer, Stephan; Schilcher, Kurt

2013-01-01

Although classification of astrocytic tumors is standardized by the WHO grading system, which is mainly based on microscopy-derived, histomorphological features, there is great interobserver variability. The main causes are thought to be the complexity of morphological details varying from tumor to tumor and from patient to patient, variations in the technical histopathological procedures like staining protocols, and finally the individual experience of the diagnosing pathologist. Thus, to raise astrocytoma grading to a more objective standard, this paper proposes a methodology based on atomic force microscopy (AFM) derived images made from histopathological samples in combination with data mining techniques. By comparing AFM images with corresponding light microscopy images of the same area, the progressive formation of cavities due to cell necrosis was identified as a typical morphological marker for a computer-assisted analysis. Using genetic programming as a tool for feature analysis, a best model was created that achieved 94.74% classification accuracy in distinguishing grade II tumors from grade IV ones. While utilizing modern image analysis techniques, AFM may become an important tool in astrocytic tumor diagnosis. By this way patients suffering from grade II tumors are identified unambiguously, having a less risk for malignant transformation. They would benefit from early adjuvant therapies.

[Isolation and identification of specific sequences correlated to cytoplasmic male sterility and fertile maintenance in cauliflower (Brassica oleracea var. botrytis)].

PubMed

Wang, Chun Guo; Chen, Xiao Qiang; Li, Hui; Zhao, Qian Cheng; Sun, De Ling; Song, Wen Qin

2008-02-01

Analysis of ISSR (Inter-Simple Sequence Repeat) and DDRT-PCR (Differential Display Reverse Transcriptase Polymerase Chain Reaction) was performed between cytoplasmic male sterility cauliflower ogura-A and its corresponding maintainer line ogura-B. Totally, 306 detectable bands were obtained by ISSR using thirty oligonucleotide primers. Commonly, six to twelve bands were produced per primer. Among all these primers only the amplification of primer ISSR3 was polymorphic, an 1100 bp specific band was only detected in maintainer line, named ISSR3(1100). Analysis of this sequence indicated that ISSR3(1100) was high homologous with the corresponding sequences of mitochondrial genome in Brassica napus and Arabidopsis thaliana,which suggested that ISSR3(1100) may derive from mitochondrial genome in cauliflower. To carry out DDRT-PCR analysis, three anchor primers and fifteen random primers were selected to combine. Totally, 1122 bands from 1 000 bp to 50 bp were detected. However, only four bands, named ogura-A 205, ogura-A383, ogura-B307 and ogura-B352, were confirmed to be different display in both lines. This result was further identified by reverse Northern dot blotting analysis. Among these four bands, ogura-A205 and ogura-A383 only express in cytoplasmic male sterility line, while ogura-B307 and ogura-B352 were only detected in maintainer line. Analysis of these sequences indicated that it was the first time that these four sequences were reported in cauliflower. Interestingly, ogura-A205 and ogura-B307 did not exhibit any similarities to other reported sequences in other species, more investigations were required to obtain further information. ogura-A383 and ogura-B352 were also two new sequences, they showed high similarities to corresponding chloroplast sequences of Arabidopsis thaliana and Brassica rapa subsp. pekinensis. So we speculated that these two sequences may derive from chloroplast genome. All these results obtained in this study offer new and significant information to investigate the molecular mechanism of cytoplasmic male sterility and fertile maintenance in cauliflower.

Comparative Study of Lectin Domains in Model Species: New Insights into Evolutionary Dynamics

PubMed Central

Van Holle, Sofie; De Schutter, Kristof; Eggermont, Lore; Tsaneva, Mariya; Dang, Liuyi; Van Damme, Els J. M.

2017-01-01

Lectins are present throughout the plant kingdom and are reported to be involved in diverse biological processes. In this study, we provide a comparative analysis of the lectin families from model species in a phylogenetic framework. The analysis focuses on the different plant lectin domains identified in five representative core angiosperm genomes (Arabidopsis thaliana, Glycine max, Cucumis sativus, Oryza sativa ssp. japonica and Oryza sativa ssp. indica). The genomes were screened for genes encoding lectin domains using a combination of Basic Local Alignment Search Tool (BLAST), hidden Markov models, and InterProScan analysis. Additionally, phylogenetic relationships were investigated by constructing maximum likelihood phylogenetic trees. The results demonstrate that the majority of the lectin families are present in each of the species under study. Domain organization analysis showed that most identified proteins are multi-domain proteins, owing to the modular rearrangement of protein domains during evolution. Most of these multi-domain proteins are widespread, while others display a lineage-specific distribution. Furthermore, the phylogenetic analyses reveal that some lectin families evolved to be similar to the phylogeny of the plant species, while others share a closer evolutionary history based on the corresponding protein domain architecture. Our results yield insights into the evolutionary relationships and functional divergence of plant lectins. PMID:28587095

Comparative analysis of 16S rRNA and amoA genes from archaea selected with organic and inorganic amendments in enrichment culture.

PubMed

Xu, Mouzhong; Schnorr, Jon; Keibler, Brandon; Simon, Holly M

2012-04-01

We took advantage of a plant-root enrichment culture system to characterize mesophilic soil archaea selected through the use of organic and inorganic amendments. Comparative analysis of 16S rRNA and amoA genes indicated that specific archaeal clades were selected under different conditions. Three amoA sequence clades were identified, while for a fourth group, identified by 16S rRNA gene analysis alone and referred to as the "root" clade, we detected no corresponding amoA gene. The amoA-containing archaea were present in media with either organic or inorganic amendments, whereas archaea representing the root clade were present only when organic amendment was used. Analysis of amoA gene abundance and expression, together with nitrification-coupled growth assays, indicated potential growth by autotrophic ammonia oxidation for members of two group 1.1b clades. Increased abundance of one of these clades, however, also occurred upon the addition of organic amendment. Finally, although amoA-containing group 1.1a archaea were present in enrichments, we detected neither expression of amoA genes nor evidence for nitrification-coupled growth of these organisms. These data support a model of a diverse metabolic community in mesophilic soil archaea that is just beginning to be characterized.

Global Qualitative Flow-Path Modeling for Local State Determination in Simulation and Analysis

NASA Technical Reports Server (NTRS)

Malin, Jane T. (Inventor); Fleming, Land D. (Inventor)

1998-01-01

For qualitative modeling and analysis, a general qualitative abstraction of power transmission variables (flow and effort) for elements of flow paths includes information on resistance, net flow, permissible directions of flow, and qualitative potential is discussed. Each type of component model has flow-related variables and an associated internal flow map, connected into an overall flow network of the system. For storage devices, the implicit power transfer to the environment is represented by "virtual" circuits that include an environmental junction. A heterogeneous aggregation method simplifies the path structure. A method determines global flow-path changes during dynamic simulation and analysis, and identifies corresponding local flow state changes that are effects of global configuration changes. Flow-path determination is triggered by any change in a flow-related device variable in a simulation or analysis. Components (path elements) that may be affected are identified, and flow-related attributes favoring flow in the two possible directions are collected for each of them. Next, flow-related attributes are determined for each affected path element, based on possibly conflicting indications of flow direction. Spurious qualitative ambiguities are minimized by using relative magnitudes and permissible directions of flow, and by favoring flow sources over effort sources when comparing flow tendencies. The results are output to local flow states of affected components.

Validation of reference genes for quantitative real-time PCR during leaf and flower development in Petunia hybrida

PubMed Central

2010-01-01

Background Identification of genes with invariant levels of gene expression is a prerequisite for validating transcriptomic changes accompanying development. Ideally expression of these genes should be independent of the morphogenetic process or environmental condition tested as well as the methods used for RNA purification and analysis. Results In an effort to identify endogenous genes meeting these criteria nine reference genes (RG) were tested in two Petunia lines (Mitchell and V30). Growth conditions differed in Mitchell and V30, and different methods were used for RNA isolation and analysis. Four different software tools were employed to analyze the data. We merged the four outputs by means of a non-weighted unsupervised rank aggregation method. The genes identified as optimal for transcriptomic analysis of Mitchell and V30 were EF1α in Mitchell and CYP in V30, whereas the least suitable gene was GAPDH in both lines. Conclusions The least adequate gene turned out to be GAPDH indicating that it should be rejected as reference gene in Petunia. The absence of correspondence of the best-suited genes suggests that assessing reference gene stability is needed when performing normalization of data from transcriptomic analysis of flower and leaf development. PMID:20056000

Two-phase Hele-Shaw flow with a moving contact line

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

Weinstein, S.J.; Ungar, L.H.; Dussan, E.B.

1988-01-01

An asymptotic analysis is presented for Hele-Shaw viscous fingering with a moving contact line at flow rates. As in problems where a thin film is present instead of a contact line, the narrow gap limit is nonuniform, and interfacial boundary conditions valid for the Hele-Shaw equations must be determined in order to predict the flow field and interface shape. Many well-posed boundary-value problems can be identified, each corresponding to a different flow regime characterized by the relative sizes of the capillary number (dimensionless velocity) and the dimensionless gap width. These problems incorporate terms corresponding to the gapwise component of themore » interfacial curvature (the curvature in the cross-sectional view of the Hele-Shaw cell) and spanwise curvature (seen in the top view of the cell) in different ways. Nonunique interface solutions typically arise as in the analogous thin film problems. The relationships between the curvature terms, the spectra of allowable solutions, and the implications for stability are discussed.« less

Possible climate-related signals in high-resolution topography of lobate debris aprons in Tempe Terra, Mars

NASA Astrophysics Data System (ADS)

Grindrod, Peter M.; Fawcett, Stephen A.

2011-10-01

Lobate debris aprons are common features in the mid-latitudes of Mars that are assumed to be the result of the flow of ice-rich material. We produce high-resolution digital elevation models of two of these features in the Tempe Terra region of Mars using HiRISE stereo images. We identify two main topographic features of different wavelength using a power spectrum analysis approach. Short wavelength features, between approximately 10 and 20 m in length, correspond to a polygonal surface texture present throughout our study area. Long wavelength features, between approximately 700 and 1800 m in length, correspond to broad ridges that are up to 20 m in amplitude. We interpret both topographic signals to be the likely result of climate change affecting the debris contribution and/or the flow regime of the lobate debris aprons. The apparent surface age of about 300 Ma could be evidence of an astronomical forcing mechanism recorded in these lobate debris aprons at this time in Mars' history.

Correspondence of the brain's functional architecture during activation and rest

PubMed Central

Smith, Stephen M.; Fox, Peter T.; Miller, Karla L.; Glahn, David C.; Fox, P. Mickle; Mackay, Clare E.; Filippini, Nicola; Watkins, Kate E.; Toro, Roberto; Laird, Angela R.; Beckmann, Christian F.

2009-01-01

Neural connections, providing the substrate for functional networks, exist whether or not they are functionally active at any given moment. However, it is not known to what extent brain regions are continuously interacting when the brain is “at rest.” In this work, we identify the major explicit activation networks by carrying out an image-based activation network analysis of thousands of separate activation maps derived from the BrainMap database of functional imaging studies, involving nearly 30,000 human subjects. Independently, we extract the major covarying networks in the resting brain, as imaged with functional magnetic resonance imaging in 36 subjects at rest. The sets of major brain networks, and their decompositions into subnetworks, show close correspondence between the independent analyses of resting and activation brain dynamics. We conclude that the full repertoire of functional networks utilized by the brain in action is continuously and dynamically “active” even when at “rest.” PMID:19620724

Monte-Carlo-based uncertainty propagation with hierarchical models—a case study in dynamic torque

NASA Astrophysics Data System (ADS)

Klaus, Leonard; Eichstädt, Sascha

2018-04-01

For a dynamic calibration, a torque transducer is described by a mechanical model, and the corresponding model parameters are to be identified from measurement data. A measuring device for the primary calibration of dynamic torque, and a corresponding model-based calibration approach, have recently been developed at PTB. The complete mechanical model of the calibration set-up is very complex, and involves several calibration steps—making a straightforward implementation of a Monte Carlo uncertainty evaluation tedious. With this in mind, we here propose to separate the complete model into sub-models, with each sub-model being treated with individual experiments and analysis. The uncertainty evaluation for the overall model then has to combine the information from the sub-models in line with Supplement 2 of the Guide to the Expression of Uncertainty in Measurement. In this contribution, we demonstrate how to carry this out using the Monte Carlo method. The uncertainty evaluation involves various input quantities of different origin and the solution of a numerical optimisation problem.

Morphometric Variation on the Cypress Aphid Cinara cupressi (Buckton) (Hemiptera: Aphididae) Associated to Urban Trees.

PubMed

Ruiz, C; Lanfranco, D; Carrillo, R; Parra, L

2014-06-01

Cinara cupressi (Buckton) is an important aphid pest of the Cupressaceae family, originally reported in Chile in 2003. Since then, it has spread over 4,000 km, contributing to conservation issues, mostly associated with native and urban trees of the Cupressaceae. In the present work, the morphometric variation of C. cupressi was examined to determine if the species present in Chile corresponds to a specific entity, and to identify variations among specimens from different localities in the study area. Colonies were collected from urban trees from northern, central, and southern Chile. Morphometric data for 14 characters in aphids from 63 localities in all the distribution ranges were measured and analyzed by multivariate analysis. Results showed that the species present in Chile corresponds to C. cupressi like a single specific entity, showing no morphological variation across the regions sampled. Our data will be discussed within the context of correct taxonomic identification for the implementation of effective biological control strategies.

Human Genome Replication Proceeds through Four Chromatin States

PubMed Central

Julienne, Hanna; Zoufir, Azedine; Audit, Benjamin; Arneodo, Alain

2013-01-01

Advances in genomic studies have led to significant progress in understanding the epigenetically controlled interplay between chromatin structure and nuclear functions. Epigenetic modifications were shown to play a key role in transcription regulation and genome activity during development and differentiation or in response to the environment. Paradoxically, the molecular mechanisms that regulate the initiation and the maintenance of the spatio-temporal replication program in higher eukaryotes, and in particular their links to epigenetic modifications, still remain elusive. By integrative analysis of the genome-wide distributions of thirteen epigenetic marks in the human cell line K562, at the 100 kb resolution of corresponding mean replication timing (MRT) data, we identify four major groups of chromatin marks with shared features. These states have different MRT, namely from early to late replicating, replication proceeds though a transcriptionally active euchromatin state (C1), a repressive type of chromatin (C2) associated with polycomb complexes, a silent state (C3) not enriched in any available marks, and a gene poor HP1-associated heterochromatin state (C4). When mapping these chromatin states inside the megabase-sized U-domains (U-shaped MRT profile) covering about 50% of the human genome, we reveal that the associated replication fork polarity gradient corresponds to a directional path across the four chromatin states, from C1 at U-domains borders followed by C2, C3 and C4 at centers. Analysis of the other genome half is consistent with early and late replication loci occurring in separate compartments, the former correspond to gene-rich, high-GC domains of intermingled chromatin states C1 and C2, whereas the latter correspond to gene-poor, low-GC domains of alternating chromatin states C3 and C4 or long C4 domains. This new segmentation sheds a new light on the epigenetic regulation of the spatio-temporal replication program in human and provides a framework for further studies in different cell types, in both health and disease. PMID:24130466

Interstellar Protons in the TeV γ-Ray SNR HESS J1731-347: Possible Evidence for the Coexistence of Hadronic and Leptonic γ-Rays

NASA Astrophysics Data System (ADS)

Fukuda, T.; Yoshiike, S.; Sano, H.; Torii, K.; Yamamoto, H.; Acero, F.; Fukui, Y.

2014-06-01

HESS J1731-347 (G353.6-0.7) is one of the TeV γ-ray supernova remnants (SNRs) that shows the shell-like morphology. We have made a new analysis of the interstellar protons toward the SNR by using both the 12CO(J = 1-0) and H I data sets. The results indicate that the TeV γ-ray shell shows significant spatial correlation with the interstellar protons at a velocity range from -90 km s-1 to -75 km s-1. The total mass of the interstellar medium (ISM) protons is estimated to be 6.4 × 104 M ⊙, 25% of which is atomic gas, and the distance corresponding to the velocity range is ~5.2 kpc, a factor of 2 larger than the previous figure, 3 kpc. We have identified the cold H I gas observed as self-absorption which shows significant correspondence with the northeastern γ-ray peak. While the good correspondence between the ISM protons and TeV γ-rays in the north of the SNR lends support to the hadronic scenario for the TeV γ-rays, the southern part of the shell shows a break in the correspondence; in particular, the southwestern rim of the SNR shell shows a significant decrease of the interstellar protons by a factor of two. We argue that this discrepancy can be explained due to leptonic γ-rays because this region coincides well with the bright shell that emits non-thermal radio continuum emission and non-thermal X-rays, suggesting that the γ-rays of HESS J1713-347 consist of both the hadronic and leptonic components. The leptonic contribution corresponds to ~20% of the total γ-rays.

Comparing the Maryland Comprehensive Cancer Control Plan With Federal Cancer Prevention and Control Recommendations

PubMed Central

Platz, Elizabeth A.; Diener-West, Marie; Hokenmaier, Sarah; Truss, Meredith; Lewis, Courtney; Kanarek, Norma F.

2015-01-01

Introduction Since the introduction of the Affordable Care Act (ACA) in 2012, 11 million more Americans now have access to preventive services via health care coverage. Several prevention-related recommendations issued by the US Preventive Services Task Force (USPSTF), Centers for Disease Control and Prevention (CDC), and Advisory Committee on Immunization Practices (ACIP) are covered under the ACA. State cancer plans often provide prevention strategies, but whether these strategies correspond to federal evidence-based recommendations is unclear. The objective of this article is to assess whether federal evidence-based recommendations, including those covered under the ACA, are included in the Maryland Comprehensive Cancer Control Plan (MCCCP). Methods A total of 19 federal recommendations pertaining to cancer prevention and control were identified. Inclusion of federal cancer-related recommendations by USPSTF, CDC, and ACIP in the MCCCP’s goals, objectives, and strategies was examined. Results Nine of the federal recommendations were issued after the MCCCP’s publication. MCCCP recommendations corresponded completely with 4 federal recommendations and corresponded only partially with 3. Reasons for partial correspondence included specification of less restrictive at-risk populations or different intervention implementers. Three federal recommendations were not mentioned in the MCCCP’s goals, objectives, and strategies. Conclusion Many cancer-related federal recommendations were released after the MCCCP’s publication and therefore do not appear in the most current version. We recommend that the results of this analysis be considered in the update of the MCCCP. Our findings underscore the need for a periodic scan for changes to federal recommendations and for adjusting state policies and programs to correspond with federal recommendations, as appropriate for Marylanders. PMID:26425867

Gene Expression Correlated with Severe Asthma Characteristics Reveals Heterogeneous Mechanisms of Severe Disease.

PubMed

Modena, Brian D; Bleecker, Eugene R; Busse, William W; Erzurum, Serpil C; Gaston, Benjamin M; Jarjour, Nizar N; Meyers, Deborah A; Milosevic, Jadranka; Tedrow, John R; Wu, Wei; Kaminski, Naftali; Wenzel, Sally E

2017-06-01

Severe asthma (SA) is a heterogeneous disease with multiple molecular mechanisms. Gene expression studies of bronchial epithelial cells in individuals with asthma have provided biological insight and underscored possible mechanistic differences between individuals. Identify networks of genes reflective of underlying biological processes that define SA. Airway epithelial cell gene expression from 155 subjects with asthma and healthy control subjects in the Severe Asthma Research Program was analyzed by weighted gene coexpression network analysis to identify gene networks and profiles associated with SA and its specific characteristics (i.e., pulmonary function tests, quality of life scores, urgent healthcare use, and steroid use), which potentially identified underlying biological processes. A linear model analysis confirmed these findings while adjusting for potential confounders. Weighted gene coexpression network analysis constructed 64 gene network modules, including modules corresponding to T1 and T2 inflammation, neuronal function, cilia, epithelial growth, and repair mechanisms. Although no network selectively identified SA, genes in modules linked to epithelial growth and repair and neuronal function were markedly decreased in SA. Several hub genes of the epithelial growth and repair module were found located at the 17q12-21 locus, near a well-known asthma susceptibility locus. T2 genes increased with severity in those treated with corticosteroids but were also elevated in untreated, mild-to-moderate disease compared with healthy control subjects. T1 inflammation, especially when associated with increased T2 gene expression, was elevated in a subgroup of younger patients with SA. In this hypothesis-generating analysis, gene expression networks in relation to asthma severity provided potentially new insight into biological mechanisms associated with the development of SA and its phenotypes.

Gene Expression Correlated with Severe Asthma Characteristics Reveals Heterogeneous Mechanisms of Severe Disease

PubMed Central

Modena, Brian D.; Bleecker, Eugene R.; Busse, William W.; Erzurum, Serpil C.; Gaston, Benjamin M.; Jarjour, Nizar N.; Meyers, Deborah A.; Milosevic, Jadranka; Tedrow, John R.; Wu, Wei; Kaminski, Naftali

2017-01-01

Rationale: Severe asthma (SA) is a heterogeneous disease with multiple molecular mechanisms. Gene expression studies of bronchial epithelial cells in individuals with asthma have provided biological insight and underscored possible mechanistic differences between individuals. Objectives: Identify networks of genes reflective of underlying biological processes that define SA. Methods: Airway epithelial cell gene expression from 155 subjects with asthma and healthy control subjects in the Severe Asthma Research Program was analyzed by weighted gene coexpression network analysis to identify gene networks and profiles associated with SA and its specific characteristics (i.e., pulmonary function tests, quality of life scores, urgent healthcare use, and steroid use), which potentially identified underlying biological processes. A linear model analysis confirmed these findings while adjusting for potential confounders. Measurements and Main Results: Weighted gene coexpression network analysis constructed 64 gene network modules, including modules corresponding to T1 and T2 inflammation, neuronal function, cilia, epithelial growth, and repair mechanisms. Although no network selectively identified SA, genes in modules linked to epithelial growth and repair and neuronal function were markedly decreased in SA. Several hub genes of the epithelial growth and repair module were found located at the 17q12–21 locus, near a well-known asthma susceptibility locus. T2 genes increased with severity in those treated with corticosteroids but were also elevated in untreated, mild-to-moderate disease compared with healthy control subjects. T1 inflammation, especially when associated with increased T2 gene expression, was elevated in a subgroup of younger patients with SA. Conclusions: In this hypothesis-generating analysis, gene expression networks in relation to asthma severity provided potentially new insight into biological mechanisms associated with the development of SA and its phenotypes. PMID:27984699

Content validity of the DSM-IV borderline and narcissistic personality disorder criteria sets.

PubMed

Blais, M A; Hilsenroth, M J; Castlebury, F D

1997-01-01

This study sought to empirically evaluate the content validity of the newly revised DSM-IV narcissistic personality disorder (NPD) and borderline personality disorder (BPD) criteria sets. Using the essential features of each disorder as construct definitions, factor analysis was used to determine how adequately the criteria sets covered the constructs. In addition, this empirical investigation sought to: 1) help define the dimensions underlying these polythetic disorders; 2) identify core features of each diagnosis; and 3) highlight the characteristics that may be most useful in diagnosing these two disorders. Ninety-one outpatients meeting DSM-IV criteria for a personality disorder (PD) were identified through a retrospective analysis of chart information. Records of these 91 patients were independently rated on all of the BPD and NPD symptom criteria for the DSM-IV. Acceptable interrater reliability (kappa estimates) was obtained for both presence or absence of a PD and symptom criteria for BPD and NPD. The factor analysis, performed separately for each disorder, identified a three-factor solution for both the DSM-IV BPD and NPD criteria sets. The results of this study provide strong support for the content validity of the NPD criteria set and moderate support for the content validly of the BPD criteria set. Three domains were found to comprise the BPD criteria set, with the essential features of interpersonal and identity instability forming one domain, and impulsivity and affective instability each identified as separate domains. Factor analysis of the NPD criteria set found three factors basically corresponding to the essential features of grandiosity, lack of empathy, and need for admiration. Therefore, the NPD criteria set adequately covers the essential or defining features of the disorder.

N-linked (N-) glycoproteomics of urinary exosomes. [Corrected].

PubMed

Saraswat, Mayank; Joenväära, Sakari; Musante, Luca; Peltoniemi, Hannu; Holthofer, Harry; Renkonen, Risto

2015-02-01

Epithelial cells lining the urinary tract secrete urinary exosomes (40-100 nm) that can be targeted to specific cells modulating their functionality. One potential targeting mechanism is adhesion between vesicle surface glycoproteins and target cells. This makes the glycopeptide analysis of exosomes important. Exosomes reflect the physiological state of the parent cells; therefore, they are a good source of biomarkers for urological and other diseases. Moreover, the urine collection is easy and noninvasive and urinary exosomes give information about renal and systemic organ systems. Accordingly, multiple studies on proteomic characterization of urinary exosomes in health and disease have been published. However, no systematic analysis of their glycoproteomic profile has been carried out to date, whereas a conserved glycan signature has been found for exosomes from urine and other sources including T cell lines and human milk. Here, we have enriched and identified the N-glycopeptides from these vesicles. These enriched N-glycopeptides were solved for their peptide sequence, glycan composition, structure, and glycosylation site using collision-induced dissociation MS/MS (CID-tandem MS) data interpreted by a publicly available software GlycopeptideId. Released glycans from the same sample was also analyzed with MALDI-MS. We have identified the N-glycoproteome of urinary exosomes. In total 126 N-glycopeptides from 51 N-glycosylation sites belonging to 37 glycoproteins were found in our results. The peptide sequences of these N-glycopeptides were identified unambiguously and their glycan composition (for 125 N-glycopeptides) and structures (for 87 N-glycopeptides) were proposed. A corresponding glycomic analysis with released N-glycans was also performed. We identified 66 unique nonmodified N-glycan compositions and in addition 13 sulfated/phosphorylated glycans were also found. This is the first systematic analysis of N-glycoproteome of urinary exosomes. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

The Human Pancreas Proteome Defined by Transcriptomics and Antibody-Based Profiling

PubMed Central

Fagerberg, Linn; Hallström, Björn M.; Schwenk, Jochen M.; Uhlén, Mathias; Korsgren, Olle; Lindskog, Cecilia

2014-01-01

The pancreas is composed of both exocrine glands and intermingled endocrine cells to execute its diverse functions, including enzyme production for digestion of nutrients and hormone secretion for regulation of blood glucose levels. To define the molecular constituents with elevated expression in the human pancreas, we employed a genome-wide RNA sequencing analysis of the human transcriptome to identify genes with elevated expression in the human pancreas. This quantitative transcriptomics data was combined with immunohistochemistry-based protein profiling to allow mapping of the corresponding proteins to different compartments and specific cell types within the pancreas down to the single cell level. Analysis of whole pancreas identified 146 genes with elevated expression levels, of which 47 revealed a particular higher expression as compared to the other analyzed tissue types, thus termed pancreas enriched. Extended analysis of in vitro isolated endocrine islets identified an additional set of 42 genes with elevated expression in these specialized cells. Although only 0.7% of all genes showed an elevated expression level in the pancreas, this fraction of transcripts, in most cases encoding secreted proteins, constituted 68% of the total mRNA in pancreas. This demonstrates the extreme specialization of the pancreas for production of secreted proteins. Among the elevated expression profiles, several previously not described proteins were identified, both in endocrine cells (CFC1, FAM159B, RBPJL and RGS9) and exocrine glandular cells (AQP12A, DPEP1, GATM and ERP27). In summary, we provide a global analysis of the pancreas transcriptome and proteome with a comprehensive list of genes and proteins with elevated expression in pancreas. This list represents an important starting point for further studies of the molecular repertoire of pancreatic cells and their relation to disease states or treatment effects. PMID:25546435

Identifying functional reorganization of spelling networks: an individual peak probability comparison approach

PubMed Central

Purcell, Jeremy J.; Rapp, Brenda

2013-01-01

Previous research has shown that damage to the neural substrates of orthographic processing can lead to functional reorganization during reading (Tsapkini et al., 2011); in this research we ask if the same is true for spelling. To examine the functional reorganization of spelling networks we present a novel three-stage Individual Peak Probability Comparison (IPPC) analysis approach for comparing the activation patterns obtained during fMRI of spelling in a single brain-damaged individual with dysgraphia to those obtained in a set of non-impaired control participants. The first analysis stage characterizes the convergence in activations across non-impaired control participants by applying a technique typically used for characterizing activations across studies: Activation Likelihood Estimate (ALE) (Turkeltaub et al., 2002). This method was used to identify locations that have a high likelihood of yielding activation peaks in the non-impaired participants. The second stage provides a characterization of the degree to which the brain-damaged individual's activations correspond to the group pattern identified in Stage 1. This involves performing a Mahalanobis distance statistics analysis (Tsapkini et al., 2011) that compares each of a control group's peak activation locations to the nearest peak generated by the brain-damaged individual. The third stage evaluates the extent to which the brain-damaged individual's peaks are atypical relative to the range of individual variation among the control participants. This IPPC analysis allows for a quantifiable, statistically sound method for comparing an individual's activation pattern to the patterns observed in a control group and, thus, provides a valuable tool for identifying functional reorganization in a brain-damaged individual with impaired spelling. Furthermore, this approach can be applied more generally to compare any individual's activation pattern with that of a set of other individuals. PMID:24399981

Community analysis of pigment patterns from 37 microalgae strains reveals new carotenoids and porphyrins characteristic of distinct strains and taxonomic groups

PubMed Central

Bérard, Jean-Baptiste; Kaas, Raymond; Pasquet, Virginie; Picot, Laurent; Cadoret, Jean-Paul

2017-01-01

Phytoplankton, with an estimated 30 000 to 1 000 000 species clustered in 12 phyla, presents a high taxonomic and ecophysiological diversity, reflected by the complex distribution of pigments among the different algal classes. High performance liquid chromatography is the gold standard method for qualitative and quantitative analysis of phytoplankton pigments in seawater and culture samples, but only a few pigments can be used as robust chemotaxonomic markers. A major challenge is thus to identify new ones, characteristic of a strain, species, class or taxon that cannot be currently identified on the basis of its pigment signature. Using an optimized extraction process coupled to a HPLC de-replication strategy, we examined the pigment composition of 37 microalgae strains, representative of the broad taxonomic diversity of marine and freshwater species (excluding cyanobacteria). For each species, the major pigments already described were unambiguously identified. We also observed the presence of several minor unidentified pigments in each chromatogram. The global analysis of pigment compositions revealed a total of 124 pigments, including 98 pigments or derivatives unidentified using the standards. Absorption spectra indicated that 35 corresponded to chlorophyll/porphyrin derivatives, 57 to carotenoids and six to derivatives having both spectral signatures. Sixty-one of these unidentified or new carotenoids and porphyrin derivatives were characteristic of particular strains or species, indicating their possible use as highly specific chemotaxonomic markers capable of identifying one strain out of the 37 selected. We developed a graphical analysis using Gephi software to give a clear representation of pigment communities among the various phytoplankton strains, and to reveal strain-characteristic and shared pigments. This made it possible to reconstruct the taxonomic evolution of microalgae classes, on the basis of the conservation, loss, and/or appearance of pigments. PMID:28231253

SU-G-BRA-07: An Innovative Fiducial-Less Tracking Method for Radiation Treatment of Abdominal Tumors by Diaphragm Disparity Analysis

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

Dick, D; Zhao, W; Wu, X

2016-06-15

Purpose: To investigate the feasibility of tracking abdominal tumors without the use of gold fiducial markers Methods: In this simulation study, an abdominal 4DCT dataset, acquired previously and containing 8 phases of the breathing cycle, was used as the testing data. Two sets of DRR images (45 and 135 degrees) were generated for each phase. Three anatomical points along the lung-diaphragm interface on each of the Digital Reconstructed Radiograph(DRR) images were identified by cross-correlation. The gallbladder, which simulates the tumor, was contoured for each phase of the breathing cycle and the corresponding centroid values serve as the measured center ofmore » the tumor. A linear model was created to correlate the diaphragm’s disparity of the three identified anatomical points with the center of the tumor. To verify the established linear model, we sequentially removed one phase of the data (i.e., 3 anatomical points and the corresponding tumor center) and created new linear models with the remaining 7 phases. Then we substituted the eliminated phase data (disparities of the 3 anatomical points) into the corresponding model to compare model-generated tumor center and the measured tumor center. Results: The maximum difference between the modeled and the measured centroid values across the 8 phases were 0.72, 0.29 and 0.30 pixels in the x, y and z directions respectively, which yielded a maximum mean-squared-error value of 0.75 pixels. The outcomes of the verification process, by eliminating each phase, produced mean-squared-errors ranging from 0.41 to 1.28 pixels. Conclusion: Gold fiducial markers, requiring surgical procedures to be implanted, are conventionally used in radiation therapy. The present work shows the feasibility of a fiducial-less tracking method for localizing abdominal tumors. Through developed diaphragm disparity analysis, the established linear model was verified with clinically accepted errors. The tracking method in real time under different radiation therapy platforms will be further investigated.« less

Gene identification for risk of relapse in stage I lung adenocarcinoma patients: a combined methodology of gene expression profiling and computational gene network analysis.

PubMed

Ludovini, Vienna; Bianconi, Fortunato; Siggillino, Annamaria; Piobbico, Danilo; Vannucci, Jacopo; Metro, Giulio; Chiari, Rita; Bellezza, Guido; Puma, Francesco; Della Fazia, Maria Agnese; Servillo, Giuseppe; Crinò, Lucio

2016-05-24

Risk assessment and treatment choice remains a challenge in early non-small-cell lung cancer (NSCLC). The aim of this study was to identify novel genes involved in the risk of early relapse (ER) compared to no relapse (NR) in resected lung adenocarcinoma (AD) patients using a combination of high throughput technology and computational analysis. We identified 18 patients (n.13 NR and n.5 ER) with stage I AD. Frozen samples of patients in ER, NR and corresponding normal lung (NL) were subjected to Microarray technology and quantitative-PCR (Q-PCR). A gene network computational analysis was performed to select predictive genes. An independent set of 79 ADs stage I samples was used to validate selected genes by Q-PCR.From microarray analysis we selected 50 genes, using the fold change ratio of ER versus NR. They were validated both in pool and individually in patient samples (ER and NR) by Q-PCR. Fourteen increased and 25 decreased genes showed a concordance between two methods. They were used to perform a computational gene network analysis that identified 4 increased (HOXA10, CLCA2, AKR1B10, FABP3) and 6 decreased (SCGB1A1, PGC, TFF1, PSCA, SPRR1B and PRSS1) genes. Moreover, in an independent dataset of ADs samples, we showed that both high FABP3 expression and low SCGB1A1 expression was associated with a worse disease-free survival (DFS).Our results indicate that it is possible to define, through gene expression and computational analysis, a characteristic gene profiling of patients with an increased risk of relapse that may become a tool for patient selection for adjuvant therapy.

Predictors of Shunt-dependent Hydrocephalus After Aneurysmal Subarachnoid Hemorrhage? A Systematic Review and Meta-Analysis.

PubMed

Xie, Zhiyi; Hu, Xin; Zan, Xin; Lin, Sen; Li, Hao; You, Chao

2017-10-01

Hydrocephalus is a well-recognized complication after aneurysmal subarachnoid hemorrhage (aSAH). This study aimed to identify predictors for shunt-dependent hydrocephalus (SDHC) after aSAH via a systematic review and meta-analysis. A systematic search was conducted using the Embase, MEDLINE, and Web of Science databases for studies pertaining to aSAH and SDHC. Risk factors were assessed by meta-analysis when they were reported by at least 2 studies. The results were presented as odd ratios or risk ratios according to the study design with the corresponding 95% confidence intervals (CI). Twenty-five studies were included. In primary analysis of 14 potential risk factors, 12 were identified as predictors of SDHC after aSAH including age ≥50 years, female gender, high Hunt-Hess grade, Glasgow Coma Scale ≤8, Fisher grade ≥3, acute hydrocephalus, external ventricular drainage insertion, intraventricular hemorrhage, postcirculation aneurysm, anterior communicating artery aneurysm, meningitis, and rebleeding. The meta-analysis based on cohort studies found a significantly increased risk for SDHC in patients with aSAH treated by coiling (risk ratio, 1.16; 95% CI, 1.05-1.29), while the meta-analysis based on case-controlled studies failed to replicate this finding (odds ratio, 1.27; 95% CI, 0.95-1.71). Several new predictors of SDHC after aSAH were identified that may assist with the early recognition and prevention of SDHC. The controversial evidence found in this study was insufficient to support the potential of neurosurgical clipping for reducing the risk of shunt dependency. Further well-designed studies are warranted to explore the effect of treatment modality on SDHC risk. Copyright © 2017 Elsevier Inc. All rights reserved.

Gene duplications in prokaryotes can be associated with environmental adaptation

PubMed Central

2010-01-01

Background Gene duplication is a normal evolutionary process. If there is no selective advantage in keeping the duplicated gene, it is usually reduced to a pseudogene and disappears from the genome. However, some paralogs are retained. These gene products are likely to be beneficial to the organism, e.g. in adaptation to new environmental conditions. The aim of our analysis is to investigate the properties of paralog-forming genes in prokaryotes, and to analyse the role of these retained paralogs by relating gene properties to life style of the corresponding prokaryotes. Results Paralogs were identified in a number of prokaryotes, and these paralogs were compared to singletons of persistent orthologs based on functional classification. This showed that the paralogs were associated with for example energy production, cell motility, ion transport, and defence mechanisms. A statistical overrepresentation analysis of gene and protein annotations was based on paralogs of the 200 prokaryotes with the highest fraction of paralog-forming genes. Biclustering of overrepresented gene ontology terms versus species was used to identify clusters of properties associated with clusters of species. The clusters were classified using similarity scores on properties and species to identify interesting clusters, and a subset of clusters were analysed by comparison to literature data. This analysis showed that paralogs often are associated with properties that are important for survival and proliferation of the specific organisms. This includes processes like ion transport, locomotion, chemotaxis and photosynthesis. However, the analysis also showed that the gene ontology terms sometimes were too general, imprecise or even misleading for automatic analysis. Conclusions Properties described by gene ontology terms identified in the overrepresentation analysis are often consistent with individual prokaryote lifestyles and are likely to give a competitive advantage to the organism. Paralogs and singletons dominate different categories of functional classification, where paralogs in particular seem to be associated with processes involving interaction with the environment. PMID:20961426

Gene duplications in prokaryotes can be associated with environmental adaptation.

PubMed

Bratlie, Marit S; Johansen, Jostein; Sherman, Brad T; Huang, Da Wei; Lempicki, Richard A; Drabløs, Finn

2010-10-20

Gene duplication is a normal evolutionary process. If there is no selective advantage in keeping the duplicated gene, it is usually reduced to a pseudogene and disappears from the genome. However, some paralogs are retained. These gene products are likely to be beneficial to the organism, e.g. in adaptation to new environmental conditions. The aim of our analysis is to investigate the properties of paralog-forming genes in prokaryotes, and to analyse the role of these retained paralogs by relating gene properties to life style of the corresponding prokaryotes. Paralogs were identified in a number of prokaryotes, and these paralogs were compared to singletons of persistent orthologs based on functional classification. This showed that the paralogs were associated with for example energy production, cell motility, ion transport, and defence mechanisms. A statistical overrepresentation analysis of gene and protein annotations was based on paralogs of the 200 prokaryotes with the highest fraction of paralog-forming genes. Biclustering of overrepresented gene ontology terms versus species was used to identify clusters of properties associated with clusters of species. The clusters were classified using similarity scores on properties and species to identify interesting clusters, and a subset of clusters were analysed by comparison to literature data. This analysis showed that paralogs often are associated with properties that are important for survival and proliferation of the specific organisms. This includes processes like ion transport, locomotion, chemotaxis and photosynthesis. However, the analysis also showed that the gene ontology terms sometimes were too general, imprecise or even misleading for automatic analysis. Properties described by gene ontology terms identified in the overrepresentation analysis are often consistent with individual prokaryote lifestyles and are likely to give a competitive advantage to the organism. Paralogs and singletons dominate different categories of functional classification, where paralogs in particular seem to be associated with processes involving interaction with the environment.

Preconditioned conjugate gradient technique for the analysis of symmetric anisotropic structures

NASA Technical Reports Server (NTRS)

Noor, Ahmed K.; Peters, Jeanne M.

1987-01-01

An efficient preconditioned conjugate gradient (PCG) technique and a computational procedure are presented for the analysis of symmetric anisotropic structures. The technique is based on selecting the preconditioning matrix as the orthotropic part of the global stiffness matrix of the structure, with all the nonorthotropic terms set equal to zero. This particular choice of the preconditioning matrix results in reducing the size of the analysis model of the anisotropic structure to that of the corresponding orthotropic structure. The similarities between the proposed PCG technique and a reduction technique previously presented by the authors are identified and exploited to generate from the PCG technique direct measures for the sensitivity of the different response quantities to the nonorthotropic (anisotropic) material coefficients of the structure. The effectiveness of the PCG technique is demonstrated by means of a numerical example of an anisotropic cylindrical panel.

Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation.

PubMed

Preissl, Sebastian; Fang, Rongxin; Huang, Hui; Zhao, Yuan; Raviram, Ramya; Gorkin, David U; Zhang, Yanxiao; Sos, Brandon C; Afzal, Veena; Dickel, Diane E; Kuan, Samantha; Visel, Axel; Pennacchio, Len A; Zhang, Kun; Ren, Bing

2018-03-01

Analysis of chromatin accessibility can reveal transcriptional regulatory sequences, but heterogeneity of primary tissues poses a significant challenge in mapping the precise chromatin landscape in specific cell types. Here we report single-nucleus ATAC-seq, a combinatorial barcoding-assisted single-cell assay for transposase-accessible chromatin that is optimized for use on flash-frozen primary tissue samples. We apply this technique to the mouse forebrain through eight developmental stages. Through analysis of more than 15,000 nuclei, we identify 20 distinct cell populations corresponding to major neuronal and non-neuronal cell types. We further define cell-type-specific transcriptional regulatory sequences, infer potential master transcriptional regulators and delineate developmental changes in forebrain cellular composition. Our results provide insight into the molecular and cellular dynamics that underlie forebrain development in the mouse and establish technical and analytical frameworks that are broadly applicable to other heterogeneous tissues.

Spatiotemporal Bayesian analysis of Lyme disease in New York state, 1990-2000.

PubMed

Chen, Haiyan; Stratton, Howard H; Caraco, Thomas B; White, Dennis J

2006-07-01

Mapping ordinarily increases our understanding of nontrivial spatial and temporal heterogeneities in disease rates. However, the large number of parameters required by the corresponding statistical models often complicates detailed analysis. This study investigates the feasibility of a fully Bayesian hierarchical regression approach to the problem and identifies how it outperforms two more popular methods: crude rate estimates (CRE) and empirical Bayes standardization (EBS). In particular, we apply a fully Bayesian approach to the spatiotemporal analysis of Lyme disease incidence in New York state for the period 1990-2000. These results are compared with those obtained by CRE and EBS in Chen et al. (2005). We show that the fully Bayesian regression model not only gives more reliable estimates of disease rates than the other two approaches but also allows for tractable models that can accommodate more numerous sources of variation and unknown parameters.

Script identification from images using cluster-based templates

DOEpatents

Hochberg, J.G.; Kelly, P.M.; Thomas, T.R.

1998-12-01

A computer-implemented method identifies a script used to create a document. A set of training documents for each script to be identified is scanned into the computer to store a series of exemplary images representing each script. Pixels forming the exemplary images are electronically processed to define a set of textual symbols corresponding to the exemplary images. Each textual symbol is assigned to a cluster of textual symbols that most closely represents the textual symbol. The cluster of textual symbols is processed to form a representative electronic template for each cluster. A document having a script to be identified is scanned into the computer to form one or more document images representing the script to be identified. Pixels forming the document images are electronically processed to define a set of document textual symbols corresponding to the document images. The set of document textual symbols is compared to the electronic templates to identify the script. 17 figs.

Script identification from images using cluster-based templates

DOEpatents

Hochberg, Judith G.; Kelly, Patrick M.; Thomas, Timothy R.

1998-01-01

A computer-implemented method identifies a script used to create a document. A set of training documents for each script to be identified is scanned into the computer to store a series of exemplary images representing each script. Pixels forming the exemplary images are electronically processed to define a set of textual symbols corresponding to the exemplary images. Each textual symbol is assigned to a cluster of textual symbols that most closely represents the textual symbol. The cluster of textual symbols is processed to form a representative electronic template for each cluster. A document having a script to be identified is scanned into the computer to form one or more document images representing the script to be identified. Pixels forming the document images are electronically processed to define a set of document textual symbols corresponding to the document images. The set of document textual symbols is compared to the electronic templates to identify the script.

Large-Scale Genomic Analysis of Codon Usage in Dengue Virus and Evaluation of Its Phylogenetic Dependence

PubMed Central

Lara-Ramírez, Edgar E.; Salazar, Ma Isabel; López-López, María de Jesús; Salas-Benito, Juan Santiago; Sánchez-Varela, Alejandro

2014-01-01

The increasing number of dengue virus (DENV) genome sequences available allows identifying the contributing factors to DENV evolution. In the present study, the codon usage in serotypes 1–4 (DENV1–4) has been explored for 3047 sequenced genomes using different statistics methods. The correlation analysis of total GC content (GC) with GC content at the three nucleotide positions of codons (GC1, GC2, and GC3) as well as the effective number of codons (ENC, ENCp) versus GC3 plots revealed mutational bias and purifying selection pressures as the major forces influencing the codon usage, but with distinct pressure on specific nucleotide position in the codon. The correspondence analysis (CA) and clustering analysis on relative synonymous codon usage (RSCU) within each serotype showed similar clustering patterns to the phylogenetic analysis of nucleotide sequences for DENV1–4. These clustering patterns are strongly related to the virus geographic origin. The phylogenetic dependence analysis also suggests that stabilizing selection acts on the codon usage bias. Our analysis of a large scale reveals new feature on DENV genomic evolution. PMID:25136631

Minimal agent based model for financial markets I. Origin and self-organization of stylized facts

NASA Astrophysics Data System (ADS)

Alfi, V.; Cristelli, M.; Pietronero, L.; Zaccaria, A.

2009-02-01

We introduce a minimal agent based model for financial markets to understand the nature and self-organization of the stylized facts. The model is minimal in the sense that we try to identify the essential ingredients to reproduce the most important deviations of price time series from a random walk behavior. We focus on four essential ingredients: fundamentalist agents which tend to stabilize the market; chartist agents which induce destabilization; analysis of price behavior for the two strategies; herding behavior which governs the possibility of changing strategy. Bubbles and crashes correspond to situations dominated by chartists, while fundamentalists provide a long time stability (on average). The stylized facts are shown to correspond to an intermittent behavior which occurs only for a finite value of the number of agents N. Therefore they correspond to finite size effects which, however, can occur at different time scales. We propose a new mechanism for the self-organization of this state which is linked to the existence of a threshold for the agents to be active or not active. The feedback between price fluctuations and number of active agents represents a crucial element for this state of self-organized intermittency. The model can be easily generalized to consider more realistic variants.

Absorption and fluorescence characteristics of chromophoric dissolved organic matter in the Yangtze Estuary.

PubMed

Sun, Qiyuan; Wang, Chao; Wang, Peifang; Hou, Jun; Ao, Yanhui

2014-03-01

The Yangtze Estuary is heavily influenced by coast-continent geochemical processes and anthropogenic activity; thus, the source and distribution of chromophoric dissolved organic matter (CDOM) in the estuary are strongly impacted by these processes. Here, a series of samples were collected from across the Yangtze Estuary to investigate the source and spatial dynamics of CDOM and its components throughout the system. Three indices (a(355), spectral slope, and fluorescence) were then calculated and interpreted. The results indicated that the distribution of CDOM was dominated by allochthonous input, conservative mixing, and phase transfer. The contribution of biogenic CDOM to total CDOM increased with salinity, and three individual CDOM components were identified upon fluorescence excitation emission matrix spectroscopy and parallel factor analysis of the water samples: C1, corresponding to humic substance-like CDOM, C2, corresponding to tryptophan-like CDOM, and C3, corresponding to tyrosine-like CDOM. C1 primarily originated from a terrestrial source, C2 had widespread origins, none of which played a dominant role, and C3 mainly originated from allochthonous input in the medium salinity area. Unexpectedly, no marine humic-like component was found in the surface water of the Yangtze Estuary, possibly because turbidity decreased the depth of sunlight penetration, limiting production of this component.

The LncRNA Connectivity Map: Using LncRNA Signatures to Connect Small Molecules, LncRNAs, and Diseases.

PubMed

Yang, Haixiu; Shang, Desi; Xu, Yanjun; Zhang, Chunlong; Feng, Li; Sun, Zeguo; Shi, Xinrui; Zhang, Yunpeng; Han, Junwei; Su, Fei; Li, Chunquan; Li, Xia

2017-07-27

Well characterized the connections among diseases, long non-coding RNAs (lncRNAs) and drugs are important for elucidating the key roles of lncRNAs in biological mechanisms in various biological states. In this study, we constructed a database called LNCmap (LncRNA Connectivity Map), available at http://www.bio-bigdata.com/LNCmap/ , to establish the correlations among diseases, physiological processes, and the action of small molecule therapeutics by attempting to describe all biological states in terms of lncRNA signatures. By reannotating the microarray data from the Connectivity Map database, the LNCmap obtained 237 lncRNA signatures of 5916 instances corresponding to 1262 small molecular drugs. We provided a user-friendly interface for the convenient browsing, retrieval and download of the database, including detailed information and the associations of drugs and corresponding affected lncRNAs. Additionally, we developed two enrichment analysis methods for users to identify candidate drugs for a particular disease by inputting the corresponding lncRNA expression profiles or an associated lncRNA list and then comparing them to the lncRNA signatures in our database. Overall, LNCmap could significantly improve our understanding of the biological roles of lncRNAs and provide a unique resource to reveal the connections among drugs, lncRNAs and diseases.

Species identification of Aspergillus section Flavi isolates from Portuguese almonds using phenotypic, including MALDI-TOF ICMS, and molecular approaches.

PubMed

Rodrigues, P; Santos, C; Venâncio, A; Lima, N

2011-10-01

Section Flavi is one of the most significant sections in the genus Aspergillus. Taxonomy of this section currently depends on multivariate approaches, entailing phenotypic and molecular traits. This work aimed to identify isolates from section Flavi by combining various classic phenotypic and genotypic methods as well as the novel approach based on spectral analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF ICMS) and to evaluate the discriminatory power of the various approaches in species identification.   Aspergillus section Flavi isolates obtained from Portuguese almonds were characterized in terms of macro- and micromorphology, mycotoxin pattern, calmodulin gene sequence and MALDI-TOF protein fingerprint spectra. For each approach, dendrograms were created and results were compared. All data sets divided the isolates into three groups, corresponding to taxa closely related to Aspergillus flavus, Aspergillus parasiticus and Aspergillus tamarii. In the A. flavus clade, molecular and spectral analyses were not able to resolve between aflatoxigenic and nonaflatoxigenic isolates. In the A. parasiticus cluster, two well-resolved clades corresponded to unidentified taxa, corresponding to those isolates with mycotoxin profile different from that expected for A. parasiticus. © 2011 The Authors. Journal of Applied Microbiology © 2011 The Society for Applied Microbiology.

Community trees: Identifying codiversification in the Páramo dipteran community.

PubMed

Carstens, Bryan C; Gruenstaeudl, Michael; Reid, Noah M

2016-05-01

Groups of codistributed species that responded in a concerted manner to environmental events are expected to share patterns of evolutionary diversification. However, the identification of such groups has largely been based on qualitative, post hoc analyses. We develop here two methods (posterior predictive simulation [PPS], Kuhner-Felsenstein [K-F] analysis of variance [ANOVA]) for the analysis of codistributed species that, given a group of species with a shared pattern of diversification, allow empiricists to identify those taxa that do not codiversify (i.e., "outlier" species). The identification of outlier species makes it possible to jointly estimate the evolutionary history of co-diversifying taxa. To evaluate the approaches presented here, we collected data from Páramo dipterans, identified outlier species, and estimated a "community tree" from species that are identified as having codiversified. Our results demonstrate that dipteran communities from different Páramo habitats in the same mountain range are more closely related than communities in other ranges. We also conduct simulation testing to evaluate this approach. Results suggest that our approach provides a useful addition to comparative phylogeographic methods, while identifying aspects of the analysis that require careful interpretation. In particular, both the PPS and K-F ANOVA perform acceptably when there are one or two outlier species, but less so as the number of outliers increases. This is likely a function of the corresponding degradation of the signal of community divergence; without a strong signal from a codiversifying community, there is no dominant pattern from which to detect an outlier species. For this reason, both the magnitude of K-F distance distribution and outside knowledge about the phylogeographic history of each putative member of the community should be considered when interpreting the results. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Static and Dynamical Structural Investigations of Metal-Oxide Nanocrystals by Powder X-ray Diffraction: Colloidal Tungsten Oxide as a Case Study

DOE PAGES

Caliandro, Rocco; Sibillano, Teresa; Belviso, B. Danilo; ...

2016-02-02

In this study, we have developed a general X-ray powder diffraction (XPD) methodology for the simultaneous structural and compositional characterization of inorganic nanomaterials. The approach is validated on colloidal tungsten oxide nanocrystals (WO 3-x NCs), as a model polymorphic nanoscale material system. Rod-shaped WO 3-x NCs with different crystal structure and stoichiometry are comparatively investigated under an inert atmosphere and after prolonged air exposure. An initial structural model for the as-synthesized NCs is preliminarily identified by means of Rietveld analysis against several reference crystal phases, followed by atomic pair distribution function (PDF) refinement of the best-matching candidates (static analysis). Subtlemore » stoichiometry deviations from the corresponding bulk standards are revealed. NCs exposed to air at room temperature are monitored by XPD measurements at scheduled time intervals. The static PDF analysis is complemented with an investigation into the evolution of the WO 3-x NC structure, performed by applying the modulation enhanced diffraction technique to the whole time series of XPD profiles (dynamical analysis). Prolonged contact with ambient air is found to cause an appreciable increase in the static disorder of the O atoms in the WO 3-x NC lattice, rather than a variation in stoichiometry. Finally, the time behavior of such structural change is identified on the basis of multivariate analysis.« less

Analysis of Ninety Degree Flexure Tests for Characterization of Composite Transverse Tensile Strength

NASA Technical Reports Server (NTRS)

OBrien, T. Kevin; Krueger, Ronald

2001-01-01

Finite element (FE) analysis was performed on 3-point and 4-point bending test configurations of ninety degree oriented glass-epoxy and graphite-epoxy composite beams to identify deviations from beam theory predictions. Both linear and geometric non-linear analyses were performed using the ABAQUS finite element code. The 3-point and 4-point bending specimens were first modeled with two-dimensional elements. Three-dimensional finite element models were then performed for selected 4-point bending configurations to study the stress distribution across the width of the specimens and compare the results to the stresses computed from two-dimensional plane strain and plane stress analyses and the stresses from beam theory. Stresses for all configurations were analyzed at load levels corresponding to the measured transverse tensile strength of the material.

A cluster analysis investigation of workaholism as a syndrome.

PubMed

Aziz, Shahnaz; Zickar, Michael J

2006-01-01

Workaholism has been conceptualized as a syndrome although there have been few tests that explicitly consider its syndrome status. The authors analyzed a three-dimensional scale of workaholism developed by Spence and Robbins (1992) using cluster analysis. The authors identified three clusters of individuals, one of which corresponded to Spence and Robbins's profile of the workaholic (high work involvement, high drive to work, low work enjoyment). Consistent with previously conjectured relations with workaholism, individuals in the workaholic cluster were more likely to label themselves as workaholics, more likely to have acquaintances label them as workaholics, and more likely to have lower life satisfaction and higher work-life imbalance. The importance of considering workaholism as a syndrome and the implications for effective interventions are discussed. Copyright 2006 APA.

Variation in strontium isotope ratios of archaeological fauna in the Midwestern United States: a preliminary study

USGS Publications Warehouse

Hedman, Kristin M.; Curry, B. Brandon; Johnson, Thomas M.; Fullagar, Paul D.; Emerson, Thomas E.

2009-01-01

Strontium isotope values (87Sr/86Sr) in bone and tooth enamel have been used increasingly to identify non-local individuals within prehistoric human populations worldwide. Archaeological research in the Midwestern United States has increasingly highlighted the role of population movement in affecting interregional cultural change. However, the comparatively low level of geologic variation in the Midwestern United States might suggest a corresponding low level of strontium variation, and calls into question the sensitivity of strontium isotopes to identify non-local individuals in this region. Using strontium isotopes of archaeological fauna, we explore the degree of variability in strontium ratios across this region. Our results demonstrate measurable variation in strontium ratios and indicate the potential of strontium analysis for addressing questions of origin and population movement in the Midwestern United States.

Fetal and neonatal deaths of children of patients classified as near miss.

PubMed

Nardello, Daniele Marin; Guimarães, Alzira Maria D Avila Nery; Barreto, Ikaro Daniel de Carvalho; Gurgel, Ricardo Queiroz; Ribeiro, Eleonora Ramos de Oliveira; Gois, Cristiane Franca Lisboa

2017-01-01

identify the epidemiological aspects of early fetal and neonatal deaths in children of patients classified with near miss and the factors associated with this outcome. a cross-sectional study of 79 women identified with near miss and their newborns. The variables were analyzed using Fisher's exact test. Risk factors were estimated based on unadjusted and adjusted odds ratios, and by means of multiple correspondence analysis, with significance for p <0.05. hypertensive disorders totaled 40.5%; Of these, 58.3% had adverse fetal and neonatal outcome. The newborns admitted to the Neonatal Intensive Care Unit proved to be significant for the outcome (70.8%), gestational age <32 weeks (41.6%), birth weight <2500 (66.7%), neonatal asphyxia (50%) and early respiratory discomfort (72.2%). prematurity, neonatal asphyxia, and early respiratory distress were significant characteristics for the outcome among newborns.

Crystallization and preliminary X-ray analysis of a novel halotolerant feruloyl esterase identified from a soil metagenomic library

PubMed Central

Chen, Shang-ke; Wang, Kui; Liu, Yuhuan; Hu, Xiaopeng

2012-01-01

Feruloyl esterase cleaves the ester linkage formed between ferulic acid and polysaccharides in plant cell walls and thus has wide potential industrial applications. A novel feruloyl esterase (EstF27) identified from a soil metagenomic library was crystallized and a complete data set was collected from a single cooled crystal using an in-house X-ray source. The crystal diffracted to 2.9 Å resolution and belonged to space group P212121, with unit-cell parameters a = 94.35, b = 106.19, c = 188.51 Å, α = β = γ = 90.00°. A Matthews coefficient of 2.55 Å3 Da−1, with a corresponding solvent content of 51.84%, suggested the presence of ten protein subunits in the asymmetric unit. PMID:22750860

Characterization of a Proposed Dichorhavirus Associated with the Citrus Leprosis Disease and Analysis of the Host Response

PubMed Central

Cruz-Jaramillo, José Luis; Ruiz-Medrano, Roberto; Rojas-Morales, Lourdes; López-Buenfil, José Abel; Morales-Galván, Oscar; Chavarín-Palacio, Claudio; Ramírez-Pool, José Abrahán; Xoconostle-Cázares, Beatriz

2014-01-01

The causal agents of Citrus leprosis are viruses; however, extant diagnostic methods to identify them have failed to detect known viruses in orange, mandarin, lime and bitter orange trees with severe leprosis symptoms in Mexico, an important citrus producer. Using high throughput sequencing, a virus associated with citrus leprosis was identified, belonging to the proposed Dichorhavirus genus. The virus was termed Citrus Necrotic Spot Virus (CNSV) and contains two negative-strand RNA components; virions accumulate in the cytoplasm and are associated with plasmodesmata—channels interconnecting neighboring cells—suggesting a mode of spread within the plant. The present study provides insights into the nature of this pathogen and the corresponding plant response, which is likely similar to other pathogens that do not spread systemically in plants. PMID:25004279

Digital Gene Expression Analysis Based on De Novo Transcriptome Assembly Reveals New Genes Associated with Floral Organ Differentiation of the Orchid Plant Cymbidium ensifolium

PubMed Central

Yang, Fengxi; Zhu, Genfa

2015-01-01

Cymbidium ensifolium belongs to the genus Cymbidium of the orchid family. Owing to its spectacular flower morphology, C. ensifolium has considerable ecological and cultural value. However, limited genetic data is available for this non-model plant, and the molecular mechanism underlying floral organ identity is still poorly understood. In this study, we characterize the floral transcriptome of C. ensifolium and present, for the first time, extensive sequence and transcript abundance data of individual floral organs. After sequencing, over 10 Gb clean sequence data were generated and assembled into 111,892 unigenes with an average length of 932.03 base pairs, including 1,227 clusters and 110,665 singletons. Assembled sequences were annotated with gene descriptions, gene ontology, clusters of orthologous group terms, the Kyoto Encyclopedia of Genes and Genomes, and the plant transcription factor database. From these annotations, 131 flowering-associated unigenes, 61 CONSTANS-LIKE (COL) unigenes and 90 floral homeotic genes were identified. In addition, four digital gene expression libraries were constructed for the sepal, petal, labellum and gynostemium, and 1,058 genes corresponding to individual floral organ development were identified. Among them, eight MADS-box genes were further investigated by full-length cDNA sequence analysis and expression validation, which revealed two APETALA1/AGL9-like MADS-box genes preferentially expressed in the sepal and petal, two AGAMOUS-like genes particularly restricted to the gynostemium, and four DEF-like genes distinctively expressed in different floral organs. The spatial expression of these genes varied distinctly in different floral mutant corresponding to different floral morphogenesis, which validated the specialized roles of them in floral patterning and further supported the effectiveness of our in silico analysis. This dataset generated in our study provides new insights into the molecular mechanisms underlying floral patterning of Cymbidium and supports a valuable resource for molecular breeding of the orchid plant. PMID:26580566

RNA Sequencing of the Exercise Transcriptome in Equine Athletes

PubMed Central

Verini-Supplizi, Andrea; Barcaccia, Gianni; Albiero, Alessandro; D'Angelo, Michela; Campagna, Davide; Valle, Giorgio; Felicetti, Michela; Silvestrelli, Maurizio; Cappelli, Katia

2013-01-01

The horse is an optimal model organism for studying the genomic response to exercise-induced stress, due to its natural aptitude for athletic performance and the relative homogeneity of its genetic and environmental backgrounds. Here, we applied RNA-sequencing analysis through the use of SOLiD technology in an experimental framework centered on exercise-induced stress during endurance races in equine athletes. We monitored the transcriptional landscape by comparing gene expression levels between animals at rest and after competition. Overall, we observed a shift from coding to non-coding regions, suggesting that the stress response involves the differential expression of not annotated regions. Notably, we observed significant post-race increases of reads that correspond to repeats, especially the intergenic and intronic L1 and L2 transposable elements. We also observed increased expression of the antisense strands compared to the sense strands in intronic and regulatory regions (1 kb up- and downstream) of the genes, suggesting that antisense transcription could be one of the main mechanisms for transposon regulation in the horse under stress conditions. We identified a large number of transcripts corresponding to intergenic and intronic regions putatively associated with new transcriptional elements. Gene expression and pathway analysis allowed us to identify several biological processes and molecular functions that may be involved with exercise-induced stress. Ontology clustering reflected mechanisms that are already known to be stress activated (e.g., chemokine-type cytokines, Toll-like receptors, and kinases), as well as “nucleic acid binding” and “signal transduction activity” functions. There was also a general and transient decrease in the global rates of protein synthesis, which would be expected after strenuous global stress. In sum, our network analysis points toward the involvement of specific gene clusters in equine exercise-induced stress, including those involved in inflammation, cell signaling, and immune interactions. PMID:24391776

Automated discovery of structural features of the optic nerve head on the basis of image and genetic data

NASA Astrophysics Data System (ADS)

Christopher, Mark; Tang, Li; Fingert, John H.; Scheetz, Todd E.; Abramoff, Michael D.

2014-03-01

Evaluation of optic nerve head (ONH) structure is a commonly used clinical technique for both diagnosis and monitoring of glaucoma. Glaucoma is associated with characteristic changes in the structure of the ONH. We present a method for computationally identifying ONH structural features using both imaging and genetic data from a large cohort of participants at risk for primary open angle glaucoma (POAG). Using 1054 participants from the Ocular Hypertension Treatment Study, ONH structure was measured by application of a stereo correspondence algorithm to stereo fundus images. In addition, the genotypes of several known POAG genetic risk factors were considered for each participant. ONH structural features were discovered using both a principal component analysis approach to identify the major modes of variance within structural measurements and a linear discriminant analysis approach to capture the relationship between genetic risk factors and ONH structure. The identified ONH structural features were evaluated based on the strength of their associations with genotype and development of POAG by the end of the OHTS study. ONH structural features with strong associations with genotype were identified for each of the genetic loci considered. Several identified ONH structural features were significantly associated (p < 0.05) with the development of POAG after Bonferroni correction. Further, incorporation of genetic risk status was found to substantially increase performance of early POAG prediction. These results suggest incorporating both imaging and genetic data into ONH structural modeling significantly improves the ability to explain POAG-related changes to ONH structure.

Genetic analysis of atherosclerosis identifies a major susceptibility locus in the major histocompatibility complex of mice.

PubMed

Grainger, Andrew T; Jones, Michael B; Li, Jing; Chen, Mei-Hua; Manichaikul, Ani; Shi, Weibin

2016-11-01

Recent genome-wide association studies (GWAS) have identified over 50 significant loci containing common variants associated with coronary artery disease. However, these variants explain only 26% of the genetic heritability of the disease, suggesting that many more variants remain to be discovered. Here, we examined the genetic basis underlying the marked difference between SM/J-Apoe -/- and BALB/cJ-Apoe -/- mice in atherosclerotic lesion formation. 206 female F 2 mice generated from an intercross between the two Apoe -/- strains were fed 12 weeks of western diet. Atherosclerotic lesion sizes in the aortic root were measured and 149 genetic markers genotyped across the entire genome. A significant locus, named Ath49 (LOD score: 4.18), for atherosclerosis was mapped to the H2 complex [mouse major histocompatibility complex (MHC)] on chromosome 17. Bioinformatic analysis identified 12 probable candidate genes, including Tnfrsf21, Adgrf1, Adgrf5, Mep1a, and Pla2g7. Corresponding human genomic regions of Ath49 showed significant association with coronary heart disease. Five suggestive loci on chromosomes 1, 4, 5, and 8 for atherosclerosis were also identified. Atherosclerotic lesion sizes were significantly correlated with HDL but not with non-HDL cholesterol, triglyceride or glucose levels in the F 2 cohort. We have identified the MHC as a major genetic determinant of atherosclerosis, highlighting the importance of inflammation in atherogenesis. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

O-Acetylation of Arabidopsis Hemicellulose Xyloglucan Requires AXY4 or AXY4L, Proteins with a TBL and DUF231 Domain[W][OA

PubMed Central

Gille, Sascha; de Souza, Amancio; Xiong, Guangyan; Benz, Monique; Cheng, Kun; Schultink, Alex; Reca, Ida-Barbara; Pauly, Markus

2011-01-01

In an Arabidopsis thaliana forward genetic screen aimed at identifying mutants with altered structures of their hemicellulose xyloglucan (axy mutants) using oligosaccharide mass profiling, two nonallelic mutants (axy4-1 and axy4-2) that have a 20 to 35% reduction in xyloglucan O-acetylation were identified. Mapping of the mutation in axy4-1 identified AXY4, a type II transmembrane protein with a Trichome Birefringence-Like domain and a domain of unknown function (DUF231). Loss of AXY4 transcript results in a complete lack of O-acetyl substituents on xyloglucan in several tissues, except seeds. Seed xyloglucan is instead O-acetylated by the paralog AXY4like, as demonstrated by the analysis of the corresponding T-DNA insertional lines. Wall fractionation analysis of axy4 knockout mutants indicated that only a fraction containing xyloglucan is non-O-acetylated. Hence, AXY4/AXY4L is required for the O-acetylation of xyloglucan, and we propose that these proteins represent xyloglucan-specific O-acetyltransferases, although their donor and acceptor substrates have yet to be identified. An Arabidopsis ecotype, Ty-0, has reduced xyloglucan O-acetylation due to mutations in AXY4, demonstrating that O-acetylation of xyloglucan does not impact the plant’s fitness in its natural environment. The relationship of AXY4 with another previously identified group of Arabidopsis proteins involved in general wall O-acetylation, reduced wall acetylation, is discussed. PMID:22086088

A toxicology-based review of fentanyl-related deaths in New Mexico (1986-2007).

PubMed

Krinsky, Clarissa S; Lathrop, Sarah L; Crossey, Michael; Baker, Ginger; Zumwalt, Ross

2011-12-01

Since its approval in the United States, fentanyl has become increasingly popular for the medical management of pain and as a substance of abuse. Fentanyl is unique among the opioids in its widespread use with a transdermal delivery system, which contributes to its unique pharmacokinetics and abuse potential. We examined the demographics of deaths with fentanyl identified on toxicologic analysis and reviewed specific challenges in the laboratory detection of postmortem fentanyl levels. The New Mexico Office of the Medical Investigator database was searched for all cases from January 1986 through December 2007 with fentanyl reported as present or quantified. Those deaths with a cause of death identified as drug overdose were then analyzed separately. From 1986 to 2007, 154 cases were identified with fentanyl present in postmortem samples, with 96 of the cases identified as fentanyl-related drug overdoses. The number of fentanyl-related deaths has increased over the past 20 years, corresponding to both statewide increases in the medical use of fentanyl and the abuse of prescription opioids. The demographics of these fentanyl-related overdoses showed that subjects were more likely to be female, white non-Hispanic, and older than those in previously described overdose deaths. Several cases were identified with central and peripheral blood samples and antemortem and postmortem samples available for fentanyl quantification. Given the uncharacteristic demographics of fentanyl-related deaths and the complexity of the laboratory analysis of fentanyl, forensic scientists must use caution in both the detection and interpretation of fentanyl concentrations.

Heritability of Nociception IV: Neuropathic pain assays are genetically distinct across methods of peripheral nerve injury

PubMed Central

Young, Erin E.; Costigan, Michael; Herbert, Teri A.; Lariviere, William R.

2013-01-01

Prior genetic correlation analysis of 22 heritable behavioral measures of nociception and hypersensitivity in the mouse identified five genetically distinct pain types. In the present study, we reanalyzed that dataset and included the results of an additional nine assays of nociception and hypersensitivity to: 1) replicate the previously identified five pain types; 2) test whether any of the newly added pain assays represent novel genetically distinct pain types; 3) test the level of genetic relatedness among nine commonly employed neuropathic pain assays. Multivariate analysis of pairwise correlations between assays shows that the newly added zymosan-induced heat hypersensitivity assay does not conform to the two previously identified groups of heat hypersensitivity assays and cyclophosphamide-induced cystitis, the first organ-specific visceral pain model examined, is genetically distinct from other inflammatory assays. The four included mechanical hypersensitivity assays are genetically distinct, and do not comprise a single pain type as previously reported. Among the nine neuropathic pain assays including autotomy, chemotherapy, nerve ligation and spared nerve injury assays, at least four genetically distinct types of neuropathic sensory abnormalities were identified, corresponding to differences in nerve injury method. In addition, two itch assays and Comt genotype were compared to the expanded set of nociception and hypersensitivity assays. Comt genotype was strongly related only to spontaneous inflammatory nociception assays. These results indicate the priority for continued investigation of genetic mechanisms in several assays newly identified to represent genetically distinct pain types. PMID:24071598

Analysis of E. rutaecarpa Alkaloids Constituents In Vitro and In Vivo by UPLC-Q-TOF-MS Combined with Diagnostic Fragment

PubMed Central

Yang, Shenshen; Tian, Meng; Yuan, Lei; Deng, Haoyue; Wang, Lei; Li, Aizhu; Hou, Zhiguo; Li, Yubo

2016-01-01

Evodia rutaecarpa (Juss.) Benth. (Rutaceae) dried ripe fruit is used for dispelling colds, soothing liver, and analgesia. Pharmacological research has proved that alkaloids are the main active ingredients of E. rutaecarpa. This study aimed to rapidly classify and identify the alkaloids constituents of E. rutaecarpa by using UPLC-Q-TOF-MS coupled with diagnostic fragments. Furthermore, the effects of the material base of E. rutaecarpa bioactive ingredients in vivo were examined such that the transitional components in the blood of rats intragastrically given E. rutaecarpa were analyzed and identified. In this study, the type of alcohol extraction of E. rutaecarpa and the corresponding blood sample were used for the analysis by UPLC-Q-TOF-MS in positive ion mode. After reviewing much of the literature and collected information on the fragments, we obtained some diagnostic fragments of the alkaloids. Combining the diagnostic fragments with the technology of UPLC-Q-TOF-MS, we identified the compounds of E. rutaecarpa and blood samples and compared the ion fragment information with that of the alkaloids in E. rutaecarpa. A total of 17 alkaloids components and 6 blood components were identified. The proposed method was rapid, accurate, and sensitive. Therefore, this technique can reliably and practically analyze the chemical constituents in traditional Chinese medicine (TCM). PMID:27446630

Nuclear factors that bind to the enhancer region of nondefective Friend murine leukemia virus.

PubMed Central

Manley, N R; O'Connell, M A; Sharp, P A; Hopkins, N

1989-01-01

Nondefective Friend murine leukemia virus (MuLV) causes erythroleukemia when injected into newborn NFS mice, while Moloney MuLV causes T-cell lymphoma. Exchange of the Friend virus enhancer region, a sequence of about 180 nucleotides including the direct repeat and a short 3'-adjacent segment, for the corresponding region in Moloney MuLV confers the ability to cause erythroid disease on Moloney MuLV. We have used the electrophoretic mobility shift assay and methylation interference analysis to identify cellular factors which bind to the Friend virus enhancer region and compared these with factors, previously identified, that bind to the Moloney virus direct repeat (N. A. Speck and D. Baltimore, Mol. Cell. Biol. 7:1101-1110, 1987). We identified five binding sites for sequence-specific DNA-binding proteins in the Friend virus enhancer region. While some binding sites are present in both the Moloney and Friend virus enhancers, both viruses contain unique sites not present in the other. Although none of the factors identified in this report which bind to these unique sites are present exclusively in T cells or erythroid cells, they bind to three regions of the enhancer shown by genetic analysis to encode disease specificity and thus are candidates to mediate the tissue-specific expression and distinct disease specificities encoded by these virus enhancer elements. Images PMID:2778872

Global transcriptional landscape and promoter mapping of the gut commensal Bifidobacterium breve UCC2003.

PubMed

Bottacini, Francesca; Zomer, Aldert; Milani, Christian; Ferrario, Chiara; Lugli, Gabriele Andrea; Egan, Muireann; Ventura, Marco; van Sinderen, Douwe

2017-12-28

Bifidobacterium breve represents a common member of the infant gut microbiota and its presence in the gut has been associated with host well being. For this reason it is relevant to investigate and understand the molecular mechanisms underlying the establishment, persistence and activities of this gut commensal in the host environment. The assessment of vegetative promoters in the bifidobacterial prototype Bifidobacterium breve UCC2003 was performed employing a combination of RNA tiling array analysis and cDNA sequencing. Canonical -10 (TATAAT) and -35 (TTGACA) sequences were identified upstream of transcribed genes or operons, where deviations from this consensus correspond to transcription level variations. A Random Forest analysis assigned the -10 region of B. breve promoters as the element most impacting on the level of transcription, followed by the spacer length and the 5'-UTR length of transcripts. Furthermore, our transcriptome study also identified rho-independent termination as the most common and effective termination signal of highly and moderately transcribed operons in B. breve. The present study allowed us to identify genes and operons that are actively transcribed in this organism during logarithmic growth, and link promoter elements with levels of transcription of essential genes in this organism. As homologs of many of our identified genes are present across the whole genus Bifidobacterium, our dataset constitutes a transcriptomic reference to be used for future investigations of gene expression in members of this genus.

Genome-wide association studies of autoimmune vitiligo identify 23 new risk loci and highlight key pathways and regulatory variants.

PubMed

Jin, Ying; Andersen, Genevieve; Yorgov, Daniel; Ferrara, Tracey M; Ben, Songtao; Brownson, Kelly M; Holland, Paulene J; Birlea, Stanca A; Siebert, Janet; Hartmann, Anke; Lienert, Anne; van Geel, Nanja; Lambert, Jo; Luiten, Rosalie M; Wolkerstorfer, Albert; Wietze van der Veen, J P; Bennett, Dorothy C; Taïeb, Alain; Ezzedine, Khaled; Kemp, E Helen; Gawkrodger, David J; Weetman, Anthony P; Kõks, Sulev; Prans, Ele; Kingo, Külli; Karelson, Maire; Wallace, Margaret R; McCormack, Wayne T; Overbeck, Andreas; Moretti, Silvia; Colucci, Roberta; Picardo, Mauro; Silverberg, Nanette B; Olsson, Mats; Valle, Yan; Korobko, Igor; Böhm, Markus; Lim, Henry W; Hamzavi, Iltefat; Zhou, Li; Mi, Qing-Sheng; Fain, Pamela R; Santorico, Stephanie A; Spritz, Richard A

2016-11-01

Vitiligo is an autoimmune disease in which depigmented skin results from the destruction of melanocytes, with epidemiological association with other autoimmune diseases. In previous linkage and genome-wide association studies (GWAS1 and GWAS2), we identified 27 vitiligo susceptibility loci in patients of European ancestry. We carried out a third GWAS (GWAS3) in European-ancestry subjects, with augmented GWAS1 and GWAS2 controls, genome-wide imputation, and meta-analysis of all three GWAS, followed by an independent replication. The combined analyses, with 4,680 cases and 39,586 controls, identified 23 new significantly associated loci and 7 suggestive loci. Most encode immune and apoptotic regulators, with some also associated with other autoimmune diseases, as well as several melanocyte regulators. Bioinformatic analyses indicate a predominance of causal regulatory variation, some of which corresponds to expression quantitative trait loci (eQTLs) at these loci. Together, the identified genes provide a framework for the genetic architecture and pathobiology of vitiligo, highlight relationships with other autoimmune diseases and melanoma, and offer potential targets for treatment.

Genome-wide association studies of autoimmune vitiligo identify 23 new risk loci and highlight key pathways and regulatory variants

PubMed Central

Jin, Ying; Andersen, Genevieve; Yorgov, Daniel; Ferrara, Tracey M; Ben, Songtao; Brownson, Kelly M; Holland, Paulene J; Birlea, Stanca A; Siebert, Janet; Hartmann, Anke; Lienert, Anne; van Geel, Nanja; Lambert, Jo; Luiten, Rosalie M; Wolkerstorfer, Albert; van der Veen, JP Wietze; Bennett, Dorothy C; Taïeb, Alain; Ezzedine, Khaled; Kemp, E Helen; Gawkrodger, David J; Weetman, Anthony P; Kõks, Sulev; Prans, Ele; Kingo, Külli; Karelson, Maire; Wallace, Margaret R; McCormack, Wayne T; Overbeck, Andreas; Moretti, Silvia; Colucci, Roberta; Picardo, Mauro; Silverberg, Nanette B; Olsson, Mats; Valle, Yan; Korobko, Igor; Böhm, Markus; Lim, Henry W.; Hamzavi, Iltefat; Zhou, Li; Mi, Qing-Sheng; Fain, Pamela R.; Santorico, Stephanie A; Spritz, Richard A

2016-01-01

Vitiligo is an autoimmune disease in which depigmented skin results from destruction of melanocytes1, with epidemiologic association with other autoimmune diseases2. In previous linkage and genome-wide association studies (GWAS1, GWAS2), we identified 27 vitiligo susceptibility loci in patients of European (EUR) ancestry. We carried out a third GWAS (GWAS3) in EUR subjects, with augmented GWAS1 and GWAS2 controls, genome-wide imputation, and meta-analysis of all three GWAS, followed by an independent replication. The combined analyses, with 4,680 cases and 39,586 controls, identified 23 new loci and 7 suggestive loci, most encoding immune and apoptotic regulators, some also associated with other autoimmune diseases, as well as several melanocyte regulators. Bioinformatic analyses indicate a predominance of causal regulatory variation, some corresponding to eQTL at these loci. Together, the identified genes provide a framework for vitiligo genetic architecture and pathobiology, highlight relationships to other autoimmune diseases and melanoma, and offer potential targets for treatment. PMID:27723757

Taxonomic changes and description of two new species for the Phyllodactylus lanei complex (Gekkota: Phyllodactylidae) in Mexico.

PubMed

RamÍrez-Reyes, Tonatiuh; Flores-Villela, Oscar

2018-04-10

An integrative taxonomy approach was implemented based on analysis of genetic, phylogenetic, morphological and ecological data to identify the cryptic diversity within the Phyllodactylus lanei complex. At least six species can be identified, of which four are currently considered subspecies: Phyllodactylus lanei, Phyllodactylus rupinus, Phyllodactylus isabelae, Phyllodactylus lupitae and two corresponding to undescribed taxa, which are identified and described in this contribution. These differ from other Mexican geckos in several characters: genetic distance (DNAmt), position in molecular phylogeny (concatened data DNAmt+DNAnu), species tree, morphological characters such as snout-vent length, longitudinal scales, tubercles from head to tail, interorbital scales, scales across venter, third labial-snout scales and rows of tubercles across dorsum; there are also differences in their bioclimatic profiles (temperature and precipitation) and geographical distribution. The most recent studies on taxonomy and evolution of Mexican geckos (Phyllodactylus) show that the diversity of this group of reptiles is currently underestimated, suggesting that more research and conservation efforts are should be addressed at these lizards.

Proteomic analysis of a compatible interaction between sugarcane and Sporisorium scitamineum.

PubMed

Barnabas, Leonard; Ashwin, N M R; Kaverinathan, K; Trentin, Anna Rita; Pivato, Micaela; Sundar, A Ramesh; Malathi, P; Viswanathan, R; Rosana, O B; Neethukrishna, K; Carletti, Paolo; Arrigoni, Giorgio; Masi, Antonio; Agrawal, Ganesh Kumar; Rakwal, Randeep

2016-04-01

Smut caused by Sporisorium scitamineum is one of the important diseases of sugarcane with global significance. Despite the intriguing nature of sugarcane, S. scitamineum interaction, several pertinent aspects remain unexplored. This study investigates the proteome level alterations occurring in the meristem of a S. scitamineum infected susceptible sugarcane cultivar at whip emergence stage. Differentially abundant proteins were identified by 2DE coupled with MALDI-TOF/TOF-MS. Comprehensively, 53 sugarcane proteins identified were related to defence, stress, metabolism, protein folding, energy, and cell division; in addition, a putative effector of S. scitamineum, chorismate mutase, was identified. Transcript expression vis-à-vis the activity of phenylalanine ammonia lyase was relatively higher in the infected meristem. Abundance of seven candidate proteins in 2D gel profiles was in correlation with its corresponding transcript expression levels as validated by qRT-PCR. Furthermore, this study has opened up new perspectives on the interaction between sugarcane and S. scitamineum. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

"Not Homeless Yet. I'm Kind of Couch Surfing": Finding Identities for People at a Homeless Shelter.

PubMed

Terui, Sachiko; Hsieh, Elaine

2016-01-01

The meanings of homelessness are fluid and socially constructed, providing resources and limitations for individuals to negotiate their identities and relationships in everyday life. In this study, we examine the strategies and corresponding resources utilized by people who are homeless to cope with the labeling of a homeless identity and to redefine their identities. We used constant comparative analysis to examine in-depth interviews with 16 participants (male = 11, female = 5) who access a local homeless shelter in the southwest United States for resources. We identified three strategies that homeless people adopt to cope with the labeling of homeless identity: (a) differentiating oneself from others who are homeless, (b) prioritizing certain aspects of life, and (c) embracing the status of homelessness. Although these strategies have been identified in previous literature, the authors extend this line of research by identifying the common resources people who are homeless utilize when adopting these strategies, which entail important implications for theory development and practical implications.

MOLE 2.0: advanced approach for analysis of biomacromolecular channels

PubMed Central

2013-01-01

Background Channels and pores in biomacromolecules (proteins, nucleic acids and their complexes) play significant biological roles, e.g., in molecular recognition and enzyme substrate specificity. Results We present an advanced software tool entitled MOLE 2.0, which has been designed to analyze molecular channels and pores. Benchmark tests against other available software tools showed that MOLE 2.0 is by comparison quicker, more robust and more versatile. As a new feature, MOLE 2.0 estimates physicochemical properties of the identified channels, i.e., hydropathy, hydrophobicity, polarity, charge, and mutability. We also assessed the variability in physicochemical properties of eighty X-ray structures of two members of the cytochrome P450 superfamily. Conclusion Estimated physicochemical properties of the identified channels in the selected biomacromolecules corresponded well with the known functions of the respective channels. Thus, the predicted physicochemical properties may provide useful information about the potential functions of identified channels. The MOLE 2.0 software is available at http://mole.chemi.muni.cz. PMID:23953065

Unsupervised Clustering of Subcellular Protein Expression Patterns in High-Throughput Microscopy Images Reveals Protein Complexes and Functional Relationships between Proteins

PubMed Central

Handfield, Louis-François; Chong, Yolanda T.; Simmons, Jibril; Andrews, Brenda J.; Moses, Alan M.

2013-01-01

Protein subcellular localization has been systematically characterized in budding yeast using fluorescently tagged proteins. Based on the fluorescence microscopy images, subcellular localization of many proteins can be classified automatically using supervised machine learning approaches that have been trained to recognize predefined image classes based on statistical features. Here, we present an unsupervised analysis of protein expression patterns in a set of high-resolution, high-throughput microscope images. Our analysis is based on 7 biologically interpretable features which are evaluated on automatically identified cells, and whose cell-stage dependency is captured by a continuous model for cell growth. We show that it is possible to identify most previously identified localization patterns in a cluster analysis based on these features and that similarities between the inferred expression patterns contain more information about protein function than can be explained by a previous manual categorization of subcellular localization. Furthermore, the inferred cell-stage associated to each fluorescence measurement allows us to visualize large groups of proteins entering the bud at specific stages of bud growth. These correspond to proteins localized to organelles, revealing that the organelles must be entering the bud in a stereotypical order. We also identify and organize a smaller group of proteins that show subtle differences in the way they move around the bud during growth. Our results suggest that biologically interpretable features based on explicit models of cell morphology will yield unprecedented power for pattern discovery in high-resolution, high-throughput microscopy images. PMID:23785265

Analysis of blood-based gene expression in idiopathic Parkinson disease.

PubMed

Shamir, Ron; Klein, Christine; Amar, David; Vollstedt, Eva-Juliane; Bonin, Michael; Usenovic, Marija; Wong, Yvette C; Maver, Ales; Poths, Sven; Safer, Hershel; Corvol, Jean-Christophe; Lesage, Suzanne; Lavi, Ofer; Deuschl, Günther; Kuhlenbaeumer, Gregor; Pawlack, Heike; Ulitsky, Igor; Kasten, Meike; Riess, Olaf; Brice, Alexis; Peterlin, Borut; Krainc, Dimitri

2017-10-17

To examine whether gene expression analysis of a large-scale Parkinson disease (PD) patient cohort produces a robust blood-based PD gene signature compared to previous studies that have used relatively small cohorts (≤220 samples). Whole-blood gene expression profiles were collected from a total of 523 individuals. After preprocessing, the data contained 486 gene profiles (n = 205 PD, n = 233 controls, n = 48 other neurodegenerative diseases) that were partitioned into training, validation, and independent test cohorts to identify and validate a gene signature. Batch-effect reduction and cross-validation were performed to ensure signature reliability. Finally, functional and pathway enrichment analyses were applied to the signature to identify PD-associated gene networks. A gene signature of 100 probes that mapped to 87 genes, corresponding to 64 upregulated and 23 downregulated genes differentiating between patients with idiopathic PD and controls, was identified with the training cohort and successfully replicated in both an independent validation cohort (area under the curve [AUC] = 0.79, p = 7.13E-6) and a subsequent independent test cohort (AUC = 0.74, p = 4.2E-4). Network analysis of the signature revealed gene enrichment in pathways, including metabolism, oxidation, and ubiquitination/proteasomal activity, and misregulation of mitochondria-localized genes, including downregulation of COX4I1 , ATP5A1 , and VDAC3 . We present a large-scale study of PD gene expression profiling. This work identifies a reliable blood-based PD signature and highlights the importance of large-scale patient cohorts in developing potential PD biomarkers. © 2017 American Academy of Neurology.

Breed-specific ancestry studies and genome-wide association analysis highlight an association between the MYH9 gene and heat tolerance in Alaskan sprint racing sled dogs.

PubMed

Huson, Heather J; vonHoldt, Bridgett M; Rimbault, Maud; Byers, Alexandra M; Runstadler, Jonathan A; Parker, Heidi G; Ostrander, Elaine A

2012-02-01

Alaskan sled dogs are a genetically distinct population shaped by generations of selective interbreeding with purebred dogs to create a group of high-performance athletes. As a result of selective breeding strategies, sled dogs present a unique opportunity to employ admixture-mapping techniques to investigate how breed composition and trait selection impact genomic structure. We used admixture mapping to investigate genetic ancestry across the genomes of two classes of sled dogs, sprint and long-distance racers, and combined that with genome-wide association studies (GWAS) to identify regions that correlate with performance-enhancing traits. The sled dog genome is enhanced by differential contributions from four non-admixed breeds (Alaskan Malamute, Siberian Husky, German Shorthaired Pointer, and Borzoi). A principal components analysis (PCA) of 115,000 genome-wide SNPs clearly resolved the sprint and distance populations as distinct genetic groups, with longer blocks of linkage disequilibrium (LD) observed in the distance versus sprint dogs (7.5-10 and 2.5-3.75 kb, respectively). Furthermore, we identified eight regions with the genomic signal from either a selective sweep or an association analysis, corroborated by an excess of ancestry when comparing sprint and distance dogs. A comparison of elite and poor-performing sled dogs identified a single region significantly associated with heat tolerance. Within the region we identified seven SNPs within the myosin heavy chain 9 gene (MYH9) that were significantly associated with heat tolerance in sprint dogs, two of which correspond to conserved promoter and enhancer regions in the human ortholog.

Screening of polyhydroxyalkanoate-producing bacteria and PhaC-encoding genes in two hypersaline microbial mats from Guerrero Negro, Baja California Sur, Mexico.

PubMed

Martínez-Gutiérrez, Carolina A; Latisnere-Barragán, Hever; García-Maldonado, José Q; López-Cortés, Alejandro

2018-01-01

Hypersaline microbial mats develop through seasonal and diel fluctuations, as well as under several physicochemical variables. Hence, resident microorganisms commonly employ strategies such as the synthesis of polyhydroxyalkanoates (PHAs) in order to resist changing and stressful conditions. However, the knowledge of bacterial PHA production in hypersaline microbial mats has been limited to date, particularly in regard to medium-chain length PHAs (mcl-PHAs), which have biotechnological applications due to their plastic properties. The aim of this study was to obtain evidence for PHA production in two hypersaline microbial mats of Guerrero Negro, Mexico by searching for PHA granules and PHA synthase genes in isolated bacterial strains and environmental samples. Six PHA-producing strains were identified by 16S rRNA gene sequencing; three of them corresponded to a Halomonas sp. In addition, Paracoccus sp., Planomicrobium sp. and Staphylococcus sp. were also identified as PHA producers. Presumptive PHA granules and PHA synthases genes were detected in both sampling sites. Moreover, phylogenetic analysis showed that most of the phylotypes were distantly related to putative PhaC synthases class I sequences belonging to members of the classes Alphaproteobacteria and Gammaproteobacteria distributed within eight families, with higher abundances corresponding mainly to Rhodobacteraceae and Rhodospirillaceae. This analysis also showed that PhaC synthases class II sequences were closely related to those of Pseudomonas putida , suggesting the presence of this group, which is probably involved in the production of mcl-PHA in the mats. According to our state of knowledge, this study reports for the first time the occurrence of phaC and phaC1 sequences in hypersaline microbial mats, suggesting that these ecosystems may be a novel source for the isolation of short- and medium-chain length PHA producers.

Fine-mapping the MHC locus in juvenile idiopathic arthritis (JIA) reveals genetic heterogeneity corresponding to distinct adult inflammatory arthritic diseases

PubMed Central

Hinks, A; Cobb, J; Ainsworth, H C; Marion, M C; Comeau, M E; Sudman, M; Han, B; Becker, M L; Bohnsack, J F; de Bakker, P I W; Haas, J P; Hazen, M; Lovell, D J; Nigrovic, P A; Nordal, E; Punnaro, M; Rosenberg, A M; Rygg, M; Wise, C A; Videm, V; Wedderburn, L R; Yarwood, A; Yeung, R S M; Prahalad, S; Langefeld, C D; Raychaudhuri, S; Thompson, S D; Thomson, W

2017-01-01

Objectives Juvenile idiopathic arthritis (JIA) is a heterogeneous group of diseases, comprising seven categories. Genetic data could potentially be used to help redefine JIA categories and improve the current classification system. The human leucocyte antigen (HLA) region is strongly associated with JIA. Fine-mapping of the region was performed to look for similarities and differences in HLA associations between the JIA categories and define correspondences with adult inflammatory arthritides. Methods Dense genotype data from the HLA region, from the Immunochip array for 5043 JIA cases and 14 390 controls, were used to impute single-nucleotide polymorphisms, HLA classical alleles and amino acids. Bivariate analysis was performed to investigate genetic correlation between the JIA categories. Conditional analysis was used to identify additional effects within the region. Comparison of the findings with those in adult inflammatory arthritic diseases was performed. Results We identified category-specific associations and have demonstrated for the first time that rheumatoid factor (RF)-negative polyarticular JIA and oligoarticular JIA are genetically similar in their HLA associations. We also observe that each JIA category potentially has an adult counterpart. The RF-positive polyarthritis association at HLA-DRB1 amino acid at position 13 mirrors the association in adult seropositive rheumatoid arthritis (RA). Interestingly, the combined oligoarthritis and RF-negative polyarthritis dataset shares the same association with adult seronegative RA. Conclusions The findings suggest the value of using genetic data in helping to classify the categories of this heterogeneous disease. Mapping JIA categories to adult counterparts could enable shared knowledge of disease pathogenesis and aetiology and facilitate transition from paediatric to adult services. PMID:27998952