Quantitative Analysis of Global Proteome and Lysine Acetylome Reveal the Differential Impacts of VPA and SAHA on HL60 Cells.

PubMed

Zhu, Xiaoyu; Liu, Xin; Cheng, Zhongyi; Zhu, Jun; Xu, Lei; Wang, Fengsong; Qi, Wulin; Yan, Jiawei; Liu, Ning; Sun, Zimin; Liu, Huilan; Peng, Xiaojun; Hao, Yingchan; Zheng, Nan; Wu, Quan

2016-01-29

Valproic acid (VPA) and suberoylanilide hydroxamic acid (SAHA) are both HDAC inhibitors (HDACi). Previous studies indicated that both inhibitors show therapeutic effects on acute myeloid leukaemia (AML), while the differential impacts of the two different HDACi on AML treatment still remains elusive. In this study, using 3-plex SILAC based quantitative proteomics technique, anti-acetyllysine antibody based affinity enrichment, high resolution LC-MS/MS and intensive bioinformatic analysis, the quantitative proteome and acetylome in SAHA and VPA treated AML HL60 cells were extensively studied. In total, 5,775 proteins and 1,124 lysine acetylation sites were successfully obtained in response to VAP and SAHA treatment. It is found that VPA and SAHA treatment differently induced proteome and acetylome profiling in AML HL60 cells. This study revealed the differential impacts of VPA and SAHA on proteome/acetylome in AML cells, deepening our understanding of HDAC inhibitor mediated AML therapeutics.

Quantitative study of flavonoids in leaves of citrus plants.

PubMed

Kawaii, S; Tomono, Y; Katase, E; Ogawa, K; Yano, M; Koizumi, M; Ito, C; Furukawa, H

2000-09-01

Leaf flavonoids were quantitatively determined in 68 representative or economically important Citrus species, cultivars, and near-Citrus relatives. Contents of 23 flavonoids including 6 polymethoxylated flavones were analyzed by means of reversed phase HPLC analysis. Principal component analysis revealed that the 7 associations according to Tanaka's classification were observed, but some do overlap each other. Group VII species could be divided into two different subgroups, namely, the first-10-species class and the last-19-species class according to Tanaka's classification numbers.

Multidimensional quantitative analysis of mRNA expression within intact vertebrate embryos.

PubMed

Trivedi, Vikas; Choi, Harry M T; Fraser, Scott E; Pierce, Niles A

2018-01-08

For decades, in situ hybridization methods have been essential tools for studies of vertebrate development and disease, as they enable qualitative analyses of mRNA expression in an anatomical context. Quantitative mRNA analyses typically sacrifice the anatomy, relying on embryo microdissection, dissociation, cell sorting and/or homogenization. Here, we eliminate the trade-off between quantitation and anatomical context, using quantitative in situ hybridization chain reaction (qHCR) to perform accurate and precise relative quantitation of mRNA expression with subcellular resolution within whole-mount vertebrate embryos. Gene expression can be queried in two directions: read-out from anatomical space to expression space reveals co-expression relationships in selected regions of the specimen; conversely, read-in from multidimensional expression space to anatomical space reveals those anatomical locations in which selected gene co-expression relationships occur. As we demonstrate by examining gene circuits underlying somitogenesis, quantitative read-out and read-in analyses provide the strengths of flow cytometry expression analyses, but by preserving subcellular anatomical context, they enable bi-directional queries that open a new era for in situ hybridization. © 2018. Published by The Company of Biologists Ltd.

Pink Ribbons and Red Dresses: A Mixed Methods Content Analysis of Media Coverage of Breast Cancer and Heart Disease.

PubMed

Champion, Claudine; Berry, Tanya R; Kingsley, Bethan; Spence, John C

2016-10-01

This research examined media coverage of breast cancer (n = 145) and heart disease and stroke (n = 39) news articles, videos, advertisements, and images in a local Canadian context through quantitative and thematic content analyses. Quantitative analysis revealed significant differences between coverage of the diseases in placement, survivors as a source of information, health agency, human interest stories, citation of a research study, the inclusion of risk statistics, discussion of preventative behaviors, and tone used. The thematic analysis revealed themes that characterized a "typical" breast cancer survivor and indicated that "good" citizens and businesses should help the cause of breast cancer. Themes for heart disease and stroke articulated individual responsibility and the ways fundraising reinforced femininity and privilege. Findings provide insight on how these diseases are framed in local Canadian media, which might impact an individual's understanding of the disease.

Isobaric Tags for Relative and Absolute Quantitation-Based Proteomic Analysis of Patent and Constricted Ductus Arteriosus Tissues Confirms the Systemic Regulation of Ductus Arteriosus Closure.

PubMed

Hong, Haifa; Ye, Lincai; Chen, Huiwen; Xia, Yu; Liu, Yue; Liu, Jinfen; Lu, Yanan; Zhang, Haibo

2015-08-01

We aimed to evaluate global changes in protein expression associated with patency by undertaking proteomic analysis of human constricted and patent ductus arteriosus (DA). Ten constricted and 10 patent human DAs were excised from infants with ductal-dependent heart disease during surgery. Using isobaric tags for relative and absolute quantitation-based quantitative proteomics, 132 differentially expressed proteins were identified. Of 132 proteins, voltage-gated sodium channel 1.3 (SCN3A), myosin 1d (Myo1d), Rho GTPase activating protein 26 (ARHGAP26), and retinitis pigmentosa 1 (RP1) were selected for validation by Western blot and quantitative real-time polymerase chain reaction analyses. Significant upregulation of SCN3A, Myo1d, and RP1 messenger RNA, and protein levels was observed in the patent DA group (all P ≤ 0.048). ARHGAP26 messenger RNA and protein levels were decreased in patent DA tissue (both P ≤ 0.018). Immunohistochemistry analysis revealed that Myo1d, ARHGAP26, and RP1 were specifically expressed in the subendothelial region of constricted DAs; however, diffuse expression of these proteins was noted in the patent group. Proteomic analysis revealed global changes in the expression of proteins that regulate oxygen sensing, ion channels, smooth muscle cell migration, nervous system, immune system, and metabolism, suggesting a basis for the systemic regulation of DA patency by diverse signaling pathways, which will be confirmed in further studies.

Olfactory function in chemical workers exposed to acrylate and methacrylate vapors.

PubMed Central

Schwartz, B S; Doty, R L; Monroe, C; Frye, R; Barker, S

1989-01-01

An investigation of the olfactory function of 731 workers at a chemical facility which manufacturers acrylates and methacrylates was undertaken using a standardized quantitative test. In a cross-sectional analysis of the data, no associations of chemical exposure with olfactory test scores were observed. A nested case-control study designed to evaluate the cumulative effects of exposure on olfactory function, however, revealed elevated crude exposure odds ratios (95% confidence interval) of 2.0 (1.1, 3.8) for all workers and 6.0 (1.7, 21.5) for workers who never smoked cigarettes. Logistic regression analysis, adjusting for multiple confounders, revealed exposure odds ratios of 2.8 (1.1, 7.0) and 13.5 (2.1, 87.6) in these same groups, respectively, and a dose-response relationship between olfactory dysfunction and cumulative exposure scores--semi-quantitative indices of lifetime exposure to the acrylates. The data also revealed decreasing exposure odds ratios with increasing duration since last exposure to these chemicals, suggesting that the effects may be reversible. PMID:2784947

A dynamic regression analysis tool for quantitative assessment of bacterial growth written in Python.

PubMed

Hoeflinger, Jennifer L; Hoeflinger, Daniel E; Miller, Michael J

2017-01-01

Herein, an open-source method to generate quantitative bacterial growth data from high-throughput microplate assays is described. The bacterial lag time, maximum specific growth rate, doubling time and delta OD are reported. Our method was validated by carbohydrate utilization of lactobacilli, and visual inspection revealed 94% of regressions were deemed excellent. Copyright © 2016 Elsevier B.V. All rights reserved.

Characteristics of calls to the Israeli hotline during the Intifada.

PubMed

Gilat, Itzhak; Latzer, Yael

2007-08-01

The present study examined the help-seeking characteristics of callers to the ten Israeli hotline centers during the Intifada - the Palestinian uprising in the Israeli administered territories. The research method combined quantitative and qualitative analyses of the volunteers' written reports. The quantitative analysis was conducted on a sample of 21,315 structured forms, and the qualitative content analysis was carried out on a sample of 498 verbal descriptions of calls. The quantitative analysis revealed a U-shaped curve illustrating the frequency of Intifada-related calls in relation to the time of the study. The qualitative analysis showed that the main complaints of the callers were focused on direct and masked manifestations of anxiety and feelings of helplessness. The implications of the findings are discussed in terms of understanding the unique psychological response to a new kind of stress, as seen from the perspective of calls to a hotline.

Macroscopic X-ray Powder Diffraction Scanning: Possibilities for Quantitative and Depth-Selective Parchment Analysis.

PubMed

Vanmeert, Frederik; De Nolf, Wout; Dik, Joris; Janssens, Koen

2018-06-05

At or below the surface of painted works of art, valuable information is present that provides insights into an object's past, such as the artist's technique and the creative process that was followed or its conservation history but also on its current state of preservation. Various noninvasive techniques have been developed over the past 2 decades that can probe this information either locally (via point analysis) or on a macroscopic scale (e.g., full-field imaging and raster scanning). Recently macroscopic X-ray powder diffraction (MA-XRPD) mapping using laboratory X-ray sources was developed. This method can visualize highly specific chemical distributions at the macroscale (dm 2 ). In this work we demonstrate the synergy between the quantitative aspects of powder diffraction and the noninvasive scanning capability of MA-XRPD highlighting the potential of the method to reveal new types of information. Quantitative data derived from a 15th/16th century illuminated sheet of parchment revealed three lead white pigments with different hydrocerussite-cerussite compositions in specific pictorial elements, while quantification analysis of impurities in the blue azurite pigment revealed two distinct azurite types: one rich in barite and one in quartz. Furthermore, on the same artifact, the depth-selective possibilities of the method that stem from an exploitation of the shift of the measured diffraction peaks with respect to reference data are highlighted. The influence of different experimental parameters on the depth-selective analysis results is briefly discussed. Promising stratigraphic information could be obtained, even though the analysis is hampered by not completely understood variations in the unit cell dimensions of the crystalline pigment phases.

Multiplex Quantitative Histologic Analysis of Human Breast Cancer Cell Signaling and Cell Fate

DTIC Science & Technology

2010-05-01

Breast cancer, cell signaling, cell proliferation, histology, image analysis 15. NUMBER OF PAGES - 51 16. PRICE CODE 17. SECURITY CLASSIFICATION...revealed by individual stains in multiplex combinations; and (3) software (FARSIGHT) for automated multispectral image analysis that (i) segments...Task 3. Develop computational algorithms for multispectral immunohistological image analysis FARSIGHT software was developed to quantify intrinsic

Functional characterization and quantitative expression analysis of two GnRH-related peptide receptors in the mosquito, Aedes aegypti.

PubMed

Oryan, Alireza; Wahedi, Azizia; Paluzzi, Jean-Paul V

2018-03-04

To cope with stressful events such as flight, organisms have evolved various regulatory mechanisms, often involving control by endocrine-derived factors. In insects, two stress-related factors include the gonadotropin-releasing hormone-related peptides adipokinetic hormone (AKH) and corazonin (CRZ). AKH is a pleiotropic hormone best known as a substrate liberator of proteins, lipids, and carbohydrates. Although a universal function has not yet been elucidated, CRZ has been shown to have roles in pigmentation, ecdysis or act as a cardiostimulatory factor. While both these neuropeptides and their respective receptors (AKHR and CRZR) have been characterized in several organisms, details on their specific roles within the disease vector, Aedes aegypti, remain largely unexplored. Here, we obtained three A. aegypti AKHR transcript variants and further identified the A. aegypti CRZR receptor. Receptor expression using a heterologous functional assay revealed that these receptors exhibit a highly specific response for their native ligands. Developmental quantitative expression analysis of CRZR revealed enrichment during the pupal and adult stages. In adults, quantitative spatial expression analysis revealed CRZR transcript in a variety of organs including head, thoracic ganglia, primary reproductive organs (ovary and testis), as well as male carcass. This suggest CRZ may play a role in ecdysis, and neuronal expression of CRZR indicates a possible role for CRZ within the nervous system. Quantitative developmental expression analysis of AKHR identified significant transcript enrichment in early adult stages. AKHR transcript was observed in the head, thoracic ganglia, accessory reproductive tissues and the carcass of adult females, while it was detected in the abdominal ganglia and enriched significantly in the carcass of adult males, which supports the known function of AKH in energy metabolism. Collectively, given the enrichment of CRZR and AKHR in the primary and secondary sex organs, respectively, of adult mosquitoes, these neuropeptides may play a role in regulating mosquito reproductive biology. Copyright © 2018 Elsevier Inc. All rights reserved.

Quantitative Proteomics Identifies Activation of Hallmark Pathways of Cancer in Patient Melanoma.

PubMed

Byrum, Stephanie D; Larson, Signe K; Avaritt, Nathan L; Moreland, Linley E; Mackintosh, Samuel G; Cheung, Wang L; Tackett, Alan J

2013-03-01

Molecular pathways regulating melanoma initiation and progression are potential targets of therapeutic development for this aggressive cancer. Identification and molecular analysis of these pathways in patients has been primarily restricted to targeted studies on individual proteins. Here, we report the most comprehensive analysis of formalin-fixed paraffin-embedded human melanoma tissues using quantitative proteomics. From 61 patient samples, we identified 171 proteins varying in abundance among benign nevi, primary melanoma, and metastatic melanoma. Seventy-three percent of these proteins were validated by immunohistochemistry staining of malignant melanoma tissues from the Human Protein Atlas database. Our results reveal that molecular pathways involved with tumor cell proliferation, motility, and apoptosis are mis-regulated in melanoma. These data provide the most comprehensive proteome resource on patient melanoma and reveal insight into the molecular mechanisms driving melanoma progression.

Comparing quantitative analysis on revealed comparative advantages of aquatic products trade of china and ASEAN based on 21st century maritime silk road

NASA Astrophysics Data System (ADS)

Luo, X. F.; Han, Y. H.; Li, Z. W.

2017-11-01

As the world’s leading aquaculture, aquatic production and trading country, China’s development of aquatic products trade with ASEAN is facing a historic opportunity in the favourable circumstances of construction of the 21st century Maritime Silk Road. In order to make guidance of the product selection and transformation for corresponding export enterprises, this article makes a quantitative analysis the Revealed Comparative Advantage of aquatic products trade from China and ASEAN respectively based on the HS classification and thoroughly compares the RCA indices. The comparison results show that the international competitiveness of aquatic products structures of China and ASEAN are quite different with few overlaps of strong competitive products, and there is a great gap between the two areas in many kinds of products.

Quantitative analysis and feature recognition in 3-D microstructural data sets

NASA Astrophysics Data System (ADS)

Lewis, A. C.; Suh, C.; Stukowski, M.; Geltmacher, A. B.; Spanos, G.; Rajan, K.

2006-12-01

A three-dimensional (3-D) reconstruction of an austenitic stainless-steel microstructure was used as input for an image-based finite-element model to simulate the anisotropic elastic mechanical response of the microstructure. The quantitative data-mining and data-warehousing techniques used to correlate regions of high stress with critical microstructural features are discussed. Initial analysis of elastic stresses near grain boundaries due to mechanical loading revealed low overall correlation with their location in the microstructure. However, the use of data-mining and feature-tracking techniques to identify high-stress outliers revealed that many of these high-stress points are generated near grain boundaries and grain edges (triple junctions). These techniques also allowed for the differentiation between high stresses due to boundary conditions of the finite volume reconstructed, and those due to 3-D microstructural features.

Quantitative analysis of the polarization characteristics of atherosclerotic plaques

NASA Astrophysics Data System (ADS)

Gubarkova, Ekaterina V.; Kirillin, Michail Y.; Dudenkova, Varvara V.; Kiseleva, Elena B.; Moiseev, Alexander A.; Gelikonov, Grigory V.; Timofeeva, Lidia B.; Fiks, Ilya I.; Feldchtein, Felix I.; Gladkova, Natalia D.

2016-04-01

In this study we demonstrate the capability of cross-polarization optical coherence tomography (CP OCT) to assess collagen and elastin fibers condition in atherosclerotic plaques basing on ratio of the OCT signal levels in cross- and co- polarizations. We consider the depolarization factor (DF) and the effective birefringence (Δn) as quantitative characteristics of CP OCT images. We revealed that calculation of both DF and Δn in the region of interest (fibrous cap) yields a statistically significant difference between stable and unstable plaques (0.46+/-0.21 vs 0.09+/-0.04 for IDF; (4.7+/-1.0)•10-4 vs (2.5+/-0.7)•10-4 for Δn p<0.05). In parallel with CP OCT we used the nonlinear microscopy for analysis of thin cross-section of atherosclerotic plaque, revealing the different average isotropy index of collagen and elastin fibers for stable and unstable plaques (0.30 +/- 0.10 vs 0.70 +/- 0.08; p<0.001). The proposed approach for quantitative assessment of CP OCT images allows cross-scattering and birefringence characterization of stable and unstable atherosclerotic plaques.

T1, diffusion tensor, and quantitative magnetization transfer imaging of the hippocampus in an Alzheimer's disease mouse model.

PubMed

Whittaker, Heather T; Zhu, Shenghua; Di Curzio, Domenico L; Buist, Richard; Li, Xin-Min; Noy, Suzanna; Wiseman, Frances K; Thiessen, Jonathan D; Martin, Melanie

2018-07-01

Alzheimer's disease (AD) pathology causes microstructural changes in the brain. These changes, if quantified with magnetic resonance imaging (MRI), could be studied for use as an early biomarker for AD. The aim of our study was to determine if T 1 relaxation, diffusion tensor imaging (DTI), and quantitative magnetization transfer imaging (qMTI) metrics could reveal changes within the hippocampus and surrounding white matter structures in ex vivo transgenic mouse brains overexpressing human amyloid precursor protein with the Swedish mutation. Delineation of hippocampal cell layers using DTI color maps allows more detailed analysis of T 1 -weighted imaging, DTI, and qMTI metrics, compared with segmentation of gross anatomy based on relaxation images, and with analysis of DTI or qMTI metrics alone. These alterations are observed in the absence of robust intracellular Aβ accumulation or plaque deposition as revealed by histology. This work demonstrates that multiparametric quantitative MRI methods are useful for characterizing changes within the hippocampal substructures and surrounding white matter tracts of mouse models of AD. Copyright © 2018. Published by Elsevier Inc.

The Student Perception of Faculty Scale: Development, Testing and Practical Application

ERIC Educational Resources Information Center

Mueller, Thomas S.

2017-01-01

This study involved a sample group of students residing in residential halls at a state university in a qualitative and quantitative analysis to measure their perceptions of the university's faculty. Exploratory, then confirmatory, factor analysis revealed a 3-factor model representing teaching faculty: a negative, emotionally challenging…

Visualization and Quantitative Analysis of Crack-Tip Plastic Zone in Pure Nickel

NASA Astrophysics Data System (ADS)

Kelton, Randall; Sola, Jalal Fathi; Meletis, Efstathios I.; Huang, Haiying

2018-05-01

Changes in surface morphology have long been thought to be associated with crack propagation in metallic materials. We have studied areal surface texture changes around crack tips in an attempt to understand the correlations between surface texture changes and crack growth behavior. Detailed profiling of the fatigue sample surface was carried out at short fatigue intervals. An image processing algorithm was developed to calculate the surface texture changes. Quantitative analysis of the crack-tip plastic zone, crack-arrested sites near triple points, and large surface texture changes associated with crack release from arrested locations was carried out. The results indicate that surface texture imaging enables visualization of the development of plastic deformation around a crack tip. Quantitative analysis of the surface texture changes reveals the effects of local microstructures on the crack growth behavior.

Identification of ginseng root using quantitative X-ray microtomography.

PubMed

Ye, Linlin; Xue, Yanling; Wang, Yudan; Qi, Juncheng; Xiao, Tiqiao

2017-07-01

The use of X-ray phase-contrast microtomography for the investigation of Chinese medicinal materials is advantageous for its nondestructive, in situ , and three-dimensional quantitative imaging properties. The X-ray phase-contrast microtomography quantitative imaging method was used to investigate the microstructure of ginseng, and the phase-retrieval method is also employed to process the experimental data. Four different ginseng samples were collected and investigated; these were classified according to their species, production area, and sample growth pattern. The quantitative internal characteristic microstructures of ginseng were extracted successfully. The size and position distributions of the calcium oxalate cluster crystals (COCCs), important secondary metabolites that accumulate in ginseng, are revealed by the three-dimensional quantitative imaging method. The volume and amount of the COCCs in different species of the ginseng are obtained by a quantitative analysis of the three-dimensional microstructures, which shows obvious difference among the four species of ginseng. This study is the first to provide evidence of the distribution characteristics of COCCs to identify four types of ginseng, with regard to species authentication and age identification, by X-ray phase-contrast microtomography quantitative imaging. This method is also expected to reveal important relationships between COCCs and the occurrence of the effective medicinal components of ginseng.

Qualitative and quantitative studies of chemical composition of sandarac resin by GC-MS.

PubMed

Kononenko, I; de Viguerie, L; Rochut, S; Walter, Ph

2017-01-01

The chemical composition of sandarac resin was investigated qualitatively and quantitatively by gas chromatography-mass spectrometry (GC-MS). Six compounds with labdane and pimarane skeletons were identified in the resin. The obtained mass spectra were interpreted and the mass spectrometric behaviour of these diterpenoids under EI conditions was described. Quantitative analysis by the method of internal standard revealed that identified diterpenoids represent only 10-30% of the analysed sample. The sandarac resin from different suppliers was analysed (from Kremer, Okhra, Color Rare, La Marchande de Couleurs, L'Atelier Montessori, Hevea). The analysis of different lumps of resins showed that the chemical composition differs from one lump to another, varying mainly in the relative distributions of the components.

Quantitative analysis of virgin coconut oil in cream cosmetics preparations using fourier transform infrared (FTIR) spectroscopy.

PubMed

Rohman, A; Man, Yb Che; Sismindari

2009-10-01

Today, virgin coconut oil (VCO) is becoming valuable oil and is receiving an attractive topic for researchers because of its several biological activities. In cosmetics industry, VCO is excellent material which functions as a skin moisturizer and softener. Therefore, it is important to develop a quantitative analytical method offering a fast and reliable technique. Fourier transform infrared (FTIR) spectroscopy with sample handling technique of attenuated total reflectance (ATR) can be successfully used to analyze VCO quantitatively in cream cosmetic preparations. A multivariate analysis using calibration of partial least square (PLS) model revealed the good relationship between actual value and FTIR-predicted value of VCO with coefficient of determination (R2) of 0.998.

A versatile pipeline for the multi-scale digital reconstruction and quantitative analysis of 3D tissue architecture

PubMed Central

Morales-Navarrete, Hernán; Segovia-Miranda, Fabián; Klukowski, Piotr; Meyer, Kirstin; Nonaka, Hidenori; Marsico, Giovanni; Chernykh, Mikhail; Kalaidzidis, Alexander; Zerial, Marino; Kalaidzidis, Yannis

2015-01-01

A prerequisite for the systems biology analysis of tissues is an accurate digital three-dimensional reconstruction of tissue structure based on images of markers covering multiple scales. Here, we designed a flexible pipeline for the multi-scale reconstruction and quantitative morphological analysis of tissue architecture from microscopy images. Our pipeline includes newly developed algorithms that address specific challenges of thick dense tissue reconstruction. Our implementation allows for a flexible workflow, scalable to high-throughput analysis and applicable to various mammalian tissues. We applied it to the analysis of liver tissue and extracted quantitative parameters of sinusoids, bile canaliculi and cell shapes, recognizing different liver cell types with high accuracy. Using our platform, we uncovered an unexpected zonation pattern of hepatocytes with different size, nuclei and DNA content, thus revealing new features of liver tissue organization. The pipeline also proved effective to analyse lung and kidney tissue, demonstrating its generality and robustness. DOI: http://dx.doi.org/10.7554/eLife.11214.001 PMID:26673893

Comprehensive Quantitative Analysis on Privacy Leak Behavior

PubMed Central

Fan, Lejun; Wang, Yuanzhuo; Jin, Xiaolong; Li, Jingyuan; Cheng, Xueqi; Jin, Shuyuan

2013-01-01

Privacy information is prone to be leaked by illegal software providers with various motivations. Privacy leak behavior has thus become an important research issue of cyber security. However, existing approaches can only qualitatively analyze privacy leak behavior of software applications. No quantitative approach, to the best of our knowledge, has been developed in the open literature. To fill this gap, in this paper we propose for the first time four quantitative metrics, namely, possibility, severity, crypticity, and manipulability, for privacy leak behavior analysis based on Privacy Petri Net (PPN). In order to compare the privacy leak behavior among different software, we further propose a comprehensive metric, namely, overall leak degree, based on these four metrics. Finally, we validate the effectiveness of the proposed approach using real-world software applications. The experimental results demonstrate that our approach can quantitatively analyze the privacy leak behaviors of various software types and reveal their characteristics from different aspects. PMID:24066046

Comprehensive quantitative analysis on privacy leak behavior.

PubMed

Fan, Lejun; Wang, Yuanzhuo; Jin, Xiaolong; Li, Jingyuan; Cheng, Xueqi; Jin, Shuyuan

2013-01-01

Privacy information is prone to be leaked by illegal software providers with various motivations. Privacy leak behavior has thus become an important research issue of cyber security. However, existing approaches can only qualitatively analyze privacy leak behavior of software applications. No quantitative approach, to the best of our knowledge, has been developed in the open literature. To fill this gap, in this paper we propose for the first time four quantitative metrics, namely, possibility, severity, crypticity, and manipulability, for privacy leak behavior analysis based on Privacy Petri Net (PPN). In order to compare the privacy leak behavior among different software, we further propose a comprehensive metric, namely, overall leak degree, based on these four metrics. Finally, we validate the effectiveness of the proposed approach using real-world software applications. The experimental results demonstrate that our approach can quantitatively analyze the privacy leak behaviors of various software types and reveal their characteristics from different aspects.

Risk Factors for Chronic Subdural Hematoma Recurrence Identified Using Quantitative Computed Tomography Analysis of Hematoma Volume and Density.

PubMed

Stavrinou, Pantelis; Katsigiannis, Sotirios; Lee, Jong Hun; Hamisch, Christina; Krischek, Boris; Mpotsaris, Anastasios; Timmer, Marco; Goldbrunner, Roland

2017-03-01

Chronic subdural hematoma (CSDH), a common condition in elderly patients, presents a therapeutic challenge with recurrence rates of 33%. We aimed to identify specific prognostic factors for recurrence using quantitative analysis of hematoma volume and density. We retrospectively reviewed radiographic and clinical data of 227 CSDHs in 195 consecutive patients who underwent evacuation of the hematoma through a single burr hole, 2 burr holes, or a mini-craniotomy. To examine the relationship between hematoma recurrence and various clinical, radiologic, and surgical factors, we used quantitative image-based analysis to measure the hematoma and trapped air volumes and the hematoma densities. Recurrence of CSDH occurred in 35 patients (17.9%). Multivariate logistic regression analysis revealed that the percentage of hematoma drained and postoperative CSDH density were independent risk factors for recurrence. All 3 evacuation methods were equally effective in draining the hematoma (71.7% vs. 73.7% vs. 71.9%) without observable differences in postoperative air volume captured in the subdural space. Quantitative image analysis provided evidence that percentage of hematoma drained and postoperative CSDH density are independent prognostic factors for subdural hematoma recurrence. Copyright © 2016 Elsevier Inc. All rights reserved.

Quantitative Analysis of Signaling Networks across Differentially Embedded Tumors Highlights Interpatient Heterogeneity in Human Glioblastoma

PubMed Central

2015-01-01

Glioblastoma multiforme (GBM) is the most aggressive malignant primary brain tumor, with a dismal mean survival even with the current standard of care. Although in vitro cell systems can provide mechanistic insight into the regulatory networks governing GBM cell proliferation and migration, clinical samples provide a more physiologically relevant view of oncogenic signaling networks. However, clinical samples are not widely available and may be embedded for histopathologic analysis. With the goal of accurately identifying activated signaling networks in GBM tumor samples, we investigated the impact of embedding in optimal cutting temperature (OCT) compound followed by flash freezing in LN2 vs immediate flash freezing (iFF) in LN2 on protein expression and phosphorylation-mediated signaling networks. Quantitative proteomic and phosphoproteomic analysis of 8 pairs of tumor specimens revealed minimal impact of the different sample processing strategies and highlighted the large interpatient heterogeneity present in these tumors. Correlation analyses of the differentially processed tumor sections identified activated signaling networks present in selected tumors and revealed the differential expression of transcription, translation, and degradation associated proteins. This study demonstrates the capability of quantitative mass spectrometry for identification of in vivo oncogenic signaling networks from human tumor specimens that were either OCT-embedded or immediately flash-frozen. PMID:24927040

A Thematic Analysis of Edwin L. Godkin's Editorials in the "Nation," 1865-1899.

ERIC Educational Resources Information Center

Lee, Richard W.

This thematic analysis of Edward L. Godkin's editorials appearing in the "Nation" seeks to reveal the major themes on which he wrote and then, by quantitative analysis, to provide some order to the themes and to study the interaction of the themes. Five hundred and twelve editorials, written over a period of 35 years and representing…

Qualitative and Quantitative Analyses of Glycogen in Human Milk.

PubMed

Matsui-Yatsuhashi, Hiroko; Furuyashiki, Takashi; Takata, Hiroki; Ishida, Miyuki; Takumi, Hiroko; Kakutani, Ryo; Kamasaka, Hiroshi; Nagao, Saeko; Hirose, Junko; Kuriki, Takashi

2017-02-22

Identification as well as a detailed analysis of glycogen in human milk has not been shown yet. The present study confirmed that glycogen is contained in human milk by qualitative and quantitative analyses. High-performance anion exchange chromatography (HPAEC) and high-performance size exclusion chromatography with a multiangle laser light scattering detector (HPSEC-MALLS) were used for qualitative analysis of glycogen in human milk. Quantitative analysis was carried out by using samples obtained from the individual milks. The result revealed that the concentration of human milk glycogen varied depending on the mother's condition-such as the period postpartum and inflammation. The amounts of glycogen in human milk collected at 0 and 1-2 months postpartum were higher than in milk collected at 3-14 months postpartum. In the milk from mothers with severe mastitis, the concentration of glycogen was about 40 times higher than that in normal milk.

StWRKY8 transcription factor regulates benzylisoquinoline alkaloid pathway in potato conferring resistance to late blight.

PubMed

Yogendra, Kalenahalli N; Dhokane, Dhananjay; Kushalappa, Ajjamada C; Sarmiento, Felipe; Rodriguez, Ernesto; Mosquera, Teresa

2017-03-01

The resistance to late blight is either qualitative or quantitative in nature. Quantitative resistance is durable, but challenging due to polygenic inheritance. In the present study, the diploid potato genotypes resistant and susceptible to late blight, were profiled for metabolites. Tissue specific metabolite analysis of benzylisoquinoline alkaloids (BIAs) in response to pathogen infection revealed increased accumulation of morphinone, codeine-6-glucuronide and morphine-3-glucuronides. These BIAs are antimicrobial compounds and possibly involved in cell wall reinforcement, especially through cross-linking cell wall pectins. Quantitative reverse transcription-PCR studies revealed higher expressions of TyDC, NCS, COR-2 and StWRKY8 transcription factor genes, in resistant genotypes than in susceptible genotype, following pathogen inoculation. A luciferase transient expression assay confirmed the binding of the StWRKY8 TF to promoters of downstream genes, elucidating a direct regulatory role on BIAs biosynthetic genes. Sequence analysis of StWRKY8 in potato genotypes revealed polymorphism in the WRKY DNA binding domain in the susceptible genotype, which is important for the regulatory function of this gene. A complementation assay of StWRKY8 in Arabidopsis wrky33 mutant background was associated with decreased fungal biomass. In conclusion, StWRKY8 regulates the biosynthesis of BIAs that are both antimicrobial and reinforce cell walls to contain the pathogen to initial infection. Copyright © 2017 Elsevier B.V. All rights reserved.

Quantitative habitability.

PubMed

Shock, Everett L; Holland, Melanie E

2007-12-01

A framework is proposed for a quantitative approach to studying habitability. Considerations of environmental supply and organismal demand of energy lead to the conclusions that power units are most appropriate and that the units for habitability become watts per organism. Extreme and plush environments are revealed to be on a habitability continuum, and extreme environments can be quantified as those where power supply only barely exceeds demand. Strategies for laboratory and field experiments are outlined that would quantify power supplies, power demands, and habitability. An example involving a comparison of various metabolisms pursued by halophiles is shown to be well on the way to a quantitative habitability analysis.

Quantitative proteomic analysis of human lung tumor xenografts treated with the ectopic ATP synthase inhibitor citreoviridin.

PubMed

Wu, Yi-Hsuan; Hu, Chia-Wei; Chien, Chih-Wei; Chen, Yu-Ju; Huang, Hsuan-Cheng; Juan, Hsueh-Fen

2013-01-01

ATP synthase is present on the plasma membrane of several types of cancer cells. Citreoviridin, an ATP synthase inhibitor, selectively suppresses the proliferation and growth of lung cancer without affecting normal cells. However, the global effects of targeting ectopic ATP synthase in vivo have not been well defined. In this study, we performed quantitative proteomic analysis using isobaric tags for relative and absolute quantitation (iTRAQ) and provided a comprehensive insight into the complicated regulation by citreoviridin in a lung cancer xenograft model. With high reproducibility of the quantitation, we obtained quantitative proteomic profiling with 2,659 proteins identified. Bioinformatics analysis of the 141 differentially expressed proteins selected by their relative abundance revealed that citreoviridin induces alterations in the expression of glucose metabolism-related enzymes in lung cancer. The up-regulation of enzymes involved in gluconeogenesis and storage of glucose indicated that citreoviridin may reduce the glycolytic intermediates for macromolecule synthesis and inhibit cell proliferation. Using comprehensive proteomics, the results identify metabolic aspects that help explain the antitumorigenic effect of citreoviridin in lung cancer, which may lead to a better understanding of the links between metabolism and tumorigenesis in cancer therapy.

Quantitative Proteomic Analysis of Human Lung Tumor Xenografts Treated with the Ectopic ATP Synthase Inhibitor Citreoviridin

PubMed Central

Wu, Yi-Hsuan; Hu, Chia-Wei; Chien, Chih-Wei; Chen, Yu-Ju; Huang, Hsuan-Cheng; Juan, Hsueh-Fen

2013-01-01

ATP synthase is present on the plasma membrane of several types of cancer cells. Citreoviridin, an ATP synthase inhibitor, selectively suppresses the proliferation and growth of lung cancer without affecting normal cells. However, the global effects of targeting ectopic ATP synthase in vivo have not been well defined. In this study, we performed quantitative proteomic analysis using isobaric tags for relative and absolute quantitation (iTRAQ) and provided a comprehensive insight into the complicated regulation by citreoviridin in a lung cancer xenograft model. With high reproducibility of the quantitation, we obtained quantitative proteomic profiling with 2,659 proteins identified. Bioinformatics analysis of the 141 differentially expressed proteins selected by their relative abundance revealed that citreoviridin induces alterations in the expression of glucose metabolism-related enzymes in lung cancer. The up-regulation of enzymes involved in gluconeogenesis and storage of glucose indicated that citreoviridin may reduce the glycolytic intermediates for macromolecule synthesis and inhibit cell proliferation. Using comprehensive proteomics, the results identify metabolic aspects that help explain the antitumorigenic effect of citreoviridin in lung cancer, which may lead to a better understanding of the links between metabolism and tumorigenesis in cancer therapy. PMID:23990911

Systematic profiling of Caenorhabditis elegans locomotive behaviors reveals additional components in G-protein Gαq signaling.

PubMed

Yu, Hui; Aleman-Meza, Boanerges; Gharib, Shahla; Labocha, Marta K; Cronin, Christopher J; Sternberg, Paul W; Zhong, Weiwei

2013-07-16

Genetic screens have been widely applied to uncover genetic mechanisms of movement disorders. However, most screens rely on human observations of qualitative differences. Here we demonstrate the application of an automatic imaging system to conduct a quantitative screen for genes regulating the locomotive behavior in Caenorhabditis elegans. Two hundred twenty-seven neuronal signaling genes with viable homozygous mutants were selected for this study. We tracked and recorded each animal for 4 min and analyzed over 4,400 animals of 239 genotypes to obtain a quantitative, 10-parameter behavioral profile for each genotype. We discovered 87 genes whose inactivation causes movement defects, including 50 genes that had never been associated with locomotive defects. Computational analysis of the high-content behavioral profiles predicted 370 genetic interactions among these genes. Network partition revealed several functional modules regulating locomotive behaviors, including sensory genes that detect environmental conditions, genes that function in multiple types of excitable cells, and genes in the signaling pathway of the G protein Gαq, a protein that is essential for animal life and behavior. We developed quantitative epistasis analysis methods to analyze the locomotive profiles and validated the prediction of the γ isoform of phospholipase C as a component in the Gαq pathway. These results provided a system-level understanding of how neuronal signaling genes coordinate locomotive behaviors. This study also demonstrated the power of quantitative approaches in genetic studies.

A Fan-tastic Quantitative Exploration of Ohm's Law

NASA Astrophysics Data System (ADS)

Mitchell, Brandon; Ekey, Robert; McCullough, Roy; Reitz, William

2018-02-01

Teaching simple circuits and Ohm's law to students in the introductory classroom has been extensively investigated through the common practice of using incandescent light bulbs to help students develop a conceptual foundation before moving on to quantitative analysis. However, the bulb filaments' resistance has a large temperature dependence, which makes them less suitable as a tool for quantitative analysis. Some instructors show that light bulbs do not obey Ohm's law either outright or through inquiry-based laboratory experiments. Others avoid the subject altogether by using bulbs strictly for qualitative purposes and then later switching to resistors for a numerical analysis, or by changing the operating conditions of the bulb so that it is "barely" glowing. It seems incongruous to develop a conceptual basis for the behavior of simple circuits using bulbs only to later reveal that they do not follow Ohm's law. Recently, small computer fans were proposed as a suitable replacement of bulbs for qualitative analysis of simple circuits where the current is related to the rotational speed of the fans. In this contribution, we demonstrate that fans can also be used for quantitative measurements and provide suggestions for successful classroom implementation.

Originality Detection Software in a Graduate Policy Course: A Mixed-Methods Evaluation of Plagiarism

ERIC Educational Resources Information Center

Dreuth Zeman, Laura; Steen, Julie A.; Metz Zeman, Natalie

2011-01-01

The authors used a mixed-methods approach to evaluate the use of Turnitin originality detection software in a graduate social work course. Qualitative analysis of student responses revealed positive and negative spent completing assignments, and the tone of the class. Quantitative analysis of students' originality scores indicated a short-term…

Component analysis of Iranian crack; a newly abused narcotic substance in iran.

PubMed

Farhoudian, Ali; Sadeghi, Mandana; Khoddami Vishteh, Hamid Reza; Moazen, Babak; Fekri, Monir; Rahimi Movaghar, Afarin

2014-01-01

Iranian crack is a new form of narcotic substance that has found widespread prevalence in Iran in the past years. Crack only nominally resembles crack cocaine as it is widely different in its clinical signs. Thus the present study aims to quantify the chemical combination of this drug. The samples included 18 specimen of Crack collected from different zones of Tehran, Iran. All specimens were in the form of inodorous cream solid powdery substance. TLC and HPLC methods were used to perform semi-quantitative and quantitative analysis of the components, respectively. The TLC analysis showed no cocaine compound in the specimens while they all revealed to contain heroin, codeine, morphine and caffeine. All but two specimens contained thebaine. None of the specimens contained amphetamine, benzodiazepines, tricyclic antidepressants, aspirin, barbiturates, tramadol and buprenorphine. Acetaminophen was found in four specimens. HPLC revealed heroin to be the foundation substance in all specimens and most of them contained a significant amount of acetylcodeine. The present analysis of the chemical combination of Crack showed that this substance is a heroin-based narcotic which is basically different from the cocaine-based crack used in Western countries. Studies like the present one at different time points, especially when abnormal clinical signs are detected, can reveal the chemical combination of the target substance and contribute to the clinical management of its acute or chronic poisoning.

Quantitative proteomics reveals the mechanism and consequence of gliotoxin-mediated dysregulation of the methionine cycle in Aspergillus niger.

PubMed

Manzanares-Miralles, Lara; Sarikaya-Bayram, Özlem; Smith, Elizabeth B; Dolan, Stephen K; Bayram, Özgür; Jones, Gary W; Doyle, Sean

2016-01-10

Gliotoxin (GT) is a redox-active metabolite, produced by Aspergillus fumigatus, which inhibits the growth of other fungi. Here we demonstrate how Aspergillus niger responds to GT exposure. Quantitative proteomics revealed that GT dysregulated the abundance of 378 proteins including those involved in methionine metabolism and induced de novo abundance of two S-adenosylmethionine (SAM)-dependent methyltransferases. Increased abundance of enzymes S-adenosylhomocysteinase (p=0.0018) required for homocysteine generation from S-adenosylhomocysteine (SAH), and spermidine synthase (p=0.0068), involved in the recycling of Met, was observed. Analysis of Met-related metabolites revealed significant increases in the levels of Met and adenosine, in correlation with proteomic data. Methyltransferase MT-II is responsible for bisthiobis(methylthio)gliotoxin (BmGT) formation, deletion of MT-II abolished BmGT formation and led to increased GT sensitivity in A. niger. Proteomic analysis also revealed that GT exposure also significantly (p<0.05) increased hydrolytic enzyme abundance, including glycoside hydrolases (n=22) and peptidases (n=16). We reveal that in an attempt to protect against the detrimental affects of GT, methyltransferase-mediated GT thiomethylation alters cellular pathways involving Met and SAM, with consequential dysregulation of hydrolytic enzyme abundance in A. niger. Thus, it provides new opportunities to exploit the response of GT-naïve fungi to GT. Copyright © 2015 Elsevier B.V. All rights reserved.

Persulfidation proteome reveals the regulation of protein function by hydrogen sulfide in diverse biological processes in Arabidopsis.

PubMed

Aroca, Angeles; Benito, Juan M; Gotor, Cecilia; Romero, Luis C

2017-10-13

Hydrogen sulfide-mediated signaling pathways regulate many physiological and pathophysiological processes in mammalian and plant systems. The molecular mechanism by which hydrogen sulfide exerts its action involves the post-translational modification of cysteine residues to form a persulfidated thiol motif, a process called protein persulfidation. We have developed a comparative and quantitative proteomic analysis approach for the detection of endogenous persulfidated proteins in wild-type Arabidopsis and L-CYSTEINE DESULFHYDRASE 1 mutant leaves using the tag-switch method. The 2015 identified persulfidated proteins were isolated from plants grown under controlled conditions, and therefore, at least 5% of the entire Arabidopsis proteome may undergo persulfidation under baseline conditions. Bioinformatic analysis revealed that persulfidated cysteines participate in a wide range of biological functions, regulating important processes such as carbon metabolism, plant responses to abiotic and biotic stresses, plant growth and development, and RNA translation. Quantitative analysis in both genetic backgrounds reveals that protein persulfidation is mainly involved in primary metabolic pathways such as the tricarboxylic acid cycle, glycolysis, and the Calvin cycle, suggesting that this protein modification is a new regulatory component in these pathways. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Proteomic characterization of EL4 lymphoma-derived tumors upon chemotherapy treatment reveals potential roles for lysosomes and caspase-6 during tumor cell death in vivo.

PubMed

Kramer, David A; Eldeeb, Mohamed A; Wuest, Melinda; Mercer, John; Fahlman, Richard P

2017-06-01

The murine mouse lymphoblastic lymphoma cell line (EL4) tumor model is an established in vivo apoptosis model for the investigation of novel cancer imaging agents and immunological treatments due to the rapid and significant response of the EL4 tumors to cyclophosphamide and etoposide combination chemotherapy. Despite the utility of this model system in cancer research, little is known regarding the molecular details of in vivo tumor cell death. Here, we report the first in-depth quantitative proteomic analysis of the changes that occur in these tumors upon cyclophosphamide and etoposide treatment in vivo. Using a label-free quantitative proteomic approach a total of 5838 proteins were identified in the treated and untreated tumors, of which 875 were determined to change in abundance with statistical significance. Initial analysis of the data reveals changes that may have been predicted, such as the downregulation of ribosomes, but demonstrates the robustness of the dataset. Analysis of the dataset also reveals the unexpected downregulation of caspase-3 and an upregulation of caspase-6 in addition to a global upregulation of lysosomal proteins in the bulk of the tumor. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Accuracy Enhancement of Raman Spectroscopy Using Complementary Laser-Induced Breakdown Spectroscopy (LIBS) with Geologically Mixed Samples.

PubMed

Choi, Soojin; Kim, Dongyoung; Yang, Junho; Yoh, Jack J

2017-04-01

Quantitative Raman analysis was carried out with geologically mixed samples that have various matrices. In order to compensate the matrix effect in Raman shift, laser-induced breakdown spectroscopy (LIBS) analysis was performed. Raman spectroscopy revealed the geological materials contained in the mixed samples. However, the analysis of a mixture containing different matrices was inaccurate due to the weak signal of the Raman shift, interference, and the strong matrix effect. On the other hand, the LIBS quantitative analysis of atomic carbon and calcium in mixed samples showed high accuracy. In the case of the calcite and gypsum mixture, the coefficient of determination of atomic carbon using LIBS was 0.99, while the signal using Raman was less than 0.9. Therefore, the geological composition of the mixed samples is first obtained using Raman and the LIBS-based quantitative analysis is then applied to the Raman outcome in order to construct highly accurate univariate calibration curves. The study also focuses on a method to overcome matrix effects through the two complementary spectroscopic techniques of Raman spectroscopy and LIBS.

Dynamically monitoring the gene expression of dual fluorophore in the cell cycle with quantitative spectrum analysis

NASA Astrophysics Data System (ADS)

Lee, Ja-Yun; Wu, Tzong-Yuan; Hsu, I.-Jen

2008-04-01

The cloning and transcription techniques on gene cloned fluorescent proteins have been widely used in many applications. They have been used as reporters of some conditions in a series of reactions. However, it is usually difficult to monitor the specific target with the exactly number of proteins during the process in turbid media, especially at micrometer scales. We successfully revealed an alternative way to monitor the cell cycle behavior and quantitatively analyzed the target cells with green and red fluorescent proteins (GFP and RFP) during different phases of the cell cycle by quantitatively analyzing its behavior and also monitoring its spatial distribution.

Quantitative phosphoproteomics reveals new roles for the protein phosphatase PP6 in mitotic cells.

PubMed

Rusin, Scott F; Schlosser, Kate A; Adamo, Mark E; Kettenbach, Arminja N

2015-10-13

Protein phosphorylation is an important regulatory mechanism controlling mitotic progression. Protein phosphatase 6 (PP6) is an essential enzyme with conserved roles in chromosome segregation and spindle assembly from yeast to humans. We applied a baculovirus-mediated gene silencing approach to deplete HeLa cells of the catalytic subunit of PP6 (PP6c) and analyzed changes in the phosphoproteome and proteome in mitotic cells by quantitative mass spectrometry-based proteomics. We identified 408 phosphopeptides on 272 proteins that increased and 298 phosphopeptides on 220 proteins that decreased in phosphorylation upon PP6c depletion in mitotic cells. Motif analysis of the phosphorylated sites combined with bioinformatics pathway analysis revealed previously unknown PP6c-dependent regulatory pathways. Biochemical assays demonstrated that PP6c opposed casein kinase 2-dependent phosphorylation of the condensin I subunit NCAP-G, and cellular analysis showed that depletion of PP6c resulted in defects in chromosome condensation and segregation in anaphase, consistent with dysregulation of condensin I function in the absence of PP6 activity. Copyright © 2015, American Association for the Advancement of Science.

Quantitative phosphoproteomics reveals new roles for the protein phosphatase PP6 in mitotic cells

PubMed Central

Rusin, Scott F.; Schlosser, Kate A.; Adamo, Mark E.; Kettenbach, Arminja N.

2017-01-01

Protein phosphorylation is an important regulatory mechanism controlling mitotic progression. Protein phosphatase 6 (PP6) is an essential enzyme with conserved roles in chromosome segregation and spindle assembly from yeast to humans. We applied a baculovirus-mediated gene silencing approach to deplete HeLa cells of the catalytic subunit of PP6 (PP6c) and analyzed changes in the phosphoproteome and proteome in mitotic cells by quantitative mass spectrometry–based proteomics. We identified 408 phosphopeptides on 272 proteins that increased and 298 phosphopeptides on 220 proteins that decreased in phosphorylation upon PP6c depletion in mitotic cells. Motif analysis of the phosphorylated sites combined with bioinformatics pathway analysis revealed previously unknown PP6c–dependent regulatory pathways. Biochemical assays demonstrated that PP6c opposed casein kinase 2–dependent phosphorylation of the condensin I subunit NCAP-G, and cellular analysis showed that depletion of PP6c resulted in defects in chromosome condensation and segregation in anaphase, consistent with dysregulation of condensin I function in the absence of PP6 activity. PMID:26462736

qSR: a quantitative super-resolution analysis tool reveals the cell-cycle dependent organization of RNA Polymerase I in live human cells.

PubMed

Andrews, J O; Conway, W; Cho, W -K; Narayanan, A; Spille, J -H; Jayanth, N; Inoue, T; Mullen, S; Thaler, J; Cissé, I I

2018-05-09

We present qSR, an analytical tool for the quantitative analysis of single molecule based super-resolution data. The software is created as an open-source platform integrating multiple algorithms for rigorous spatial and temporal characterizations of protein clusters in super-resolution data of living cells. First, we illustrate qSR using a sample live cell data of RNA Polymerase II (Pol II) as an example of highly dynamic sub-diffractive clusters. Then we utilize qSR to investigate the organization and dynamics of endogenous RNA Polymerase I (Pol I) in live human cells, throughout the cell cycle. Our analysis reveals a previously uncharacterized transient clustering of Pol I. Both stable and transient populations of Pol I clusters co-exist in individual living cells, and their relative fraction vary during cell cycle, in a manner correlating with global gene expression. Thus, qSR serves to facilitate the study of protein organization and dynamics with very high spatial and temporal resolutions directly in live cell.

Fibrotic-like changes in degenerate human intervertebral discs revealed by quantitative proteomic analysis.

PubMed

Yee, A; Lam, M P Y; Tam, V; Chan, W C W; Chu, I K; Cheah, K S E; Cheung, K M C; Chan, D

2016-03-01

Intervertebral disc degeneration (IDD) can lead to symptomatic conditions including sciatica and back pain. The purpose of this study is to understand the extracellular matrix (ECM) changes in disc biology through comparative proteomic analysis of degenerated and non-degenerated human intervertebral disc (IVD) tissues of different ages. Seven non-degenerated (11-46 years of age) and seven degenerated (16-53 years of age) annulus fibrosus (AF) and nucleus pulposus (NP) samples were used. Proteins were extracted using guanidine hydrochloride, separated from large proteoglycans (PGs) by caesium chloride (CsCl) density gradient ultracentrifugation, and identified using liquid chromatography (LC) coupled with tandem mass spectrometry (MS/MS). For quantitative comparison, proteins were labeled with iTRAQ reagents. Collagen fibrils in the NP were assessed using scanning electron microscopy (SEM). In the AF, quantitative analysis revealed increased levels of HTRA1, COMP and CILP in degeneration when compared with samples from older individuals. Fibronectin showed increment with age and degeneration. In the NP, more CILP and CILP2 were present in degenerated samples of younger individuals. Reduced protein solubility was observed in degenerated and older non-degenerated samples correlated with an accumulation of type I collagen in the insoluble fibers. Characterization of collagen fibrils in the NP revealed smaller mean fibril diameters and decreased porosity in the degenerated samples. Our study identified distinct matrix changes associated with aging and degeneration in the intervertebral discs (IVDs). The nature of the ECM changes, together with observed decreased in solubility and changes in fibril diameter is consistent with a fibrotic-like environment. Copyright © 2015 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

Methodological Issues and Further Research in the Study of Reading Comprehension with Different Levels of Knowledge.

ERIC Educational Resources Information Center

Qian, Gaoyin

Some methodological issues in the study of levels of knowledge are reviewed, and needs for further research are explored, drawing on an analysis of 12 studies reported since the late 1970s. In the 12 studies, 16 quantitative experiments were conducted. These were assessed for internal and external validity. Analysis revealed some shortcomings in…

Quantitative changes in proteins responsible for flavonoid and anthocyanin biosynthesis in strawberry fruit at different ripening stages: A targeted quantitative proteomic investigation employing multiple reaction monitoring.

PubMed

Song, Jun; Du, Lina; Li, Li; Kalt, Wilhelmina; Palmer, Leslie Campbell; Fillmore, Sherry; Zhang, Ying; Zhang, ZhaoQi; Li, XiHong

2015-06-03

To better understand the regulation of flavonoid and anthocyanin biosynthesis, a targeted quantitative proteomic investigation employing LC-MS with multiple reaction monitoring was conducted on two strawberry cultivars at three ripening stages. This quantitative proteomic workflow was improved through an OFFGEL electrophoresis to fractionate peptides from total protein digests. A total of 154 peptide transitions from 47 peptides covering 21 proteins and isoforms related to anthocyanin biosynthesis were investigated. The normalized protein abundance, which was measured using isotopically-labeled standards, was significantly changed concurrently with increased anthocyanin content and advanced fruit maturity. The protein abundance of phenylalanine ammonia-lyase; anthocyanidin synthase, chalcone isomerase; flavanone 3-hydroxylase; dihydroflavonol 4-reductase, UDP-glucose:flavonoid-3-O-glucosyltransferase, cytochrome c and cytochrome C oxidase subunit 2, was all significantly increased in fruit of more advanced ripeness. An interaction between cultivar and maturity was also shown with respect to chalcone isomerase. The good correlation between protein abundance and anthocyanin content suggested that a metabolic control point may exist for anthocyanin biosynthesis. This research provides insights into the process of anthocyanin formation in strawberry fruit at the level of protein concentration and reveals possible candidates in the regulation of anthocyanin formation during fruit ripening. To gain insight into the molecular mechanisms contributing to flavonoids and anthocyanin biosynthesis and regulation of strawberry fruit during ripening is challenging due to limited molecular biology tools and established hypothesis. Our targeted proteomic approach employing LC-MS/MS analysis and MRM technique to quantify proteins in relation to flavonoids and anthocyanin biosynthesis and regulation in strawberry fruit during fruit ripening is novel. The identification of peptides and proteins provided reliable design and validation of quantitative approaches using SRM on targeted proteins proposed involved in strawberry fruit. Our data revealed the identifying candidate proteins and their quantitative changes in relation to fruit ripening and flavonoids and anthocyanin biosynthesis and regulation. More importantly, this quantitative proteomic data is also compared with chemical analysis to reveal possible control levels of this important quality trait. Although, MRM approach is not new in plant biology research, the application has been very rare. This is the first systematic multi-targeted interrogation of the possible regulation of entire pathway of flavonoids and anthocyanin biosynthesis in strawberry fruit at different ripening stages using quantitative MRM technique on mass spectrometry. Our results demonstrate the power of targeted quantitative mass spectrometry data for analysis of proteins in biological regulation. These results indicate that distinct and diverse control of flavonoids and anthocyanin biosynthesis mechanisms at metabolism and proteins levels. This important and complementary knowledge will be useful for systematically characterizing the flavonoids and anthocyanin biosynthesis pathway of any fruit/plant species. Copyright © 2015. Published by Elsevier B.V.

An analysis toolbox to explore mesenchymal migration heterogeneity reveals adaptive switching between distinct modes

PubMed Central

Shafqat-Abbasi, Hamdah; Kowalewski, Jacob M; Kiss, Alexa; Gong, Xiaowei; Hernandez-Varas, Pablo; Berge, Ulrich; Jafari-Mamaghani, Mehrdad; Lock, John G; Strömblad, Staffan

2016-01-01

Mesenchymal (lamellipodial) migration is heterogeneous, although whether this reflects progressive variability or discrete, 'switchable' migration modalities, remains unclear. We present an analytical toolbox, based on quantitative single-cell imaging data, to interrogate this heterogeneity. Integrating supervised behavioral classification with multivariate analyses of cell motion, membrane dynamics, cell-matrix adhesion status and F-actin organization, this toolbox here enables the detection and characterization of two quantitatively distinct mesenchymal migration modes, termed 'Continuous' and 'Discontinuous'. Quantitative mode comparisons reveal differences in cell motion, spatiotemporal coordination of membrane protrusion/retraction, and how cells within each mode reorganize with changed cell speed. These modes thus represent distinctive migratory strategies. Additional analyses illuminate the macromolecular- and cellular-scale effects of molecular targeting (fibronectin, talin, ROCK), including 'adaptive switching' between Continuous (favored at high adhesion/full contraction) and Discontinuous (low adhesion/inhibited contraction) modes. Overall, this analytical toolbox now facilitates the exploration of both spontaneous and adaptive heterogeneity in mesenchymal migration. DOI: http://dx.doi.org/10.7554/eLife.11384.001 PMID:26821527

Lignin metabolism involves Botrytis cinerea BcGs1- induced defense response in tomato.

PubMed

Yang, Chenyu; Liang, Yingbo; Qiu, Dewen; Zeng, Hongmei; Yuan, Jingjing; Yang, Xiufen

2018-06-04

BcGs1, a cell wall-degrading enzyme (CWDE), was originally derived from Botrytis cinerea. Our previous study revealed that BcGs1 could trigger defense responses and protect plants against various pathogens. We researched the defense response mechanism underlying this BcGs1 elicitation in tomato. We revealed that the two domains were required for BcGs1's full necrosis activity. According to analysis and quantitative real-time PCR of the up-regulated proteins and genes filtered by iTRAQ-based quantitative proteome approach, oxidative metabolism and phenylpropanoid metabolism were speculated to be involved in BcGs1-triggered defense response in tomato. Furthermore, experimental evidence showed that BcGs1 triggered reactive oxygen species (ROS) burst and increased the level of phenylalanine-ammonia lyase (PAL) and peroxidase (POD) enzyme activity, as well as lignin accumulation. Moreover, histochemical analysis revealed that infiltration of BcGs1 in tomato leaves exhibited cell wall thickening compared with untreated plants. The results suggested that BcGs1 activated the basal defense response included lignin metabolism contributed to BcGs1-induced resistance to Botrytis. cinerea infection in tomato.

Vector analysis of ecoenzyme activities reveal constraints on coupled C, N and P dynamics

EPA Science Inventory

We developed a quantitative method for estimating resource allocation strategies of microbial communities based on the proportional activities of four, key extracellular enzymes, 1,4-ß-glucosidase (BG), leucine amino-peptidase (LAP), 1,4-ß-N-acetylglucosaminidase (NAG...

Screening circular RNA related to chemotherapeutic resistance in breast cancer.

PubMed

Gao, Danfeng; Zhang, Xiufen; Liu, Beibei; Meng, Dong; Fang, Kai; Guo, Zijian; Li, Lihua

2017-09-01

We aimed to identify circular RNAs (circRNAs) associated with breast cancer chemoresistance. CircRNA microarray expression profiles were obtained from Adriamycin (ADM) resistant MCF-7 breast cancer cells (MCF-7/ADM) and parental MCF-7 cells and were validated using quantitative real-time reverse transcription PCR. The expression data were analyzed bioinformatically. We detected 3093 circRNAs and identified 18 circRNAs that are differentially expressed between MCF-7/ADM and MCF-7 cells; after validating by quantitative real-time reverse transcription PCR, we predicted the possible miRNAs and potential target genes of the seven upregulated circRNAs using TargetScan and miRanda. The bioinformatics analysis revealed several target genes related to cancer-related signaling pathways. Additionally, we discovered a regulatory role of the circ_0006528-miR-7-5p-Raf1 axis in ADM-resistant breast cancer. These results revealed that circRNAs may play a role in breast cancer chemoresistance and that hsa_circ_0006528 might be a promising candidate for further functional analysis.

Quantitation of Rotundone in Grapefruit (Citrus paradisi) Peel and Juice by Stable Isotope Dilution Assay.

PubMed

Nakanishi, Akira; Fukushima, Yusuke; Miyazawa, Norio; Yoshikawa, Keisuke; Maeda, Tomoko; Kurobayashi, Yoshiko

2017-06-21

Aroma extract dilution analyses of the aromas of peels and juices of white and pink grapefruits revealed that rotundone, responsible for peppery, spicy, and woody odors, was detected for the first time at high flavor dilution factors of 256-1024. In both juices, rotundone was detected at the highest flavor dilution factor of 1024. Rotundone in grapefruits was quantitated by a stable isotope dilution assay with a newly synthesized deuterium-labeled internal standard, rotundone-d 2,3 : its levels were 2180 and 1920 ng/kg in white and pink grapefruit peels and 29.6 and 49.8 ng/kg in white and pink grapefruit juices, respectively. On the basis of these results, sensory analysis was performed to assess the effects of rotundone on a white grapefruit juice aroma reconstitute. This sensory analysis revealed that rotundone does not impart a woody odor or affect any of the existing attributes, but increases various attributes, thus confirming that rotundone is indispensable for the aroma of grapefruit juice.

Label-free quantitative proteomics reveals differentially regulated proteins in the latex of sticky diseased Carica papaya L. plants

PubMed Central

Rodrigues, Silas P.; Ventura, José A.; Aguilar, Clemente; Nakayasu, Ernesto S.; Choi, HyungWon; Sobreira, Tiago J. P.; Nohara, Lilian L.; Wermelinger, Luciana S.; Almeida, Igor C.; Zingali, Russolina B.; Fernandes, Patricia M. B.

2012-01-01

Papaya meleira virus (PMeV) is so far the only described laticifer-infecting virus, the causal agent of papaya (Carica papaya L.) sticky disease. The effects of PMeV on the laticifers’ regulatory network were addressed here through the proteomic analysis of papaya latex. Using both 1-DE- and 1D-LC-ESI-MS/MS, 160 unique papaya latex proteins were identified, representing 122 new proteins in the latex of this plant. Quantitative analysis by normalized spectral counting revealed 10 down-regulated proteins in the latex of diseased plants, 9 cysteine proteases (chymopapain) and 1 latex serine proteinase inhibitor. A repression of papaya latex proteolytic activity during PMeV infection was hypothesized. This was further confirmed by enzymatic assays that showed a reduction of cysteine-protease-associated proteolytic activity in the diseased papaya latex. These findings are discussed in the context of plant responses against pathogens and may greatly contribute to understand the roles of laticifers in plant stress responses. PMID:22465191

Quantitative analysis of naphthenic acids in water by liquid chromatography-accurate mass time-of-flight mass spectrometry.

PubMed

Hindle, Ralph; Noestheden, Matthew; Peru, Kerry; Headley, John

2013-04-19

This study details the development of a routine method for quantitative analysis of oil sands naphthenic acids, which are a complex class of compounds found naturally and as contaminants in oil sands process waters from Alberta's Athabasca region. Expanding beyond classical naphthenic acids (CnH2n-zO2), those compounds conforming to the formula CnH2n-zOx (where 2≥x≤4) were examined in commercial naphthenic acid and environmental water samples. HPLC facilitated a five-fold reduction in ion suppression when compared to the more commonly used flow injection analysis. A comparison of 39 model naphthenic acids revealed significant variability in response factors, demonstrating the necessity of using naphthenic acid mixtures for quantitation, rather than model compounds. It was also demonstrated that naphthenic acidic heterogeneity (commercial and environmental) necessitates establishing a single NA mix as the standard against which all quantitation is performed. The authors present the first ISO17025 accredited method for the analysis of naphthenic acids in water using HPLC high resolution accurate mass time-of-flight mass spectrometry. The method detection limit was 1mg/L total oxy-naphthenic acids (Sigma technical mix). Copyright © 2013 Elsevier B.V. All rights reserved.

Involvement of GABA Transporters in Atropine-Treated Myopic Retina As Revealed by iTRAQ Quantitative Proteomics

PubMed Central

2015-01-01

Atropine, a muscarinic antagonist, is known to inhibit myopia progression in several animal models and humans. However, the mode of action is not established yet. In this study, we compared quantitative iTRAQ proteomic analysis in the retinas collected from control and lens-induced myopic (LIM) mouse eyes treated with atropine. The myopic group received a (−15D) spectacle lens over the right eye on postnatal day 10 with or without atropine eye drops starting on postnatal day 24. Axial length was measured by optical low coherence interferometry (OLCI), AC-Master, and refraction was measured by automated infrared photorefractor at postnatal 24, 38, and 52 days. Retinal tissue samples were pooled from six eyes for each group. The experiments were repeated twice, and technical replicates were also performed for liquid chromatography–tandem mass spectrometry (LC–MS/MS) analysis. MetaCore was used to perform protein profiling for pathway analysis. We identified a total of 3882 unique proteins with <1% FDR by analyzing the samples in replicates for two independent experiments. This is the largest number of mouse retina proteome reported to date. Thirty proteins were found to be up-regulated (ratio for myopia/control > global mean ratio + 1 standard deviation), and 28 proteins were down-regulated (ratio for myopia/control < global mean ratio - 1 standard deviation) in myopic eyes as compared with control retinas. Pathway analysis using MetaCore revealed regulation of γ-aminobutyric acid (GABA) levels in the myopic eyes. Detailed analysis of the quantitative proteomics data showed that the levels of GABA transporter 1 (GAT-1) were elevated in myopic retina and significantly reduced after atropine treatment. These results were further validated with immunohistochemistry and Western blot analysis. In conclusion, this study provides a comprehensive quantitative proteomic analysis of atropine-treated mouse retina and suggests the involvement of GABAergic signaling in the antimyopic effects of atropine in mouse eyes. The GABAergic transmission in the neural retina plays a pivotal role in the maintenance of axial eye growth in mammals. PMID:25211393

Reciprocal contribution analysis of the left and right hips while walking

NASA Astrophysics Data System (ADS)

Tsuruoka, Yuriko; Tamura, Yoshiyasu; Shibasaki, Ryosuke

2007-10-01

The physical posture of even healthy university students is easy to collapse when walking with textbooks and other heavy loads during university attendance. Consequently, they may experience lower-back pain or knee pain. However, the resulting burden of this stress to the left and right lower-back has not previously been quantitatively analyzed. In this study, we employed a Relative Power Contribution (RPC) analysis approach to quantitatively investigate and compare the reciprocal contribution between the left and right lower-backs while walking with a bag and without a bag. Quantitative data were collected by two accelerometers installed on the subjects. Results for the subjects walking with and without a bag indicated that the contribution of the left and right lower-backs decreased by up to 21% ( p<0.05). Some disorder occurs in the feedback relations of the movement in both lower-backs and as a result, it was understood to cause much discomfort in these areas. This analysis reveals the quantitative relations of left and right lower-backs, which are difficult to discern from the original data. The results can be useful for preventive healthcare for lower-back and knee pains.

Gene cloning, expression and functional characterization of a proliferation-inducing ligand (APRIL) from hedgehog (Erinaceus europaeus).

PubMed

Cui, Xian-Wei; Xiao, Wen; Ji, Chen-Bo; Tian, Ai-Ying; Zhang, Jie; Zhang, Shuang-Quan

2012-05-01

Here we describe the identification of the hedgehog Erinaceus europaeus homologue of a proliferation-inducing ligand (APRIL) of the TNF family (designated heAPRIL). Hedgehog APRIL contains two cysteine residues (Cys(196) and Cys(211)), a furin protease cleavage site and a conserved putative N-glycosylation site (Asn(124)). Real-time quantitative PCR (qPCR) analysis revealed that heAPRIL could be detected in various tissues. MTT assays and flow cytometric analysis revealed that Nus-hesAPRIL and hesAPRIL could promote the survival/proliferation of splenic B cells. Laser scanning confocal microscopy analysis showed GFP-hesAPRIL could successfully bind to the APRIL receptors of lymphocytes.

Patient-focused goal planning process and outcome after spinal cord injury rehabilitation: quantitative and qualitative audit.

PubMed

Byrnes, Michelle; Beilby, Janet; Ray, Patricia; McLennan, Renee; Ker, John; Schug, Stephan

2012-12-01

To evaluate the process and outcome of a multidisciplinary inpatient goal planning rehabilitation programme on physical, social and psychological functioning for patients with spinal cord injury. Clinical audit: quantitative and qualitative analyses. Specialist spinal injury unit, Perth, Australia. Consecutive series of 100 newly injured spinal cord injury inpatients. MAIN MEASURE(S): The Needs Assessment Checklist (NAC), patient-focused goal planning questionnaire and goal planning progress form. The clinical audit of 100 spinal cord injured patients revealed that 547 goal planning meetings were held with 8531 goals stipulated in total. Seventy-five per cent of the goals set at the first goal planning meeting were achieved by the second meeting and the rate of goal achievements at subsequent goal planning meetings dropped to 56%. Based on quantitative analysis of physical, social and psychological functioning, the 100 spinal cord injury patients improved significantly from baseline to discharge. Furthermore, qualitative analysis revealed benefits consistently reported by spinal cord injury patients of the goal planning rehabilitation programme in improvements to their physical, social and psychological adjustment to injury. The findings of this clinical audit underpin the need for patient-focused goal planning rehabilitation programmes which are tailored to the individual's needs and involve a comprehensive multidisciplinary team.

[Quantitative histoenzymatic analysis of the adenohypophysis and adrenal cortex during the early stages of involution].

PubMed

Prochukhanov, R A; Rostovtseva, T I

1977-11-01

A method of quantitative histenzymatic analysis was applied for determination of the involution changes of the neuroendocrine system. The activity of NAD- and NADP-reductases, acid and alkaline phosphatases, glucose-6-phosphoric dehydrogenase, 3-OH-steroid-dehydrogenase, 11-hydroxysteroid dehydrogenases was investigated in the adenohypophysis and in the adrenal cortex of rats aged 4 and 12 months. There were revealed peculiarities attending the structural-metabolic provision of physiological reconstructions of the neuro-endocrine system under conditions of the estral cycle at the early involution stages. An initial reduction of the cell ular-vascular transport with the retention of the functional activity of the intracellular organoids was demonstrated in ageing animals.

Coercivity degradation caused by inhomogeneous grain boundaries in sintered Nd-Fe-B permanent magnets

NASA Astrophysics Data System (ADS)

Chen, Hansheng; Yun, Fan; Qu, Jiangtao; Li, Yingfei; Cheng, Zhenxiang; Fang, Ruhao; Ye, Zhixiao; Ringer, Simon P.; Zheng, Rongkun

2018-05-01

Quantitative correlation between intrinsic coercivity and grain boundaries in three dimensions is critical to further improve the performance of sintered Nd-Fe-B permanent magnets. Here, we quantitatively reveal the local composition variation across and especially along grain boundaries using the powerful atomic-scale analysis technique known as atom probe tomography. We also estimate the saturation magnetization, magnetocrystalline anisotropy constant, and exchange stiffness of the grain boundaries on the basis of the experimentally determined structure and composition. Finally, using micromagnetic simulations, we quantify the intrinsic coercivity degradation caused by inhomogeneous grain boundaries. This approach can be applied to other magnetic materials for the analysis and optimization of magnetic properties.

Examining Practical Relevance of the Coursework of Doctoral Leadership Programs

ERIC Educational Resources Information Center

Li, Jinyi; Friedel, Janice; Rusche, Philip

2011-01-01

This quantitative study investigated the extent to which doctoral leadership programs are practically relevant. Results revealed that community college leaders and leadership program faculty did not differ significantly on the importance ratings on the American Association of Community Colleges (AACC) competencies. The subsequent analysis,…

Value Perceptions as Influences upon Engagement

ERIC Educational Resources Information Center

Swanson, Lee A.

2009-01-01

This study was designed to assess whether changes in stakeholders' perceptions about the value generated by an institution might influence the nature of their engagement with it. Quantitative and qualitative analysis of research data revealed a positive correlation between stakeholders who believed an institution generated social or economic value…

Mass Spectrometry Analysis of Spatial Protein Networks by Colocalization Analysis (COLA).

PubMed

Mardakheh, Faraz K

2017-01-01

A major challenge in systems biology is comprehensive mapping of protein interaction networks. Crucially, such interactions are often dynamic in nature, necessitating methods that can rapidly mine the interactome across varied conditions and treatments to reveal change in the interaction networks. Recently, we described a fast mass spectrometry-based method to reveal functional interactions in mammalian cells on a global scale, by revealing spatial colocalizations between proteins (COLA) (Mardakheh et al., Mol Biosyst 13:92-105, 2017). As protein localization and function are inherently linked, significant colocalization between two proteins is a strong indication for their functional interaction. COLA uses rapid complete subcellular fractionation, coupled with quantitative proteomics to generate a subcellular localization profile for each protein quantified by the mass spectrometer. Robust clustering is then applied to reveal significant similarities in protein localization profiles, indicative of colocalization.

Quantitative protein localization signatures reveal an association between spatial and functional divergences of proteins.

PubMed

Loo, Lit-Hsin; Laksameethanasan, Danai; Tung, Yi-Ling

2014-03-01

Protein subcellular localization is a major determinant of protein function. However, this important protein feature is often described in terms of discrete and qualitative categories of subcellular compartments, and therefore it has limited applications in quantitative protein function analyses. Here, we present Protein Localization Analysis and Search Tools (PLAST), an automated analysis framework for constructing and comparing quantitative signatures of protein subcellular localization patterns based on microscopy images. PLAST produces human-interpretable protein localization maps that quantitatively describe the similarities in the localization patterns of proteins and major subcellular compartments, without requiring manual assignment or supervised learning of these compartments. Using the budding yeast Saccharomyces cerevisiae as a model system, we show that PLAST is more accurate than existing, qualitative protein localization annotations in identifying known co-localized proteins. Furthermore, we demonstrate that PLAST can reveal protein localization-function relationships that are not obvious from these annotations. First, we identified proteins that have similar localization patterns and participate in closely-related biological processes, but do not necessarily form stable complexes with each other or localize at the same organelles. Second, we found an association between spatial and functional divergences of proteins during evolution. Surprisingly, as proteins with common ancestors evolve, they tend to develop more diverged subcellular localization patterns, but still occupy similar numbers of compartments. This suggests that divergence of protein localization might be more frequently due to the development of more specific localization patterns over ancestral compartments than the occupation of new compartments. PLAST enables systematic and quantitative analyses of protein localization-function relationships, and will be useful to elucidate protein functions and how these functions were acquired in cells from different organisms or species. A public web interface of PLAST is available at http://plast.bii.a-star.edu.sg.

Quantitative Protein Localization Signatures Reveal an Association between Spatial and Functional Divergences of Proteins

PubMed Central

Loo, Lit-Hsin; Laksameethanasan, Danai; Tung, Yi-Ling

2014-01-01

Protein subcellular localization is a major determinant of protein function. However, this important protein feature is often described in terms of discrete and qualitative categories of subcellular compartments, and therefore it has limited applications in quantitative protein function analyses. Here, we present Protein Localization Analysis and Search Tools (PLAST), an automated analysis framework for constructing and comparing quantitative signatures of protein subcellular localization patterns based on microscopy images. PLAST produces human-interpretable protein localization maps that quantitatively describe the similarities in the localization patterns of proteins and major subcellular compartments, without requiring manual assignment or supervised learning of these compartments. Using the budding yeast Saccharomyces cerevisiae as a model system, we show that PLAST is more accurate than existing, qualitative protein localization annotations in identifying known co-localized proteins. Furthermore, we demonstrate that PLAST can reveal protein localization-function relationships that are not obvious from these annotations. First, we identified proteins that have similar localization patterns and participate in closely-related biological processes, but do not necessarily form stable complexes with each other or localize at the same organelles. Second, we found an association between spatial and functional divergences of proteins during evolution. Surprisingly, as proteins with common ancestors evolve, they tend to develop more diverged subcellular localization patterns, but still occupy similar numbers of compartments. This suggests that divergence of protein localization might be more frequently due to the development of more specific localization patterns over ancestral compartments than the occupation of new compartments. PLAST enables systematic and quantitative analyses of protein localization-function relationships, and will be useful to elucidate protein functions and how these functions were acquired in cells from different organisms or species. A public web interface of PLAST is available at http://plast.bii.a-star.edu.sg. PMID:24603469

Quantitative and Qualitative Evaluations of the Enhanced Logo-autobiography Program for Korean-American Women.

PubMed

Sung, Kyung Mi; Bernstein, Kunsook

2017-12-01

This study extends Bernstein et al.'s (2016) investigation of the effects of the Enhanced Logo-autobiography Program on Korean-American women's depressive symptoms, coping strategies, purpose in life, and posttraumatic growth by analyzing quantitative and qualitative data. This study's participants significantly improved on quantitative measures of depression, coping strategies, purpose in life, and post-traumatic growth at eight weeks post-intervention and follow-up. The qualitative content analysis revealed 17 themes with five essential themes. The program's activity to promote purpose in life through posttraumatic growth facilitated participants' recovery from traumatic experiences. Standardized guidelines are needed to conduct this program in Korean community centers.

Global Relative Quantification with Liquid Chromatography–Matrix-assisted Laser Desorption Ionization Time-of-flight (LC-MALDI-TOF)—Cross–validation with LTQ-Orbitrap Proves Reliability and Reveals Complementary Ionization Preferences*

PubMed Central

Hessling, Bernd; Büttner, Knut; Hecker, Michael; Becher, Dörte

2013-01-01

Quantitative LC-MALDI is an underrepresented method, especially in large-scale experiments. The additional fractionation step that is needed for most MALDI-TOF-TOF instruments, the comparatively long analysis time, and the very limited number of established software tools for the data analysis render LC-MALDI a niche application for large quantitative analyses beside the widespread LC–electrospray ionization workflows. Here, we used LC-MALDI in a relative quantification analysis of Staphylococcus aureus for the first time on a proteome-wide scale. Samples were analyzed in parallel with an LTQ-Orbitrap, which allowed cross-validation with a well-established workflow. With nearly 850 proteins identified in the cytosolic fraction and quantitative data for more than 550 proteins obtained with the MASCOT Distiller software, we were able to prove that LC-MALDI is able to process highly complex samples. The good correlation of quantities determined via this method and the LTQ-Orbitrap workflow confirmed the high reliability of our LC-MALDI approach for global quantification analysis. Because the existing literature reports differences for MALDI and electrospray ionization preferences and the respective experimental work was limited by technical or methodological constraints, we systematically compared biochemical attributes of peptides identified with either instrument. This genome-wide, comprehensive study revealed biases toward certain peptide properties for both MALDI-TOF-TOF- and LTQ-Orbitrap-based approaches. These biases are based on almost 13,000 peptides and result in a general complementarity of the two approaches that should be exploited in future experiments. PMID:23788530

Global relative quantification with liquid chromatography-matrix-assisted laser desorption ionization time-of-flight (LC-MALDI-TOF)--cross-validation with LTQ-Orbitrap proves reliability and reveals complementary ionization preferences.

PubMed

Hessling, Bernd; Büttner, Knut; Hecker, Michael; Becher, Dörte

2013-10-01

Quantitative LC-MALDI is an underrepresented method, especially in large-scale experiments. The additional fractionation step that is needed for most MALDI-TOF-TOF instruments, the comparatively long analysis time, and the very limited number of established software tools for the data analysis render LC-MALDI a niche application for large quantitative analyses beside the widespread LC-electrospray ionization workflows. Here, we used LC-MALDI in a relative quantification analysis of Staphylococcus aureus for the first time on a proteome-wide scale. Samples were analyzed in parallel with an LTQ-Orbitrap, which allowed cross-validation with a well-established workflow. With nearly 850 proteins identified in the cytosolic fraction and quantitative data for more than 550 proteins obtained with the MASCOT Distiller software, we were able to prove that LC-MALDI is able to process highly complex samples. The good correlation of quantities determined via this method and the LTQ-Orbitrap workflow confirmed the high reliability of our LC-MALDI approach for global quantification analysis. Because the existing literature reports differences for MALDI and electrospray ionization preferences and the respective experimental work was limited by technical or methodological constraints, we systematically compared biochemical attributes of peptides identified with either instrument. This genome-wide, comprehensive study revealed biases toward certain peptide properties for both MALDI-TOF-TOF- and LTQ-Orbitrap-based approaches. These biases are based on almost 13,000 peptides and result in a general complementarity of the two approaches that should be exploited in future experiments.

Probing lipid membrane electrostatics

NASA Astrophysics Data System (ADS)

Yang, Yi

The electrostatic properties of lipid bilayer membranes play a significant role in many biological processes. Atomic force microscopy (AFM) is highly sensitive to membrane surface potential in electrolyte solutions. With fully characterized probe tips, AFM can perform quantitative electrostatic analysis of lipid membranes. Electrostatic interactions between Silicon nitride probes and supported zwitterionic dioleoylphosphatidylcholine (DOPC) bilayer with a variable fraction of anionic dioleoylphosphatidylserine (DOPS) were measured by AFM. Classical Gouy-Chapman theory was used to model the membrane electrostatics. The nonlinear Poisson-Boltzmann equation was numerically solved with finite element method to provide the potential distribution around the AFM tips. Theoretical tip-sample electrostatic interactions were calculated with the surface integral of both Maxwell and osmotic stress tensors on tip surface. The measured forces were interpreted with theoretical forces and the resulting surface charge densities of the membrane surfaces were in quantitative agreement with the Gouy-Chapman-Stern model of membrane charge regulation. It was demonstrated that the AFM can quantitatively detect membrane surface potential at a separation of several screening lengths, and that the AFM probe only perturbs the membrane surface potential by <2%. One important application of this technique is to estimate the dipole density of lipid membrane. Electrostatic analysis of DOPC lipid bilayers with the AFM reveals a repulsive force between the negatively charged probe tips and the zwitterionic lipid bilayers. This unexpected interaction has been analyzed quantitatively to reveal that the repulsion is due to a weak external field created by the internai membrane dipole moment. The analysis yields a dipole moment of 1.5 Debye per lipid with a dipole potential of +275 mV for supported DOPC membranes. This new ability to quantitatively measure the membrane dipole density in a noninvasive manner will be useful in identifying the biological effects of the dipole potential. Finally, heterogeneous model membranes were studied with fluid electric force microscopy (FEFM). Electrostatic mapping was demonstrated with 50 nm resolution. The capabilities of quantitative electrostatic measurement and lateral charge density mapping make AFM a unique and powerful probe of membrane electrostatics.

Nonlinear optical microscopy: use of second harmonic generation and two-photon microscopy for automated quantitative liver fibrosis studies.

PubMed

Sun, Wanxin; Chang, Shi; Tai, Dean C S; Tan, Nancy; Xiao, Guangfa; Tang, Huihuan; Yu, Hanry

2008-01-01

Liver fibrosis is associated with an abnormal increase in an extracellular matrix in chronic liver diseases. Quantitative characterization of fibrillar collagen in intact tissue is essential for both fibrosis studies and clinical applications. Commonly used methods, histological staining followed by either semiquantitative or computerized image analysis, have limited sensitivity, accuracy, and operator-dependent variations. The fibrillar collagen in sinusoids of normal livers could be observed through second-harmonic generation (SHG) microscopy. The two-photon excited fluorescence (TPEF) images, recorded simultaneously with SHG, clearly revealed the hepatocyte morphology. We have systematically optimized the parameters for the quantitative SHG/TPEF imaging of liver tissue and developed fully automated image analysis algorithms to extract the information of collagen changes and cell necrosis. Subtle changes in the distribution and amount of collagen and cell morphology are quantitatively characterized in SHG/TPEF images. By comparing to traditional staining, such as Masson's trichrome and Sirius red, SHG/TPEF is a sensitive quantitative tool for automated collagen characterization in liver tissue. Our system allows for enhanced detection and quantification of sinusoidal collagen fibers in fibrosis research and clinical diagnostics.

Assessment of a Competency-Based Undergraduate Course on Genetic and Genomics.

PubMed

Kronk, Rebecca; Colbert, Alison; Lengetti, Evelyn

2017-08-24

In response to new demands in the nursing profession, an innovative undergraduate genetics course was designed based on the Essential Nursing Competencies and Curricula Guidelines for Genetics and Genomics. Reflective journaling and storytelling were used as major pedagogies, alongside more traditional approaches. Thematic content analysis of student reflections revealed transformational learning as the major theme emerging from genomic and genetic knowledge acquisition. Quantitative analyses of precourse/postcourse student self-assessments of competencies revealed significant findings.

Using normalization 3D model for automatic clinical brain quantative analysis and evaluation

NASA Astrophysics Data System (ADS)

Lin, Hong-Dun; Yao, Wei-Jen; Hwang, Wen-Ju; Chung, Being-Tau; Lin, Kang-Ping

2003-05-01

Functional medical imaging, such as PET or SPECT, is capable of revealing physiological functions of the brain, and has been broadly used in diagnosing brain disorders by clinically quantitative analysis for many years. In routine procedures, physicians manually select desired ROIs from structural MR images and then obtain physiological information from correspondent functional PET or SPECT images. The accuracy of quantitative analysis thus relies on that of the subjectively selected ROIs. Therefore, standardizing the analysis procedure is fundamental and important in improving the analysis outcome. In this paper, we propose and evaluate a normalization procedure with a standard 3D-brain model to achieve precise quantitative analysis. In the normalization process, the mutual information registration technique was applied for realigning functional medical images to standard structural medical images. Then, the standard 3D-brain model that shows well-defined brain regions was used, replacing the manual ROIs in the objective clinical analysis. To validate the performance, twenty cases of I-123 IBZM SPECT images were used in practical clinical evaluation. The results show that the quantitative analysis outcomes obtained from this automated method are in agreement with the clinical diagnosis evaluation score with less than 3% error in average. To sum up, the method takes advantage of obtaining precise VOIs, information automatically by well-defined standard 3-D brain model, sparing manually drawn ROIs slice by slice from structural medical images in traditional procedure. That is, the method not only can provide precise analysis results, but also improve the process rate for mass medical images in clinical.

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.

Duplex Quantitative PCR Assay for Detection of Haemophilus influenzae That Distinguishes Fucose- and Protein D-Negative Strains

PubMed Central

de Gier, Camilla; Pickering, Janessa L.; Richmond, Peter C.; Thornton, Ruth B.

2016-01-01

We have developed a specific Haemophilus influenzae quantitative PCR (qPCR) that also identifies fucose-negative and protein D-negative strains. Analysis of 100 H. influenzae isolates, 28 Haemophilus haemolyticus isolates, and 14 other bacterial species revealed 100% sensitivity (95% confidence interval [CI], 96% to 100%) and 100% specificity (95% CI, 92% to 100%) for this assay. The evaluation of 80 clinical specimens demonstrated a strong correlation between semiquantitative culture and the qPCR (P < 0.001). PMID:27335148

Quantitatively in Situ Imaging Silver Nanowire Hollowing Kinetics

DOE PAGES

Yu, Le; Yan, Zhongying; Cai, Zhonghou; ...

2016-09-28

We report the in-situ investigation of the morphological evolution of silver nanowires to hollow silver oxide nanotubes using transmission x-ray microscopy (TXM). Complex silver diffusion kinetics and hollowing process via the Kirkendall effect have been captured in real time. Further quantitative x-ray absorption analysis reveals the difference between the longitudinal and radial diffusions. In conclusion, the diffusion coefficient of silver in its oxide nanoshell is, for the first time, calculated to be 1.2 × 10 -13 cm 2/s from the geometrical parameters extracted from the TXM images.

A Dual-Color Reporter Assay of Cohesin-Mediated Gene Regulation in Budding Yeast Meiosis.

PubMed

Fan, Jinbo; Jin, Hui; Yu, Hong-Guo

2017-01-01

In this chapter, we describe a quantitative fluorescence-based assay of gene expression using the ratio of the reporter green fluorescence protein (GFP) to the internal red fluorescence protein (RFP) control. With this dual-color heterologous reporter assay, we have revealed cohesin-regulated genes and discovered a cis-acting DNA element, the Ty1-LTR, which interacts with cohesin and regulates gene expression during yeast meiosis. The method described here provides an effective cytological approach for quantitative analysis of global gene expression in budding yeast meiosis.

Pupil movements to light and accommodative stimulation - A comparative study.

NASA Technical Reports Server (NTRS)

Semmlow, J.; Stark, L.

1973-01-01

Isolation and definition of specific response components in pupil reflexes through comparison of the dynamic features of light-induced and accommodation-induced pupil movements. A quantitative analysis of the behavior of the complex nonlinear pupil responses reveals the presence of two independent nonlinear characteristics: a range-dependent gain and a direction dependence or movement asymmetry. These nonlinear properties are attributed to motor processes because they are observable in pupil responses to both light and accommodation stimuli. The possible mechanisms and consequences of these pupil response characteristics are quantitatively defined and discussed.

Making the Most of Instructional Coaches

ERIC Educational Resources Information Center

Kane, Britnie Delinger; Rosenquist, Brooks

2018-01-01

Although coaching holds great promise for professional development, instructional coaches are often asked to take on responsibilities that are not focused on improving instruction. The authors discuss a quantitative study of four school districts and a qualitative analysis of a single district that, together, reveal how hiring practices and school…

Changing Knowledge and the Academic Profession in Portugal

ERIC Educational Resources Information Center

Santiago, Rui; Carvalho, Teresa; Ferreira, Andreia

2015-01-01

The paper analyses the Portuguese academics' perceptions about changes in their research activities and modes of knowledge production. Quantitative data gathered from an on-line national survey have been used to develop this analysis. Results reveal that the majority of academics declared that they were not involved in knowledge and technology…

Community College Students' Perceptions of Effective Communication in Online Learning

ERIC Educational Resources Information Center

Parker, Donna Alice Hill

2012-01-01

This quantitative research project analyzed the application of instructional communication tools and techniques used by community college students to determine how they perceive communication in their online classes. Online students from a community college participated in this study by completing an electronic survey. Data analysis revealed that…

Interventions for Behaviorally Disordered Students: A Quantitative Review and Methodological Critique.

ERIC Educational Resources Information Center

Skiba, Russell; Casey, Ann

1985-01-01

Results of three forms of meta-analysis on 41 studies involving behavior disorders revealed powerful effects of treatment: both interventions targeting classroom behavior and those attributable to a behavioral orientation were somewhat more powerful and robust. Methodological flaws, however, are cited. Recommendations for solidifying the research…

Dissociable brain biomarkers of fluid intelligence.

PubMed

Paul, Erick J; Larsen, Ryan J; Nikolaidis, Aki; Ward, Nathan; Hillman, Charles H; Cohen, Neal J; Kramer, Arthur F; Barbey, Aron K

2016-08-15

Cognitive neuroscience has long sought to understand the biological foundations of human intelligence. Decades of research have revealed that general intelligence is correlated with two brain-based biomarkers: the concentration of the brain biochemical N-acetyl aspartate (NAA) measured by proton magnetic resonance spectroscopy (MRS) and total brain volume measured using structural MR imaging (MRI). However, the relative contribution of these biomarkers in predicting performance on core facets of human intelligence remains to be well characterized. In the present study, we sought to elucidate the role of NAA and brain volume in predicting fluid intelligence (Gf). Three canonical tests of Gf (BOMAT, Number Series, and Letter Sets) and three working memory tasks (Reading, Rotation, and Symmetry span tasks) were administered to a large sample of healthy adults (n=211). We conducted exploratory factor analysis to investigate the factor structure underlying Gf independent from working memory and observed two Gf components (verbal/spatial and quantitative reasoning) and one working memory component. Our findings revealed a dissociation between two brain biomarkers of Gf (controlling for age and sex): NAA concentration correlated with verbal/spatial reasoning, whereas brain volume correlated with quantitative reasoning and working memory. A follow-up analysis revealed that this pattern of findings is observed for males and females when analyzed separately. Our results provide novel evidence that distinct brain biomarkers are associated with specific facets of human intelligence, demonstrating that NAA and brain volume are independent predictors of verbal/spatial and quantitative facets of Gf. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Fluvial drainage networks: the fractal approach as an improvement of quantitative geomorphic analyses

NASA Astrophysics Data System (ADS)

Melelli, Laura; Liucci, Luisa; Vergari, Francesca; Ciccacci, Sirio; Del Monte, Maurizio

2014-05-01

Drainage basins are primary landscape units for geomorphological investigations. Both hillslopes and river drainage system are fundamental components in drainage basins analysis. As other geomorphological systems, also the drainage basins aim to an equilibrium condition where the sequence of erosion, transport and sedimentation approach to a condition of minimum energy effort. This state is revealed by a typical geometry of landforms and of drainage net. Several morphometric indexes can measure how much a drainage basin is far from the theoretical equilibrium configuration, revealing possible external disarray. In active tectonic areas, the drainage basins have a primary importance in order to highlight style, amount and rate of tectonic impulses, and morphometric indexes allow to estimate the tectonic activity classes of different sectors in a study area. Moreover, drainage rivers are characterized by a self-similarity structure; this promotes the use of fractals theory to investigate the system. In this study, fractals techniques are employed together with quantitative geomorphological analysis to study the Upper Tiber Valley (UTV), a tectonic intermontane basin located in northern Apennines (Umbria, central Italy). The area is the result of different tectonic phases. From Late Pliocene until present time the UTV is strongly controlled by a regional uplift and by an extensional phase with different sets of normal faults playing a fundamental role in basin morphology. Thirty-four basins are taken into account for the quantitative analysis, twenty on the left side of the basin, the others on the right side. Using fractals dimension of drainage networks, Horton's laws results, concavity and steepness indexes, and hypsometric curves, this study aims to obtain an evolutionary model of the UTV, where the uplift is compared to local subsidence induced by normal fault activity. The results highlight a well defined difference between western and eastern tributary basins, suggesting a greater disequilibrium in the last ones. The quantitative analysis points out the segments of the basin boundaries where the fault activity is more efficient and the resulting geomorphological implications.

Quantitative refractive index distribution of single cell by combining phase-shifting interferometry and AFM imaging.

PubMed

Zhang, Qinnan; Zhong, Liyun; Tang, Ping; Yuan, Yingjie; Liu, Shengde; Tian, Jindong; Lu, Xiaoxu

2017-05-31

Cell refractive index, an intrinsic optical parameter, is closely correlated with the intracellular mass and concentration. By combining optical phase-shifting interferometry (PSI) and atomic force microscope (AFM) imaging, we constructed a label free, non-invasive and quantitative refractive index of single cell measurement system, in which the accurate phase map of single cell was retrieved with PSI technique and the cell morphology with nanoscale resolution was achieved with AFM imaging. Based on the proposed AFM/PSI system, we achieved quantitative refractive index distributions of single red blood cell and Jurkat cell, respectively. Further, the quantitative change of refractive index distribution during Daunorubicin (DNR)-induced Jurkat cell apoptosis was presented, and then the content changes of intracellular biochemical components were achieved. Importantly, these results were consistent with Raman spectral analysis, indicating that the proposed PSI/AFM based refractive index system is likely to become a useful tool for intracellular biochemical components analysis measurement, and this will facilitate its application for revealing cell structure and pathological state from a new perspective.

On sweat analysis for quantitative estimation of dehydration during physical exercise.

PubMed

Ring, Matthias; Lohmueller, Clemens; Rauh, Manfred; Eskofier, Bjoern M

2015-08-01

Quantitative estimation of water loss during physical exercise is of importance because dehydration can impair both muscular strength and aerobic endurance. A physiological indicator for deficit of total body water (TBW) might be the concentration of electrolytes in sweat. It has been shown that concentrations differ after physical exercise depending on whether water loss was replaced by fluid intake or not. However, to the best of our knowledge, this fact has not been examined for its potential to quantitatively estimate TBW loss. Therefore, we conducted a study in which sweat samples were collected continuously during two hours of physical exercise without fluid intake. A statistical analysis of these sweat samples revealed significant correlations between chloride concentration in sweat and TBW loss (r = 0.41, p <; 0.01), and between sweat osmolality and TBW loss (r = 0.43, p <; 0.01). A quantitative estimation of TBW loss resulted in a mean absolute error of 0.49 l per estimation. Although the precision has to be improved for practical applications, the present results suggest that TBW loss estimation could be realizable using sweat samples.

Time-Resolved Fluorescent Immunochromatography of Aflatoxin B1 in Soybean Sauce: A Rapid and Sensitive Quantitative Analysis.

PubMed

Wang, Du; Zhang, Zhaowei; Li, Peiwu; Zhang, Qi; Zhang, Wen

2016-07-14

Rapid and quantitative sensing of aflatoxin B1 with high sensitivity and specificity has drawn increased attention of studies investigating soybean sauce. A sensitive and rapid quantitative immunochromatographic sensing method was developed for the detection of aflatoxin B1 based on time-resolved fluorescence. It combines the advantages of time-resolved fluorescent sensing and immunochromatography. The dynamic range of a competitive and portable immunoassay was 0.3-10.0 µg·kg(-1), with a limit of detection (LOD) of 0.1 µg·kg(-1) and recoveries of 87.2%-114.3%, within 10 min. The results showed good correlation (R² > 0.99) between time-resolved fluorescent immunochromatographic strip test and high performance liquid chromatography (HPLC). Soybean sauce samples analyzed using time-resolved fluorescent immunochromatographic strip test revealed that 64.2% of samples contained aflatoxin B1 at levels ranging from 0.31 to 12.5 µg·kg(-1). The strip test is a rapid, sensitive, quantitative, and cost-effective on-site screening technique in food safety analysis.

In silico quantitative structure-toxicity relationship study of aromatic nitro compounds.

PubMed

Pasha, Farhan Ahmad; Neaz, Mohammad Morshed; Cho, Seung Joo; Ansari, Mohiuddin; Mishra, Sunil Kumar; Tiwari, Sharvan

2009-05-01

Small molecules often have toxicities that are a function of molecular structural features. Minor variations in structural features can make large difference in such toxicity. Consequently, in silico techniques may be used to correlate such molecular toxicities with their structural features. Relative to nine different sets of aromatic nitro compounds having known observed toxicities against different targets, we developed ligand-based 2D quantitative structure-toxicity relationship models using 20 selected topological descriptors. The topological descriptors have several advantages such as conformational independency, facile and less time-consuming computation to yield good results. Multiple linear regression analysis was used to correlate variations of toxicity with molecular properties. The information index on molecular size, lopping centric index and Kier flexibility index were identified as fundamental descriptors for different kinds of toxicity, and further showed that molecular size, branching and molecular flexibility might be particularly important factors in quantitative structure-toxicity relationship analysis. This study revealed that topological descriptor-guided quantitative structure-toxicity relationship provided a very useful, cost and time-efficient, in silico tool for describing small-molecule toxicities.

Predictive value of EEG in postanoxic encephalopathy: A quantitative model-based approach.

PubMed

Efthymiou, Evdokia; Renzel, Roland; Baumann, Christian R; Poryazova, Rositsa; Imbach, Lukas L

2017-10-01

The majority of comatose patients after cardiac arrest do not regain consciousness due to severe postanoxic encephalopathy. Early and accurate outcome prediction is therefore essential in determining further therapeutic interventions. The electroencephalogram is a standardized and commonly available tool used to estimate prognosis in postanoxic patients. The identification of pathological EEG patterns with poor prognosis relies however primarily on visual EEG scoring by experts. We introduced a model-based approach of EEG analysis (state space model) that allows for an objective and quantitative description of spectral EEG variability. We retrospectively analyzed standard EEG recordings in 83 comatose patients after cardiac arrest between 2005 and 2013 in the intensive care unit of the University Hospital Zürich. Neurological outcome was assessed one month after cardiac arrest using the Cerebral Performance Category. For a dynamic and quantitative EEG analysis, we implemented a model-based approach (state space analysis) to quantify EEG background variability independent from visual scoring of EEG epochs. Spectral variability was compared between groups and correlated with clinical outcome parameters and visual EEG patterns. Quantitative assessment of spectral EEG variability (state space velocity) revealed significant differences between patients with poor and good outcome after cardiac arrest: Lower mean velocity in temporal electrodes (T4 and T5) was significantly associated with poor prognostic outcome (p<0.005) and correlated with independently identified visual EEG patterns such as generalized periodic discharges (p<0.02). Receiver operating characteristic (ROC) analysis confirmed the predictive value of lower state space velocity for poor clinical outcome after cardiac arrest (AUC 80.8, 70% sensitivity, 15% false positive rate). Model-based quantitative EEG analysis (state space analysis) provides a novel, complementary marker for prognosis in postanoxic encephalopathy. Copyright © 2017 Elsevier B.V. All rights reserved.

Deciphering of the Human Interferon-Regulated Proteome by Mass Spectrometry-Based Quantitative Analysis Reveals Extent and Dynamics of Protein Induction and Repression

PubMed Central

Megger, Dominik A.; Philipp, Jos; Le-Trilling, Vu Thuy Khanh; Sitek, Barbara; Trilling, Mirko

2017-01-01

Interferons (IFNs) are pleotropic cytokines secreted upon encounter of pathogens and tumors. Applying their antipathogenic, antiproliferative, and immune stimulatory capacities, recombinant IFNs are frequently prescribed as drugs to treat different diseases. IFNs act by changing the gene expression profile of cells. Due to characteristics such as rapid gene induction and signaling, IFNs also represent prototypical model systems for various aspects of biomedical research (e.g., signal transduction). In regard to the signaling and activated promoters, IFNs can be subdivided into two groups. Here, alterations of the cellular proteome of human cells treated with IFNα and IFNγ were elucidated in a time-resolved manner by quantitative proteome analysis. The majority of protein regulations were strongly IFN type and time dependent. In addition to the expected upregulation of IFN-responsive proteins, an astonishing number of proteins became profoundly repressed especially by IFNγ. Thus, our comprehensive analysis revealed important insights into the human IFN-regulated proteome and its dynamics of protein induction and repression. Interestingly, the new class of IFN-repressed genes comprises known host factors for highly relevant pathogens such as HIV, dengue virus, and hepatitis C virus. PMID:28959263

Deciphering of the Human Interferon-Regulated Proteome by Mass Spectrometry-Based Quantitative Analysis Reveals Extent and Dynamics of Protein Induction and Repression.

PubMed

Megger, Dominik A; Philipp, Jos; Le-Trilling, Vu Thuy Khanh; Sitek, Barbara; Trilling, Mirko

2017-01-01

Interferons (IFNs) are pleotropic cytokines secreted upon encounter of pathogens and tumors. Applying their antipathogenic, antiproliferative, and immune stimulatory capacities, recombinant IFNs are frequently prescribed as drugs to treat different diseases. IFNs act by changing the gene expression profile of cells. Due to characteristics such as rapid gene induction and signaling, IFNs also represent prototypical model systems for various aspects of biomedical research (e.g., signal transduction). In regard to the signaling and activated promoters, IFNs can be subdivided into two groups. Here, alterations of the cellular proteome of human cells treated with IFNα and IFNγ were elucidated in a time-resolved manner by quantitative proteome analysis. The majority of protein regulations were strongly IFN type and time dependent. In addition to the expected upregulation of IFN-responsive proteins, an astonishing number of proteins became profoundly repressed especially by IFNγ. Thus, our comprehensive analysis revealed important insights into the human IFN-regulated proteome and its dynamics of protein induction and repression. Interestingly, the new class of IFN-repressed genes comprises known host factors for highly relevant pathogens such as HIV, dengue virus, and hepatitis C virus.

Image Analysis of DNA Fiber and Nucleus in Plants.

PubMed

Ohmido, Nobuko; Wako, Toshiyuki; Kato, Seiji; Fukui, Kiichi

2016-01-01

Advances in cytology have led to the application of a wide range of visualization methods in plant genome studies. Image analysis methods are indispensable tools where morphology, density, and color play important roles in the biological systems. Visualization and image analysis methods are useful techniques in the analyses of the detailed structure and function of extended DNA fibers (EDFs) and interphase nuclei. The EDF is the highest in the spatial resolving power to reveal genome structure and it can be used for physical mapping, especially for closely located genes and tandemly repeated sequences. One the other hand, analyzing nuclear DNA and proteins would reveal nuclear structure and functions. In this chapter, we describe the image analysis protocol for quantitatively analyzing different types of plant genome, EDFs and interphase nuclei.

Structure and Function of Iron-Loaded Synthetic Melanin

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

Li, Yiwen; Xie, Yijun; Wang, Zhao

We describe a synthetic method for increasing and controlling the iron loading of synthetic melanin nanoparticles and use the resulting materials to perform a systematic quantitative investigation on their structure- property relationship. A comprehensive analysis by magnetometry, electron paramagnetic resonance, and nuclear magnetic relaxation dispersion reveals the complexities of their magnetic behavior and how these intraparticle magnetic interactions manifest in useful material properties such as their performance as MRI contrast agents. This analysis allows predictions of the optimal iron loading through a quantitative modeling of antiferromagnetic coupling that arises from proximal iron ions. This study provides a detailed understanding ofmore » this complex class of synthetic biomaterials and gives insight into interactions and structures prevalent in naturally occurring melanins.« less

Quantitative analysis of backflow of reversible pump-turbine in generating mode

NASA Astrophysics Data System (ADS)

Liu, K. H.; Zhang, Y. N.; Li, J. W.; Xian, H. Z.

2016-05-01

Significant vibration and pressure fluctuations are usually observed when pump- turbine is operated during the off-design conditions, especially turbine brake and runaway. The root cause of these instability phenomena is the abnormal unsteady flow (especially the backflow) inside the pump-turbine. In the present paper, numerical simulation method is adopted to investigate the characteristics of the flow inside the whole passage of pump-turbine with two guide vane openings (6° and 21° respectively) and three kinds of operating conditions (turbine, runaway and turbine braking respectively). A quantitative analysis of backflow is performed in both the axial and radial directions and the generation and development of backflow in the pump turbine are revealed with great details.

Quantitative Proteomics of the Tonoplast Reveals a Role for Glycolytic Enzymes in Salt Tolerance[C][W

PubMed Central

Barkla, Bronwyn J.; Vera-Estrella, Rosario; Hernández-Coronado, Marcela; Pantoja, Omar

2009-01-01

To examine the role of the tonoplast in plant salt tolerance and identify proteins involved in the regulation of transporters for vacuolar Na+ sequestration, we exploited a targeted quantitative proteomics approach. Two-dimensional differential in-gel electrophoresis analysis of free flow zonal electrophoresis separated tonoplast fractions from control, and salt-treated Mesembryanthemum crystallinum plants revealed the membrane association of glycolytic enzymes aldolase and enolase, along with subunits of the vacuolar H+-ATPase V-ATPase. Protein blot analysis confirmed coordinated salt regulation of these proteins, and chaotrope treatment indicated a strong tonoplast association. Reciprocal coimmunoprecipitation studies revealed that the glycolytic enzymes interacted with the V-ATPase subunit B VHA-B, and aldolase was shown to stimulate V-ATPase activity in vitro by increasing the affinity for ATP. To investigate a physiological role for this association, the Arabidopsis thaliana cytoplasmic enolase mutant, los2, was characterized. These plants were salt sensitive, and there was a specific reduction in enolase abundance in the tonoplast from salt-treated plants. Moreover, tonoplast isolated from mutant plants showed an impaired ability for aldolase stimulation of V-ATPase hydrolytic activity. The association of glycolytic proteins with the tonoplast may not only channel ATP to the V-ATPase, but also directly upregulate H+-pump activity. PMID:20028841

Quantitative proteomics of the tonoplast reveals a role for glycolytic enzymes in salt tolerance.

PubMed

Barkla, Bronwyn J; Vera-Estrella, Rosario; Hernández-Coronado, Marcela; Pantoja, Omar

2009-12-01

To examine the role of the tonoplast in plant salt tolerance and identify proteins involved in the regulation of transporters for vacuolar Na(+) sequestration, we exploited a targeted quantitative proteomics approach. Two-dimensional differential in-gel electrophoresis analysis of free flow zonal electrophoresis separated tonoplast fractions from control, and salt-treated Mesembryanthemum crystallinum plants revealed the membrane association of glycolytic enzymes aldolase and enolase, along with subunits of the vacuolar H(+)-ATPase V-ATPase. Protein blot analysis confirmed coordinated salt regulation of these proteins, and chaotrope treatment indicated a strong tonoplast association. Reciprocal coimmunoprecipitation studies revealed that the glycolytic enzymes interacted with the V-ATPase subunit B VHA-B, and aldolase was shown to stimulate V-ATPase activity in vitro by increasing the affinity for ATP. To investigate a physiological role for this association, the Arabidopsis thaliana cytoplasmic enolase mutant, los2, was characterized. These plants were salt sensitive, and there was a specific reduction in enolase abundance in the tonoplast from salt-treated plants. Moreover, tonoplast isolated from mutant plants showed an impaired ability for aldolase stimulation of V-ATPase hydrolytic activity. The association of glycolytic proteins with the tonoplast may not only channel ATP to the V-ATPase, but also directly upregulate H(+)-pump activity.

Application of relativistic electrons for the quantitative analysis of trace elements

NASA Astrophysics Data System (ADS)

Hoffmann, D. H. H.; Brendel, C.; Genz, H.; Löw, W.; Richter, A.

1984-04-01

Particle induced X-ray emission methods (PIXE) have been extended to relativistic electrons to induce X-ray emission (REIXE) for quantitative trace-element analysis. The electron beam (20 ≤ E0≤ 70 MeV) was supplied by the Darmstadt electron linear accelerator DALINAC. Systematic measurements of absolute K-, L- and M-shell ionization cross sections revealed a scaling behaviour of inner-shell ionization cross sections from which X-ray production cross sections can be deduced for any element of interest for a quantitative sample investigation. Using a multielemental mineral monazite sample from Malaysia the sensitivity of REIXE is compared to well established methods of trace-element analysis like proton- and X-ray-induced X-ray fluorescence analysis. The achievable detection limit for very heavy elements amounts to about 100 ppm for the REIXE method. As an example of an application the investigation of a sample prepared from manganese nodules — picked up from the Pacific deep sea — is discussed, which showed the expected high mineral content of Fe, Ni, Cu and Ti, although the search for aliquots of Pt did not show any measurable content within an upper limit of 250 ppm.

A Comparison of Mathematics Teachers' and Professors' Views on Secondary Preparation for Tertiary Calculus

ERIC Educational Resources Information Center

Wade, Carol; Sonnert, Gerhard; Sadler, Philip M.; Hazari, Zahra; Watson, Charity

2016-01-01

This article compares the views of teachers and professors about the transition from secondary mathematics to tertiary calculus. Quantitative analysis revealed five categories where teachers and professors differed significantly in the relative frequency of addressing them. Using the rite of passage theory, the separation and incorporation phases…

Whole genome structural analysis of Caribbean hair sheep reveals quantitative link to West African ancestry

USDA-ARS?s Scientific Manuscript database

Hair sheep of Caribbean origin have become an important part of the U.S. sheep industry. Lack of wool eliminates a number of health concerns and drastically reduces the cost of production. More importantly, Caribbean hair sheep demonstrate robust performance even in the presence of drug resistant ga...

Stress and Grief of a Perinatal Loss: Integrating Qualitative and Quantitative Methods.

ERIC Educational Resources Information Center

Thomas, Volker; Striegel, Phil

1995-01-01

Examined how parents grieve loss of a baby through miscarriage or stillbirth. Interviewed 26 couples 2 weeks after a perinatal loss. Ethnographic content analysis revealed 12 themes closely related to resources, meaning of the stressful event, and coping strategies, all of which are elements, of Hill's ABC-X stress model. (JBJ)

Explaining Hong Kong Students' International Achievement in Civic Learning

ERIC Educational Resources Information Center

Kennedy, Kerry J.; Lijuan, Li

2016-01-01

This study identifies predictors of Hong Kong students' civic learning. It has adopted a cross-sectional quantitative design using secondary data from the 2009 International Civics and Citizenship Education Study (ICCS 2009; Schulz et al., 2010). Multi-level analysis reveals that most of the variance in student achievement can be accounted for by…

Fellows' Perceptions of a Mandatory Reflective Electronic Portfolio in a Geriatric Medicine Fellowship Program

ERIC Educational Resources Information Center

Ruiz, Jorge G.; Qadri, Syeda S.; Karides, Marina; Castillo, Carmen; Milanez, Marcos; Roos, Bernard A.

2009-01-01

Electronic portfolios (ePortfolios) can be useful for evaluating and documenting mastery of competencies. We investigated geriatric medicine fellows' perceptions of an ePortfolio. We conducted surveys and focus groups followed by quantitative and qualitative data analysis. Our study revealed that fellows considered the ePortfolio acceptable and…

Learning Difficulties Experienced by Grade 12 South African Students in the Chemical Representation of Phenomena

ERIC Educational Resources Information Center

Ramnarain, Umesh; Joseph, Aleyamma

2012-01-01

This study investigated the learning difficulties of grade 12 South African students in a national chemistry examination. A quantitative analysis of students' performance in the examination revealed there was a significant difference between student performance in questions where students needed to execute a transformation across levels of…

A large scale joint analysis of flowering time reveals independent temperate adaptations in maize

USDA-ARS?s Scientific Manuscript database

Modulating days to flowering is a key mechanism in plants for adapting to new environments, and variation in days to flowering drives population structure by limiting mating. To elucidate the genetic architecture of flowering across maize, a quantitative trait, we mapped flowering in five global pop...

Prospective Teachers' Metaphorical Perceptions on the Concept of Science

ERIC Educational Resources Information Center

Aysegul, Derman; Serdar, Derman

2015-01-01

The aim of this study is to reveal prospective teachers' perceptions of the concept of science by asking them to use metaphors to describe it. A metaphor elicitation method was employed in this study. The data obtained from the study were considered with both quantitative and qualitative (Content Analysis) analyses. The study determined the…

Infrared spectroscopy reveals both qualitative and quantitative differences in equine subchondral bone during maturation

NASA Astrophysics Data System (ADS)

Kobrina, Yevgeniya; Isaksson, Hanna; Sinisaari, Miikka; Rieppo, Lassi; Brama, Pieter A.; van Weeren, René; Helminen, Heikki J.; Jurvelin, Jukka S.; Saarakkala, Simo

2010-11-01

The collagen phase in bone is known to undergo major changes during growth and maturation. The objective of this study is to clarify whether Fourier transform infrared (FTIR) microspectroscopy, coupled with cluster analysis, can detect quantitative and qualitative changes in the collagen matrix of subchondral bone in horses during maturation and growth. Equine subchondral bone samples (n = 29) from the proximal joint surface of the first phalanx are prepared from two sites subjected to different loading conditions. Three age groups are studied: newborn (0 days old), immature (5 to 11 months old), and adult (6 to 10 years old) horses. Spatial collagen content and collagen cross-link ratio are quantified from the spectra. Additionally, normalized second derivative spectra of samples are clustered using the k-means clustering algorithm. In quantitative analysis, collagen content in the subchondral bone increases rapidly between the newborn and immature horses. The collagen cross-link ratio increases significantly with age. In qualitative analysis, clustering is able to separate newborn and adult samples into two different groups. The immature samples display some nonhomogeneity. In conclusion, this is the first study showing that FTIR spectral imaging combined with clustering techniques can detect quantitative and qualitative changes in the collagen matrix of subchondral bone during growth and maturation.

Quantitative Glycoproteomics Analysis Reveals Changes in N-Glycosylation Level Associated with Pancreatic Ductal Adenocarcinoma

PubMed Central

2015-01-01

Glycosylation plays an important role in epithelial cancers, including pancreatic ductal adenocarcinoma. However, little is known about the glycoproteome of the human pancreas or its alterations associated with pancreatic tumorigenesis. Using quantitative glycoproteomics approach, we investigated protein N-glycosylation in pancreatic tumor tissue in comparison with normal pancreas and chronic pancreatitis tissue. The study lead to the discovery of a roster of glycoproteins with aberrant N-glycosylation level associated with pancreatic cancer, including mucin-5AC (MUC5AC), carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5), insulin-like growth factor binding protein (IGFBP3), and galectin-3-binding protein (LGALS3BP). Pathway analysis of cancer-associated aberrant glycoproteins revealed an emerging phenomenon that increased activity of N-glycosylation was implicated in several pancreatic cancer pathways, including TGF-β, TNF, NF-kappa-B, and TFEB-related lysosomal changes. In addition, the study provided evidence that specific N-glycosylation sites within certain individual proteins can have significantly altered glycosylation occupancy in pancreatic cancer, reflecting the complexity of the molecular mechanisms underlying cancer-associated glycosylation events. PMID:24471499

Label-free quantitative proteomics reveals differentially regulated proteins in the latex of sticky diseased Carica papaya L. plants.

PubMed

Rodrigues, Silas P; Ventura, José A; Aguilar, Clemente; Nakayasu, Ernesto S; Choi, HyungWon; Sobreira, Tiago J P; Nohara, Lilian L; Wermelinger, Luciana S; Almeida, Igor C; Zingali, Russolina B; Fernandes, Patricia M B

2012-06-18

Papaya meleira virus (PMeV) is so far the only described laticifer-infecting virus, the causal agent of papaya (Carica papaya L.) sticky disease. The effects of PMeV on the laticifers' regulatory network were addressed here through the proteomic analysis of papaya latex. Using both 1-DE- and 1D-LC-ESI-MS/MS, 160 unique papaya latex proteins were identified, representing 122 new proteins in the latex of this plant. Quantitative analysis by normalized spectral counting revealed 10 down-regulated proteins in the latex of diseased plants, 9 cysteine proteases (chymopapain) and 1 latex serine proteinase inhibitor. A repression of papaya latex proteolytic activity during PMeV infection was hypothesized. This was further confirmed by enzymatic assays that showed a reduction of cysteine-protease-associated proteolytic activity in the diseased papaya latex. These findings are discussed in the context of plant responses against pathogens and may greatly contribute to understand the roles of laticifers in plant stress responses. Copyright © 2012 Elsevier B.V. All rights reserved.

[Recurrence of chronic active Epstein-Barr virus infection presenting with myelopathy after umbilical cord blood transplantation].

PubMed

Watanabe, Shohei; Okada, Masaya; Tokugawa, Tazuko; Sawada, Akihiro; Ogawa, Hiroyasu; Yoshikawa, Hiroo

2014-01-01

A 38-year-old man was admitted to our hospital with neck pain, dysesthesia of both hands, and weakness of the left upper limb. He had been diagnosed with a chronic active Epstein-Barr virus infection (CAEBV) at the age of 34 and had undergone umbilical cord blood transplantation at the age of 37. MRI of the spinal cord revealed an intramedullary hyperintense lesion on T₂-weighted images with gadolinium enhancement. Because his laboratory tests revealed proliferation of CD19(+) lymphocytes in the peripheral blood, and EBV DNA was detected in both peripheral blood and CSF, he was diagnosed as having post-transplant EBV associated lymphoproliferative disease. However, chemotherapy did not alleviate his symptoms. At a later time, quantitative chimerism analysis of his CSF showed a higher proportion of lymphocytes that had originated from the recipient. Finally, he was diagnosed as having a recurrence of CAEBV in the central nervous system, and his symptoms were restored by intrathecal chemotherapy (methotrexate, cytosine arabinoside, and prednisolone). Quantitative chimerism analysis of CSF was useful for diagnosing the recurrence of CAEBV in the central nervous system.

Quantitative glycoproteomics analysis reveals changes in N-glycosylation level associated with pancreatic ductal adenocarcinoma.

PubMed

Pan, Sheng; Chen, Ru; Tamura, Yasuko; Crispin, David A; Lai, Lisa A; May, Damon H; McIntosh, Martin W; Goodlett, David R; Brentnall, Teresa A

2014-03-07

Glycosylation plays an important role in epithelial cancers, including pancreatic ductal adenocarcinoma. However, little is known about the glycoproteome of the human pancreas or its alterations associated with pancreatic tumorigenesis. Using quantitative glycoproteomics approach, we investigated protein N-glycosylation in pancreatic tumor tissue in comparison with normal pancreas and chronic pancreatitis tissue. The study lead to the discovery of a roster of glycoproteins with aberrant N-glycosylation level associated with pancreatic cancer, including mucin-5AC (MUC5AC), carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5), insulin-like growth factor binding protein (IGFBP3), and galectin-3-binding protein (LGALS3BP). Pathway analysis of cancer-associated aberrant glycoproteins revealed an emerging phenomenon that increased activity of N-glycosylation was implicated in several pancreatic cancer pathways, including TGF-β, TNF, NF-kappa-B, and TFEB-related lysosomal changes. In addition, the study provided evidence that specific N-glycosylation sites within certain individual proteins can have significantly altered glycosylation occupancy in pancreatic cancer, reflecting the complexity of the molecular mechanisms underlying cancer-associated glycosylation events.

In-depth Qualitative and Quantitative Profiling of Tyrosine Phosphorylation Using a Combination of Phosphopeptide Immunoaffinity Purification and Stable Isotope Dimethyl Labeling*

PubMed Central

Boersema, Paul J.; Foong, Leong Yan; Ding, Vanessa M. Y.; Lemeer, Simone; van Breukelen, Bas; Philp, Robin; Boekhorst, Jos; Snel, Berend; den Hertog, Jeroen; Choo, Andre B. H.; Heck, Albert J. R.

2010-01-01

Several mass spectrometry-based assays have emerged for the quantitative profiling of cellular tyrosine phosphorylation. Ideally, these methods should reveal the exact sites of tyrosine phosphorylation, be quantitative, and not be cost-prohibitive. The latter is often an issue as typically several milligrams of (stable isotope-labeled) starting protein material are required to enable the detection of low abundance phosphotyrosine peptides. Here, we adopted and refined a peptidecentric immunoaffinity purification approach for the quantitative analysis of tyrosine phosphorylation by combining it with a cost-effective stable isotope dimethyl labeling method. We were able to identify by mass spectrometry, using just two LC-MS/MS runs, more than 1100 unique non-redundant phosphopeptides in HeLa cells from about 4 mg of starting material without requiring any further affinity enrichment as close to 80% of the identified peptides were tyrosine phosphorylated peptides. Stable isotope dimethyl labeling could be incorporated prior to the immunoaffinity purification, even for the large quantities (mg) of peptide material used, enabling the quantification of differences in tyrosine phosphorylation upon pervanadate treatment or epidermal growth factor stimulation. Analysis of the epidermal growth factor-stimulated HeLa cells, a frequently used model system for tyrosine phosphorylation, resulted in the quantification of 73 regulated unique phosphotyrosine peptides. The quantitative data were found to be exceptionally consistent with the literature, evidencing that such a targeted quantitative phosphoproteomics approach can provide reproducible results. In general, the combination of immunoaffinity purification of tyrosine phosphorylated peptides with large scale stable isotope dimethyl labeling provides a cost-effective approach that can alleviate variation in sample preparation and analysis as samples can be combined early on. Using this approach, a rather complete qualitative and quantitative picture of tyrosine phosphorylation signaling events can be generated. PMID:19770167

Quantitative analysis of diet structure by real-time PCR, reveals different feeding patterns by two dominant grasshopper species

PubMed Central

Huang, Xunbing; Wu, Huihui; McNeill, Mark Richard; Qin, Xinghu; Ma, Jingchuan; Tu, Xiongbing; Cao, Guangchun; Wang, Guangjun; Nong, Xiangqun; Zhang, Zehua

2016-01-01

Studies on grasshopper diets have historically employed a range of methodologies, each with certain advantages and disadvantages. For example, some methodologies are qualitative instead of quantitative. Others require long experimental periods or examine population-level effects, only. In this study, we used real-time PCR to examine diets of individual grasshoppers. The method has the advantage of being both fast and quantitative. Using two grasshopper species, Oedaleus asiaticus and Dasyhippus barbipes, we designed ITS primer sequences for their three main host plants, Stipa krylovii, Leymus chinensis and Cleistogenes squarrosa and used real-time PCR method to test diet structure both qualitatively and quantitatively. The lowest detection efficiency of the three grass species was ~80% with a strong correlation between actual and PCR-measured food intake. We found that Oedaleus asiaticus maintained an unchanged diet structure across grasslands with different grass communities. By comparison, Dasyhippus barbipes changed its diet structure. These results revealed why O. asiaticus distribution is mainly confined to Stipa-dominated grassland, and D. barbipes is more widely distributed across Inner Mongolia. Overall, real-time PCR was shown to be a useful tool for investigating grasshopper diets, which in turn offers some insight into grasshopper distributions and improved pest management. PMID:27562455

Analysis of Fundus Shape in Highly Myopic Eyes by Using Curvature Maps Constructed from Optical Coherence Tomography

PubMed Central

Miyake, Masahiro; Yamashiro, Kenji; Akagi-Kurashige, Yumiko; Oishi, Akio; Tsujikawa, Akitaka; Hangai, Masanori; Yoshimura, Nagahisa

2014-01-01

Purpose To evaluate fundus shape in highly myopic eyes using color maps created through optical coherence tomography (OCT) image analysis. Methods We retrospectively evaluated 182 highly myopic eyes from 113 patients. After obtaining 12 lines of 9-mm radial OCT scans with the fovea at the center, the Bruch’s membrane line was plotted and its curvature was measured at 1-µm intervals in each image, which was reflected as a color topography map. For the quantitative analysis of the eye shape, mean absolute curvature and variance of curvature were calculated. Results The color maps allowed staphyloma visualization as a ring of green color at the edge and as that of orange-red color at the bottom. Analyses of mean and variance of curvature revealed that eyes with myopic choroidal neovascularization tended to have relatively flat posterior poles with smooth surfaces, while eyes with chorioretinal atrophy exhibited a steep, curved shape with an undulated surface (P<0.001). Furthermore, eyes with staphylomas and those without clearly differed in terms of mean curvature and the variance of curvature: 98.4% of eyes with staphylomas had mean curvature ≥7.8×10−5 [1/µm] and variance of curvature ≥0.26×10−8 [1/µm]. Conclusions We established a novel method to analyze posterior pole shape by using OCT images to construct curvature maps. Our quantitative analysis revealed that fundus shape is associated with myopic complications. These values were also effective in distinguishing eyes with staphylomas from those without. This tool for the quantitative evaluation of eye shape should facilitate future research of myopic complications. PMID:25259853

The Quantitative Analysis of Chennai Automotive Industry Cluster

NASA Astrophysics Data System (ADS)

Bhaskaran, Ethirajan

2016-07-01

Chennai, also called as Detroit of India due to presence of Automotive Industry producing over 40 % of the India's vehicle and components. During 2001-2002, the Automotive Component Industries (ACI) in Ambattur, Thirumalizai and Thirumudivakkam Industrial Estate, Chennai has faced problems on infrastructure, technology, procurement, production and marketing. The objective is to study the Quantitative Performance of Chennai Automotive Industry Cluster before (2001-2002) and after the CDA (2008-2009). The methodology adopted is collection of primary data from 100 ACI using quantitative questionnaire and analyzing using Correlation Analysis (CA), Regression Analysis (RA), Friedman Test (FMT), and Kruskall Wallis Test (KWT).The CA computed for the different set of variables reveals that there is high degree of relationship between the variables studied. The RA models constructed establish the strong relationship between the dependent variable and a host of independent variables. The models proposed here reveal the approximate relationship in a closer form. KWT proves, there is no significant difference between three locations clusters with respect to: Net Profit, Production Cost, Marketing Costs, Procurement Costs and Gross Output. This supports that each location has contributed for development of automobile component cluster uniformly. The FMT proves, there is no significant difference between industrial units in respect of cost like Production, Infrastructure, Technology, Marketing and Net Profit. To conclude, the Automotive Industries have fully utilized the Physical Infrastructure and Centralised Facilities by adopting CDA and now exporting their products to North America, South America, Europe, Australia, Africa and Asia. The value chain analysis models have been implemented in all the cluster units. This Cluster Development Approach (CDA) model can be implemented in industries of under developed and developing countries for cost reduction and productivity increase.

Quantitative and Qualitative Differences in Morphological Traits Revealed between Diploid Fragaria Species

PubMed Central

SARGENT, DANIEL J.; GEIBEL, M.; HAWKINS, J. A.; WILKINSON, M. J.; BATTEY, N. H.; SIMPSON, D. W.

2004-01-01

• Background and Aims The aims of this investigation were to highlight the qualitative and quantitative diversity apparent between nine diploid Fragaria species and produce interspecific populations segregating for a large number of morphological characters suitable for quantitative trait loci analysis. • Methods A qualitative comparison of eight described diploid Fragaria species was performed and measurements were taken of 23 morphological traits from 19 accessions including eight described species and one previously undescribed species. A principal components analysis was performed on 14 mathematically unrelated traits from these accessions, which partitioned the species accessions into distinct morphological groups. Interspecific crosses were performed with accessions of species that displayed significant quantitative divergence and, from these, populations that should segregate for a range of quantitative traits were raised. • Key Results Significant differences between species were observed for all 23 morphological traits quantified and three distinct groups of species accessions were observed after the principal components analysis. Interspecific crosses were performed between these groups, and F2 and backcross populations were raised that should segregate for a range of morphological characters. In addition, the study highlighted a number of distinctive morphological characters in many of the species studied. • Conclusions Diploid Fragaria species are morphologically diverse, yet remain highly interfertile, making the group an ideal model for the study of the genetic basis of phenotypic differences between species through map-based investigation using quantitative trait loci. The segregating interspecific populations raised will be ideal for such investigations and could also provide insights into the nature and extent of genome evolution within this group. PMID:15469944

Quantitation of influenza virus using field flow fractionation and multi-angle light scattering for quantifying influenza A particles

PubMed Central

Bousse, Tatiana; Shore, David A.; Goldsmith, Cynthia S.; Hossain, M. Jaber; Jang, Yunho; Davis, Charles T.; Donis, Ruben O.; Stevens, James

2017-01-01

Summary Recent advances in instrumentation and data analysis in field flow fractionation and multi-angle light scattering (FFF-MALS) have enabled greater use of this technique to characterize and quantitate viruses. In this study, the FFF-MALS technique was applied to the characterization and quantitation of type A influenza virus particles to assess its usefulness for vaccine preparation. The use of FFF-MALS for quantitation and measurement of control particles provided data accurate to within 5% of known values, reproducible with a coefficient of variation of 1.9 %. The methods, sensitivity and limit of detection were established by analyzing different volumes of purified virus, which produced a linear regression with fitting value R2 of 0.99. FFF-MALS was further applied to detect and quantitate influenza virus in the supernatant of infected MDCK cells and allantoic fluids of infected eggs. FFF fractograms of the virus present in these different fluids revealed similar distribution of monomeric and oligomeric virions. However, the monomer fraction of cell grown virus has greater size variety. Notably, β-propialactone (BPL) inactivation of influenza viruses did not influence any of the FFF-MALS measurements. Quantitation analysis by FFF-MALS was compared to infectivity assays and real-time RT-PCR (qRT-PCR) and the limitations of each assay were discussed. PMID:23916678

Single-Cell Based Quantitative Assay of Chromosome Transmission Fidelity

PubMed Central

Zhu, Jin; Heinecke, Dominic; Mulla, Wahid A.; Bradford, William D.; Rubinstein, Boris; Box, Andrew; Haug, Jeffrey S.; Li, Rong

2015-01-01

Errors in mitosis are a primary cause of chromosome instability (CIN), generating aneuploid progeny cells. Whereas a variety of factors can influence CIN, under most conditions mitotic errors are rare events that have been difficult to measure accurately. Here we report a green fluorescent protein−based quantitative chromosome transmission fidelity (qCTF) assay in budding yeast that allows sensitive and quantitative detection of CIN and can be easily adapted to high-throughput analysis. Using the qCTF assay, we performed genome-wide quantitative profiling of genes that affect CIN in a dosage-dependent manner and identified genes that elevate CIN when either increased (icCIN) or decreased in copy number (dcCIN). Unexpectedly, qCTF screening also revealed genes whose change in copy number quantitatively suppress CIN, suggesting that the basal error rate of the wild-type genome is not minimized, but rather, may have evolved toward an optimal level that balances both stability and low-level karyotype variation for evolutionary adaptation. PMID:25823586

Single-Cell Based Quantitative Assay of Chromosome Transmission Fidelity.

PubMed

Zhu, Jin; Heinecke, Dominic; Mulla, Wahid A; Bradford, William D; Rubinstein, Boris; Box, Andrew; Haug, Jeffrey S; Li, Rong

2015-03-30

Errors in mitosis are a primary cause of chromosome instability (CIN), generating aneuploid progeny cells. Whereas a variety of factors can influence CIN, under most conditions mitotic errors are rare events that have been difficult to measure accurately. Here we report a green fluorescent protein-based quantitative chromosome transmission fidelity (qCTF) assay in budding yeast that allows sensitive and quantitative detection of CIN and can be easily adapted to high-throughput analysis. Using the qCTF assay, we performed genome-wide quantitative profiling of genes that affect CIN in a dosage-dependent manner and identified genes that elevate CIN when either increased (icCIN) or decreased in copy number (dcCIN). Unexpectedly, qCTF screening also revealed genes whose change in copy number quantitatively suppress CIN, suggesting that the basal error rate of the wild-type genome is not minimized, but rather, may have evolved toward an optimal level that balances both stability and low-level karyotype variation for evolutionary adaptation. Copyright © 2015 Zhu et al.

Quantitative proteomic study of Aspergillus Fumigatus secretome revealed deamidation of secretory enzymes.

PubMed

Adav, Sunil S; Ravindran, Anita; Sze, Siu Kwan

2015-04-24

Aspergillus sp. plays an essential role in lignocellulosic biomass recycling and is also exploited as cell factories for the production of industrial enzymes. This study profiled the secretome of Aspergillus fumigatus when grown with cellulose, xylan and starch by high throughput quantitative proteomics using isobaric tags for relative and absolute quantification (iTRAQ). Post translational modifications (PTMs) of proteins play a critical role in protein functions. However, our understanding of the PTMs in secretory proteins is limited. Here, we present the identification of PTMs such as deamidation of secreted proteins of A. fumigatus. This study quantified diverse groups of extracellular secreted enzymes and their functional classification revealed cellulases and glycoside hydrolases (32.9%), amylases (0.9%), hemicellulases (16.2%), lignin degrading enzymes (8.1%), peptidases and proteases (11.7%), chitinases, lipases and phosphatases (7.6%), and proteins with unknown function (22.5%). The comparison of quantitative iTRAQ results revealed that cellulose and xylan stimulates expression of specific cellulases and hemicellulases, and their abundance level as a function of substrate. In-depth data analysis revealed deamidation as a major PTM of key cellulose hydrolyzing enzymes like endoglucanases, cellobiohydrolases and glucosidases. Hemicellulose degrading endo-1,4-beta-xylanase, monosidases, xylosidases, lignin degrading laccase, isoamyl alcohol oxidase and oxidoreductases were also found to be deamidated. The filamentous fungi play an essential role in lignocellulosic biomass recycling and fungal strains belonging to Aspergillus were also exploited as cell factories for the production of organic acids, pharmaceuticals, and industrially important enzymes. In this study, extracellular proteins secreted by thermophilic A. fumigatus when grown with cellulose, xylan and starch were profiled using isobaric tags for relative and absolute quantification (iTRAQ) by adopting liquid chromatography tandem mass spectrometry. The comparison of quantitative iTRAQ results revealed that cellulose and xylan stimulate expression of specific cellulases and hemicellulases, and expression level as a function of substrate. Post translational modifications revealed deamidation of key cellulases including endoglucanases, cellobiohydrolases and glucosidases; and hemicellulases and lignin degrading enzymes. The knowledge on deamidated enzymes along with specific sites of modifications could be crucial information for further functional studies of these enzymes of A. fumigatus. Copyright © 2015 Elsevier B.V. All rights reserved.

Combinatorial modification of human histone H4 quantitated by two-dimensional liquid chromatography coupled with top down mass spectrometry.

PubMed

Pesavento, James J; Bullock, Courtney R; LeDuc, Richard D; Mizzen, Craig A; Kelleher, Neil L

2008-05-30

Quantitative proteomics has focused heavily on correlating protein abundances, ratios, and dynamics by developing methods that are protein expression-centric (e.g. isotope coded affinity tag, isobaric tag for relative and absolute quantification, etc.). These methods effectively detect changes in protein abundance but fail to provide a comprehensive perspective of the diversity of proteins such as histones, which are regulated by post-translational modifications. Here, we report the characterization of modified forms of HeLa cell histone H4 with a dynamic range >10(4) using a strictly Top Down mass spectrometric approach coupled with two dimensions of liquid chromatography. This enhanced dynamic range enabled the precise characterization and quantitation of 42 forms uniquely modified by combinations of methylation and acetylation, including those with trimethylated Lys-20, monomethylated Arg-3, and the novel dimethylated Arg-3 (each <1% of all H4 forms). Quantitative analyses revealed distinct trends in acetylation site occupancy depending on Lys-20 methylation state. Because both modifications are dynamically regulated through the cell cycle, we simultaneously investigated acetylation and methylation kinetics through three cell cycle phases and used these data to statistically assess the robustness of our quantitative analysis. This work represents the most comprehensive analysis of histone H4 forms present in human cells reported to date.

Morphometric Analysis of Chemoreception Organ in Male and Female Ticks (Acari: Ixodidae).

PubMed

Josek, Tanya; Allan, Brian F; Alleyne, Marianne

2018-05-04

The Haller's organ plays a crucial role in a tick's ability to detect hosts. Even though this sensory organ is vital to tick survival, the morphology of this organ is not well understood. The objective of this study was to characterize variation in the morphological components of the Haller's organ of three medically important tick species using quantitative methods. The Haller's organs of Ixodes scapularis Say (Ixodida: Ixodidae) (black-legged tick), Amblyomma americanum (L.) (Ixodida: Ixodidae) (lone star tick), and Dermacentor variabilis (Say) (Ixodida: Ixodidae) (American dog tick) were morphologically analyzed using environmental scanning electron microscopy and geometric morphometrics, and the results were statistically interpreted using canonical variate analysis. Our data reveal significant, quantitative differences in the morphology of the Haller's organ among all three tick species and that in D. variabilis the sensory structure is sexually dimorphic. Studies like this can serve as a quantitative basis for further studies on sensor physiology, behavior, and tick species life history, potentially leading to novel methods for the prevention of tick-borne disease.

Variation in seed dormancy quantitative trait loci in Arabidopsis thaliana originating from one site.

PubMed

Silady, Rebecca A; Effgen, Sigi; Koornneef, Maarten; Reymond, Matthieu

2011-01-01

A Quantitative Trait Locus (QTL) analysis was performed using two novel Recombinant Inbred Line (RIL) populations, derived from the progeny between two Arabidopsis thaliana genotypes collected at the same site in Kyoto (Japan) crossed with the reference laboratory strain Landsberg erecta (Ler). We used these two RIL populations to determine the genetic basis of seed dormancy and flowering time, which are assumed to be the main traits controlling life history variation in Arabidopsis. The analysis revealed quantitative variation for seed dormancy that is associated with allelic variation at the seed dormancy QTL DOG1 (for Delay Of Germination 1) in one population and at DOG6 in both. These DOG QTL have been previously identified using mapping populations derived from accessions collected at different sites around the world. Genetic variation within a population may enhance its ability to respond accurately to variation within and between seasons. In contrast, variation for flowering time, which also segregated within each mapping population, is mainly governed by the same QTL.

X-ray vision of fuel sprays.

PubMed

Wang, Jin

2005-03-01

With brilliant synchrotron X-ray sources, microsecond time-resolved synchrotron X-ray radiography and tomography have been used to elucidate the detailed three-dimensional structure and dynamics of high-pressure high-speed fuel sprays in the near-nozzle region. The measurement allows quantitative determination of the fuel distribution in the optically impenetrable region owing to the multiple scattering of visible light by small atomized fuel droplets surrounding the jet. X-radiographs of the jet-induced shock waves prove that the fuel jets become supersonic under appropriate injection conditions and that the quantitative analysis of the thermodynamic properties of the shock waves can also be derived from the most direct measurement. In other situations where extremely axial-asymmetric sprays are encountered, mass deconvolution and cross-sectional fuel distribution models can be computed based on the monochromatic and time-resolved X-radiographic images collected from various rotational orientations of the sprays. Such quantitative analysis reveals the never-before-reported characteristics and most detailed near-nozzle mass distribution of highly transient fuel sprays.

Interrelation of structure and operational states in cascading failure of overloading lines in power grids

NASA Astrophysics Data System (ADS)

Xue, Fei; Bompard, Ettore; Huang, Tao; Jiang, Lin; Lu, Shaofeng; Zhu, Huaiying

2017-09-01

As the modern power system is expected to develop to a more intelligent and efficient version, i.e. the smart grid, or to be the central backbone of energy internet for free energy interactions, security concerns related to cascading failures have been raised with consideration of catastrophic results. The researches of topological analysis based on complex networks have made great contributions in revealing structural vulnerabilities of power grids including cascading failure analysis. However, existing literature with inappropriate assumptions in modeling still cannot distinguish the effects between the structure and operational state to give meaningful guidance for system operation. This paper is to reveal the interrelation between network structure and operational states in cascading failure and give quantitative evaluation by integrating both perspectives. For structure analysis, cascading paths will be identified by extended betweenness and quantitatively described by cascading drop and cascading gradient. Furthermore, the operational state for cascading paths will be described by loading level. Then, the risk of cascading failure along a specific cascading path can be quantitatively evaluated considering these two factors. The maximum cascading gradient of all possible cascading paths can be used as an overall metric to evaluate the entire power grid for its features related to cascading failure. The proposed method is tested and verified on IEEE30-bus system and IEEE118-bus system, simulation evidences presented in this paper suggests that the proposed model can identify the structural causes for cascading failure and is promising to give meaningful guidance for the protection of system operation in the future.

Quantitative analysis of 18F-NaF dynamic PET/CT cannot differentiate malignant from benign lesions in multiple myeloma

PubMed Central

Sachpekidis, Christos; Hillengass, Jens; Goldschmidt, Hartmut; Anwar, Hoda; Haberkorn, Uwe; Dimitrakopoulou-Strauss, Antonia

2017-01-01

A renewed interest has been recently developed for the highly sensitive bone-seeking radiopharmaceutical 18F-NaF. Aim of the present study is to evaluate the potential utility of quantitative analysis of 18F-NaF dynamic PET/CT data in differentiating malignant from benign degenerative lesions in multiple myeloma (MM). 80 MM patients underwent whole-body PET/CT and dynamic PET/CT scanning of the pelvis with 18F-NaF. PET/CT data evaluation was based on visual (qualitative) assessment, semi-quantitative (SUV) calculations, and absolute quantitative estimations after application of a 2-tissue compartment model and a non-compartmental approach leading to the extraction of fractal dimension (FD). In total 263 MM lesions were demonstrated on 18F-NaF PET/CT. Semi-quantitative and quantitative evaluations were performed for 25 MM lesions as well as for 25 benign, degenerative and traumatic lesions. Mean SUVaverage for MM lesions was 11.9 and mean SUVmax was 23.2. Respectively, SUVaverage and SUVmax for degenerative lesions were 13.5 and 20.2. Kinetic analysis of 18F-NaF revealed the following mean values for MM lesions: K1 = 0.248 (1/min), k3 = 0.359 (1/min), influx (Ki) = 0.107 (1/min), FD = 1.382, while the respective values for degenerative lesions were: K1 = 0.169 (1/min), k3 = 0.422 (1/min), influx (Ki) = 0.095 (1/min), FD = 1. 411. No statistically significant differences between MM and benign degenerative disease regarding SUVaverage, SUVmax, K1, k3 and influx (Ki) were demonstrated. FD was significantly higher in degenerative than in malignant lesions. The present findings show that quantitative analysis of 18F-NaF PET data cannot differentiate malignant from benign degenerative lesions in MM patients, supporting previously published results, which reflect the limited role of 18F-NaF PET/CT in the diagnostic workup of MM. PMID:28913153

UPLC-MS/MS quantitative analysis and structural fragmentation study of five Parmotrema lichens from the Eastern Ghats.

PubMed

Kumar, K; Siva, Bandi; Sarma, V U M; Mohabe, Satish; Reddy, A Madhusudana; Boustie, Joel; Tiwari, Ashok K; Rao, N Rama; Babu, K Suresh

2018-07-15

Comparative phytochemical analysis of five lichen species [Parmotrema tinctorum (Delise ex Nyl.) Hale, P. andinum (Mull. Arg.) Hale, P. praesorediosum (Nyl.) Hale, P. grayanum (Hue) Hale, P. austrosinense (Zahlbr.) Hale] of Parmotrema genus were performed using two complementary UPLC-MS systems. The first system consists of high resolution UPLC-QToF-MS/MS spectrometer and the second system consisted of UPLC-MS/MS in Multiple Reaction Monitoring (MRM) mode for quantitative analysis of major constituents in the selected lichen species. The individual compounds (47 compounds) were identified using Q-ToF-MS/MS, via comparison of the exact molecular masses from their MS/MS spectra, the comparison of literature data and retention times to those of standard compounds which were isolated from crude extract of abundant lichen, P. tinctorum. The analysis also allowed us to identify unknown peaks/compounds, which were further characterized by their mass fragmentation studies. The quantitative MRM analysis was useful to have a better discrimination of species according to their chemical profile. Moreover, the determination of antioxidant activities (ABTS + inhibition) and Advance Glycation Endproducts (AGEs) inhibition carried out for the crude extracts revealed a potential antiglycaemic activity to be confirmed for P. austrosinense. Copyright © 2018 Elsevier B.V. All rights reserved.

The effects of physical activity on impulsive choice: Influence of sensitivity to reinforcement amount and delay

PubMed Central

Strickland, Justin C.; Feinstein, Max A.; Lacy, Ryan T.; Smith, Mark A.

2016-01-01

Impulsive choice is a diagnostic feature and/or complicating factor for several psychological disorders and may be examined in the laboratory using delay-discounting procedures. Recent investigators have proposed using quantitative measures of analysis to examine the behavioral processes contributing to impulsive choice. The purpose of this study was to examine the effects of physical activity (i.e., wheel running) on impulsive choice in a single-response, discrete-trial procedure using two quantitative methods of analysis. To this end, rats were assigned to physical activity or sedentary groups and trained to respond in a delay-discounting procedure. In this procedure, one lever always produced one food pellet immediately, whereas a second lever produced three food pellets after a 0, 10, 20, 40, or 80-second delay. Estimates of sensitivity to reinforcement amount and sensitivity to reinforcement delay were determined using (1) a simple linear analysis and (2) an analysis of logarithmically transformed response ratios. Both analyses revealed that physical activity decreased sensitivity to reinforcement amount and sensitivity to reinforcement delay. These findings indicate that (1) physical activity has significant but functionally opposing effects on the behavioral processes that contribute to impulsive choice and (2) both quantitative methods of analysis are appropriate for use in single-response, discrete-trial procedures. PMID:26964905

Common and distinct neural correlates of personal and vicarious reward: A quantitative meta-analysis

PubMed Central

Morelli, Sylvia A.; Sacchet, Matthew D.; Zaki, Jamil

2015-01-01

Individuals experience reward not only when directly receiving positive outcomes (e.g., food or money), but also when observing others receive such outcomes. This latter phenomenon, known as vicarious reward, is a perennial topic of interest among psychologists and economists. More recently, neuroscientists have begun exploring the neuroanatomy underlying vicarious reward. Here we present a quantitative whole-brain meta-analysis of this emerging literature. We identified 25 functional neuroimaging studies that included contrasts between vicarious reward and a neutral control, and subjected these contrasts to an activation likelihood estimate (ALE) meta-analysis. This analysis revealed a consistent pattern of activation across studies, spanning structures typically associated with the computation of value (especially ventromedial prefrontal cortex) and mentalizing (including dorsomedial prefrontal cortex and superior temporal sulcus). We further quantitatively compared this activation pattern to activation foci from a previous meta-analysis of personal reward. Conjunction analyses yielded overlapping VMPFC activity in response to personal and vicarious reward. Contrast analyses identified preferential engagement of the nucleus accumbens in response to personal as compared to vicarious reward, and in mentalizing-related structures in response to vicarious as compared to personal reward. These data shed light on the common and unique components of the reward that individuals experience directly and through their social connections. PMID:25554428

Quantitative analysis of proteome extracted from barley crowns grown under different drought conditions

PubMed Central

Vítámvás, Pavel; Urban, Milan O.; Škodáček, Zbynek; Kosová, Klára; Pitelková, Iva; Vítámvás, Jan; Renaut, Jenny; Prášil, Ilja T.

2015-01-01

Barley cultivar Amulet was used to study the quantitative proteome changes through different drought conditions utilizing two-dimensional difference gel electrophoresis (2D-DIGE). Plants were cultivated for 10 days under different drought conditions. To obtain control and differentially drought-treated plants, the soil water content was kept at 65, 35, and 30% of soil water capacity (SWC), respectively. Osmotic potential, water saturation deficit, 13C discrimination, and dehydrin accumulation were monitored during sampling of the crowns for proteome analysis. Analysis of the 2D-DIGE gels revealed 105 differentially abundant spots; most were differentially abundant between the controls and drought-treated plants, and 25 spots displayed changes between both drought conditions. Seventy-six protein spots were successfully identified by tandem mass spectrometry. The most frequent functional categories of the identified proteins can be put into the groups of: stress-associated proteins, amino acid metabolism, carbohydrate metabolism, as well as DNA and RNA regulation and processing. Their possible role in the response of barley to drought stress is discussed. Our study has shown that under drought conditions barley cv. Amulet decreased its growth and developmental rates, displayed a shift from aerobic to anaerobic metabolism, and exhibited increased levels of several protective proteins. Comparison of the two drought treatments revealed plant acclimation to milder drought (35% SWC); but plant damage under more severe drought treatment (30% SWC). The results obtained revealed that cv. Amulet is sensitive to drought stress. Additionally, four spots revealing a continuous and significant increase with decreasing SWC (UDP-glucose 6-dehydrogenase, glutathione peroxidase, and two non-identified) could be good candidates for testing of their protein phenotyping capacity together with proteins that were significantly distinguished in both drought treatments. PMID:26175745

Quantitative workflow based on NN for weighting criteria in landfill suitability mapping

NASA Astrophysics Data System (ADS)

Abujayyab, Sohaib K. M.; Ahamad, Mohd Sanusi S.; Yahya, Ahmad Shukri; Ahmad, Siti Zubaidah; Alkhasawneh, Mutasem Sh.; Aziz, Hamidi Abdul

2017-10-01

Our study aims to introduce a new quantitative workflow that integrates neural networks (NNs) and multi criteria decision analysis (MCDA). Existing MCDA workflows reveal a number of drawbacks, because of the reliance on human knowledge in the weighting stage. Thus, new workflow presented to form suitability maps at the regional scale for solid waste planning based on NNs. A feed-forward neural network employed in the workflow. A total of 34 criteria were pre-processed to establish the input dataset for NN modelling. The final learned network used to acquire the weights of the criteria. Accuracies of 95.2% and 93.2% achieved for the training dataset and testing dataset, respectively. The workflow was found to be capable of reducing human interference to generate highly reliable maps. The proposed workflow reveals the applicability of NN in generating landfill suitability maps and the feasibility of integrating them with existing MCDA workflows.

[Applications of mathematical statistics methods on compatibility researches of traditional Chinese medicines formulae].

PubMed

Mai, Lan-Yin; Li, Yi-Xuan; Chen, Yong; Xie, Zhen; Li, Jie; Zhong, Ming-Yu

2014-05-01

The compatibility of traditional Chinese medicines (TCMs) formulae containing enormous information, is a complex component system. Applications of mathematical statistics methods on the compatibility researches of traditional Chinese medicines formulae have great significance for promoting the modernization of traditional Chinese medicines and improving clinical efficacies and optimizations of formulae. As a tool for quantitative analysis, data inference and exploring inherent rules of substances, the mathematical statistics method can be used to reveal the working mechanisms of the compatibility of traditional Chinese medicines formulae in qualitatively and quantitatively. By reviewing studies based on the applications of mathematical statistics methods, this paper were summarized from perspective of dosages optimization, efficacies and changes of chemical components as well as the rules of incompatibility and contraindication of formulae, will provide the references for further studying and revealing the working mechanisms and the connotations of traditional Chinese medicines.

Quantitative Proteomic Analysis Reveals That Anti-Cancer Effects of Selenium-Binding Protein 1 In Vivo Are Associated with Metabolic Pathways

PubMed Central

Ying, Qi; Ansong, Emmanuel; Diamond, Alan M.; Lu, Zhaoxin; Yang, Wancai; Bie, Xiaomei

2015-01-01

Previous studies have shown the tumor-suppressive role of selenium-binding protein 1 (SBP1), but the underlying mechanisms are unclear. In this study, we found that induction of SBP1 showed significant inhibition of colorectal cancer cell growth and metastasis in mice. We further employed isobaric tags for relative and absolute quantitation (iTRAQ) to identify proteins that were involved in SBP1-mediated anti-cancer effects in tumor tissues. We identified 132 differentially expressed proteins, among them, 53 proteins were upregulated and 79 proteins were downregulated. Importantly, many of the differentially altered proteins were associated with lipid/glucose metabolism, which were also linked to Glycolysis, MAPK, Wnt, NF-kB, NOTCH and epithelial-mesenchymal transition (EMT) signaling pathways. These results have revealed a novel mechanism that SBP1-mediated cancer inhibition is through altering lipid/glucose metabolic signaling pathways. PMID:25974208

Fusing Quantitative Requirements Analysis with Model-based Systems Engineering

NASA Technical Reports Server (NTRS)

Cornford, Steven L.; Feather, Martin S.; Heron, Vance A.; Jenkins, J. Steven

2006-01-01

A vision is presented for fusing quantitative requirements analysis with model-based systems engineering. This vision draws upon and combines emergent themes in the engineering milieu. "Requirements engineering" provides means to explicitly represent requirements (both functional and non-functional) as constraints and preferences on acceptable solutions, and emphasizes early-lifecycle review, analysis and verification of design and development plans. "Design by shopping" emphasizes revealing the space of options available from which to choose (without presuming that all selection criteria have previously been elicited), and provides means to make understandable the range of choices and their ramifications. "Model-based engineering" emphasizes the goal of utilizing a formal representation of all aspects of system design, from development through operations, and provides powerful tool suites that support the practical application of these principles. A first step prototype towards this vision is described, embodying the key capabilities. Illustrations, implications, further challenges and opportunities are outlined.

Clusters of Insomnia Disorder: An Exploratory Cluster Analysis of Objective Sleep Parameters Reveals Differences in Neurocognitive Functioning, Quantitative EEG, and Heart Rate Variability

PubMed Central

Miller, Christopher B.; Bartlett, Delwyn J.; Mullins, Anna E.; Dodds, Kirsty L.; Gordon, Christopher J.; Kyle, Simon D.; Kim, Jong Won; D'Rozario, Angela L.; Lee, Rico S.C.; Comas, Maria; Marshall, Nathaniel S.; Yee, Brendon J.; Espie, Colin A.; Grunstein, Ronald R.

2016-01-01

Study Objectives: To empirically derive and evaluate potential clusters of Insomnia Disorder through cluster analysis from polysomnography (PSG). We hypothesized that clusters would differ on neurocognitive performance, sleep-onset measures of quantitative (q)-EEG and heart rate variability (HRV). Methods: Research volunteers with Insomnia Disorder (DSM-5) completed a neurocognitive assessment and overnight PSG measures of total sleep time (TST), wake time after sleep onset (WASO), and sleep onset latency (SOL) were used to determine clusters. Results: From 96 volunteers with Insomnia Disorder, cluster analysis derived at least two clusters from objective sleep parameters: Insomnia with normal objective sleep duration (I-NSD: n = 53) and Insomnia with short sleep duration (I-SSD: n = 43). At sleep onset, differences in HRV between I-NSD and I-SSD clusters suggest attenuated parasympathetic activity in I-SSD (P < 0.05). Preliminary work suggested three clusters by retaining the I-NSD and splitting the I-SSD cluster into two: I-SSD A (n = 29): defined by high WASO and I-SSD B (n = 14): a second I-SSD cluster with high SOL and medium WASO. The I-SSD B cluster performed worse than I-SSD A and I-NSD for sustained attention (P ≤ 0.05). In an exploratory analysis, q-EEG revealed reduced spectral power also in I-SSD B before (Delta, Alpha, Beta-1) and after sleep-onset (Beta-2) compared to I-SSD A and I-NSD (P ≤ 0.05). Conclusions: Two insomnia clusters derived from cluster analysis differ in sleep onset HRV. Preliminary data suggest evidence for three clusters in insomnia with differences for sustained attention and sleep-onset q-EEG. Clinical Trial Registration: Insomnia 100 sleep study: Australia New Zealand Clinical Trials Registry (ANZCTR) identification number 12612000049875. URL: https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=347742. Citation: Miller CB, Bartlett DJ, Mullins AE, Dodds KL, Gordon CJ, Kyle SD, Kim JW, D'Rozario AL, Lee RS, Comas M, Marshall NS, Yee BJ, Espie CA, Grunstein RR. Clusters of Insomnia Disorder: an exploratory cluster analysis of objective sleep parameters reveals differences in neurocognitive functioning, quantitative EEG, and heart rate variability. SLEEP 2016;39(11):1993–2004. PMID:27568796

Study on Analysis of Variance on the indigenous wild and cultivated rice species of Manipur Valley

NASA Astrophysics Data System (ADS)

Medhabati, K.; Rohinikumar, M.; Rajiv Das, K.; Henary, Ch.; Dikash, Th.

2012-10-01

The analysis of variance revealed considerable variation among the cultivars and the wild species for yield and other quantitative characters in both the years of investigation. The highly significant differences among the cultivars in year wise and pooled analysis of variance for all the 12 characters reveal that there are enough genetic variabilities for all the characters studied. The existence of genetic variability is of paramount importance for starting a judicious plant breeding programme. Since introduced high yielding rice cultivars usually do not perform well. Improvement of indigenous cultivars is a clear choice for increase of rice production. The genetic variability of 37 rice germplasms in 12 agronomic characters estimated in the present study can be used in breeding programme

Transcriptome- Assisted Label-Free Quantitative Proteomics Analysis Reveals Novel Insights into Piper nigrum—Phytophthora capsici Phytopathosystem

PubMed Central

Mahadevan, Chidambareswaren; Krishnan, Anu; Saraswathy, Gayathri G.; Surendran, Arun; Jaleel, Abdul; Sakuntala, Manjula

2016-01-01

Black pepper (Piper nigrum L.), a tropical spice crop of global acclaim, is susceptible to Phytophthora capsici, an oomycete pathogen which causes the highly destructive foot rot disease. A systematic understanding of this phytopathosystem has not been possible owing to lack of genome or proteome information. In this study, we explain an integrated transcriptome-assisted label-free quantitative proteomics pipeline to study the basal immune components of black pepper when challenged with P. capsici. We report a global identification of 532 novel leaf proteins from black pepper, of which 518 proteins were functionally annotated using BLAST2GO tool. A label-free quantitation of the protein datasets revealed 194 proteins common to diseased and control protein datasets of which 22 proteins showed significant up-regulation and 134 showed significant down-regulation. Ninety-three proteins were identified exclusively on P. capsici infected leaf tissues and 245 were expressed only in mock (control) infected samples. In-depth analysis of our data gives novel insights into the regulatory pathways of black pepper which are compromised during the infection. Differential down-regulation was observed in a number of critical pathways like carbon fixation in photosynthetic organism, cyano-amino acid metabolism, fructose, and mannose metabolism, glutathione metabolism, and phenylpropanoid biosynthesis. The proteomics results were validated with real-time qRT-PCR analysis. We were also able to identify the complete coding sequences for all the proteins of which few selected genes were cloned and sequence characterized for further confirmation. Our study is the first report of a quantitative proteomics dataset in black pepper which provides convincing evidence on the effectiveness of a transcriptome-based label-free proteomics approach for elucidating the host response to biotic stress in a non-model spice crop like P. nigrum, for which genome information is unavailable. Our dataset will serve as a useful resource for future studies in this plant. Data are available via ProteomeXchange with identifier PXD003887. PMID:27379110

Transcriptome- Assisted Label-Free Quantitative Proteomics Analysis Reveals Novel Insights into Piper nigrum-Phytophthora capsici Phytopathosystem.

PubMed

Mahadevan, Chidambareswaren; Krishnan, Anu; Saraswathy, Gayathri G; Surendran, Arun; Jaleel, Abdul; Sakuntala, Manjula

2016-01-01

Black pepper (Piper nigrum L.), a tropical spice crop of global acclaim, is susceptible to Phytophthora capsici, an oomycete pathogen which causes the highly destructive foot rot disease. A systematic understanding of this phytopathosystem has not been possible owing to lack of genome or proteome information. In this study, we explain an integrated transcriptome-assisted label-free quantitative proteomics pipeline to study the basal immune components of black pepper when challenged with P. capsici. We report a global identification of 532 novel leaf proteins from black pepper, of which 518 proteins were functionally annotated using BLAST2GO tool. A label-free quantitation of the protein datasets revealed 194 proteins common to diseased and control protein datasets of which 22 proteins showed significant up-regulation and 134 showed significant down-regulation. Ninety-three proteins were identified exclusively on P. capsici infected leaf tissues and 245 were expressed only in mock (control) infected samples. In-depth analysis of our data gives novel insights into the regulatory pathways of black pepper which are compromised during the infection. Differential down-regulation was observed in a number of critical pathways like carbon fixation in photosynthetic organism, cyano-amino acid metabolism, fructose, and mannose metabolism, glutathione metabolism, and phenylpropanoid biosynthesis. The proteomics results were validated with real-time qRT-PCR analysis. We were also able to identify the complete coding sequences for all the proteins of which few selected genes were cloned and sequence characterized for further confirmation. Our study is the first report of a quantitative proteomics dataset in black pepper which provides convincing evidence on the effectiveness of a transcriptome-based label-free proteomics approach for elucidating the host response to biotic stress in a non-model spice crop like P. nigrum, for which genome information is unavailable. Our dataset will serve as a useful resource for future studies in this plant. Data are available via ProteomeXchange with identifier PXD003887.

Metaphors of Primary School Students Relating to the Concept of Global Warming

ERIC Educational Resources Information Center

Dogru, Mustafa; Sarac, Esra

2013-01-01

The purpose of this study is to reveal the metaphors of primary school students (n = 362) relating to the concept of global warming. Data collected by completing the expression of "global warming is like..., because..." of the students were analysed by use of qualitative and quantitative data analysis techniques. According to findings of…

In the Eye of the Beholder: Mothers' Perceptions of Poor Neighborhoods as Places to Raise Children

ERIC Educational Resources Information Center

Dahl, Trayci; Ceballo, Rosario; Huerta, Marisela

2010-01-01

This study explores how mothers facing similar neighborhood conditions evaluate their neighborhoods as places to raise children. The authors relied upon a triangulation of methods, using both quantitative and qualitative methodologies, with a sample of 91 low-income mothers. Content analysis of qualitative interviews revealed that mothers often…

How Are Notions of Childcare Similar or Different among American, Chinese, Japanese and Swedish Teachers?

ERIC Educational Resources Information Center

Izumi-Taylor, Satomi; Lee, Yu-Yuan; Franceschini, Louis

2011-01-01

The purpose of this study was to examine similarities and differences in the perceptions of childcare among American, Chinese, Japanese and Swedish early childhood teachers. Participants consisted of 78 American teachers, 156 Chinese teachers, 158 Japanese teachers, and 157 Swedish teachers. The results of quantitative analysis revealed that these…

Conjunct Use in Business News Stories and Academic Journal Articles: A Comparative Study.

ERIC Educational Resources Information Center

Morrow, Phillip R.

1989-01-01

A quantitative analysis of the use of conjuncts in two genres of written English, business news stories and academic journal articles, revealed a much higher frequency of conjunct use in the journal articles. A brief discussion focuses on the pedagogical implications of this study, and suggestions for further research are presented. (26…

MAPPING TOXICANT-INDUCED NERVOUS SYSTEM DAMAGE WITH A CUPRIC SILVER STAIN: A QUANTITATIVE ANALYSIS OF NEURAL DEGENERATION INDUCED BY 3,4-METHYLENEDIOXYMETHAMPETHAMINE (MDMA)

EPA Science Inventory

The purpose of structural assessments in neurotoxicology is to provide a convincing picture of the location and extent of damage to the nervous system. ilver stains that selectively reveal neural degeneration hold particular promise in this regard. n this chapter we describe resu...

Investigating Early Childhood Teachers' Understandings of and Practices in Education for Sustainability in Queensland: A Japan-Australia Research Collaboration

ERIC Educational Resources Information Center

Inoue, Michiko; O'Gorman, Lyndal; Davis, Julie

2016-01-01

In a study undertaken in Queensland, Australia, analysis of a survey that included both qualitative and quantitative questions revealed that, like their Japanese counterparts, early childhood teachers do not have well-developed ideas and practices in education for sustainability (EfS). Instead, they mainly practise traditional nature-based…

Strategies for Effecting System-Wide Pedagogical Change: Identifying and Addressing the Gap between Organizational and Pedagogical Implementation

ERIC Educational Resources Information Center

Weinberger, Yehudith

2018-01-01

The study described here analyses a faculty-wide change designed to foster the communication proficiencies of students in a large teacher education college, gathering data from various sources over three years of the new agenda's implementation. Qualitative and quantitative data analysis revealed that implementation was progressing on two distinct…

Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq

PubMed Central

Shepard, Peter J.; Choi, Eun-A; Lu, Jente; Flanagan, Lisa A.; Hertel, Klemens J.; Shi, Yongsheng

2011-01-01

Alternative polyadenylation (APA) of mRNAs has emerged as an important mechanism for post-transcriptional gene regulation in higher eukaryotes. Although microarrays have recently been used to characterize APA globally, they have a number of serious limitations that prevents comprehensive and highly quantitative analysis. To better characterize APA and its regulation, we have developed a deep sequencing-based method called Poly(A) Site Sequencing (PAS-Seq) for quantitatively profiling RNA polyadenylation at the transcriptome level. PAS-Seq not only accurately and comprehensively identifies poly(A) junctions in mRNAs and noncoding RNAs, but also provides quantitative information on the relative abundance of polyadenylated RNAs. PAS-Seq analyses of human and mouse transcriptomes showed that 40%–50% of all expressed genes produce alternatively polyadenylated mRNAs. Furthermore, our study detected evolutionarily conserved polyadenylation of histone mRNAs and revealed novel features of mitochondrial RNA polyadenylation. Finally, PAS-Seq analyses of mouse embryonic stem (ES) cells, neural stem/progenitor (NSP) cells, and neurons not only identified more poly(A) sites than what was found in the entire mouse EST database, but also detected significant changes in the global APA profile that lead to lengthening of 3′ untranslated regions (UTR) in many mRNAs during stem cell differentiation. Together, our PAS-Seq analyses revealed a complex landscape of RNA polyadenylation in mammalian cells and the dynamic regulation of APA during stem cell differentiation. PMID:21343387

Quantitative filter forensics for indoor particle sampling.

PubMed

Haaland, D; Siegel, J A

2017-03-01

Filter forensics is a promising indoor air investigation technique involving the analysis of dust which has collected on filters in central forced-air heating, ventilation, and air conditioning (HVAC) or portable systems to determine the presence of indoor particle-bound contaminants. In this study, we summarize past filter forensics research to explore what it reveals about the sampling technique and the indoor environment. There are 60 investigations in the literature that have used this sampling technique for a variety of biotic and abiotic contaminants. Many studies identified differences between contaminant concentrations in different buildings using this technique. Based on this literature review, we identified a lack of quantification as a gap in the past literature. Accordingly, we propose an approach to quantitatively link contaminants extracted from HVAC filter dust to time-averaged integrated air concentrations. This quantitative filter forensics approach has great potential to measure indoor air concentrations of a wide variety of particle-bound contaminants. Future studies directly comparing quantitative filter forensics to alternative sampling techniques are required to fully assess this approach, but analysis of past research suggests the enormous possibility of this approach. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

3D/4D multiscale imaging in acute lymphoblastic leukemia cells: visualizing dynamics of cell death

NASA Astrophysics Data System (ADS)

Sarangapani, Sreelatha; Mohan, Rosmin Elsa; Patil, Ajeetkumar; Lang, Matthew J.; Asundi, Anand

2017-06-01

Quantitative phase detection is a new methodology that provides quantitative information on cellular morphology to monitor the cell status, drug response and toxicity. In this paper the morphological changes in acute leukemia cells treated with chitosan were detected using d'Bioimager a robust imaging system. Quantitative phase image of the cells was obtained with numerical analysis. Results show that the average area and optical volume of the chitosan treated cells is significantly reduced when compared with the control cells, which reveals the effect of chitosan on the cancer cells. From the results it can be attributed that d'Bioimager can be used as a non-invasive imaging alternative to measure the morphological changes of the living cells in real time.

Quantitative functional characterization of conserved molecular interactions in the active site of mannitol 2-dehydrogenase

PubMed Central

Lucas, James E; Siegel, Justin B

2015-01-01

Enzyme active site residues are often highly conserved, indicating a significant role in function. In this study we quantitate the functional contribution for all conserved molecular interactions occurring within a Michaelis complex for mannitol 2-dehydrogenase derived from Pseudomonas fluorescens (pfMDH). Through systematic mutagenesis of active site residues, we reveal that the molecular interactions in pfMDH mediated by highly conserved residues not directly involved in reaction chemistry can be as important to catalysis as those directly involved in the reaction chemistry. This quantitative analysis of the molecular interactions within the pfMDH active site provides direct insight into the functional role of each molecular interaction, several of which were unexpected based on canonical sequence conservation and structural analyses. PMID:25752240

Quantitative genetic analysis of brain copper and zinc in BXD recombinant inbred mice.

PubMed

Jones, Leslie C; McCarthy, Kristin A; Beard, John L; Keen, Carl L; Jones, Byron C

2006-01-01

Copper and zinc are trace nutrients essential for normal brain function, yet an excess of these elements can be toxic. It is important therefore that these metals be closely regulated. We recently conducted a quantitative trait loci (QTL) analysis to identify chromosomal regions in the mouse containing possible regulatory genes. The animals came from 15 strains of the BXD/Ty recombinant inbred (RI) strain panel and the brain regions analyzed were frontal cortex, caudate-putamen, nucleus accumbens and ventral midbrain. Several QTL were identified for copper and/or zinc, most notably on chromosomes 1, 8, 16 and 17. Genetic correlational analysis also revealed associations between these metals and dopamine, cocaine responses, saccharine preference, immune response and seizure susceptibility. Notably, the QTL on chromosome 17 is also associated with seizure susceptibility and contains the histocompatibility H2 complex. This work shows that regulation of zinc and copper is under polygenic influence and is intimately related to CNS function. Future work will reveal genes underlying the QTL and how they interact with other genes and the environment. More importantly, revelation of the genetic underpinnings of copper and zinc brain homeostasis will aid our understanding of neurological diseases that are related to copper and zinc imbalance.

Expression quantitative trait loci and genetic regulatory network analysis reveals that Gabra2 is involved in stress responses in the mouse.

PubMed

Dai, Jiajuan; Wang, Xusheng; Chen, Ying; Wang, Xiaodong; Zhu, Jun; Lu, Lu

2009-11-01

Previous studies have revealed that the subunit alpha 2 (Gabra2) of the gamma-aminobutyric acid receptor plays a critical role in the stress response. However, little is known about the gentetic regulatory network for Gabra2 and the stress response. We combined gene expression microarray analysis and quantitative trait loci (QTL) mapping to characterize the genetic regulatory network for Gabra2 expression in the hippocampus of BXD recombinant inbred (RI) mice. Our analysis found that the expression level of Gabra2 exhibited much variation in the hippocampus across the BXD RI strains and between the parental strains, C57BL/6J, and DBA/2J. Expression QTL (eQTL) mapping showed three microarray probe sets of Gabra2 to have highly significant linkage likelihood ratio statistic (LRS) scores. Gene co-regulatory network analysis showed that 10 genes, including Gria3, Chka, Drd3, Homer1, Grik2, Odz4, Prkag2, Grm5, Gabrb1, and Nlgn1 are directly or indirectly associated with stress responses. Eleven genes were implicated as Gabra2 downstream genes through mapping joint modulation. The genetical genomics approach demonstrates the importance and the potential power of the eQTL studies in identifying genetic regulatory networks that contribute to complex traits, such as stress responses.

Proteome Analysis Using Isobaric Tags for Relative and Absolute Analysis Quantitation (iTRAQ) Reveals Alterations in Stress-Induced Dysfunctional Chicken Muscle.

PubMed

Xing, Tong; Wang, Chong; Zhao, Xue; Dai, Chen; Zhou, Guanghong; Xu, Xinglian

2017-04-05

The current study was designed to investigate changes in the protein profiles of pale, soft, and exudative (PSE)-like muscles of broilers subjected to transportation under high-temperature conditions, using isobaric tags for relative and absolute analysis quantitation (iTRAQ). Arbor Acres chickens (n = 112) were randomly divided into two treatments: unstressed control (CON) and 0.5 h of transport (T). Birds were transported according to a designed protocol. Pectoralis major (PM) muscle samples in the T group were collected and classified as normal (T-NOR) or PSE-like (T-PSE). Plasma activities of stress indicators, muscle microstructure, and proteome were measured. Results indicated that broilers in the T-PSE group exhibited higher activities of plasma stress indicators. The microstructure of T-PSE group showed a looser network and larger intercellular spaces in comparison to the other groups. Proteomic analysis, based on iTRAQ, revealed 29 differentially expressed proteins in the T-NOR and T-PSE groups that were involved in protein turnover, signal transduction, stress and defense, calcium handling, cell structure, and metabolism. In particular, proteins relating to the glycolysis pathway, calcium signaling, and molecular chaperones exhibited significant differences that may contribute to the inferior post-mortem meat quality. Overall, the proteomic results provide a further understanding of the mechanism of meat quality changes in response to stress.

SCOPA and META-SCOPA: software for the analysis and aggregation of genome-wide association studies of multiple correlated phenotypes.

PubMed

Mägi, Reedik; Suleimanov, Yury V; Clarke, Geraldine M; Kaakinen, Marika; Fischer, Krista; Prokopenko, Inga; Morris, Andrew P

2017-01-11

Genome-wide association studies (GWAS) of single nucleotide polymorphisms (SNPs) have been successful in identifying loci contributing genetic effects to a wide range of complex human diseases and quantitative traits. The traditional approach to GWAS analysis is to consider each phenotype separately, despite the fact that many diseases and quantitative traits are correlated with each other, and often measured in the same sample of individuals. Multivariate analyses of correlated phenotypes have been demonstrated, by simulation, to increase power to detect association with SNPs, and thus may enable improved detection of novel loci contributing to diseases and quantitative traits. We have developed the SCOPA software to enable GWAS analysis of multiple correlated phenotypes. The software implements "reverse regression" methodology, which treats the genotype of an individual at a SNP as the outcome and the phenotypes as predictors in a general linear model. SCOPA can be applied to quantitative traits and categorical phenotypes, and can accommodate imputed genotypes under a dosage model. The accompanying META-SCOPA software enables meta-analysis of association summary statistics from SCOPA across GWAS. Application of SCOPA to two GWAS of high-and low-density lipoprotein cholesterol, triglycerides and body mass index, and subsequent meta-analysis with META-SCOPA, highlighted stronger association signals than univariate phenotype analysis at established lipid and obesity loci. The META-SCOPA meta-analysis also revealed a novel signal of association at genome-wide significance for triglycerides mapping to GPC5 (lead SNP rs71427535, p = 1.1x10 -8 ), which has not been reported in previous large-scale GWAS of lipid traits. The SCOPA and META-SCOPA software enable discovery and dissection of multiple phenotype association signals through implementation of a powerful reverse regression approach.

New features of global climatology revealed by satellite-derived oceanic rainfall maps

NASA Technical Reports Server (NTRS)

Rao, M. S. V.; Theon, J. S.

1977-01-01

Quantitative rainfall maps over the oceanic areas of the globe were derived from the Nimbus 5 Electrically Scanning Microwave Radiometer (ESMR) data. Analysis of satellite derived oceanic rainfall maps reveal certain distinctive characteristics of global patterns for the years 1973-74. The main ones are (1) the forking of the Intertropical Convergence Zone in the Pacific, (2) a previously unrecognized rain area in the South Atlantic, (3) the bimodal behavior of rainbelts in the Indian Ocean and (4) the large interannual variability in oceanic rainfall. These features are discussed.

Image-guided convection-enhanced delivery of muscimol to the primate brain

PubMed Central

Heiss, John D.; Walbridge, Stuart; Asthagiri, Ashok R.; Lonser, Russell R.

2009-01-01

Object Muscimol is a potent γ-aminobutyric acid-A receptor agonist (GABAA) that temporarily and selectively suppresses neurons. Targeted muscimol-suppression of neuronal structures could provide insight into the pathophysiology and treatment of a variety of neurologic disorders. To determine if muscimol delivered to the brain by convection-enhanced delivery (CED) could be monitored using a co-infused surrogate magnetic resonance (MR)-imaging tracer, we perfused the striata of primates with tritiated muscimol and gadolinium-DTPA. Methods Three primates underwent convective co-infusion of 3H-muscimol (0.8 μM) and gadolinium-DTPA (−5 mM) into the bilateral striata. Primates underwent serial MR-imaging during infusion and animals were sacrificed immediately after infusion. Post-mortem quantitative autoradiography and histological analysis was performed. Results MR-imaging revealed that infusate (tritiated muscimol and gadolinium-DTPA) distribution was clearly discernible from the non-infused parenchyma. Real-time MR-imaging of the infusion revealed the precise region of anatomic perfusion in each animal. Imaging analysis during infusion revealed that the distribution volume of infusate linearly increased (R=0.92) with volume of infusion. Overall, the mean (±S.D.) volume of distribution to volume of infusion ratio was 8.2±1.3. Autoradiographic analysis revealed that MR-imaging of gadolinium-DTPA closely correlated with the distribution of 3H-muscimol and precisely estimated its volume of distribution (mean difference in volume of distribution, 7.4%). Quantitative autoradiograms revealed that muscimol was homogeneously distributed over the perfused region in a square-shaped concentration profile. Conclusions Muscimol can be effectively delivered to clinically relevant volumes of the primate brain. Moreover, the distribution of muscimol can be tracked by co-infusion of gadolinium-DTPA using MR-imaging. The ability to accurately monitor and control the anatomic extent of muscimol distribution during its convection-enhanced delivery will enhance safety, permit correlations of muscimol distribution with clinical effect, and should lead to an improved understanding of the pathophysiologic processes underlying a variety of neurologic disorders. PMID:19715424

Quantitation of flavonoid constituents in citrus fruits.

PubMed

Kawaii, S; Tomono, Y; Katase, E; Ogawa, K; Yano, M

1999-09-01

Twenty-four flavonoids have been determined in 66 Citrus species and near-citrus relatives, grown in the same field and year, by means of reversed phase high-performance liquid chromatography analysis. Statistical methods have been applied to find relations among the species. The F ratios of 21 flavonoids obtained by applying ANOVA analysis are significant, indicating that a classification of the species using these variables is reasonable to pursue. Principal component analysis revealed that the distributions of Citrus species belonging to different classes were largely in accordance with Tanaka's classification system.

Quantitative Proteomics Analysis of Streptomyces coelicolor Development Demonstrates That Onset of Secondary Metabolism Coincides with Hypha Differentiation*

PubMed Central

Manteca, Angel; Sanchez, Jesus; Jung, Hye R.; Schwämmle, Veit; Jensen, Ole N.

2010-01-01

Streptomyces species produce many clinically important secondary metabolites, including antibiotics and antitumorals. They have a complex developmental cycle, including programmed cell death phenomena, that makes this bacterium a multicellular prokaryotic model. There are two differentiated mycelial stages: an early compartmentalized vegetative mycelium (first mycelium) and a multinucleated reproductive mycelium (second mycelium) arising after programmed cell death processes. In the present study, we made a detailed proteomics analysis of the distinct developmental stages of solid confluent Streptomyces coelicolor cultures using iTRAQ (isobaric tags for relative and absolute quantitation) labeling and LC-MS/MS. A new experimental approach was developed to obtain homogeneous samples at each developmental stage (temporal protein analysis) and also to obtain membrane and cytosolic protein fractions (spatial protein analysis). A total of 345 proteins were quantified in two biological replicates. Comparative bioinformatics analyses revealed the switch from primary to secondary metabolism between the initial compartmentalized mycelium and the multinucleated hyphae. PMID:20224110

'Ogura'-based 'CMS' lines with different nuclear backgrounds of cabbage revealed substantial diversity at morphological and molecular levels.

PubMed

Parkash, Chander; Kumar, Sandeep; Singh, Rajender; Kumar, Ajay; Kumar, Satish; Dey, Shyam Sundar; Bhatia, Reeta; Kumar, Raj

2018-01-01

A comprehensive study on characterization and genetic diversity analysis was carried out in 16 'Ogura'-based 'CMS' lines of cabbage using 14 agro-morphological traits and 29 SSR markers. Agro-morphological characterization depicted considerable variations for different horticultural traits studied. The genotype, ZHA-2, performed better for most of the economically important quantitative traits. Further, gross head weight (0.76), head length (0.60) and head width (0.83) revealed significant positive correlation with net head weight. Dendrogram based on 10 quantitative traits exhibited considerable diversity among different CMS lines and principle component analysis (PCA) indicated that net and gross head weight, and head length and width are the main components of divergence between 16 CMS lines of cabbage. In molecular study, a total of 58 alleles were amplified by 29 SSR primers, averaging to 2.0 alleles in each locus. High mean values of Shannon's Information index (0.62), expected (0.45) and observed (0.32) heterozygosity and polymorphic information content (0.35) depicted substantial polymorphism. Dendrogram based on Jaccard's similarity coefficient constructed two major groups and eight sub-groups, which revealed substantial diversity among different CMS lines. In overall, based on agro-morphological and molecular studies genotype RRMA, ZHA-2 and RCA were found most divergent. Hence, they have immense potential in future breeding programs for the high-yielding hybrid development in cabbage.

The Effect of Concept Mapping on Student Understanding and Correlation with Student Learning Styles

NASA Astrophysics Data System (ADS)

Mosley, William G.

This study investigated the use of concept mapping as a pedagogical strategy to promote change in the learning styles of pre-nursing students. Students' individual learning styles revealed two subsets of students; those who demonstrated a learning style that favors abstract conceptualization and those who demonstrated a learning style that favors concrete experience. Students in the experimental groups performed concept mapping activities designed to facilitate an integrative understanding of interactions between various organ systems of the body while the control group received a traditional didactic instruction without performing concept mapping activities. Both qualitative and quantitative data were collected in order to measure differences in student achievement. Analysis of the quantitative data revealed no significant change in the learning styles of students in either the control or experimental groups. Learning style groups were analyzed qualitatively for recurring or emergent themes that students identified as facilitating their learning. An analysis of qualitative data revealed that most students in the pre-nursing program were able to identify concepts within the class based upon visual cues, and a majority of these students exhibited the learning style of abstract conceptualization. As the laboratory experience for the course involves an examination of the anatomical structures of the human body, a visual identification of these structures seemed to be the most logical method to measure students' ability to identify anatomical structures.

Quantitative evaluation of contrast-enhanced ultrasound after intravenous administration of a microbubble contrast agent for differentiation of benign and malignant thyroid nodules: assessment of diagnostic accuracy.

PubMed

Nemec, Ursula; Nemec, Stefan F; Novotny, Clemens; Weber, Michael; Czerny, Christian; Krestan, Christian R

2012-06-01

To investigate the diagnostic accuracy, through quantitative analysis, of contrast-enhanced ultrasound (CEUS), using a microbubble contrast agent, in the differentiation of thyroid nodules. This prospective study enrolled 46 patients with solitary, scintigraphically non-functional thyroid nodules. These patients were scheduled for surgery and underwent preoperative CEUS with pulse-inversion harmonic imaging after intravenous microbubble contrast medium administration. Using histology as a standard of reference, time-intensity curves of benign and malignant nodules were compared by means of peak enhancement and wash-out enhancement relative to the baseline intensity using a mixed model ANOVA. ROC analysis was performed to assess the diagnostic accuracy in the differentiation of benign and malignant nodules on CEUS. The complete CEUS data of 42 patients (31/42 [73.8%] benign and 11/42 [26.2%] malignant nodules) revealed a significant difference (P < 0.001) in enhancement between benign and malignant nodules. Furthermore, based on ROC analysis, CEUS demonstrated sensitivity of 76.9%, specificity of 84.8% and accuracy of 82.6%. Quantitative analysis of CEUS using a microbubble contrast agent allows the differentiation of benign and malignant thyroid nodules and may potentially serve, in addition to grey-scale and Doppler ultrasound, as an adjunctive tool in the assessment of patients with thyroid nodules. • Contrast-enhanced ultrasound (CEUS) helps differentiate between benign and malignant thyroid nodules. • Quantitative CEUS analysis yields sensitivity of 76.9% and specificity of 84.8%. • CEUS may be a potentially useful adjunct in assessing thyroid nodules.

Influence of sample preparation and reliability of automated numerical refocusing in stain-free analysis of dissected tissues with quantitative phase digital holographic microscopy

NASA Astrophysics Data System (ADS)

Kemper, Björn; Lenz, Philipp; Bettenworth, Dominik; Krausewitz, Philipp; Domagk, Dirk; Ketelhut, Steffi

2015-05-01

Digital holographic microscopy (DHM) has been demonstrated to be a versatile tool for high resolution non-destructive quantitative phase imaging of surfaces and multi-modal minimally-invasive monitoring of living cell cultures in-vitro. DHM provides quantitative monitoring of physiological processes through functional imaging and structural analysis which, for example, gives new insight into signalling of cellular water permeability and cell morphology changes due to toxins and infections. Also the analysis of dissected tissues quantitative DHM phase contrast prospects application fields by stain-free imaging and the quantification of tissue density changes. We show that DHM allows imaging of different tissue layers with high contrast in unstained tissue sections. As the investigation of fixed samples represents a very important application field in pathology, we also analyzed the influence of the sample preparation. The retrieved data demonstrate that the quality of quantitative DHM phase images of dissected tissues depends strongly on the fixing method and common staining agents. As in DHM the reconstruction is performed numerically, multi-focus imaging is achieved from a single digital hologram. Thus, we evaluated the automated refocussing feature of DHM for application on different types of dissected tissues and revealed that on moderately stained samples highly reproducible holographic autofocussing can be achieved. Finally, it is demonstrated that alterations of the spatial refractive index distribution in murine and human tissue samples represent a reliable absolute parameter that is related of different degrees of inflammation in experimental colitis and Crohn's disease. This paves the way towards the usage of DHM in digital pathology for automated histological examinations and further studies to elucidate the translational potential of quantitative phase microscopy for the clinical management of patients, e.g., with inflammatory bowel disease.

A Quantitative Analysis of Latino Acculturation and Alcohol Use: Myth Versus Reality.

PubMed

Alvarez, Miriam J; Frietze, Gabriel; Ramos, Corin; Field, Craig; Zárate, Michael A

2017-07-01

Research on health among Latinos often focuses on acculturation processes and the associated stressors that influence drinking behavior. Given the common use of acculturation measures and the state of the knowledge on alcohol-related health among Latino populations, the current analyses tested the efficacy of acculturation measures to predict various indicators of alcohol consumption. Specifically, this quantitative review assessed the predictive utility of acculturation on alcohol consumption behaviors (frequency, volume, and quantity). Two main analyses were conducted-a p-curve analysis and a meta-analysis of the observed associations between acculturation and drinking behavior. Results demonstrated that current measures of acculturation are a statistically significant predictor of alcohol use (Z = -20.75, p < 0.0001). The meta-analysis included a cumulative sample size of 29,589 Latino participants across 31 studies. A random-effects model yielded a weighted average correlation of 0.16 (95% confidence interval = 0.12, 0.19). Additional subgroup analyses examined the effects of gender and using different scales to measure acculturation. Altogether, results demonstrated that acculturation is a useful predictor of alcohol use. In addition, the meta-analysis revealed that a small positive correlation exists between acculturation and alcohol use in Latinos with a between-study variance of only 1.5% (τ 2  = 0.015). Our analyses reveal that the association between current measures of acculturation and alcohol use is relatively small. Copyright © 2017 by the Research Society on Alcoholism.

Quantitative and Qualitative Analysis of Bacteria in Er(III) Solution by Thin-Film Magnetopheresis

PubMed Central

Zborowski, Maciej; Tada, Yoko; Malchesky, Paul S.; Hall, Geraldine S.

1993-01-01

Magnetic deposition, quantitation, and identification of bacteria reacting with the paramagnetic trivalent lanthanide ion, Er3+, was evaluated. The magnetic deposition method was dubbed thin-film magnetopheresis. The optimization of the magnetic deposition protocol was accomplished with Escherichia coli as a model organism in 150 mM NaCl and 5 mM ErCl3 solution. Three gram-positive bacteria, Staphylococcus epidermidis, Staphylococcus saprophyticus, and Enterococcus faecalis, and four gram-negative bacteria, E. coli, Pseudomonas aeruginosa, Proteus mirabilis, and Klebsiella pneumoniae, were subsequently investigated. Quantitative analysis consisted of the microscopic cell count and a scattered-light scanning of the magnetically deposited material aided by the computer data acquisition system. Qualitative analysis consisted of Gram stain differentiation and fluorescein isothiocyanate staining in combination with selected antisera against specific types of bacteria on the solid substrate. The magnetic deposition protocol allowed quantitative detection of E. coli down to the concentration of 105 CFU ml-1, significant in clinical diagnosis applications such as urinary tract infections. Er3+ did not interfere with the typical appearance of the Gram-stained bacteria nor with the antigen recognition by the antibody in the immunohistological evaluations. Indirect antiserum-fluorescein isothiocyanate labelling correctly revealed the presence of E. faecalis and P. aeruginosa in the magnetically deposited material obtained from the mixture of these two bacterial species. On average, the reaction of gram-positive organisms was significantly stronger to the magnetic field in the presence of Er3+ than the reaction of gram-negative organisms. The thin-film magnetophoresis offers promise as a rapid method for quantitative and qualitative analysis of bacteria in solutions such as urine or environmental water. Images PMID:16348916

Comparison of longitudinal excursion of a nerve-phantom model using quantitative ultrasound imaging and motion analysis system methods: A convergent validity study.

PubMed

Paquette, Philippe; El Khamlichi, Youssef; Lamontagne, Martin; Higgins, Johanne; Gagnon, Dany H

2017-08-01

Quantitative ultrasound imaging is gaining popularity in research and clinical settings to measure the neuromechanical properties of the peripheral nerves such as their capability to glide in response to body segment movement. Increasing evidence suggests that impaired median nerve longitudinal excursion is associated with carpal tunnel syndrome. To date, psychometric properties of longitudinal nerve excursion measurements using quantitative ultrasound imaging have not been extensively investigated. This study investigates the convergent validity of the longitudinal nerve excursion by comparing measures obtained using quantitative ultrasound imaging with those determined with a motion analysis system. A 38-cm long rigid nerve-phantom model was used to assess the longitudinal excursion in a laboratory environment. The nerve-phantom model, immersed in a 20-cm deep container filled with a gelatin-based solution, was moved 20 times using a linear forward and backward motion. Three light-emitting diodes were used to record nerve-phantom excursion with a motion analysis system, while a 5-cm linear transducer allowed simultaneous recording via ultrasound imaging. Both measurement techniques yielded excellent association ( r  = 0.99) and agreement (mean absolute difference between methods = 0.85 mm; mean relative difference between methods = 7.48 %). Small discrepancies were largely found when larger excursions (i.e. > 10 mm) were performed, revealing slight underestimation of the excursion by the ultrasound imaging analysis software. Quantitative ultrasound imaging is an accurate method to assess the longitudinal excursion of an in vitro nerve-phantom model and appears relevant for future research protocols investigating the neuromechanical properties of the peripheral nerves.

A comparative analysis of human plasma and serum proteins by combining native PAGE, whole-gel slicing and quantitative LC-MS/MS: Utilizing native MS-electropherograms in proteomic analysis for discovering structure and interaction-correlated differences.

PubMed

Wen, Meiling; Jin, Ya; Manabe, Takashi; Chen, Shumin; Tan, Wen

2017-12-01

MS identification has long been used for PAGE-separated protein bands, but global and systematic quantitation utilizing MS after PAGE has remained rare and not been reported for native PAGE. Here we reported on a new method combining native PAGE, whole-gel slicing and quantitative LC-MS/MS, aiming at comparative analysis on not only abundance, but also structures and interactions of proteins. A pair of human plasma and serum samples were used as test samples and separated on a native PAGE gel. Six lanes of each sample were cut, each lane was further sliced into thirty-five 1.1 mm × 1.1 mm squares and all the squares were subjected to standardized procedures of in-gel digestion and quantitative LC-MS/MS. The results comprised 958 data rows that each contained abundance values of a protein detected in one square in eleven gel lanes (one plasma lane excluded). The data were evaluated to have satisfactory reproducibility of assignment and quantitation. Totally 315 proteins were assigned, with each protein assigned in 1-28 squares. The abundance distributions in the plasma and serum gel lanes were reconstructed for each protein, named as "native MS-electropherograms". Comparison of the electropherograms revealed significant plasma-versus-serum differences on 33 proteins in 87 squares (fold difference > 2 or < 0.5, p < 0.05). Many of the differences matched with accumulated knowledge on protein interactions and proteolysis involved in blood coagulation, complement and wound healing processes. We expect this method would be useful to provide more comprehensive information in comparative proteomic analysis, on both quantities and structures/interactions. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Sample normalization methods in quantitative metabolomics.

PubMed

Wu, Yiman; Li, Liang

2016-01-22

To reveal metabolomic changes caused by a biological event in quantitative metabolomics, it is critical to use an analytical tool that can perform accurate and precise quantification to examine the true concentration differences of individual metabolites found in different samples. A number of steps are involved in metabolomic analysis including pre-analytical work (e.g., sample collection and storage), analytical work (e.g., sample analysis) and data analysis (e.g., feature extraction and quantification). Each one of them can influence the quantitative results significantly and thus should be performed with great care. Among them, the total sample amount or concentration of metabolites can be significantly different from one sample to another. Thus, it is critical to reduce or eliminate the effect of total sample amount variation on quantification of individual metabolites. In this review, we describe the importance of sample normalization in the analytical workflow with a focus on mass spectrometry (MS)-based platforms, discuss a number of methods recently reported in the literature and comment on their applicability in real world metabolomics applications. Sample normalization has been sometimes ignored in metabolomics, partially due to the lack of a convenient means of performing sample normalization. We show that several methods are now available and sample normalization should be performed in quantitative metabolomics where the analyzed samples have significant variations in total sample amounts. Copyright © 2015 Elsevier B.V. All rights reserved.

Characterizing microstructural features of biomedical samples by statistical analysis of Mueller matrix images

NASA Astrophysics Data System (ADS)

He, Honghui; Dong, Yang; Zhou, Jialing; Ma, Hui

2017-03-01

As one of the salient features of light, polarization contains abundant structural and optical information of media. Recently, as a comprehensive description of polarization property, the Mueller matrix polarimetry has been applied to various biomedical studies such as cancerous tissues detections. In previous works, it has been found that the structural information encoded in the 2D Mueller matrix images can be presented by other transformed parameters with more explicit relationship to certain microstructural features. In this paper, we present a statistical analyzing method to transform the 2D Mueller matrix images into frequency distribution histograms (FDHs) and their central moments to reveal the dominant structural features of samples quantitatively. The experimental results of porcine heart, intestine, stomach, and liver tissues demonstrate that the transformation parameters and central moments based on the statistical analysis of Mueller matrix elements have simple relationships to the dominant microstructural properties of biomedical samples, including the density and orientation of fibrous structures, the depolarization power, diattenuation and absorption abilities. It is shown in this paper that the statistical analysis of 2D images of Mueller matrix elements may provide quantitative or semi-quantitative criteria for biomedical diagnosis.

Fast and solvent-free quantitation of boar taint odorants in pig fat by stable isotope dilution analysis-dynamic headspace-thermal desorption-gas chromatography/time-of-flight mass spectrometry.

PubMed

Fischer, Jochen; Haas, Torsten; Leppert, Jan; Lammers, Peter Schulze; Horner, Gerhard; Wüst, Matthias; Boeker, Peter

2014-09-01

Boar taint is a specific off-odour of boar meat products, known to be caused by at least three unpleasant odorants, with very low odour thresholds. Androstenone is a boar pheromone produced in the testes, whereas skatole and indole originate from the microbial breakdown of tryptophan in the intestinal tract. A new procedure, applying stable isotope dilution analysis (SIDA) and dynamic headspace-thermal desorption-gas chromatography/time-of-flight mass spectrometry (dynHS-TD-GC/TOFMS) for the simultaneous quantitation of these boar taint compounds in pig fat was elaborated and validated in this paper. The new method is characterised by a simple and solvent-free dynamic headspace sampling. The deuterated compounds d3-androstenone, d3-skatole and d6-indole were used as internal standards to eliminate matrix effects. The method validation performed revealed low limits of detection (LOD) and quantitation (LOQ) with high accuracy and precision, thus confirming the feasibility of the new dynHS-TD-GC/TOFMS approach for routine analysis. Copyright © 2014 Elsevier Ltd. All rights reserved.

Identification and Quantitation of Asparagine and Citrulline Using High-Performance Liquid Chromatography (HPLC)

PubMed Central

Bai, Cheng; Reilly, Charles C.; Wood, Bruce W.

2007-01-01

High-performance liquid chromatography (HPLC) analysis was used for identification of two problematic ureides, asparagine and citrulline. We report here a technique that takes advantage of the predictable delay in retention time of the co-asparagine/citrulline peak to enable both qualitative and quantitative analysis of asparagine and citrulline using the Platinum EPS reverse-phase C18 column (Alltech Associates). Asparagine alone is eluted earlier than citrulline alone, but when both of them are present in biological samples they may co-elute. HPLC retention times for asparagine and citrulline were influenced by other ureides in the mixture. We found that at various asparagines and citrulline ratios [= 3:1, 1:1, and 1:3; corresponding to 75:25, 50:50, and 25:75 (μMol ml−1/μMol ml−1)], the resulting peak exhibited different retention times. Adjustment of ureide ratios as internal standards enables peak identification and quantification. Both chemicals were quantified in xylem sap samples of pecan [Carya illinoinensis (Wangenh.) K. Koch] trees. Analysis revealed that tree nickel nutrition status affects relative concentrations of Urea Cycle intermediates, asparagine and citrulline, present in sap. Consequently, we concluded that the HPLC methods are presented to enable qualitative and quantitative analysis of these metabolically important ureides. PMID:19662174

Identification and quantitation of asparagine and citrulline using high-performance liquid chromatography (HPLC).

PubMed

Bai, Cheng; Reilly, Charles C; Wood, Bruce W

2007-03-28

High-performance liquid chromatography (HPLC) analysis was used for identification of two problematic ureides, asparagine and citrulline. We report here a technique that takes advantage of the predictable delay in retention time of the co-asparagine/citrulline peak to enable both qualitative and quantitative analysis of asparagine and citrulline using the Platinum EPS reverse-phase C18 column (Alltech Associates). Asparagine alone is eluted earlier than citrulline alone, but when both of them are present in biological samples they may co-elute. HPLC retention times for asparagine and citrulline were influenced by other ureides in the mixture. We found that at various asparagines and citrulline ratios [= 3:1, 1:1, and 1:3; corresponding to 75:25, 50:50, and 25:75 (microMol ml(-1)/microMol ml(-1))], the resulting peak exhibited different retention times. Adjustment of ureide ratios as internal standards enables peak identification and quantification. Both chemicals were quantified in xylem sap samples of pecan [Carya illinoinensis (Wangenh.) K. Koch] trees. Analysis revealed that tree nickel nutrition status affects relative concentrations of Urea Cycle intermediates, asparagine and citrulline, present in sap. Consequently, we concluded that the HPLC methods are presented to enable qualitative and quantitative analysis of these metabolically important ureides.

Widespread age-related differences in the human brain microstructure revealed by quantitative magnetic resonance imaging.

PubMed

Callaghan, Martina F; Freund, Patrick; Draganski, Bogdan; Anderson, Elaine; Cappelletti, Marinella; Chowdhury, Rumana; Diedrichsen, Joern; Fitzgerald, Thomas H B; Smittenaar, Peter; Helms, Gunther; Lutti, Antoine; Weiskopf, Nikolaus

2014-08-01

A pressing need exists to disentangle age-related changes from pathologic neurodegeneration. This study aims to characterize the spatial pattern and age-related differences of biologically relevant measures in vivo over the course of normal aging. Quantitative multiparameter maps that provide neuroimaging biomarkers for myelination and iron levels, parameters sensitive to aging, were acquired from 138 healthy volunteers (age range: 19-75 years). Whole-brain voxel-wise analysis revealed a global pattern of age-related degeneration. Significant demyelination occurred principally in the white matter. The observed age-related differences in myelination were anatomically specific. In line with invasive histologic reports, higher age-related differences were seen in the genu of the corpus callosum than the splenium. Iron levels were significantly increased in the basal ganglia, red nucleus, and extensive cortical regions but decreased along the superior occipitofrontal fascicle and optic radiation. This whole-brain pattern of age-associated microstructural differences in the asymptomatic population provides insight into the neurobiology of aging. The results help build a quantitative baseline from which to examine and draw a dividing line between healthy aging and pathologic neurodegeneration. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Widespread age-related differences in the human brain microstructure revealed by quantitative magnetic resonance imaging☆

PubMed Central

Callaghan, Martina F.; Freund, Patrick; Draganski, Bogdan; Anderson, Elaine; Cappelletti, Marinella; Chowdhury, Rumana; Diedrichsen, Joern; FitzGerald, Thomas H.B.; Smittenaar, Peter; Helms, Gunther; Lutti, Antoine; Weiskopf, Nikolaus

2014-01-01

A pressing need exists to disentangle age-related changes from pathologic neurodegeneration. This study aims to characterize the spatial pattern and age-related differences of biologically relevant measures in vivo over the course of normal aging. Quantitative multiparameter maps that provide neuroimaging biomarkers for myelination and iron levels, parameters sensitive to aging, were acquired from 138 healthy volunteers (age range: 19–75 years). Whole-brain voxel-wise analysis revealed a global pattern of age-related degeneration. Significant demyelination occurred principally in the white matter. The observed age-related differences in myelination were anatomically specific. In line with invasive histologic reports, higher age-related differences were seen in the genu of the corpus callosum than the splenium. Iron levels were significantly increased in the basal ganglia, red nucleus, and extensive cortical regions but decreased along the superior occipitofrontal fascicle and optic radiation. This whole-brain pattern of age-associated microstructural differences in the asymptomatic population provides insight into the neurobiology of aging. The results help build a quantitative baseline from which to examine and draw a dividing line between healthy aging and pathologic neurodegeneration. PMID:24656835

Diversity in ATP concentrations in a single bacterial cell population revealed by quantitative single-cell imaging

PubMed Central

Yaginuma, Hideyuki; Kawai, Shinnosuke; Tabata, Kazuhito V.; Tomiyama, Keisuke; Kakizuka, Akira; Komatsuzaki, Tamiki; Noji, Hiroyuki; Imamura, Hiromi

2014-01-01

Recent advances in quantitative single-cell analysis revealed large diversity in gene expression levels between individual cells, which could affect the physiology and/or fate of each cell. In contrast, for most metabolites, the concentrations were only measureable as ensemble averages of many cells. In living cells, adenosine triphosphate (ATP) is a critically important metabolite that powers many intracellular reactions. Quantitative measurement of the absolute ATP concentration in individual cells has not been achieved because of the lack of reliable methods. In this study, we developed a new genetically-encoded ratiometric fluorescent ATP indicator “QUEEN”, which is composed of a single circularly-permuted fluorescent protein and a bacterial ATP binding protein. Unlike previous FRET-based indicators, QUEEN was apparently insensitive to bacteria growth rate changes. Importantly, intracellular ATP concentrations of numbers of bacterial cells calculated from QUEEN fluorescence were almost equal to those from firefly luciferase assay. Thus, QUEEN is suitable for quantifying the absolute ATP concentration inside bacteria cells. Finally, we found that, even for a genetically-identical Escherichia coli cell population, absolute concentrations of intracellular ATP were significantly diverse between individual cells from the same culture, by imaging QUEEN signals from single cells. PMID:25283467

Targeted Metabolomic Pathway Analysis and Validation Revealed Glutamatergic Disorder in the Prefrontal Cortex among the Chronic Social Defeat Stress Mice Model of Depression.

PubMed

Wang, Wei; Guo, Hua; Zhang, Shu-Xiao; Li, Juan; Cheng, Ke; Bai, Shun-Jie; Yang, De-Yu; Wang, Hai-Yang; Liang, Zi-Hong; Liao, Li; Sun, Lin; Xie, Peng

2016-10-07

Major depressive disorder (MDD) is a severe psychiatric disease that has critically affected life quality for millions of people. Chronic stress is gradually recognized as a primary pathogenesis risk factor of MDD. Despite the remarkable progress in mechanism research, the pathogenesis mechanism of MDD is still not well understood. Therefore, we conducted a liquid chromatography-tandem mass spectrometry (LC-MS/MS) detection of 25 major metabolites of tryptophanic, GABAergic, and catecholaminergic pathways in the prefontal cortex (PFC) of mice in chronic social defeat stress (CSDS). The depressed mice exhibit significant reduction of glutamate in the GABAergic pathway and an increase of L-DOPA and vanillylmandelic acid in catecholaminergic pathways. The data of real-time-quantitative polymerase chain reaction (RT-qPCR) and Western blotting analysis revealed an altered level of glutamatergic circuitry. The metabolomic and molecular data reveal that the glutamatergic disorder in mice shed lights to reveal a mechanism on depression-like and stress resilient phenotype.

Studies on the key aroma compounds in raw (unheated) and heated Japanese soy sauce.

PubMed

Kaneko, Shu; Kumazawa, Kenji; Nishimura, Osamu

2013-04-10

An investigation using the aroma extract dilution analysis (AEDA) technique of the aroma concentrate from a raw Japanese soy sauce and the heated soy sauce revealed 40 key aroma compounds including 7 newly identified compounds. Among them, 5(or 2)-ethyl-4-hydroxy-2(or 5)-methyl-3(2H)-furanone and 3-hydroxy-4,5-dimethyl-2(5H)-furanone exhibited the highest flavor dilution (FD) factor of 2048, followed by 3-(methylthio)propanal, 4-ethyl-2-methoxyphenol, and 4-hydroxy-2,5-dimethyl-3(2H)-furanone having FD factors from 128 to 512 in the raw soy sauce. Furthermore, comparative AEDAs, a quantitative analysis, and a sensory analysis demonstrated that whereas most of the key aroma compounds in the raw soy sauce were common in the heated soy sauce, some of the Strecker aldehydes and 4-vinylphenols contributed less to the raw soy sauce aroma. The model decarboxylation reactions of the phenolic acids during heating of the raw soy sauce revealed that although all reactions resulted in low yields, the hydroxycinnamic acid derivatives were much more reactive than the hydroxybenzoic acid derivatives due to the stable reaction intermediates. Besides the quantitative analyses of the soy sauces, the estimation of the reaction yields of the phenolic compounds in the heated soy sauce revealed that although only the 4-vinylphenols increased during heating of the raw soy sauce, they might not mainly be formed as decarboxylation products from the corresponding hydroxycinnamic acids but from the other proposed precursors, such as lignin, shakuchirin, and esters with arabinoxylan.

How Citation Boosts Promote Scientific Paradigm Shifts and Nobel Prizes

PubMed Central

Mazloumian, Amin; Eom, Young-Ho; Helbing, Dirk; Lozano, Sergi; Fortunato, Santo

2011-01-01

Nobel Prizes are commonly seen to be among the most prestigious achievements of our times. Based on mining several million citations, we quantitatively analyze the processes driving paradigm shifts in science. We find that groundbreaking discoveries of Nobel Prize Laureates and other famous scientists are not only acknowledged by many citations of their landmark papers. Surprisingly, they also boost the citation rates of their previous publications. Given that innovations must outcompete the rich-gets-richer effect for scientific citations, it turns out that they can make their way only through citation cascades. A quantitative analysis reveals how and why they happen. Science appears to behave like a self-organized critical system, in which citation cascades of all sizes occur, from continuous scientific progress all the way up to scientific revolutions, which change the way we see our world. Measuring the “boosting effect” of landmark papers, our analysis reveals how new ideas and new players can make their way and finally triumph in a world dominated by established paradigms. The underlying “boost factor” is also useful to discover scientific breakthroughs and talents much earlier than through classical citation analysis, which by now has become a widespread method to measure scientific excellence, influencing scientific careers and the distribution of research funds. Our findings reveal patterns of collective social behavior, which are also interesting from an attention economics perspective. Understanding the origin of scientific authority may therefore ultimately help to explain how social influence comes about and why the value of goods depends so strongly on the attention they attract. PMID:21573229

How citation boosts promote scientific paradigm shifts and nobel prizes.

PubMed

Mazloumian, Amin; Eom, Young-Ho; Helbing, Dirk; Lozano, Sergi; Fortunato, Santo

2011-05-04

Nobel Prizes are commonly seen to be among the most prestigious achievements of our times. Based on mining several million citations, we quantitatively analyze the processes driving paradigm shifts in science. We find that groundbreaking discoveries of Nobel Prize Laureates and other famous scientists are not only acknowledged by many citations of their landmark papers. Surprisingly, they also boost the citation rates of their previous publications. Given that innovations must outcompete the rich-gets-richer effect for scientific citations, it turns out that they can make their way only through citation cascades. A quantitative analysis reveals how and why they happen. Science appears to behave like a self-organized critical system, in which citation cascades of all sizes occur, from continuous scientific progress all the way up to scientific revolutions, which change the way we see our world. Measuring the "boosting effect" of landmark papers, our analysis reveals how new ideas and new players can make their way and finally triumph in a world dominated by established paradigms. The underlying "boost factor" is also useful to discover scientific breakthroughs and talents much earlier than through classical citation analysis, which by now has become a widespread method to measure scientific excellence, influencing scientific careers and the distribution of research funds. Our findings reveal patterns of collective social behavior, which are also interesting from an attention economics perspective. Understanding the origin of scientific authority may therefore ultimately help to explain how social influence comes about and why the value of goods depends so strongly on the attention they attract.

Quantitative Analysis of Defects in Silicon. [to predict energy conversion efficiency of silicon samples for solar cells

NASA Technical Reports Server (NTRS)

Natesh, R.; Smith, J. M.; Qidwai, H. A.; Bruce, T.

1979-01-01

The evaluation and prediction of the conversion efficiency for a variety of silicon samples with differences in structural defects, such as grain boundaries, twin boundaries, precipitate particles, dislocations, etc. are discussed. Quantitative characterization of these structural defects, which were revealed by etching the surface of silicon samples, is performed by using an image analyzer. Due to different crystal growth and fabrication techniques the various types of silicon contain a variety of trace impurity elements and structural defects. The two most important criteria in evaluating the various silicon types for solar cell applications are cost and conversion efficiency.

Trend of De La Salle Lipa Education Graduates' Performance in the Licensure Examination for Teachers

ERIC Educational Resources Information Center

Kalaw, Maria Theresa B.

2017-01-01

This study aimed to examine the trend of performance of De La Salle Lipa (DLSL) education graduates in the Licensure Examination for Teachers (LET). Quantitative trend analysis employed on the data collected from records officially released by the Professional Regulation Commission (PRC) for the years 2011 to 2015 revealed that the performance of…

Stories in Networks and Networks in Stories: A Tri-Modal Model for Mixed-Methods Social Network Research on Teachers

ERIC Educational Resources Information Center

Baker-Doyle, Kira J.

2015-01-01

Social network research on teachers and schools has risen exponentially in recent years as an innovative method to reveal the role of social networks in education. However, scholars are still exploring ways to incorporate traditional quantitative methods of Social Network Analysis (SNA) with qualitative approaches to social network research. This…

Marketable Job Skills for High School Students: What We Learned from an Evaluation of after School Matters

ERIC Educational Resources Information Center

Alexander, Kendra P.; Hirsch, Barton J.

2012-01-01

This article summarizes findings from an experimental evaluation of After School Matters (ASM), a paid, apprenticeship-based, after-school program in Chicago for high school students. Analysis of quantitative data from a mock job interview revealed that ASM participants did not demonstrate more marketable job skills than youth in the control…

The Use of Cohesive Devices in Argumentative Writing by Chinese EFL Learners at Different Proficiency Levels

ERIC Educational Resources Information Center

Yang, Wenxing; Sun, Ying

2012-01-01

This article reports on a study that comparatively investigated the differences and similarities in the (incorrect) use of cohesive devices by second-year and fourth-year undergraduate Chinese EFL learners in their argumentative writings. Via detailed analysis of the quantitative and qualitative data, this study seeks to reveal if the patterns of…

Spectral imaging of histological and cytological specimens

NASA Astrophysics Data System (ADS)

Rothmann, Chana; Malik, Zvi

1999-05-01

Evaluation of cell morphology by bright field microscopy is the pillar of histopathological diagnosis. The need for quantitative and objective parameters for diagnosis has given rise to the development of morphometric methods. The development of spectral imaging for biological and medical applications introduced both fields to large amounts of information extracted from a single image. Spectroscopic analysis is based on the ability of a stained histological specimen to absorb, reflect, or emit photons in ways characteristic to its interactions with specific dyes. Spectral information obtained from a histological specimen is stored in a cube whose appellate signifies the two spatial dimensions of a flat sample (x and y) and the third dimension, the spectrum, representing the light intensity for every wavelength. The spectral information stored in the cube can be further processed by morphometric analysis and quantitative procedures. Such a procedure is spectral-similarity mapping (SSM), which enables the demarcation of areas occupied by the same type of material. SSM constructs new images of the specimen, revealing areas with similar stain-macromolecule characteristics and enhancing subcellular features. Spectral imaging combined with SSM reveals nuclear organization through the differentiation stages as well as in apoptotic and necrotic conditions and identifies specifically the nucleoli domains.

Significance of the gate voltage-dependent mobility in the electrical characterization of organic field effect transistors

NASA Astrophysics Data System (ADS)

Kim, Jong Beom; Lee, Dong Ryeol

2018-04-01

We studied the effect of the addition of free hole- and electron-rich organic molecules to organic semiconductors (OSCs) in organic field effect transistors (OFETs) on the gate voltage-dependent mobility. The drain current versus gate voltage characteristics were quantitatively analyzed using an OFET mobility model of power law behavior based on hopping transport in an OSC. This analysis distinguished the threshold voltage shifts, depending on the materials and structures of the OFET device, and properly estimated the hopping transport of the charge carriers induced by the gate bias within the OSC from the power law exponent parameter. The addition of pentacene or C60 molecules to a one-monolayer pentacene-based OFET shifted the threshold voltages negatively or positively, respectively, due to the structural changes that occurred in the OFET device. On the other hand, the power law parameters revealed that the addition of charge carriers of the same or opposite polarity enhanced or hindered hopping transport, respectively. This study revealed the need for a quantitative analysis of the gate voltage-dependent mobility while distinguishing this effect from the threshold voltage effect in order to understand OSC hopping transport in OFETs.

A broader understanding of care managers' attitudes of advance care planning: a concurrent nested design.

PubMed

Aultman, Julie; Baughman, Kristin R; Ludwick, Ruth

2018-05-18

To examine barriers of advance care planning (ACP) experienced by care managers (CMs) through a mixed methods approach. A concurrent nested design was used to acquire a deeper understanding of ACP, and to identify nuances between quantitative and qualitative data. Past quantitative studies on providers have identified barriers related to time, culture, knowledge, responsibility, and availability of legal documents. These barriers, and accompanying attitudes and feelings, have been taken at face value without rich qualitative data to identify under what conditions and to what extent a barrier impacts care. A two-part multisite, mixed methods study was conducted using surveys and focus groups. Surveys were completed by 458 CMs at 10 Area Agencies on Aging and 62 participated in one of 8 focus groups. Data were analyzed using a concurrent nested design with individual data analysis and a merged data approach. There were three main distinctions between the quantitative and qualitative data. First, while CMs reported on the survey that ACP was not too time consuming, focus group data revealed that time was an issue especially related to competing priorities. Second on the survey 60% of the CMS reported they had enough knowledge, but qualitative data revealed about more nuances. Last, the reported comfort levels in the quantitative data were less overt in the qualitative date where additional feelings and attitudes were revealed, e.g., frustration with families, preferences for more physician involvement. CMs reported their attitudes about ACP, clarified through a rigorous mixed methods analysis. Care managers can successfully lead ACP discussions, but require further education, resources, and team-based guidance. ACP is essential for reducing emotional, social, and financial burdens associated with health care decision-making, and CMs can positively impact ACP discussions when appropriately supported by the clinical community. The many nuances in the ACP process that we found illustrate the need for ongoing discussions, education and research on this important topic. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Quantitative contrast-enhanced ultrasound evaluation of pathological complete response in patients with locally advanced breast cancer receiving neoadjuvant chemotherapy.

PubMed

Wan, Cai-Feng; Liu, Xue-Song; Wang, Lin; Zhang, Jie; Lu, Jin-Song; Li, Feng-Hua

2018-06-01

To clarify whether the quantitative parameters of contrast-enhanced ultrasound (CEUS) can be used to predict pathological complete response (pCR) in patients with locally advanced breast cancer receiving neoadjuvant chemotherapy (NAC). Fifty-one patients with histologically proved locally advanced breast cancer scheduled for NAC were enrolled. The quantitative data for CEUS and the tumor diameter were collected at baseline and before surgery, and compared with the pathological response. Multiple logistic regression analysis was performed to examine quantitative parameters at CEUS and the tumor diameter to predict the pCR, and receiver operating characteristic (ROC) curve analysis was used as a summary statistic. Multiple logistic regression analysis revealed that PEAK (the maximum intensity of the time-intensity curve during bolus transit), PEAK%, TTP% (time to peak), and diameter% were significant independent predictors of pCR, and the area under the ROC curve was 0.932(Az 1 ), and the sensitivity and specificity to predict pCR were 93.7% and 80.0%. The area under the ROC curve for the quantitative parameters was 0.927(Az 2 ), and the sensitivity and specificity to predict pCR were 81.2% and 94.3%. For diameter%, the area under the ROC curve was 0.786 (Az 3 ), and the sensitivity and specificity to predict pCR were 93.8% and 54.3%. The values of Az 1 and Az 2 were significantly higher than that of Az 3 (P = 0.027 and P = 0.034, respectively). However, there was no significant difference between the values of Az 1 and Az 2 (P = 0.825). Quantitative analysis of tumor blood perfusion with CEUS is superior to diameter% to predict pCR, and can be used as a functional technique to evaluate tumor response to NAC. Copyright © 2018. Published by Elsevier B.V.

Accurate Quantitation and Analysis of Nitrofuran Metabolites, Chloramphenicol, and Florfenicol in Seafood by Ultrahigh-Performance Liquid Chromatography-Tandem Mass Spectrometry: Method Validation and Regulatory Samples.

PubMed

Aldeek, Fadi; Hsieh, Kevin C; Ugochukwu, Obiadada N; Gerard, Ghislain; Hammack, Walter

2018-05-23

We developed and validated a method for the extraction, identification, and quantitation of four nitrofuran metabolites, 3-amino-2-oxazolidinone (AOZ), 3-amino-5-morpholinomethyl-2-oxazolidinone (AMOZ), semicarbazide (SC), and 1-aminohydantoin (AHD), as well as chloramphenicol and florfenicol in a variety of seafood commodities. Samples were extracted by liquid-liquid extraction techniques, analyzed by ultrahigh-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS), and quantitated using commercially sourced, derivatized nitrofuran metabolites, with their isotopically labeled internal standards in-solvent. We obtained recoveries of 90-100% at various fortification levels. The limit of detection (LOD) was set at 0.25 ng/g for AMOZ and AOZ, 1 ng/g for AHD and SC, and 0.1 ng/g for the phenicols. Various extraction methods, standard stability, derivatization efficiency, and improvements to conventional quantitation techniques were also investigated. We successfully applied this method to the identification and quantitation of nitrofuran metabolites and phenicols in 102 imported seafood products. Our results revealed that four of the samples contained residues from banned veterinary drugs.

The effects of physical activity on impulsive choice: Influence of sensitivity to reinforcement amount and delay.

PubMed

Strickland, Justin C; Feinstein, Max A; Lacy, Ryan T; Smith, Mark A

2016-05-01

Impulsive choice is a diagnostic feature and/or complicating factor for several psychological disorders and may be examined in the laboratory using delay-discounting procedures. Recent investigators have proposed using quantitative measures of analysis to examine the behavioral processes contributing to impulsive choice. The purpose of this study was to examine the effects of physical activity (i.e., wheel running) on impulsive choice in a single-response, discrete-trial procedure using two quantitative methods of analysis. To this end, rats were assigned to physical activity or sedentary groups and trained to respond in a delay-discounting procedure. In this procedure, one lever always produced one food pellet immediately, whereas a second lever produced three food pellets after a 0, 10, 20, 40, or 80-s delay. Estimates of sensitivity to reinforcement amount and sensitivity to reinforcement delay were determined using (1) a simple linear analysis and (2) an analysis of logarithmically transformed response ratios. Both analyses revealed that physical activity decreased sensitivity to reinforcement amount and sensitivity to reinforcement delay. These findings indicate that (1) physical activity has significant but functionally opposing effects on the behavioral processes that contribute to impulsive choice and (2) both quantitative methods of analysis are appropriate for use in single-response, discrete-trial procedures. Copyright © 2016 Elsevier B.V. All rights reserved.

Evaluation of acute ischemic stroke using quantitative EEG: a comparison with conventional EEG and CT scan.

PubMed

Murri, L; Gori, S; Massetani, R; Bonanni, E; Marcella, F; Milani, S

1998-06-01

The sensitivity of quantitative electroencephalogram (EEG) was compared with that of conventional EEG in patients with acute ischaemic stroke. In addition, a correlation between quantitative EEG data and computerized tomography (CT) scan findings was carried out for all the areas of lesion in order to reassess the actual role of EEG in the evaluation of stroke. Sixty-five patients were tested with conventional and quantitative EEG within 24 h from the onset of neurological symptoms, whereas CT scan was performed within 4 days from the onset of stroke. EEG was recorded from 19 electrodes placed upon the scalp according to the International 10-20 System. Spectral analysis was carried out on 30 artefact-free 4-sec epochs. For each channel absolute and relative power were calculated for the delta, theta, alpha and beta frequency bands and such data were successively represented in colour-coded maps. Ten patients with extensive lesions documented by CT scan were excluded. The results indicated that conventional EEG revealed abnormalities in 40 of 55 cases, while EEG mapping showed abnormalities in 46 of 55 cases: it showed focal abnormalities in five cases and nonfocal abnormalities in one of six cases which had appeared to be normal according to visual inspection of EEG. In a further 11 cases, where the conventional EEG revealed abnormalities in one hemisphere, the quantitative EEG and maps allowed to further localize abnormal activity in a more localized way. The sensitivity of both methods was higher for frontocentral, temporal and parieto-occipital cortical-subcortical infarctions than for basal ganglia and internal capsule lesions; however, quantitative EEG was more efficient for all areas of lesion in detecting cases that had appeared normal by visual inspection and was clearly superior in revealing focal abnormalities. When we considered the electrode related to which the maximum power of the delta frequency band is recorded, a fairly close correlation was found between the localization of the maximum delta power and the position of lesions documented by CT scan for all areas of lesion excepting those located in the striatocapsular area.

Expression analysis of a heat-inducible, Myo-inositol-1-phosphate synthase (MIPS) gene from wheat and the alternatively spliced variants of rice and Arabidopsis.

PubMed

Khurana, Neetika; Chauhan, Harsh; Khurana, Paramjit

2012-01-01

Molecular dissection and a deeper analysis of the heat stress response mechanism in wheat have been poorly understood so far. This study delves into the molecular basis of action of TaMIPS, a heat stress-inducible enzyme that was identified through PCR-select subtraction technology, which is named here as TaMIPS2. MIPS (L-Myo-inositol-phosphate synthase) is important for the normal growth and development in plants. Expression profiling showed that TaMIPS2 is expressed during different developing seed stages upon heat stress. Also, the transcript levels increase in unfertilized ovaries and significant amounts are present during the recovery period providing evidence that MIPS is crucial for its role in heat stress recovery and flower development. Alternatively spliced forms from rice and Arabidopsis were also identified and their expression analysis revealed that apart from heat stress, some of the spliced variants were also inducible by drought, NaCl, Cold, ABA, BR, SA and mannitol. In silico promoter analysis revealed various cis-elements that could contribute for the differential regulation of MIPS in different plant systems. Phylogenetic analysis indicated that MIPS are highly conserved among monocots and dicots and TaMIPS2 grouped specifically with monocots. Comparative analyses was undertaken by different experimental approaches, i.e., semi-quantitative RT-PCR, quantitative RT-PCR, Genevestigator as a reference expression tool and motif analysis to predict the possible function of TaMIPS2 in regulating the different aspects of plant development under abiotic stress in wheat.

Validated ¹H and 13C Nuclear Magnetic Resonance Methods for the Quantitative Determination of Glycerol in Drug Injections.

PubMed

Lu, Jiaxi; Wang, Pengli; Wang, Qiuying; Wang, Yanan; Jiang, Miaomiao

2018-05-15

In the current study, we employed high-resolution proton and carbon nuclear magnetic resonance spectroscopy (¹H and 13 C NMR) for quantitative analysis of glycerol in drug injections without any complex pre-treatment or derivatization on samples. The established methods were validated with good specificity, linearity, accuracy, precision, stability, and repeatability. Our results revealed that the contents of glycerol were convenient to calculate directly via the integration ratios of peak areas with an internal standard in ¹H NMR spectra, while the integration of peak heights were proper for 13 C NMR in combination with an external calibration of glycerol. The developed methods were both successfully applied in drug injections. Quantitative NMR methods showed an extensive prospect for glycerol determination in various liquid samples.

Remote quantitative analysis of minerals based on multispectral line-calibrated laser-induced breakdown spectroscopy (LIBS).

PubMed

Wan, Xiong; Wang, Peng

2014-01-01

Laser-induced breakdown spectroscopy (LIBS) is a feasible remote sensing technique used for mineral analysis in some unapproachable places where in situ probing is needed, such as analysis of radioactive elements in a nuclear leak or the detection of elemental compositions and contents of minerals on planetary and lunar surfaces. Here a compact custom 15 m focus optical component, combining a six times beam expander with a telescope, has been built, with which the laser beam of a 1064 nm Nd ; YAG laser is focused on remote minerals. The excited LIBS signals that reveal the elemental compositions of minerals are collected by another compact single lens-based signal acquisition system. In our remote LIBS investigations, the LIBS spectra of an unknown ore have been detected, from which the metal compositions are obtained. In addition, a multi-spectral line calibration (MSLC) method is proposed for the quantitative analysis of elements. The feasibility of the MSLC and its superiority over a single-wavelength determination have been confirmed by comparison with traditional chemical analysis of the copper content in the ore.

Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the α subunit of protein kinase CK2

PubMed Central

Takahashi, Yuji; Shomura, Ayahiko; Sasaki, Takuji; Yano, Masahiro

2001-01-01

Hd6 is a quantitative trait locus involved in rice photoperiod sensitivity. It was detected in backcross progeny derived from a cross between the japonica variety Nipponbare and the indica variety Kasalath. To isolate a gene at Hd6, we used a large segregating population for the high-resolution and fine-scale mapping of Hd6 and constructed genomic clone contigs around the Hd6 region. Linkage analysis with P1-derived artificial chromosome clone-derived DNA markers delimited Hd6 to a 26.4-kb genomic region. We identified a gene encoding the α subunit of protein kinase CK2 (CK2α) in this region. The Nipponbare allele of CK2α contains a premature stop codon, and the resulting truncated product is undoubtedly nonfunctional. Genetic complementation analysis revealed that the Kasalath allele of CK2α increases days-to-heading. Map-based cloning with advanced backcross progeny enabled us to identify a gene underlying a quantitative trait locus even though it exhibited a relatively small effect on the phenotype. PMID:11416158

Quantitative analysis of 18F-NaF dynamic PET/CT cannot differentiate malignant from benign lesions in multiple myeloma.

PubMed

Sachpekidis, Christos; Hillengass, Jens; Goldschmidt, Hartmut; Anwar, Hoda; Haberkorn, Uwe; Dimitrakopoulou-Strauss, Antonia

2017-01-01

A renewed interest has been recently developed for the highly sensitive bone-seeking radiopharmaceutical 18 F-NaF. Aim of the present study is to evaluate the potential utility of quantitative analysis of 18 F-NaF dynamic PET/CT data in differentiating malignant from benign degenerative lesions in multiple myeloma (MM). 80 MM patients underwent whole-body PET/CT and dynamic PET/CT scanning of the pelvis with 18 F-NaF. PET/CT data evaluation was based on visual (qualitative) assessment, semi-quantitative (SUV) calculations, and absolute quantitative estimations after application of a 2-tissue compartment model and a non-compartmental approach leading to the extraction of fractal dimension (FD). In total 263 MM lesions were demonstrated on 18 F-NaF PET/CT. Semi-quantitative and quantitative evaluations were performed for 25 MM lesions as well as for 25 benign, degenerative and traumatic lesions. Mean SUV average for MM lesions was 11.9 and mean SUV max was 23.2. Respectively, SUV average and SUV max for degenerative lesions were 13.5 and 20.2. Kinetic analysis of 18 F-NaF revealed the following mean values for MM lesions: K 1 = 0.248 (1/min), k 3 = 0.359 (1/min), influx (K i ) = 0.107 (1/min), FD = 1.382, while the respective values for degenerative lesions were: K 1 = 0.169 (1/min), k 3 = 0.422 (1/min), influx (K i ) = 0.095 (1/min), FD = 1. 411. No statistically significant differences between MM and benign degenerative disease regarding SUV average , SUV max , K 1 , k 3 and influx (K i ) were demonstrated. FD was significantly higher in degenerative than in malignant lesions. The present findings show that quantitative analysis of 18 F-NaF PET data cannot differentiate malignant from benign degenerative lesions in MM patients, supporting previously published results, which reflect the limited role of 18 F-NaF PET/CT in the diagnostic workup of MM.

Reliability and validity evidence of the Assessment of Language Use in Social Contexts for Adults (ALUSCA).

PubMed

Valente, Ana Rita S; Hall, Andreia; Alvelos, Helena; Leahy, Margaret; Jesus, Luis M T

2018-04-12

The appropriate use of language in context depends on the speaker's pragmatic language competencies. A coding system was used to develop a specific and adult-focused self-administered questionnaire to adults who stutter and adults who do not stutter, The Assessment of Language Use in Social Contexts for Adults, with three categories: precursors, basic exchanges, and extended literal/non-literal discourse. This paper presents the content validity, item analysis, reliability coefficients and evidences of construct validity of the instrument. Content validity analysis was based on a two-stage process: first, 11 pragmatic questionnaires were assessed to identify items that probe each pragmatic competency and to create the first version of the instrument; second, items were assessed qualitatively by an expert panel composed by adults who stutter and controls, and quantitatively and qualitatively by an expert panel composed by clinicians. A pilot study was conducted with five adults who stutter and five controls to analyse items and calculate reliability. Construct validity evidences were obtained using the hypothesized relationships method and factor analysis with 28 adults who stutter and 28 controls. Concerning content validity, the questionnaires assessed up to 13 pragmatic competencies. Qualitative and quantitative analysis revealed ambiguities in items construction. Disagreement between experts was solved through item modification. The pilot study showed that the instrument presented internal consistency and temporal stability. Significant differences between adults who stutter and controls and different response profiles revealed the instrument's underlying construct. The instrument is reliable and presented evidences of construct validity.

Quantitative DNA Methylation Analysis Identifies a Single CpG Dinucleotide Important for ZAP-70 Expression and Predictive of Prognosis in Chronic Lymphocytic Leukemia

PubMed Central

Claus, Rainer; Lucas, David M.; Stilgenbauer, Stephan; Ruppert, Amy S.; Yu, Lianbo; Zucknick, Manuela; Mertens, Daniel; Bühler, Andreas; Oakes, Christopher C.; Larson, Richard A.; Kay, Neil E.; Jelinek, Diane F.; Kipps, Thomas J.; Rassenti, Laura Z.; Gribben, John G.; Döhner, Hartmut; Heerema, Nyla A.; Marcucci, Guido; Plass, Christoph; Byrd, John C.

2012-01-01

Purpose Increased ZAP-70 expression predicts poor prognosis in chronic lymphocytic leukemia (CLL). Current methods for accurately measuring ZAP-70 expression are problematic, preventing widespread application of these tests in clinical decision making. We therefore used comprehensive DNA methylation profiling of the ZAP-70 regulatory region to identify sites important for transcriptional control. Patients and Methods High-resolution quantitative DNA methylation analysis of the entire ZAP-70 gene regulatory regions was conducted on 247 samples from patients with CLL from four independent clinical studies. Results Through this comprehensive analysis, we identified a small area in the 5′ regulatory region of ZAP-70 that showed large variability in methylation in CLL samples but was universally methylated in normal B cells. High correlation with mRNA and protein expression, as well as activity in promoter reporter assays, revealed that within this differentially methylated region, a single CpG dinucleotide and neighboring nucleotides are particularly important in ZAP-70 transcriptional regulation. Furthermore, by using clustering approaches, we identified a prognostic role for this site in four independent data sets of patients with CLL using time to treatment, progression-free survival, and overall survival as clinical end points. Conclusion Comprehensive quantitative DNA methylation analysis of the ZAP-70 gene in CLL identified important regions responsible for transcriptional regulation. In addition, loss of methylation at a specific single CpG dinucleotide in the ZAP-70 5′ regulatory sequence is a highly predictive and reproducible biomarker of poor prognosis in this disease. This work demonstrates the feasibility of using quantitative specific ZAP-70 methylation analysis as a relevant clinically applicable prognostic test in CLL. PMID:22564988

Effect of excess lithium in LiMn2O4 and Li1.15Mn1.85O4 electrodes revealed by quantitative analysis of soft X-ray absorption spectroscopy

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

Zhuo, Zengqing; Olalde-Velasco, Paul.; Chin, Timothy

We performed a comparative study of the soft x-ray absorption spectroscopy of the LiMn2O4 and Li1.15Mn1.85O4 electrode materials with a quantitative analysis of the Mn oxidation states. The revealed redox evolution of Mn upon the electrochemical cycling clarifies the effect of the excess Li in the materials, which naturally explains the different electrochemical performance. The spectral analysis perfectly agrees with the different initial cycling capacities of the two materials. The results show unambiguously that Mn3+ starts to dominate the electrode surface after only one cycle. More importantly, the data show that, while LiMn2O4 electrodes follow the nominal Mn redox evolution,more » the formation of Mn3+ on the electrode surface is largely retarded for the Li1.15Mn1.85O4 during most of the electrochemical process. Such a different surface Mn redox behavior leads to differences in the detrimental effects of Mn2+ formation on the surface, which is observed directly after only two cycles. Our results provide strong evidence that a key effect of the (bulk) excess Li doping is actually due to processes on the electrode surfaces.« less

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

Global Profiling of Protein Lysine Malonylation in Escherichia coli Reveals Its Role in Energy Metabolism.

PubMed

Qian, Lili; Nie, Litong; Chen, Ming; Liu, Ping; Zhu, Jun; Zhai, Linhui; Tao, Sheng-Ce; Cheng, Zhongyi; Zhao, Yingming; Tan, Minjia

2016-06-03

Protein lysine malonylation is a recently identified post-translational modification (PTM), which is evolutionarily conserved from bacteria to mammals. Although analysis of lysine malonylome in mammalians suggested that this modification was related to energy metabolism, the substrates and biological roles of malonylation in prokaryotes are still poorly understood. In this study, we performed qualitative and quantitative analyses to globally identify lysine malonylation substrates in Escherichia coli. We identified 1745 malonylation sites in 594 proteins in E. coli, representing the first and largest malonylome data set in prokaryotes up to date. Bioinformatic analyses showed that lysine malonylation was significantly enriched in protein translation, energy metabolism pathways and fatty acid biosynthesis, implying the potential roles of protein malonylation in bacterial physiology. Quantitative proteomics by fatty acid synthase inhibition in both auxotrophic and prototrophic E. coli strains revealed that lysine malonylation is closely associated with E. coli fatty acid metabolism. Protein structural analysis and mutagenesis experiment suggested malonylation could impact enzymatic activity of citrate synthase, a key enzyme in citric acid (TCA) cycle. Further comparative analysis among lysine malonylome, succinylome and acetylome data showed that these three modifications could participate in some similar enriched metabolism pathways, but they could also possibly play distinct roles such as in fatty acid synthesis. These data expanded our knowledge of lysine malonylation in prokaryotes, providing a resource for functional study of lysine malonylation in bacteria.

Protein content and functional characteristics of serum-purified exosomes from patients with colorectal cancer revealed by quantitative proteomics.

PubMed

Chen, Yanyu; Xie, Yong; Xu, Lai; Zhan, Shaohua; Xiao, Yi; Gao, Yanpan; Wu, Bin; Ge, Wei

2017-02-15

Tumor cells of colorectal cancer (CRC) release exosomes into the circulation. These exosomes can mediate communication between cells and affect various tumor-related processes in their target cells. We present a quantitative proteomics analysis of the exosomes purified from serum of patients with CRC and normal volunteers; data are available via ProteomeXchange with identifier PXD003875. We identified 918 proteins with an overlap of 725 Gene IDs in the Exocarta proteins list. Compared with the serum-purified exosomes (SPEs) of normal volunteers, we found 36 proteins upregulated and 22 proteins downregulated in the SPEs of CRC patients. Bioinformatics analysis revealed that upregulated proteins are involved in processes that modulate the pretumorigenic microenvironment for metastasis. In contrast, differentially expressed proteins (DEPs) that play critical roles in tumor growth and cell survival were principally downregulated. Our study demonstrates that SPEs of CRC patients play a pivotal role in promoting the tumor invasiveness, but have minimal influence on putative alterations in tumor survival or proliferation. According to bioinformatics analysis, we speculate that the protein contents of exosomes might be associated with whether they are involved in premetastatic niche establishment or growth and survival of metastatic tumor cells. This information will be helpful in elucidating the pathophysiological functions of tumor-derived exosomes, and aid in the development of CRC diagnostics and therapeutics. © 2016 UICC.

Effect of excess lithium in LiMn2O4 and Li1.15Mn1.85O4 electrodes revealed by quantitative analysis of soft X-ray absorption spectroscopy

DOE PAGES

Zhuo, Zengqing; Olalde-Velasco, Paul.; Chin, Timothy; ...

2017-02-27

We performed a comparative study of the soft x-ray absorption spectroscopy of the LiMn2O4 and Li1.15Mn1.85O4 electrode materials with a quantitative analysis of the Mn oxidation states. The revealed redox evolution of Mn upon the electrochemical cycling clarifies the effect of the excess Li in the materials, which naturally explains the different electrochemical performance. The spectral analysis perfectly agrees with the different initial cycling capacities of the two materials. The results show unambiguously that Mn3+ starts to dominate the electrode surface after only one cycle. More importantly, the data show that, while LiMn2O4 electrodes follow the nominal Mn redox evolution,more » the formation of Mn3+ on the electrode surface is largely retarded for the Li1.15Mn1.85O4 during most of the electrochemical process. Such a different surface Mn redox behavior leads to differences in the detrimental effects of Mn2+ formation on the surface, which is observed directly after only two cycles. Our results provide strong evidence that a key effect of the (bulk) excess Li doping is actually due to processes on the electrode surfaces.« less

Novel glioblastoma markers with diagnostic and prognostic value identified through transcriptome analysis.

PubMed

Reddy, Sreekanth P; Britto, Ramona; Vinnakota, Katyayni; Aparna, Hebbar; Sreepathi, Hari Kishore; Thota, Balaram; Kumari, Arpana; Shilpa, B M; Vrinda, M; Umesh, Srikantha; Samuel, Cini; Shetty, Mitesh; Tandon, Ashwani; Pandey, Paritosh; Hegde, Sridevi; Hegde, A S; Balasubramaniam, Anandh; Chandramouli, B A; Santosh, Vani; Kondaiah, Paturu; Somasundaram, Kumaravel; Rao, M R Satyanarayana

2008-05-15

Current methods of classification of astrocytoma based on histopathologic methods are often subjective and less accurate. Although patients with glioblastoma have grave prognosis, significant variability in patient outcome is observed. Therefore, the aim of this study was to identify glioblastoma diagnostic and prognostic markers through microarray analysis. We carried out transcriptome analysis of 25 diffusely infiltrating astrocytoma samples [WHO grade II--diffuse astrocytoma, grade III--anaplastic astrocytoma, and grade IV--glioblastoma (GBM)] using cDNA microarrays containing 18,981 genes. Several of the markers identified were also validated by real-time reverse transcription quantitative PCR and immunohistochemical analysis on an independent set of tumor samples (n = 100). Survival analysis was carried out for two markers on another independent set of retrospective cases (n = 51). We identified several differentially regulated grade-specific genes. Independent validation by real-time reverse transcription quantitative PCR analysis found growth arrest and DNA-damage-inducible alpha (GADD45alpha) and follistatin-like 1 (FSTL1) to be up-regulated in most GBMs (both primary and secondary), whereas superoxide dismutase 2 and adipocyte enhancer binding protein 1 were up-regulated in the majority of primary GBM. Further, identification of the grade-specific expression of GADD45alpha and FSTL1 by immunohistochemical staining reinforced our findings. Analysis of retrospective GBM cases with known survival data revealed that cytoplasmic overexpression of GADD45alpha conferred better survival while the coexpression of FSTL1 with p53 was associated with poor survival. Our study reveals that GADD45alpha and FSTLI are GBM-specific whereas superoxide dismutase 2 and adipocyte enhancer binding protein 1 are primary GBM-specific diagnostic markers. Whereas GADD45alpha overexpression confers a favorable prognosis, FSTL1 overexpression is a hallmark of poor prognosis in GBM patients.

Predicting Team Performance through Human Behavioral Sensing and Quantitative Workflow Instrumentation

DTIC Science & Technology

2016-07-27

make risk-informed decisions during serious games . Statistical models of intra- game performance were developed to determine whether behaviors in...specific facets of the gameplay workflow were predictive of analytical performance and games outcomes. A study of over seventy instrumented teams revealed...more accurate game decisions. 2 Keywords: Humatics · Serious Games · Human-System Interaction · Instrumentation · Teamwork · Communication Analysis

Attitudes of Students and Faculty toward Using Computer Technology and Twitter for Online Learning and Student Engagement: A Cross-Sectional Analysis

ERIC Educational Resources Information Center

Ramirez, Dulce M.

2017-01-01

The increasing use of online pedagogy in higher education has revealed a need to analyze factors contributing to student engagement in online courses. Throughout the past decade, social media has been a growing influence in higher education. This quantitative cross-sectional study examined the attitudes of students and faculty towards computer…

Serum proteome profiling in canine idiopathic dilated cardiomyopathy using TMT-based quantitative proteomics approach.

PubMed

Bilić, Petra; Guillemin, Nicolas; Kovačević, Alan; Beer Ljubić, Blanka; Jović, Ines; Galan, Asier; Eckersall, Peter David; Burchmore, Richard; Mrljak, Vladimir

2018-05-15

Idiopathic dilated cardiomyopathy (iDCM) is a primary myocardial disorder with an unknown aetiology, characterized by reduced contractility and ventricular dilation of the left or both ventricles. Naturally occurring canine iDCM was used herein to identify serum proteomic signature of the disease compared to the healthy state, providing an insight into underlying mechanisms and revealing proteins with biomarker potential. To achieve this, we used high-throughput label-based quantitative LC-MS/MS proteomics approach and bioinformatics analysis of the in silico inferred interactome protein network created from the initial list of differential proteins. To complement the proteomic analysis, serum biochemical parameters and levels of know biomarkers of cardiac function were measured. Several proteins with biomarker potential were identified, such as inter-alpha-trypsin inhibitor heavy chain H4, microfibril-associated glycoprotein 4 and apolipoprotein A-IV, which were validated using an independent method (Western blotting) and showed high specificity and sensitivity according to the receiver operating characteristic curve analysis. Bioinformatics analysis revealed involvement of different pathways in iDCM, such as complement cascade activation, lipoprotein particles dynamics, elastic fibre formation, GPCR signalling and respiratory electron transport chain. Idiopathic dilated cardiomyopathy is a severe primary myocardial disease of unknown cause, affecting both humans and dogs. This study is a contribution to the canine heart disease research by means of proteomic and bioinformatic state of the art analyses, following similar approach in human iDCM research. Importantly, we used serum as non-invasive and easily accessible biological source of information and contributed to the scarce data on biofluid proteome research on this topic. Bioinformatics analysis revealed biological pathways modulated in canine iDCM with potential of further targeted research. Also, several proteins with biomarker potential have been identified and successfully validated. Copyright © 2018 Elsevier B.V. All rights reserved.

Dissecting genetic architecture of grape proanthocyanidin composition through quantitative trait locus mapping

PubMed Central

2012-01-01

Background Proanthocyanidins (PAs), or condensed tannins, are flavonoid polymers, widespread throughout the plant kingdom, which provide protection against herbivores while conferring organoleptic and nutritive values to plant-derived foods, such as wine. However, the genetic basis of qualitative and quantitative PA composition variation is still poorly understood. To elucidate the genetic architecture of the complex grape PA composition, we first carried out quantitative trait locus (QTL) analysis on a 191-individual pseudo-F1 progeny. Three categories of PA variables were assessed: total content, percentages of constitutive subunits and composite ratio variables. For nine functional candidate genes, among which eight co-located with QTLs, we performed association analyses using a diversity panel of 141 grapevine cultivars in order to identify causal SNPs. Results Multiple QTL analysis revealed a total of 103 and 43 QTLs, respectively for seed and skin PA variables. Loci were mainly of additive effect while some loci were primarily of dominant effect. Results also showed a large involvement of pairwise epistatic interactions in shaping PA composition. QTLs for PA variables in skin and seeds differed in number, position, involvement of epistatic interaction and allelic effect, thus revealing different genetic determinisms for grape PA composition in seeds and skin. Association results were consistent with QTL analyses in most cases: four out of nine tested candidate genes (VvLAR1, VvMYBPA2, VvCHI1, VvMYBPA1) showed at least one significant association with PA variables, especially VvLAR1 revealed as of great interest for further functional investigation. Some SNP-phenotype associations were observed only in the diversity panel. Conclusions This study presents the first QTL analysis on grape berry PA composition with a comparison between skin and seeds, together with an association study. Our results suggest a complex genetic control for PA traits and different genetic architectures for grape PA composition between berry skin and seeds. This work also uncovers novel genomic regions for further investigation in order to increase our knowledge of the genetic basis of PA composition. PMID:22369244

Automated quantitative histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary growth.

PubMed

Sankar, Martial; Nieminen, Kaisa; Ragni, Laura; Xenarios, Ioannis; Hardtke, Christian S

2014-02-11

Among various advantages, their small size makes model organisms preferred subjects of investigation. Yet, even in model systems detailed analysis of numerous developmental processes at cellular level is severely hampered by their scale. For instance, secondary growth of Arabidopsis hypocotyls creates a radial pattern of highly specialized tissues that comprises several thousand cells starting from a few dozen. This dynamic process is difficult to follow because of its scale and because it can only be investigated invasively, precluding comprehensive understanding of the cell proliferation, differentiation, and patterning events involved. To overcome such limitation, we established an automated quantitative histology approach. We acquired hypocotyl cross-sections from tiled high-resolution images and extracted their information content using custom high-throughput image processing and segmentation. Coupled with automated cell type recognition through machine learning, we could establish a cellular resolution atlas that reveals vascular morphodynamics during secondary growth, for example equidistant phloem pole formation. DOI: http://dx.doi.org/10.7554/eLife.01567.001.

A quantitative framework for whole-body coordination reveals specific deficits in freely walking ataxic mice

PubMed Central

Machado, Ana S; Darmohray, Dana M; Fayad, João; Marques, Hugo G; Carey, Megan R

2015-01-01

The coordination of movement across the body is a fundamental, yet poorly understood aspect of motor control. Mutant mice with cerebellar circuit defects exhibit characteristic impairments in locomotor coordination; however, the fundamental features of this gait ataxia have not been effectively isolated. Here we describe a novel system (LocoMouse) for analyzing limb, head, and tail kinematics of freely walking mice. Analysis of visibly ataxic Purkinje cell degeneration (pcd) mice reveals that while differences in the forward motion of individual paws are fully accounted for by changes in walking speed and body size, more complex 3D trajectories and, especially, inter-limb and whole-body coordination are specifically impaired. Moreover, the coordination deficits in pcd are consistent with a failure to predict and compensate for the consequences of movement across the body. These results isolate specific impairments in whole-body coordination in mice and provide a quantitative framework for understanding cerebellar contributions to coordinated locomotion. DOI: http://dx.doi.org/10.7554/eLife.07892.001 PMID:26433022

Automated quantitative histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary growth

PubMed Central

Sankar, Martial; Nieminen, Kaisa; Ragni, Laura; Xenarios, Ioannis; Hardtke, Christian S

2014-01-01

Among various advantages, their small size makes model organisms preferred subjects of investigation. Yet, even in model systems detailed analysis of numerous developmental processes at cellular level is severely hampered by their scale. For instance, secondary growth of Arabidopsis hypocotyls creates a radial pattern of highly specialized tissues that comprises several thousand cells starting from a few dozen. This dynamic process is difficult to follow because of its scale and because it can only be investigated invasively, precluding comprehensive understanding of the cell proliferation, differentiation, and patterning events involved. To overcome such limitation, we established an automated quantitative histology approach. We acquired hypocotyl cross-sections from tiled high-resolution images and extracted their information content using custom high-throughput image processing and segmentation. Coupled with automated cell type recognition through machine learning, we could establish a cellular resolution atlas that reveals vascular morphodynamics during secondary growth, for example equidistant phloem pole formation. DOI: http://dx.doi.org/10.7554/eLife.01567.001 PMID:24520159

Chemical compositions, chromatographic fingerprints and antioxidant activities of Andrographis Herba.

PubMed

Zhao, Yang; Kao, Chun-Pin; Wu, Kun-Chang; Liao, Chi-Ren; Ho, Yu-Ling; Chang, Yuan-Shiun

2014-11-10

This paper describes the development of an HPLC-UV-MS method for quantitative determination of andrographolide and dehydroandrographolide in Andrographis Herba and establishment of its chromatographic fingerprint. The method was validated for linearity, limit of detection and quantification, inter- and intra-day precisions, repeatability, stability and recovery. All the validation results of quantitative determination and fingerprinting methods were satisfactory. The developed method was then applied to assay the contents of andrographolide and dehydroandrographolide and to acquire the fingerprints of all the collected Andrographis Herba samples. Furthermore, similarity analysis and principal component analysis were used to reveal the similarities and differences between the samples on the basis of the characteristic peaks. More importantly, the DPPH free radical-scavenging and ferric reducing capacities of the Andrographis Herba samples were assayed. By bivariate correlation analysis, we found that six compounds are positively correlated to DPPH free radical scavenging and ferric reducing capacities, and four compounds are negatively correlated to DPPH free radical scavenging and ferric reducing capacities.

General description and understanding of the nonlinear dynamics of mode-locked fiber lasers.

PubMed

Wei, Huai; Li, Bin; Shi, Wei; Zhu, Xiushan; Norwood, Robert A; Peyghambarian, Nasser; Jian, Shuisheng

2017-05-02

As a type of nonlinear system with complexity, mode-locked fiber lasers are known for their complex behaviour. It is a challenging task to understand the fundamental physics behind such complex behaviour, and a unified description for the nonlinear behaviour and the systematic and quantitative analysis of the underlying mechanisms of these lasers have not been developed. Here, we present a complexity science-based theoretical framework for understanding the behaviour of mode-locked fiber lasers by going beyond reductionism. This hierarchically structured framework provides a model with variable dimensionality, resulting in a simple view that can be used to systematically describe complex states. Moreover, research into the attractors' basins reveals the origin of stochasticity, hysteresis and multistability in these systems and presents a new method for quantitative analysis of these nonlinear phenomena. These findings pave the way for dynamics analysis and system designs of mode-locked fiber lasers. We expect that this paradigm will also enable potential applications in diverse research fields related to complex nonlinear phenomena.

Mapping the Extracellular and Membrane Proteome Associated with the Vasculature and the Stroma in the Embryo*

PubMed Central

Soulet, Fabienne; Kilarski, Witold W.; Roux-Dalvai, Florence; Herbert, John M. J.; Sacewicz, Izabela; Mouton-Barbosa, Emmanuelle; Bicknell, Roy; Lalor, Patricia; Monsarrat, Bernard; Bikfalvi, Andreas

2013-01-01

In order to map the extracellular or membrane proteome associated with the vasculature and the stroma in an embryonic organism in vivo, we developed a biotinylation technique for chicken embryo and combined it with mass spectrometry and bioinformatic analysis. We also applied this procedure to implanted tumors growing on the chorioallantoic membrane or after the induction of granulation tissue. Membrane and extracellular matrix proteins were the most abundant components identified. Relative quantitative analysis revealed differential protein expression patterns in several tissues. Through a bioinformatic approach, we determined endothelial cell protein expression signatures, which allowed us to identify several proteins not yet reported to be associated with endothelial cells or the vasculature. This is the first study reported so far that applies in vivo biotinylation, in combination with robust label-free quantitative proteomics approaches and bioinformatic analysis, to an embryonic organism. It also provides the first description of the vascular and matrix proteome of the embryo that might constitute the starting point for further developments. PMID:23674615

[Phenotypic and genetic analysis of a patient presented with Tietz/Waardenburg type II a syndrome].

PubMed

Wang, Huanhuan; Tang, Lifang; Zhang, Jingmin; Hu, Qin; Chen, Yingwei; Xiao, Bing

2015-08-01

To determine the genetic cause for a patient featuring decreased pigmentation of the skin and iris, hearing loss and multiple congenital anomalies. Routine chromosomal banding was performed to analyze the karyotype of the patient and his parents. Single nucleotide polymorphism array (SNP array) was employed to identify cryptic chromosome aberrations, and quantitative real-time PCR was used to confirm the results. Karyotype analysis has revealed no obvious anomaly for the patient and his parents. SNP array analysis of the patient has demonstrated a 3.9 Mb deletion encompassing 3p13p14.1, which caused loss of entire MITF gene. The deletion was confirmed by quantitative real-time PCR. Clinical features of the patient have included severe bilateral hearing loss, decreased pigmentation of the skin and iris and multiple congenital anomalies. The patient, carrying a 3p13p14.1 deletion, has features of Tietz syndrome/Waardenburg syndrome type IIa. This case may provide additional data for the study of genotype-phenotype correlation of this disease.

Quantitative Proteomic Analysis Reveals Populus cathayana Females Are More Sensitive and Respond More Sophisticatedly to Iron Deficiency than Males.

PubMed

Zhang, Sheng; Zhang, Yunxiang; Cao, Yanchun; Lei, Yanbao; Jiang, Hao

2016-03-04

Previous studies have shown that there are significant sexual differences in the morphological and physiological responses of Populus cathayana Rehder to nitrogen and phosphorus deficiencies, but little is known about the sex-specific differences in responses to iron deficiency. In this study, the effects of iron deficiency on the morphology, physiology, and proteome of P. cathayana males and females were investigated. The results showed that iron deficiency (25 days) significantly decreased height growth, photosynthetic rate, chlorophyll content, and tissue iron concentration in both sexes. A comparison between the sexes indicated that iron-deficient males had less height inhibition and photosynthesis system II or chloroplast ultrastructural damage than iron-deficient females. iTRAQ-based quantitative proteomic analysis revealed that 144 and 68 proteins were decreased in abundance (e.g., proteins involved in photosynthesis, carbohydrate and energy metabolism, and gene expression regulation) and 78 and 39 proteins were increased in abundance (e.g., proteins involved in amino acid metabolism and stress response) according to the criterion of ratio ≥1.5 in females and males, respectively. A comparison between the sexes indicated that iron-deficient females exhibited a greater change in the proteins involved in photosynthesis, carbon and energy metabolism, the redox system, and stress responsive proteins. This study reveals females are more sensitive and have a more sophisticated response to iron deficiency compared with males and provides new insights into differential sexual responses to nutrient deficiency.

An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data.

PubMed

Vu, Trung N; Valkenborg, Dirk; Smets, Koen; Verwaest, Kim A; Dommisse, Roger; Lemière, Filip; Verschoren, Alain; Goethals, Bart; Laukens, Kris

2011-10-20

Nuclear magnetic resonance spectroscopy (NMR) is a powerful technique to reveal and compare quantitative metabolic profiles of biological tissues. However, chemical and physical sample variations make the analysis of the data challenging, and typically require the application of a number of preprocessing steps prior to data interpretation. For example, noise reduction, normalization, baseline correction, peak picking, spectrum alignment and statistical analysis are indispensable components in any NMR analysis pipeline. We introduce a novel suite of informatics tools for the quantitative analysis of NMR metabolomic profile data. The core of the processing cascade is a novel peak alignment algorithm, called hierarchical Cluster-based Peak Alignment (CluPA). The algorithm aligns a target spectrum to the reference spectrum in a top-down fashion by building a hierarchical cluster tree from peak lists of reference and target spectra and then dividing the spectra into smaller segments based on the most distant clusters of the tree. To reduce the computational time to estimate the spectral misalignment, the method makes use of Fast Fourier Transformation (FFT) cross-correlation. Since the method returns a high-quality alignment, we can propose a simple methodology to study the variability of the NMR spectra. For each aligned NMR data point the ratio of the between-group and within-group sum of squares (BW-ratio) is calculated to quantify the difference in variability between and within predefined groups of NMR spectra. This differential analysis is related to the calculation of the F-statistic or a one-way ANOVA, but without distributional assumptions. Statistical inference based on the BW-ratio is achieved by bootstrapping the null distribution from the experimental data. The workflow performance was evaluated using a previously published dataset. Correlation maps, spectral and grey scale plots show clear improvements in comparison to other methods, and the down-to-earth quantitative analysis works well for the CluPA-aligned spectra. The whole workflow is embedded into a modular and statistically sound framework that is implemented as an R package called "speaq" ("spectrum alignment and quantitation"), which is freely available from http://code.google.com/p/speaq/.

Shallow Investigations of the Deep Seafloor: Quantitative Morphology in the Levant Basin, Eastern Mediterranean

NASA Astrophysics Data System (ADS)

Kanari, M.; Ketter, T.; Tibor, G.; Schattner, U.

2017-12-01

We aim to characterize the seafloor morphology and its shallow sub-surface structures and deformations in the deep part of the Levant basin (eastern Mediterranean) using recently acquired high-resolution shallow seismic reflection data and multibeam bathymetry, which allow quantitative analysis of morphology and structure. The Levant basin at the eastern Mediterranean is considered a passive continental margin, where most of the recent geological processes were related in literature to salt tectonics rooted at the Messinian deposits from 6Ma. We analyzed two sets of recently acquired high-resolution data from multibeam bathymetry and 3.5 kHz Chirp sub-bottom seismic reflection in the deep basin of the continental shelf offshore Israel (water depths up to 2100 m). Semi-automatic mapping of seafloor features and seismic data interpretation resulted in quantitative morphological analysis of the seafloor and its underlying sediment with penetration depth up to 60 m. The quantitative analysis and its interpretation are still in progress. Preliminary results reveal distinct morphologies of four major elements: channels, faults, folds and sediment waves, validated by seismic data. From the spatial distribution and orientation analyses of these phenomena, we identify two primary process types which dominate the formation of the seafloor in the Levant basin: structural and sedimentary. Characterization of the geological and geomorphological processes forming the seafloor helps to better understand the transport mechanisms and the relations between sediment transport and deposition in deep water and the shallower parts of the shelf and slope.

Paradoxes of the comparative analysis of ground-based and satellite geodetic measurements in recent geodynamics

NASA Astrophysics Data System (ADS)

Kuzmin, Yu. O.

2017-11-01

The comparative analysis of the Earth's surface deformations measured by ground-based and satellite geodetic methods on the regional and zonal measurement scales is carried out. The displacement velocities and strain rates are compared in the active regions such as Turkmenian-Iranian zone of interaction of the Arabian and Eurasian lithospheric plates and the Kamchatka segment of the subduction of the Pacific Plate beneath the Okotsk Plate. The comparison yields a paradoxical result. With the qualitatively identical kinematics of the motion, the quantitative characteristics of the displacement velocities and rates of strain revealed by the observations using the global navigational satellite system (GNSS) are by 1-2 orders of magnitude higher than those estimated by the more accurate methods of ground-based geodesy. For resolving the revealed paradoxes, it is required to set up special studies on the joint analysis of ground-based and satellite geodetic data from the combined observation sites.

Cognitive functioning in patients with affective disorders and schizophrenia: a meta-analysis.

PubMed

Stefanopoulou, Evgenia; Manoharan, Andiappan; Landau, Sabine; Geddes, John R; Goodwin, Guy; Frangou, Sophia

2009-01-01

There is considerable evidence for cognitive dysfunction in schizophrenia and affective disorders, but the pattern of potential similarities or differences between diagnostic groups remains uncertain. The objective of this study was to conduct a quantitative review of studies on cognitive performance in schizophrenia and affective disorders. Relevant articles were identified through literature search in major databases for the period between January 1980 and December 2005. Meta-analytic treatment of the original studies revealed widespread cognitive deficits in patients with schizophrenia and affective disorders in intellectual ability and speed of information processing, in encoding and retrieval, rule discovery and in response generation and response inhibition. Differences between diagnostic groups were quantitative rather than qualitative.

Quantitation of Indoleacetic Acid Conjugates in Bean Seeds by Direct Tissue Hydrolysis 1

PubMed Central

Bialek, Krystyna; Cohen, Jerry D.

1989-01-01

Gas chromatography-selected ion monitoring-mass spectral analysis using [13C6]indole-3-acetic acid (IAA) as an internal standard provides an effective means for quantitation of IAA liberated during direct strong basic hydrolysis of bean (Phaseolus vulgaris L.) seed powder, provided that extra precautions are undertaken to exclude oxygen from the reaction vial. Direct seed powder hydrolysis revealed that the major portion of amide IAA conjugates in bean seeds are not extractable by aqueous acetone, the solvent used commonly for IAA conjugate extraction from seeds and other plant tissues. Strong basic hydrolysis of plant tissue can be used to provide new information on IAA content. Images Figure 1 PMID:16666783

Tandem transmission/reflection mode XRD instrument including XRF for in situ measurement of Martian rocks and soils

NASA Astrophysics Data System (ADS)

Delhez, Robert; Van der Gaast, S. J.; Wielders, Arno; de Boer, J. L.; Helmholdt, R. B.; van Mechelen, J.; Reiss, C.; Woning, L.; Schenk, H.

2003-02-01

The mineralogy of the surface material of Mars is the key to disclose its present and past life and climates. Clay mineral species, carbonates, and ice (water and CO2) are and/or contain their witnesses. X-ray powder diffraction (XRPD) is the most powerful analytical method to identify and quantitatively characterize minerals in complex mixtures. This paper discusses the development of a working model of an instrument consisting of a reflection mode diffractometer and a transmission mode CCD-XRPD instrument, combined with an XRF module. The CCD-XRD/XRF instrument is analogous to the instrument for Mars missions developed by Sarrazin et al. (1998). This part of the tandem instrument enables "quick and dirty" analysis of powdered (!) matter to monitor semi-quantitatively the presence of clay minerals as a group, carbonates, and ices and yields semi-quantitative chemical information from X-ray fluorescence (XRF). The reflection mode instrument (i) enables in-situ measurements of rocks and soils and quantitative information on the compounds identified, (ii) has a high resolution and reveals large spacings for accurate identification, in particular of clay mineral species, and (iii) the shape of the line profiles observed reveals the kind and approximate amounts of lattice imperfections present. It will be shown that the information obtained with the reflection mode diffractometer is crucial for finding signs of life and changes in the climate on Mars. Obviously this instrument can also be used for other extra-terrestrial research.

Dating Violence among High-Risk Young Women: A Systematic Review Using Quantitative and Qualitative Methods

PubMed Central

Joly, Lauren E.; Connolly, Jennifer

2016-01-01

Our systematic review identified 21 quantitative articles and eight qualitative articles addressing dating violence among high risk young women. The groups of high-risk young women in this review include street-involved, justice-involved, pregnant or parenting, involved with Child Protective Services, and youth diagnosed with a mental health issue. Our meta-analysis of the quantitative articles indicated that 34% (CI = 0.24–0.45) of high-risk young women report that they have been victims of physical dating violence and 45% (CI = 0.31–0.61) of these young women report perpetrating physical dating violence. Significant moderator variables included questionnaire and timeframe. Meta-synthesis of the qualitative studies revealed that high-risk young women report perpetrating dating violence to gain power and respect, whereas women report becoming victims of dating violence due to increased vulnerability. PMID:26840336

Finding the bottom and using it

PubMed Central

Sandoval, Ruben M.; Wang, Exing; Molitoris, Bruce A.

2014-01-01

Maximizing 2-photon parameters used in acquiring images for quantitative intravital microscopy, especially when high sensitivity is required, remains an open area of investigation. Here we present data on correctly setting the black level of the photomultiplier tube amplifier by adjusting the offset to allow for accurate quantitation of low intensity processes. When the black level is set too high some low intensity pixel values become zero and a nonlinear degradation in sensitivity occurs rendering otherwise quantifiable low intensity values virtually undetectable. Initial studies using a series of increasing offsets for a sequence of concentrations of fluorescent albumin in vitro revealed a loss of sensitivity for higher offsets at lower albumin concentrations. A similar decrease in sensitivity, and therefore the ability to correctly determine the glomerular permeability coefficient of albumin, occurred in vivo at higher offset. Finding the offset that yields accurate and linear data are essential for quantitative analysis when high sensitivity is required. PMID:25313346

Differentiation of Cuscuta chinensis and Cuscuta australis by HPLC-DAD-MS analysis and HPLC-UV quantitation.

PubMed

He, Xianghui; Yang, Wenzhi; Ye, Min; Wang, Qing; Guo, Dean

2011-11-01

Cuscuta chinensis and Cuscuta australis, the two botanical sources of the Chinese herbal medicine Tu-Si-Zi, were distinguished from each other based on qualitative and quantitative chemical analysis. By HPLC‑DAD‑MS, a total of 36 compounds were characterized from these two Cuscuta species, including 14 flavonoids, 17 quinic acid derivatives, and 5 lignans. In addition, HPLC‑UV was applied to determine seven major compounds (6 flavonoids plus chlorogenic acid) in 27 batches of Tu-Si-Zi. The results revealed that the amounts of the three classes of compounds varied significantly between the species. C. australis contained more flavonoids but less quinic acid derivatives and lignans than C. chinensis. Particularly, the amounts of kaempferol and astragalin in C. australis were remarkably higher than in C. chinensis. This finding could be valuable for the quality control of Tu-Si-Zi. © Georg Thieme Verlag KG Stuttgart · New York.

Quantitative analysis of dislocation arrangements induced by electromigration in a passivated Al (0.5 wt % Cu) interconnect

NASA Astrophysics Data System (ADS)

Barabash, R. I.; Ice, G. E.; Tamura, N.; Valek, B. C.; Bravman, J. C.; Spolenak, R.; Patel, J. R.

2003-05-01

Electromigration during accelerated testing can induce plastic deformation in apparently undamaged Al interconnect lines as recently revealed by white beam scanning x-ray microdiffraction. In the present article, we provide a first quantitative analysis of the dislocation structure generated in individual micron-sized Al grains during an in situ electromigration experiment. Laue reflections from individual interconnect grains show pronounced streaking during the early stages of electromigration. We demonstrate that the evolution of the dislocation structure during electromigration is highly inhomogeneous and results in the formation of unpaired randomly distributed dislocations as well as geometrically necessary dislocation boundaries. Approximately half of all unpaired dislocations are grouped within the walls. The misorientation created by each boundary and density of unpaired individual dislocations is determined. The origin of the observed plastic deformation is considered in view of the constraints for dislocation arrangements under the applied electric field during electromigration.

Establishment of a sensitive system for analysis of human vaginal microbiota on the basis of rRNA-targeted reverse transcription-quantitative PCR.

PubMed

Kurakawa, Takashi; Ogata, Kiyohito; Tsuji, Hirokazu; Kado, Yukiko; Takahashi, Takuya; Kida, Yumi; Ito, Masahiro; Okada, Nobuhiko; Nomoto, Koji

2015-04-01

Ten specific primer sets, for Lactobacillus gasseri, Lactobacillus crispatus, Atopobium vaginae, Gardnerella vaginalis, Mobiluncus curtisii, Chlamydia trachomatis/muridarum, Bifidobacterium longum subsp. longum, Bifidobacterium longum subsp. infantis, Bifidobacterium adolescentis, and Bifidobacterium angulatum, were developed for quantitative analysis of vaginal microbiota. rRNA-targeted reverse transcription-quantitative PCR (RT-qPCR) analysis of the vaginal samples from 12 healthy Japanese volunteers using the new primer sets together with 25 existing primer sets revealed the diversity of their vaginal microbiota: Lactobacilli such as L. crispatus, L. gasseri, Lactobacillus jensenii, Lactobacillus iners, and Lactobacillus vaginalis, as the major populations at 10(7) cells/ml vaginal fluid, were followed by facultative anaerobes such as Streptococcus and strict anaerobes at lower population levels of 10(4) cells/ml or less. Certain bacterial vaginosis (BV)-related bacteria, such as G. vaginalis, A. vaginae, M. curtisii, and Prevotella, were also detected in some subjects. Especially in one subject, both G. vaginalis and A. vaginae were detected at high population levels of 10(8.8) and 10(8.9) cells/ml vaginal fluid, suggesting that she is an asymptomatic BV patient. These results suggest that the RT-qPCR system is effective for accurate analysis of major vaginal commensals and diagnosis of several vaginal infections. Copyright © 2015 Elsevier B.V. All rights reserved.

Correlative SEM SERS for quantitative analysis of dimer nanoparticles.

PubMed

Timmermans, F J; Lenferink, A T M; van Wolferen, H A G M; Otto, C

2016-11-14

A Raman microscope integrated with a scanning electron microscope was used to investigate plasmonic structures by correlative SEM-SERS analysis. The integrated Raman-SEM microscope combines high-resolution electron microscopy information with SERS signal enhancement from selected nanostructures with adsorbed Raman reporter molecules. Correlative analysis is performed for dimers of two gold nanospheres. Dimers were selected on the basis of SEM images from multi aggregate samples. The effect of the orientation of the dimer with respect to the polarization state of the laser light and the effect of the particle gap size on the Raman signal intensity is observed. Additionally, calculations are performed to simulate the electric near field enhancement. These simulations are based on the morphologies observed by electron microscopy. In this way the experiments are compared with the enhancement factor calculated with near field simulations and are subsequently used to quantify the SERS enhancement factor. Large differences between experimentally observed and calculated enhancement factors are regularly detected, a phenomenon caused by nanoscale differences between the real and 'simplified' simulated structures. Quantitative SERS experiments reveal the structure induced enhancement factor, ranging from ∼200 to ∼20 000, averaged over the full nanostructure surface. The results demonstrate correlative Raman-SEM microscopy for the quantitative analysis of plasmonic particles and structures, thus enabling a new analytical method in the field of SERS and plasmonics.

Phenotypic analysis of prostate-infiltrating lymphocytes reveals TH17 and Treg skewing.

PubMed

Sfanos, Karen Sandell; Bruno, Tullia C; Maris, Charles H; Xu, Lauren; Thoburn, Christopher J; DeMarzo, Angelo M; Meeker, Alan K; Isaacs, William B; Drake, Charles G

2008-06-01

Pathologic examination of prostate glands removed from patients with prostate cancer commonly reveals infiltrating CD4+ and CD8+ T cells. Little is known about the phenotype of these cells, despite accumulating evidence suggesting a potential role for chronic inflammation in the etiology of prostate cancer. We developed a technique that samples the majority of the peripheral prostate through serial needle aspirates. CD4+ prostate-infiltrating lymphocytes (PIL) were isolated using magnetic beads and analyzed for subset skewing using both flow cytometry and quantitative reverse transcription-PCR. The transcriptional profile of fluorescence-activated cell sorted prostate-infiltrating regulatory T cells (CD4+, CD25+, GITR+) was compared with naïve, peripheral blood T cells using microarray analysis. CD4+ PIL showed a paucity of TH2 (interleukin-4-secreting) cells, a surprising finding given the generally accepted association of these cells with chronic, smoldering inflammation. Instead, CD4+ PIL seemed to be skewed towards a regulatory Treg phenotype (FoxP3+) as well as towards the TH17 phenotype (interleukin-17+). We also found that a preponderance of TH17-mediated inflammation was associated with a lower pathologic Gleason score. These protein level data were reflected at the message level, as analyzed by quantitative reverse transcription-PCR. Microarray analysis of pooled prostate-infiltrating T(reg) revealed expected Treg-associated transcripts (FoxP3, CTLA-4, GITR, LAG-3) as well as a number of unique cell surface markers that may serve as additional Treg markers. Taken together, these data suggest that TH17 and/or Treg CD4+ T cells (rather than TH2 T cells) may be involved in the development or progression of prostate cancer.

Phenotypic Analysis of Prostate-Infiltrating Lymphocytes Reveals TH17 and Treg Skewing

PubMed Central

Sfanos, Karen Sandell; Bruno, Tullia C.; Maris, Charles H.; Xu, Lauren; Thoburn, Christopher J.; DeMarzo, Angelo M.; Meeker, Alan K.; Isaacs, William B.; Drake, Charles G.

2011-01-01

Purpose Pathologic examination of prostate glands removed from patients with prostate cancer commonly reveals infiltrating CD4+ and CD8+ T cells. Little is known about the phenotype of these cells, despite accumulating evidence suggesting a potential role for chronic inflammation in the etiology of prostate cancer. Experimental Design We developed a technique that samples the majority of the peripheral prostate through serial needle aspirates. CD4+ prostate-infiltrating lymphocytes (PIL) were isolated using magnetic beads and analyzed for subset skewing using both flow cytometry and quantitative reverse transcription-PCR. The transcriptional profile of fluorescence-activated cell sorted prostate-infiltrating regulatory T cells (CD4+, CD25+, GITR+) was compared with naïve, peripheral blood T cells using microarray analysis. Results CD4+ PIL showed a paucity of TH2 (interleukin-4– secreting) cells, a surprising finding given the generally accepted association of these cells with chronic, smoldering inflammation. Instead, CD4+ PIL seemed to be skewed towards a regulatory Treg phenotype (FoxP3+) as well as towards the TH17 phenotype (interleukin-17+). We also found that a preponderance of TH17-mediated inflammation was associated with a lower pathologic Gleason score. These protein level data were reflected at the message level, as analyzed by quantitative reverse transcription-PCR. Microarray analysis of pooled prostate-infiltrating Treg revealed expected Treg-associated transcripts (FoxP3, CTLA-4, GITR, LAG-3) as well as a number of unique cell surface markers that may serve as additional Treg markers. Conclusion Taken together, these data suggest that TH17 and/or Treg CD4+ T cells (rather than TH2 T cells) may be involved in the development or progression of prostate cancer. PMID:18519750

Label-free protein profiling of formalin-fixed paraffin-embedded (FFPE) heart tissue reveals immediate mitochondrial impairment after ionising radiation.

PubMed

Azimzadeh, Omid; Scherthan, Harry; Yentrapalli, Ramesh; Barjaktarovic, Zarko; Ueffing, Marius; Conrad, Marcus; Neff, Frauke; Calzada-Wack, Julia; Aubele, Michaela; Buske, Christian; Atkinson, Michael J; Hauck, Stefanie M; Tapio, Soile

2012-04-18

Qualitative proteome profiling of formalin-fixed, paraffin-embedded (FFPE) tissue is advancing the field of clinical proteomics. However, quantitative proteome analysis of FFPE tissue is hampered by the lack of an efficient labelling method. The usage of conventional protein labelling on FFPE tissue has turned out to be inefficient. Classical labelling targets lysine residues that are blocked by the formalin treatment. The aim of this study was to establish a quantitative proteomics analysis of FFPE tissue by combining the label-free approach with optimised protein extraction and separation conditions. As a model system we used FFPE heart tissue of control and exposed C57BL/6 mice after total body irradiation using a gamma ray dose of 3 gray. We identified 32 deregulated proteins (p≤0.05) in irradiated hearts 24h after the exposure. The proteomics data were further evaluated and validated by bioinformatics and immunoblotting investigation. In good agreement with our previous results using fresh-frozen tissue, the analysis indicated radiation-induced alterations in three main biological pathways: respiratory chain, lipid metabolism and pyruvate metabolism. The label-free approach enables the quantitative measurement of radiation-induced alterations in FFPE tissue and facilitates retrospective biomarker identification using clinical archives. Copyright © 2012 Elsevier B.V. All rights reserved.

Emotion regulation in bereavement: searching for and finding emotional support in social network sites

NASA Astrophysics Data System (ADS)

Döveling, Katrin

2015-04-01

In an age of rising impact of online communication in social network sites (SNS), emotional interaction is neither limited nor restricted by time or space. Bereavement extends to the anonymity of cyberspace. What role does virtual interaction play in SNS in dealing with the basic human emotion of grief caused by the loss of a beloved person? The analysis laid out in this article provides answers in light of an interdisciplinary perspective on online bereavement. Relevant lines of research are scrutinized. After laying out the theoretical spectrum for the study, hypotheses based on a prior in-depth qualitative content analysis of 179 postings in three different German online bereavement platforms are proposed and scrutinized in a quantitative content analysis (2127 postings from 318 users). Emotion regulation patterns in SNS and similarities as well as differences in online bereavement of children, adolescents and adults are revealed. Large-scale quantitative findings into central motives, patterns, and restorative effects of online shared bereavement in regulating distress, fostering personal empowerment, and engendering meaning are presented. The article closes with implications for further analysis in memorialization practices.

An emerging strategy for evaluating the grades of Keemun black tea by combinatory liquid chromatography-Orbitrap mass spectrometry-based untargeted metabolomics and inhibition effects on α-glucosidase and α-amylase.

PubMed

Guo, Xuemei; Long, Piaopiao; Meng, Qilu; Ho, Chi-Tang; Zhang, Liang

2018-04-25

Quantitative analysis and untargeted liquid chromatography mass spectrum (LC-MS) based metabolomics of different grades of Keemun black tea (KBT) were conducted. Quantitative analysis did not show tight correlation between tea grades and contents of polyphenols, but untargeted metabolomics analysis revealed that high-grades KBT were distinguished from the low-grades. S-plot and Variable Importance (VIP) analysis gave 28 marker compounds responsible for the discrimination of different grades of KBT. The inhibitory effects of KBT on α-amylase and α-glucosidase were positively correlated to tea grades, and the correlation coefficient between each marker compound and inhibitory rate were calculated. Thirteen compounds were positively related to the anti-glycemic activity, and theasinensin A, afzelechin gallate and kaempferol-glucoside were confirmed as grade-related bioactive marker compounds by chemical and bioassay in effective fractions. This study suggested that combinatory metabolomics and bioactivities assay provided a new strategy for the classification of tea grades. Copyright © 2017 Elsevier Ltd. All rights reserved.

Quantitation of heat-shock proteins in clinical samples using mass spectrometry.

PubMed

Kaur, Punit; Asea, Alexzander

2011-01-01

Mass spectrometry (MS) is a powerful analytical tool for proteomics research and drug and biomarker discovery. MS enables identification and quantification of known and unknown compounds by revealing their structural and chemical properties. Proper sample preparation for MS-based analysis is a critical step in the proteomics workflow because the quality and reproducibility of sample extraction and preparation for downstream analysis significantly impact the separation and identification capabilities of mass spectrometers. The highly expressed proteins represent potential biomarkers that could aid in diagnosis, therapy, or drug development. Because the proteome is so complex, there is no one standard method for preparing protein samples for MS analysis. Protocols differ depending on the type of sample, source, experiment, and method of analysis. Molecular chaperones play significant roles in almost all biological functions due to their capacity for detecting intracellular denatured/unfolded proteins, initiating refolding or denaturation of such malfolded protein sequences and more recently for their role in the extracellular milieu as chaperokines. In this chapter, we describe the latest techniques for quantitating the expression of molecular chaperones in human clinical samples.

Dynamic transcriptional signature and cell fate analysis reveals plasticity of individual neural plate border cells

PubMed Central

Roellig, Daniela; Tan-Cabugao, Johanna; Esaian, Sevan; Bronner, Marianne E

2017-01-01

The ‘neural plate border’ of vertebrate embryos contains precursors of neural crest and placode cells, both defining vertebrate characteristics. How these lineages segregate from neural and epidermal fates has been a matter of debate. We address this by performing a fine-scale quantitative temporal analysis of transcription factor expression in the neural plate border of chick embryos. The results reveal significant overlap of transcription factors characteristic of multiple lineages in individual border cells from gastrula through neurula stages. Cell fate analysis using a Sox2 (neural) enhancer reveals that cells that are initially Sox2+ cells can contribute not only to neural tube but also to neural crest and epidermis. Moreover, modulating levels of Sox2 or Pax7 alters the apportionment of neural tube versus neural crest fates. Our results resolve a long-standing question and suggest that many individual border cells maintain ability to contribute to multiple ectodermal lineages until or beyond neural tube closure. DOI: http://dx.doi.org/10.7554/eLife.21620.001 PMID:28355135

Comparative analysis of Hibiscus sabdariffa (roselle) hot and cold extracts in respect to their potential for α-glucosidase inhibition.

PubMed

Rasheed, Dalia M; Porzel, Andrea; Frolov, Andrei; El Seedi, Hesham R; Wessjohann, Ludger A; Farag, Mohamed A

2018-06-01

Roselle (Hibiscus sabdariffa) is a functional food with potential health benefits, consumed either as hot or cold beverage. To ensure quality control of its various products, accurate measurement of active metabolites is warranted. Herein, we propose a combination of ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS) and nuclear magnetic resonance (NMR) analytical platforms for the untargeted characterization of metabolites in two roselle cultivars, Aswan and Sudan-1. The analyses revealed 33 metabolites, including sugars, flavonoids, anthocyanins, phenolic and aliphatic organic acids. Their relative contents in cultivars were assessed via principle component analysis (PCA) and orthogonal projection to latent structures analysis (OPLS). Impact of the different extraction methods (decoction, infusion and maceration) was compared by quantitative 1 H NMR spectroscopy, revealing cold maceration to be optimal for preserving anthocyanins, whereas infusion was more suited for recovering organic acids. The metabolite pattern revealed by the different extraction methods was found in good correlation for their ability to inhibit α-glucosidase enzyme. Copyright © 2018 Elsevier Ltd. All rights reserved.

Advanced STEM microanalysis of bimetallic nanoparticle catalysts

NASA Astrophysics Data System (ADS)

Lyman, Charles E.; Dimick, Paul S.

2012-05-01

Individual particles within bimetallic nanoparticle populations are not always identical, limiting the usefulness of bulk analysis techniques such as EXAFS. The scanning transmission electron microscope (STEM) is the only instrument able to characterize supported nanoparticle populations on a particle-by-particle basis. Quantitative elemental analyses of sub-5-nm particles reveal phase separations among particles and surface segregation within particles. This knowledge can lead to improvements in bimetallic catalysts. Advanced STEMs with field-emission guns, aberration-corrected optics, and efficient signal detection systems allow analysis of sub-nanometer particles.

Quantitative study of fruit flavonoids in citrus hybrids of King (C. nobilis) and Mukaku Kishu (C. kinokuni).

PubMed

Kawaii, S; Tomono, Y; Katase, E; Ogawa, K; Nonomura-Nakano, M; Nesumi, H; Yoshida, T; Sugiura, M; Yano, M

2001-08-01

Twenty-four Citrus hybrids of King (C. nobilis) and Mukaku Kishu (C. kinokuni) were examined for their flavonoid profiles of the edible part by reversed-phase HPLC analysis. Two hybrids (G-155 and G-156) contained higher amounts of natsudaidain than their parents, whereas the remainder of the hybrids had a character intermediate between those of King and Mukaku Kishu on the basis of polymethoxylated flavone composition. Principal component analysis revealed the distribution of the hybrids by quantifying 23 flavonoid contents.

Reversed-phase high-performance liquid chromatography of sulfur mustard in water

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

Raghuveeran, C.D.; Malhotra, R.C.; Dangi, R.S.

1993-01-01

A reversed-phase high-performance liquid chromatography method for the detection and quantitation of sulfur mustard (HD) in water is described with detection at 200 nm. The detection based on the solubility of HD in water revealed that extremely low quantities of HD (4 to 5 mg/L) only are soluble. Experience shows that water is still the medium of choice for the analysis of HD in water and aqueous effluents in spite of the minor handicap of its half-life of ca. 4 minutes, which only calls for speedy analysis.

Quantitative proteomics and systems analysis of cultured H9C2 cardiomyoblasts during differentiation over time supports a 'function follows form' model of differentiation.

PubMed

Kankeu, Cynthia; Clarke, Kylie; Van Haver, Delphi; Gevaert, Kris; Impens, Francis; Dittrich, Anna; Roderick, H Llewelyn; Passante, Egle; Huber, Heinrich J

2018-05-17

The rat cardiomyoblast cell line H9C2 has emerged as a valuable tool for studying cardiac development, mechanisms of disease and toxicology. We present here a rigorous proteomic analysis that monitored the changes in protein expression during differentiation of H9C2 cells into cardiomyocyte-like cells over time. Quantitative mass spectrometry followed by gene ontology (GO) enrichment analysis revealed that early changes in H9C2 differentiation are related to protein pathways of cardiac muscle morphogenesis and sphingolipid synthesis. These changes in the proteome were followed later in the differentiation time-course by alterations in the expression of proteins involved in cation transport and beta-oxidation. Studying the temporal profile of the H9C2 proteome during differentiation in further detail revealed eight clusters of co-regulated proteins that can be associated with early, late, continuous and transient up- and downregulation. Subsequent reactome pathway analysis based on these eight clusters further corroborated and detailed the results of the GO analysis. Specifically, this analysis confirmed that proteins related to pathways in muscle contraction are upregulated early and transiently, and proteins relevant to extracellular matrix organization are downregulated early. In contrast, upregulation of proteins related to cardiac metabolism occurs at later time points. Finally, independent validation of the proteomics results by immunoblotting confirmed hereto unknown regulators of cardiac structure and ionic metabolism. Our results are consistent with a 'function follows form' model of differentiation, whereby early and transient alterations of structural proteins enable subsequent changes that are relevant to the characteristic physiology of cardiomyocytes.

Quantitative somatosensory testing of the penis: optimizing the clinical neurological examination.

PubMed

Bleustein, Clifford B; Eckholdt, Haftan; Arezzo, Joseph C; Melman, Arnold

2003-06-01

Quantitative somatosensory testing, including vibration, pressure, spatial perception and thermal thresholds of the penis, has demonstrated neuropathy in patients with a history of erectile dysfunction of all etiologies. We evaluated which measurement of neurological function of the penis was best at predicting erectile dysfunction and examined the impact of location on the penis for quantitative somatosensory testing measurements. A total of 107 patients were evaluated. All patients were required to complete the erectile function domain of the International Index of Erectile Function (IIEF) questionnaire, of whom 24 had no complaints of erectile dysfunction and scored within the "normal" range on the IIEF. Patients were subsequently tested on ventral middle penile shaft, proximal dorsal midline penile shaft and glans penis (with foreskin retracted) for vibration, pressure, spatial perception, and warm and cold thermal thresholds. Mixed models repeated measures analysis of variance controlling for age, diabetes and hypertension revealed that method of measurement (quantitative somatosensory testing) was predictive of IIEF score (F = 209, df = 4,1315, p <0.001), while site of measurement on the penis was not. To determine the best method of measurement, we used hierarchical regression, which revealed that warm temperature was the best predictor of erectile dysfunction with pseudo R(2) = 0.19, p <0.0007. There was no significant improvement in predicting erectile dysfunction when another test was added. Using 37C and greater as the warm thermal threshold yielded a sensitivity of 88.5%, specificity 70.0% and positive predictive value 85.5%. Quantitative somatosensory testing using warm thermal threshold measurements taken at the glans penis can be used alone to assess the neurological status of the penis. Warm thermal thresholds alone offer a quick, noninvasive accurate method of evaluating penile neuropathy in an office setting.

Purification, developmental expression, and in silico characterization of α-amylase inhibitor from Echinochloa frumentacea.

PubMed

Panwar, Priyankar; Verma, A K; Dubey, Ashutosh

2018-05-01

Barnyard ( Echinochloa frumentacea ) and finger ( Eleusine coracana ) millet growing at northwestern Himalaya were explored for the α-amylase inhibitor (α-AI). The mature seeds of barnyard millet variety PRJ1 had maximum α-AI activity which increases in different developmental stage. α-AI was purified up to 22.25-fold from barnyard millet variety PRJ1. Semi-quantitative PCR of different developmental stages of barnyard millet seeds showed increased levels of the transcript from 7 to 28 days. Sequence analysis revealed that it contained 315 bp nucleotide which encodes 104 amino acid sequence with molecular weight 10.72 kDa. The predicted 3D structure of α-AI was 86.73% similar to a bifunctional inhibitor of ragi. In silico analysis of 71 α-AI protein sequences were carried out for biochemical features, homology search, multiple sequence alignment, phylogenetic tree construction, motif, and superfamily distribution of protein sequences. Analysis of multiple sequence alignment revealed the existence of conserved regions NPLP[S/G]CRWYVV[S/Q][Q/R]TCG[V/I] throughout sequences. Superfam analysis revealed that α-AI protein sequences were distributed among seven different superfamilies.

Validation of Quantitative Multimodality Analysis of Telomerase Activity in Urine Cells as a Noninvasive Diagnostic and Prognostic Tool for Prostate Cancer

DTIC Science & Technology

2005-08-01

present study, who was previously misdiagnosed with BPH and inflammation, eventually has revealed the prostate cancer with the Gleason score 7. Therefore...Noninvasive Diagnostic and Prognostic Tool for Prostate Cancer ...5a. CONTRACT NUMBER Urine Cells as a Noninvasive Diagnostic and Prognostic Tool for Prostate Cancer 5b. GRANT NUMBER W81XWH-04-1-0774 5c

An Integrated Literature Review of the Knowledge Needs of Parents with Children with Special Health Care Needs and of Instruments to Assess These Needs

ERIC Educational Resources Information Center

Adler, Kristin; Salanterä, Sanna; Leino­-Kilpi, Helena; Grädel, Barbara

2015-01-01

The purpose of this integrative (including both quantitative and qualitative studies) literature review was to identify knowledge needs of parents of a child with special health care needs and to evaluate instruments to assess these needs. The content analysis of 48 publications revealed a vast amount of knowledge needs that were categorized into…

Isolation and Identification of Lactic Acid Bacteria from Traditional Dairy Products in Baotou and Bayannur of Midwestern Inner Mongolia and q-PCR Analysis of Predominant Species

PubMed Central

2016-01-01

In this study, traditional culture method and 16S rRNA gene analysis were applied to reveal the composition and diversity of lactic acid bacteria (LAB) of fermented cow milk, huruud and urum from Baotou and Bayannur of midwestern Inner Mongolia. Also, the quantitative results of dominant LAB species in three different types of dairy products from Baotou and Bayannur were gained by quantitative polymerase chain reaction (q-PCR) technology. Two hundred and two LAB strains isolated from sixty-six samples were identified and classified into four genera, namely Enterococcus, Lactococcus, Lactobacillus, Leuconostoc, and twenty-one species and subspecies. From these isolates, Lactococcus lactis subsp. lactis (32.18%), Lactobacillus plantarum (12.38%) and Leuconosto mesenteroides (11.39%) were considered as the dominated LAB species under the condition of cultivating in MRS and M17 medium. And the q-PCR results revealed that the number of dominant species varied from samples to samples and from region to region. This study clearly shows the composition and diversity of LAB existing in fermented cow milk, huruud and urum, which could be considered as valuable resources for LAB isolation and further probiotic selection. PMID:27621691

An Integrative Platform for Three-dimensional Quantitative Analysis of Spatially Heterogeneous Metastasis Landscapes

NASA Astrophysics Data System (ADS)

Guldner, Ian H.; Yang, Lin; Cowdrick, Kyle R.; Wang, Qingfei; Alvarez Barrios, Wendy V.; Zellmer, Victoria R.; Zhang, Yizhe; Host, Misha; Liu, Fang; Chen, Danny Z.; Zhang, Siyuan

2016-04-01

Metastatic microenvironments are spatially and compositionally heterogeneous. This seemingly stochastic heterogeneity provides researchers great challenges in elucidating factors that determine metastatic outgrowth. Herein, we develop and implement an integrative platform that will enable researchers to obtain novel insights from intricate metastatic landscapes. Our two-segment platform begins with whole tissue clearing, staining, and imaging to globally delineate metastatic landscape heterogeneity with spatial and molecular resolution. The second segment of our platform applies our custom-developed SMART 3D (Spatial filtering-based background removal and Multi-chAnnel forest classifiers-based 3D ReconsTruction), a multi-faceted image analysis pipeline, permitting quantitative interrogation of functional implications of heterogeneous metastatic landscape constituents, from subcellular features to multicellular structures, within our large three-dimensional (3D) image datasets. Coupling whole tissue imaging of brain metastasis animal models with SMART 3D, we demonstrate the capability of our integrative pipeline to reveal and quantify volumetric and spatial aspects of brain metastasis landscapes, including diverse tumor morphology, heterogeneous proliferative indices, metastasis-associated astrogliosis, and vasculature spatial distribution. Collectively, our study demonstrates the utility of our novel integrative platform to reveal and quantify the global spatial and volumetric characteristics of the 3D metastatic landscape with unparalleled accuracy, opening new opportunities for unbiased investigation of novel biological phenomena in situ.

Wide-scale quantitative phosphoproteomic analysis reveals that cold treatment of T cells closely mimics soluble antibody stimulation

PubMed Central

Ji, Qinqin; Salomon, Arthur R.

2015-01-01

The activation of T-lymphocytes through antigen-mediated T-cell receptor (TCR) clustering is vital in regulating the adaptive-immune response. Although T cell receptor signaling has been extensively studied, the fundamental mechanisms for signal initiation are not fully understood. Reduced temperature initiated some of the hallmarks of TCR signaling such as increased phosphorylation and activation on ERK and calcium release from the endoplasmic reticulum as well as coalesce T-cell membrane microdomains. The precise mechanism of TCR signaling initiation due to temperature change remains obscure. One critical question is whether signaling initiated by cold treatment of T cells differs from signaling initiated by crosslinking of the T cell receptor. To address this uncertainty, a wide-scale, quantitative mass spectrometry-based phosphoproteomic analysis was performed on T cells stimulated either by temperature shift or through crosslinking of the TCR. Careful statistical comparison between the two stimulations revealed a striking level of identity between the subset of 339 sites that changed significantly with both stimulations. This study demonstrates for the first time, at unprecedented detail, that T cell cold treatment was sufficient to initiate signaling patterns nearly identical to soluble antibody stimulation, shedding new light on the mechanism of activation of these critically important immune cells. PMID:25839225

Toward a quantitative account of pitch distribution in spontaneous narrative: Method and validation

PubMed Central

Matteson, Samuel E.; Streit Olness, Gloria; Caplow, Nancy J.

2013-01-01

Pitch is well-known both to animate human discourse and to convey meaning in communication. The study of the statistical population distributions of pitch in discourse will undoubtedly benefit from methodological improvements. The current investigation examines a method that parameterizes pitch in discourse as musical pitch interval H measured in units of cents and that disaggregates the sequence of peak word-pitches using tools employed in time-series analysis and digital signal processing. The investigators test the proposed methodology by its application to distributions in pitch interval of the peak word-pitch (collectively called the discourse gamut) that occur in simulated and actual spontaneous emotive narratives obtained from 17 middle-aged African-American adults. The analysis, in rigorous tests, not only faithfully reproduced simulated distributions imbedded in realistic time series that drift and include pitch breaks, but the protocol also reveals that the empirical distributions exhibit a common hidden structure when normalized to a slowly varying mode (called the gamut root) of their respective probability density functions. Quantitative differences between narratives reveal the speakers' relative propensity for the use of pitch levels corresponding to elevated degrees of a discourse gamut (the “e-la”) superimposed upon a continuum that conforms systematically to an asymmetric Laplace distribution. PMID:23654400

Sonoelastography of Plantar Fascia: Reproducibility and Pattern Description in Healthy Subjects and Symptomatic Subjects.

PubMed

Ríos-Díaz, José; Martínez-Payá, Jacinto J; del Baño-Aledo, María Elena; de Groot-Ferrando, Ana; Botía-Castillo, Paloma; Fernández-Rodríguez, David

2015-10-01

The purpose of the work reported here was to describe the sonoelastographic appearance of the plantar fascia of healthy volunteers and patients with fasciitis. Twenty-three healthy subjects and 21 patients with plantar fasciitis were examined using B-mode and real-time sonoelastography (RTSR) scanning. B-Mode examination included fascia thickness and echotexture. Echogenicity and echovariation of the color histogram were analyzed. Fasciae were classified into type 1, blue (more elastic); type 2, blue/green (intermediate); or type 3, green (less elastic). RTSE revealed 72.7% of fasciae as type 2, with no significant association with fasciitis (χ(2) = 3.6, df = 2, p = 0.17). Quantitative analysis of the color histogram revealed a significantly greater intensity of green (mean = 77.8, 95% confidence interval [CI] = 71.9-83.6) and blue (mean = 74.2, 95% CI = 69.7-78.8) in healthy subjects. Echovariation of the color red was 33.4% higher in the fasciitis group than in the healthy group (95% CI = 16.7-50.1). Sonoelastography with quantitative analysis of echovariation can be a useful tool for evaluation of plantar fascia pathology. Copyright © 2015 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

Quantitative phosphoproteomics analysis reveals a key role of insulin growth factor 1 receptor (IGF1R) tyrosine kinase in human sperm capacitation.

PubMed

Wang, Jing; Qi, Lin; Huang, Shaoping; Zhou, Tao; Guo, Yueshuai; Wang, Gaigai; Guo, Xuejiang; Zhou, Zuomin; Sha, Jiahao

2015-04-01

One of the most important changes during sperm capacitation is the enhancement of tyrosine phosphorylation. However, the mechanisms of protein tyrosine phosphorylation during sperm capacitation are not well studied. We used label-free quantitative phosphoproteomics to investigate the overall phosphorylation events during sperm capacitation in humans and identified 231 sites with increased phosphorylation levels. Motif analysis using the NetworKIN algorithm revealed that the activity of tyrosine phosphorylation kinases insulin growth factor 1 receptor (IGF1R)/insulin receptor is significantly enriched among the up-regulated phosphorylation substrates during capacitation. Western blotting further confirmed inhibition of IGF1R with inhibitors GSK1904529A and NVP-AEW541, which inhibited the increase in tyrosine phosphorylation levels during sperm capacitation. Additionally, sperm hyperactivated motility was also inhibited by GSK1904529A and NVP-AEW541 but could be up-regulated by insulin growth factor 1, the ligand of IGF1R. Thus, the IGF1R-mediated tyrosine phosphorylation pathway may play important roles in the regulation of sperm capacitation in humans and could be a target for improvement in sperm functions in infertile men. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Relationship between Plaque Echo, Thickness and Neovascularization Assessed by Quantitative and Semi-quantitative Contrast-Enhanced Ultrasonography in Different Stenosis Groups.

PubMed

Song, Yan; Feng, Jun; Dang, Ying; Zhao, Chao; Zheng, Jie; Ruan, Litao

2017-12-01

The aim of this study was to determine the relationship between plaque echo, thickness and neovascularization in different stenosis groups using quantitative and semi-quantitative contrast-enhanced ultrasound (CEUS) in patients with carotid atherosclerosis plaque. A total of 224 plaques were divided into mild stenosis (<50%; 135 plaques, 60.27%), moderate stenosis (50%-69%; 39 plaques, 17.41%) and severe stenosis (70%-99%; 50 plaques, 22.32%) groups. Quantitative and semi-quantitative methods were used to assess plaque neovascularization and determine the relationship between plaque echo, thickness and neovascularization. Correlation analysis revealed no relationship of neovascularization with plaque echo in the groups using either quantitative or semi-quantitative methods. Furthermore, there was no correlation of neovascularization with plaque thickness using the semi-quantitative method. The ratio of areas under the curve (RAUC) was negatively correlated with plaque thickness (r = -0.317, p = 0.001) in the mild stenosis group. With the quartile method, plaque thickness of the mild stenosis group was divided into four groups, with significant differences between the 1.5-2.2 mm and ≥3.5 mm groups (p = 0.002), 2.3-2.8 mm and ≥3.5 mm groups (p <0.001) and 2.9-3.4 mm and ≥3.5 mm groups (p <0.001). Both semi-quantitative and quantitative CEUS methods characterizing neovascularization of plaque are equivalent with respect to assessing relationships between neovascularization, echogenicity and thickness. However, the quantitative method could fail for plaque <3.5 mm because of motion artifacts. Copyright © 2017 World Federation for Ultrasound in Medicine and Biology. Published by Elsevier Inc. All rights reserved.

The health impact of trade and investment agreements: a quantitative systematic review and network co-citation analysis.

PubMed

Barlow, Pepita; McKee, Martin; Basu, Sanjay; Stuckler, David

2017-03-08

Regional trade agreements are major international policy instruments that shape macro-economic and political systems. There is widespread debate as to whether and how these agreements pose risks to public health. Here we perform a comprehensive systematic review of quantitative studies of the health impact of trade and investment agreements. We identified studies from searches in PubMed, Web of Science, EMBASE, and Global Health Online. Research articles were eligible for inclusion if they were quantitative studies of the health impacts of trade and investment agreements or policy. We systematically reviewed study findings, evaluated quality using the Quality Assessment Tool from the Effective Public Health Practice Project, and performed network citation analysis to study disciplinary siloes. Seventeen quantitative studies met our inclusion criteria. There was consistent evidence that implementing trade agreements was associated with increased consumption of processed foods and sugar-sweetened beverages. Granting import licenses for patented drugs was associated with increased access to pharmaceuticals. Implementing trade agreements and associated policies was also correlated with higher cardiovascular disease incidence and higher Body Mass Index (BMI), whilst correlations with tobacco consumption, under-five mortality, maternal mortality, and life expectancy were inconclusive. Overall, the quality of studies is weak or moderately weak, and co-citation analysis revealed a relative isolation of public health from economics. We identified limitations in existing studies which preclude definitive conclusions of the health impacts of regional trade and investment agreements. Few address unobserved confounding, and many possible consequences and mechanisms linking trade and investment agreements to health remain poorly understood. Results from our co-citation analysis suggest scope for greater interdisciplinary collaboration. Notwithstanding these limitations, our results find evidence that trade agreements pose some significant health risks. Health protections in trade and investment treaties may mitigate these impacts.

Clustering Methods with Qualitative Data: A Mixed Methods Approach for Prevention Research with Small Samples

PubMed Central

Henry, David; Dymnicki, Allison B.; Mohatt, Nathaniel; Allen, James; Kelly, James G.

2016-01-01

Qualitative methods potentially add depth to prevention research, but can produce large amounts of complex data even with small samples. Studies conducted with culturally distinct samples often produce voluminous qualitative data, but may lack sufficient sample sizes for sophisticated quantitative analysis. Currently lacking in mixed methods research are methods allowing for more fully integrating qualitative and quantitative analysis techniques. Cluster analysis can be applied to coded qualitative data to clarify the findings of prevention studies by aiding efforts to reveal such things as the motives of participants for their actions and the reasons behind counterintuitive findings. By clustering groups of participants with similar profiles of codes in a quantitative analysis, cluster analysis can serve as a key component in mixed methods research. This article reports two studies. In the first study, we conduct simulations to test the accuracy of cluster assignment using three different clustering methods with binary data as produced when coding qualitative interviews. Results indicated that hierarchical clustering, K-Means clustering, and latent class analysis produced similar levels of accuracy with binary data, and that the accuracy of these methods did not decrease with samples as small as 50. Whereas the first study explores the feasibility of using common clustering methods with binary data, the second study provides a “real-world” example using data from a qualitative study of community leadership connected with a drug abuse prevention project. We discuss the implications of this approach for conducting prevention research, especially with small samples and culturally distinct communities. PMID:25946969

Statistical image quantification toward optimal scan fusion and change quantification

NASA Astrophysics Data System (ADS)

Potesil, Vaclav; Zhou, Xiang Sean

2007-03-01

Recent advance of imaging technology has brought new challenges and opportunities for automatic and quantitative analysis of medical images. With broader accessibility of more imaging modalities for more patients, fusion of modalities/scans from one time point and longitudinal analysis of changes across time points have become the two most critical differentiators to support more informed, more reliable and more reproducible diagnosis and therapy decisions. Unfortunately, scan fusion and longitudinal analysis are both inherently plagued with increased levels of statistical errors. A lack of comprehensive analysis by imaging scientists and a lack of full awareness by physicians pose potential risks in clinical practice. In this paper, we discuss several key error factors affecting imaging quantification, studying their interactions, and introducing a simulation strategy to establish general error bounds for change quantification across time. We quantitatively show that image resolution, voxel anisotropy, lesion size, eccentricity, and orientation are all contributing factors to quantification error; and there is an intricate relationship between voxel anisotropy and lesion shape in affecting quantification error. Specifically, when two or more scans are to be fused at feature level, optimal linear fusion analysis reveals that scans with voxel anisotropy aligned with lesion elongation should receive a higher weight than other scans. As a result of such optimal linear fusion, we will achieve a lower variance than naïve averaging. Simulated experiments are used to validate theoretical predictions. Future work based on the proposed simulation methods may lead to general guidelines and error lower bounds for quantitative image analysis and change detection.

Clustering Methods with Qualitative Data: a Mixed-Methods Approach for Prevention Research with Small Samples.

PubMed

Henry, David; Dymnicki, Allison B; Mohatt, Nathaniel; Allen, James; Kelly, James G

2015-10-01

Qualitative methods potentially add depth to prevention research but can produce large amounts of complex data even with small samples. Studies conducted with culturally distinct samples often produce voluminous qualitative data but may lack sufficient sample sizes for sophisticated quantitative analysis. Currently lacking in mixed-methods research are methods allowing for more fully integrating qualitative and quantitative analysis techniques. Cluster analysis can be applied to coded qualitative data to clarify the findings of prevention studies by aiding efforts to reveal such things as the motives of participants for their actions and the reasons behind counterintuitive findings. By clustering groups of participants with similar profiles of codes in a quantitative analysis, cluster analysis can serve as a key component in mixed-methods research. This article reports two studies. In the first study, we conduct simulations to test the accuracy of cluster assignment using three different clustering methods with binary data as produced when coding qualitative interviews. Results indicated that hierarchical clustering, K-means clustering, and latent class analysis produced similar levels of accuracy with binary data and that the accuracy of these methods did not decrease with samples as small as 50. Whereas the first study explores the feasibility of using common clustering methods with binary data, the second study provides a "real-world" example using data from a qualitative study of community leadership connected with a drug abuse prevention project. We discuss the implications of this approach for conducting prevention research, especially with small samples and culturally distinct communities.

Image velocimetry and spectral analysis enable quantitative characterization of larval zebrafish gut motility.

PubMed

Ganz, J; Baker, R P; Hamilton, M K; Melancon, E; Diba, P; Eisen, J S; Parthasarathy, R

2018-05-02

Normal gut function requires rhythmic and coordinated movements that are affected by developmental processes, physical and chemical stimuli, and many debilitating diseases. The imaging and characterization of gut motility, especially regarding periodic, propagative contractions driving material transport, are therefore critical goals. Previous image analysis approaches have successfully extracted properties related to the temporal frequency of motility modes, but robust measures of contraction magnitude, especially from in vivo image data, remain challenging to obtain. We developed a new image analysis method based on image velocimetry and spectral analysis that reveals temporal characteristics such as frequency and wave propagation speed, while also providing quantitative measures of the amplitude of gut motion. We validate this approach using several challenges to larval zebrafish, imaged with differential interference contrast microscopy. Both acetylcholine exposure and feeding increase frequency and amplitude of motility. Larvae lacking enteric nervous system gut innervation show the same average motility frequency, but reduced and less variable amplitude compared to wild types. Our image analysis approach enables insights into gut dynamics in a wide variety of developmental and physiological contexts and can also be extended to analyze other types of cell movements. © 2018 John Wiley & Sons Ltd.

ANTONIA perfusion and stroke. A software tool for the multi-purpose analysis of MR perfusion-weighted datasets and quantitative ischemic stroke assessment.

PubMed

Forkert, N D; Cheng, B; Kemmling, A; Thomalla, G; Fiehler, J

2014-01-01

The objective of this work is to present the software tool ANTONIA, which has been developed to facilitate a quantitative analysis of perfusion-weighted MRI (PWI) datasets in general as well as the subsequent multi-parametric analysis of additional datasets for the specific purpose of acute ischemic stroke patient dataset evaluation. Three different methods for the analysis of DSC or DCE PWI datasets are currently implemented in ANTONIA, which can be case-specifically selected based on the study protocol. These methods comprise a curve fitting method as well as a deconvolution-based and deconvolution-free method integrating a previously defined arterial input function. The perfusion analysis is extended for the purpose of acute ischemic stroke analysis by additional methods that enable an automatic atlas-based selection of the arterial input function, an analysis of the perfusion-diffusion and DWI-FLAIR mismatch as well as segmentation-based volumetric analyses. For reliability evaluation, the described software tool was used by two observers for quantitative analysis of 15 datasets from acute ischemic stroke patients to extract the acute lesion core volume, FLAIR ratio, perfusion-diffusion mismatch volume with manually as well as automatically selected arterial input functions, and follow-up lesion volume. The results of this evaluation revealed that the described software tool leads to highly reproducible results for all parameters if the automatic arterial input function selection method is used. Due to the broad selection of processing methods that are available in the software tool, ANTONIA is especially helpful to support image-based perfusion and acute ischemic stroke research projects.

Loss of Chromosome 18 in Neuroendocrine Tumors of the Small Intestine: The Enigma Remains.

PubMed

Nieser, Maike; Henopp, Tobias; Brix, Joachim; Stoß, Laura; Sitek, Barbara; Naboulsi, Wael; Anlauf, Martin; Schlitter, Anna M; Klöppel, Günter; Gress, Thomas; Moll, Roland; Bartsch, Detlef K; Heverhagen, Anna E; Knoefel, Wolfram T; Kaemmerer, Daniel; Haybaeck, Johannes; Fend, Falko; Sperveslage, Jan; Sipos, Bence

2017-01-01

Neuroendocrine tumors of the small intestine (SI-NETs) exhibit an increasing incidence and high mortality rate. Until now, no fundamental molecular event has been linked to the tumorigenesis and progression of these tumors. Only the loss of chromosome 18 (Chr18) has been shown in up to two thirds of SI-NETs, whereby the significance of this alteration is still not understood. We therefore performed the first comprehensive study to identify Chr18-related events at the genetic, epigenetic and gene/protein expression levels. We did expression analysis of all seven putative Chr18-related tumor suppressors by quantitative real-time PCR (qRT-PCR), Western blot and immunohistochemistry. Next-generation exome sequencing and SNP array analysis were performed with five SI-NETs with (partial) loss of Chr18. Finally, we analyzed all microRNAs (miRNAs) located on Chr18 by qRT-PCR, comparing Chr18+/- and Chr18+/+ SI-NETs. Only DCC (deleted in colorectal cancer) revealed loss of/greatly reduced expression in 6/21 cases (29%). No relevant loss of SMAD2, SMAD4, elongin A3 and CABLES was detected. PMAIP1 and maspin were absent at the protein level. Next-generation sequencing did not reveal relevant recurrent somatic mutations on Chr18 either in an exploratory cohort of five SI-NETs, or in a validation cohort (n = 30). SNP array analysis showed no additional losses. The quantitative analysis of all 27 Chr18-related miRNAs revealed no difference in expression between Chr18+/- and Chr18+/+ SI-NETs. DCC seems to be the only Chr18-related tumor suppressor affected by the monoallelic loss of Chr18 resulting in a loss of DCC protein expression in one third of SI-NETs. No additional genetic or epigenetic alterations were present on Chr18. © 2016 S. Karger AG, Basel.

Examining the relationship between social support availability, urban center size, and self-perceived mental health of recent immigrants to Canada: a mixed-methods analysis.

PubMed

Chadwick, Kathryn A; Collins, Patricia A

2015-03-01

The experiences of settlement in a new country (e.g., securing housing and employment, language barriers) pose numerous challenges for recent immigrants that can impede their health and well-being. Lack of social support upon arrival and during settlement may help to explain why immigrant mental health status declines over time. While most urban centers in Canada offer some settlement services, little is known about how the availability of social supports, and the health statuses of recent immigrants, varies by city size. The objective of this mixed-methods study was to examine the relationship between self-perceived mental health (SPMH), social support availability, and urban center size, for recent immigrants to Canada. The quantitative component involved analysis of 2009-2010 Canadian Community Health Survey data, selecting for only recent immigrants and for those living in either large or small urban centers. The qualitative component involved in-depth interviews with managers of settlement service organizations located in three large and three small urban centers in Canada. The quantitative analysis revealed that social support availability is positively associated with higher SPMH status, and is higher in small urban centers. In support of these findings, our interviews revealed that settlement service organizations operating in small urban centers offer more intensive social supports; interviewees attributed this difference to personal relationships in small cities, and the ease with which they can connect to other agencies to provide clients with necessary supports. Logistic regression analysis revealed, however, that recent immigrants in small urban centers are twice as likely to report low SPMH compared to those living in large urban centers. Thus, while the scope and nature of settlements services appears to vary by city size in Canada, more research is needed to understand what effect settlement services have on the health status of recent immigrants to Canada, especially in smaller urban centers. Copyright © 2015. Published by Elsevier Ltd.

Quantitation of repaglinide and metabolites in mouse whole-body thin tissue sections using droplet-based liquid microjunction surface sampling-high-performance liquid chromatography-electrospray ionization tandem mass spectrometry.

PubMed

Chen, Weiqi; Wang, Lifei; Van Berkel, Gary J; Kertesz, Vilmos; Gan, Jinping

2016-03-25

Herein, quantitation aspects of a fully automated autosampler/HPLC-MS/MS system applied for unattended droplet-based surface sampling of repaglinide dosed thin tissue sections with subsequent HPLC separation and mass spectrometric analysis of parent drug and various drug metabolites were studied. Major organs (brain, lung, liver, kidney and muscle) from whole-body thin tissue sections and corresponding organ homogenates prepared from repaglinide dosed mice were sampled by surface sampling and by bulk extraction, respectively, and analyzed by HPLC-MS/MS. A semi-quantitative agreement between data obtained by surface sampling and that by employing organ homogenate extraction was observed. Drug concentrations obtained by the two methods followed the same patterns for post-dose time points (0.25, 0.5, 1 and 2 h). Drug amounts determined in the specific tissues was typically higher when analyzing extracts from the organ homogenates. In addition, relative comparison of the levels of individual metabolites between the two analytical methods also revealed good semi-quantitative agreement. Copyright © 2015 Elsevier B.V. All rights reserved.

Quantitation of repaglinide and metabolites in mouse whole-body thin tissue sections using droplet-based liquid microjunction surface sampling-high-performance liquid chromatography-electrospray ionization tandem mass spectrometry

DOE PAGES

Chen, Weiqi; Wang, Lifei; Van Berkel, Gary J.; ...

2015-11-03

Herein, quantitation aspects of a fully automated autosampler/HPLC-MS/MS system applied for unattended droplet-based surface sampling of repaglinide dosed thin tissue sections with subsequent HPLC separation and mass spectrometric analysis of parent drug and various drug metabolites was studied. Major organs (brain, lung, liver, kidney, muscle) from whole-body thin tissue sections and corresponding organ homogenates prepared from repaglinide dosed mice were sampled by surface sampling and by bulk extraction, respectively, and analyzed by HPLC-MS/MS. A semi-quantitative agreement between data obtained by surface sampling and that by employing organ homogenate extraction was observed. Drug concentrations obtained by the two methods followed themore » same patterns for post-dose time points (0.25, 0.5, 1 and 2 h). Drug amounts determined in the specific tissues was typically higher when analyzing extracts from the organ homogenates. Furthermore, relative comparison of the levels of individual metabolites between the two analytical methods also revealed good semi-quantitative agreement.« less

Quantitation of repaglinide and metabolites in mouse whole-body thin tissue sections using droplet-based liquid microjunction surface sampling-high-performance liquid chromatography-electrospray ionization tandem mass spectrometry

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

Chen, Weiqi; Wang, Lifei; Van Berkel, Gary J.

Herein, quantitation aspects of a fully automated autosampler/HPLC-MS/MS system applied for unattended droplet-based surface sampling of repaglinide dosed thin tissue sections with subsequent HPLC separation and mass spectrometric analysis of parent drug and various drug metabolites was studied. Major organs (brain, lung, liver, kidney, muscle) from whole-body thin tissue sections and corresponding organ homogenates prepared from repaglinide dosed mice were sampled by surface sampling and by bulk extraction, respectively, and analyzed by HPLC-MS/MS. A semi-quantitative agreement between data obtained by surface sampling and that by employing organ homogenate extraction was observed. Drug concentrations obtained by the two methods followed themore » same patterns for post-dose time points (0.25, 0.5, 1 and 2 h). Drug amounts determined in the specific tissues was typically higher when analyzing extracts from the organ homogenates. Furthermore, relative comparison of the levels of individual metabolites between the two analytical methods also revealed good semi-quantitative agreement.« less

Affective outcomes of virtual reality exposure therapy for anxiety and specific phobias: a meta-analysis.

PubMed

Parsons, Thomas D; Rizzo, Albert A

2008-09-01

Virtual reality exposure therapy (VRET) is an increasingly common treatment for anxiety and specific phobias. Lacking is a quantitative meta-analysis that enhances understanding of the variability and clinical significance of anxiety reduction outcomes after VRET. Searches of electronic databases yielded 52 studies, and of these, 21 studies (300 subjects) met inclusion criteria. Although meta-analysis revealed large declines in anxiety symptoms following VRET, moderator analyses were limited due to inconsistent reporting in the VRET literature. This highlights the need for future research studies that report uniform and detailed information regarding presence, immersion, anxiety and/or phobia duration, and demographics.

Qualitative and quantitative processing of side-scan sonar data

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

Dwan, F.S.; Anderson, A.L.; Hilde, T.W.C.

1990-06-01

Modern side-scan sonar systems allow vast areas of seafloor to be rapidly imaged and quantitatively mapped in detail. The application of remote sensing image processing techniques can be used to correct for various distortions inherent in raw sonography. Corrections are possible for water column, slant-range, aspect ratio, speckle and striping noise, multiple returns, power drop-off, and for georeferencing. The final products reveal seafloor features and patterns that are geometrically correct, georeferenced, and have improved signal/noise ratio. These products can be merged with other georeferenced data bases for further database management and information extraction. In order to compare data collected bymore » different systems from a common area and to ground truth measurements and geoacoustic models, quantitative correction must be made for calibrated sonar system and bathymetry effects. Such data inversion must account for system source level, beam pattern, time-varying gain, processing gain, transmission loss, absorption, insonified area, and grazing angle effects. Seafloor classification can then be performed on the calculated back-scattering strength using Lambert's Law and regression analysis. Examples are given using both approaches: image analysis and inversion of data based on the sonar equation.« less

Digital histologic analysis reveals morphometric patterns of age-related involution in breast epithelium and stroma.

PubMed

Sandhu, Rupninder; Chollet-Hinton, Lynn; Kirk, Erin L; Midkiff, Bentley; Troester, Melissa A

2016-02-01

Complete age-related regression of mammary epithelium, often termed postmenopausal involution, is associated with decreased breast cancer risk. However, most studies have qualitatively assessed involution. We quantitatively analyzed epithelium, stroma, and adipose tissue from histologically normal breast tissue of 454 patients in the Normal Breast Study. High-resolution digital images of normal breast hematoxylin and eosin-stained slides were partitioned into epithelium, adipose tissue, and nonfatty stroma. Percentage area and nuclei per unit area (nuclear density) were calculated for each component. Quantitative data were evaluated in association with age using linear regression and cubic spline models. Stromal area decreased (P = 0.0002), and adipose tissue area increased (P < 0.0001), with an approximate 0.7% change in area for each component, until age 55 years when these area measures reached a steady state. Although epithelial area did not show linear changes with age, epithelial nuclear density decreased linearly beginning in the third decade of life. No significant age-related trends were observed for stromal or adipose nuclear density. Digital image analysis offers a high-throughput method for quantitatively measuring tissue morphometry and for objectively assessing age-related changes in adipose tissue, stroma, and epithelium. Epithelial nuclear density is a quantitative measure of age-related breast involution that begins to decline in the early premenopausal period. Copyright © 2015 Elsevier Inc. All rights reserved.

Quantitative proteomic characterization of the lung extracellular matrix in chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis.

PubMed

Åhrman, Emma; Hallgren, Oskar; Malmström, Lars; Hedström, Ulf; Malmström, Anders; Bjermer, Leif; Zhou, Xiao-Hong; Westergren-Thorsson, Gunilla; Malmström, Johan

2018-03-01

Remodeling of the extracellular matrix (ECM) is a common feature in lung diseases such as chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF). Here, we applied a sequential tissue extraction strategy to describe disease-specific remodeling of human lung tissue in disease, using end-stages of COPD and IPF. Our strategy was based on quantitative comparison of the disease proteomes, with specific focus on the matrisome, using data-independent acquisition and targeted data analysis (SWATH-MS). Our work provides an in-depth proteomic characterization of human lung tissue during impaired tissue remodeling. In addition, we show important quantitative and qualitative effects of the solubility of matrisome proteins. COPD was characterized by a disease-specific increase in ECM regulators, metalloproteinase inhibitor 3 (TIMP3) and matrix metalloproteinase 28 (MMP-28), whereas for IPF, impairment in cell adhesion proteins, such as collagen VI and laminins, was most prominent. For both diseases, we identified increased levels of proteins involved in the regulation of endopeptidase activity, with several proteins belonging to the serpin family. The established human lung quantitative proteome inventory and the construction of a tissue-specific protein assay library provides a resource for future quantitative proteomic analyses of human lung tissues. We present a sequential tissue extraction strategy to determine changes in extractability of matrisome proteins in end-stage COPD and IPF compared to healthy control tissue. Extensive quantitative analysis of the proteome changes of the disease states revealed altered solubility of matrisome proteins involved in ECM regulators and cell-ECM communication. The results highlight disease-specific remodeling mechanisms associated with COPD and IPF. Copyright © 2018 Elsevier B.V. All rights reserved.

A Pilot Study of the Noninvasive Assessment of the Lung Microbiota as a Potential Tool for the Early Diagnosis of Ventilator-Associated Pneumonia

PubMed Central

Brady, Jacob S.; Romano-Keeler, Joann; Drake, Wonder P.; Norris, Patrick R.; Jenkins, Judith M.; Isaacs, Richard J.; Boczko, Erik M.

2015-01-01

BACKGROUND: Ventilator-associated pneumonia (VAP) remains a common complication in critically ill surgical patients, and its diagnosis remains problematic. Exhaled breath contains aerosolized droplets that reflect the lung microbiota. We hypothesized that exhaled breath condensate fluid (EBCF) in hygroscopic condenser humidifier/heat and moisture exchanger (HCH/HME) filters would contain bacterial DNA that qualitatively and quantitatively correlate with pathogens isolated from quantitative BAL samples obtained for clinical suspicion of pneumonia. METHODS: Forty-eight adult patients who were mechanically ventilated and undergoing quantitative BAL (n = 51) for suspected pneumonia in the surgical ICU were enrolled. Per protocol, patients fulfilling VAP clinical criteria undergo quantitative BAL bacterial culture. Immediately prior to BAL, time-matched HCH/HME filters were collected for study of EBCF by real-time polymerase chain reaction. Additionally, convenience samples of serially collected filters in patients with BAL-diagnosed VAP were analyzed. RESULTS: Forty-nine of 51 time-matched EBCF/BAL fluid samples were fully concordant (concordance > 95% by κ statistic) relative to identified pathogens and strongly correlated with clinical cultures. Regression analysis of quantitative bacterial DNA in paired samples revealed a statistically significant positive correlation (r = 0.85). In a convenience sample, qualitative and quantitative polymerase chain reaction analysis of serial HCH/HME samples for bacterial DNA demonstrated an increase in load that preceded the suspicion of pneumonia. CONCLUSIONS: Bacterial DNA within EBCF demonstrates a high correlation with BAL fluid and clinical cultures. Bacterial DNA within EBCF increases prior to the suspicion of pneumonia. Further study of this novel approach may allow development of a noninvasive tool for the early diagnosis of VAP. PMID:25474571

Multifractal spectrum and lacunarity as measures of complexity of osseointegration.

PubMed

de Souza Santos, Daniel; Dos Santos, Leonardo Cavalcanti Bezerra; de Albuquerque Tavares Carvalho, Alessandra; Leão, Jair Carneiro; Delrieux, Claudio; Stosic, Tatijana; Stosic, Borko

2016-07-01

The goal of this study is to contribute to a better quantitative description of the early stages of osseointegration, by application of fractal, multifractal, and lacunarity analysis. Fractal, multifractal, and lacunarity analysis are performed on scanning electron microscopy (SEM) images of titanium implants that were first subjected to different treatment combinations of i) sand blasting, ii) acid etching, and iii) exposition to calcium phosphate, and were then submersed in a simulated body fluid (SBF) for 30 days. All the three numerical techniques are applied to the implant SEM images before and after SBF immersion, in order to provide a comprehensive set of common quantitative descriptors. It is found that implants subjected to different physicochemical treatments before submersion in SBF exhibit a rather similar level of complexity, while the great variety of crystal forms after SBF submersion reveals rather different quantitative measures (reflecting complexity), for different treatments. In particular, it is found that acid treatment, in most combinations with the other considered treatments, leads to a higher fractal dimension (more uniform distribution of crystals), lower lacunarity (lesser variation in gap sizes), and narrowing of the multifractal spectrum (smaller fluctuations on different scales). The current quantitative description has shown the capacity to capture the main features of complex images of implant surfaces, for several different treatments. Such quantitative description should provide a fundamental tool for future large scale systematic studies, considering the large variety of possible implant treatments and their combinations. Quantitative description of early stages of osseointegration on titanium implants with different treatments should help develop a better understanding of this phenomenon, in general, and provide basis for further systematic experimental studies. Clinical practice should benefit from such studies in the long term, by more ready access to implants of higher quality.

Hyperthyroidism stimulates mitochondrial proton leak and ATP turnover in rat hepatocytes but does not change the overall kinetics of substrate oxidation reactions.

PubMed

Harper, M E; Brand, M D

1994-08-01

Thyroid hormones have well-known effects on oxidative phosphorylation, but there is little quantitative information on their important sites of action. We have used top-down elasticity analysis, an extension of metabolic control analysis, to identify the sites of action of thyroid hormones on oxidative phosphorylation in rat hepatocytes. We divided the oxidative phosphorylation system into three blocks of reactions: the substrate oxidation subsystem, the phosphorylating subsystem, and the mitochondrial proton leak subsystem and have identified those blocks of reactions whose kinetics are significantly changed by hyperthyroidism. Our results show significant effects on the kinetics of the proton leak and the phosphorylating subsystems. Quantitative analyses revealed that 43% of the increase in resting respiration rate in hyperthyroid hepatocytes compared with euthyroid hepatocytes was due to differences in the proton leak and 59% was due to differences in the activity of the phosphorylating subsystem. There were no significant effects on the substrate oxidation subsystem. Changes in nonmitochondrial oxygen consumption accounted for -2% of the change in respiration rate. Top-down control analysis revealed that the distribution of control over the rates of mitochondrial oxygen consumption, ATP synthesis and consumption, and proton leak and over mitochondrial membrane potential (delta psi m) was similar in hepatocytes from hyperthyroid and littermate-paired euthyroid controls. The results of this study include the first complete top-down elasticity and control analyses of oxidative phosphorylation in hepatocytes from hyperthyroid rats.

Proteomics, bioinformatics and targeted gene expression analysis reveals up-regulation of cochlin and identifies other potential biomarkers in the mouse model for deafness in usher syndrome type 1F

PubMed Central

Chance, Mark R.; Chang, Jinsook; Liu, Shuqing; Gokulrangan, Giridharan; Chen, Daniel H.-C.; Lindsay, Aaron; Geng, Ruishuang; Zheng, Qing Y.; Alagramam, Kumar

2010-01-01

Proteins and protein networks associated with cochlear pathogenesis in the Ames waltzer (av) mouse, a model for deafness in Usher syndrome 1F (USH1F), were identified. Cochlear protein from wild-type and av mice at postnatal day 30, a time point in which cochlear pathology is well established, was analyzed by quantitative 2D gel electrophoresis followed by mass spectrometry (MS). The analytic gel resolved 2270 spots; 69 spots showed significant changes in intensity in the av cochlea compared with the control. The cochlin protein was identified in 20 peptide spots, most of which were up-regulated, while a few were down-regulated. Analysis of MS sequence data showed that, in the av cochlea, a set of full-length isoforms of cochlin was up-regulated, while isoforms missing the N-terminal FCH/LCCL domain were down-regulated. Protein interaction network analysis of all differentially expressed proteins was performed with Metacore software. That analysis revealed a number of statistically significant candidate protein networks predicted to be altered in the affected cochlea. Quantitative PCR (qPCR) analysis of select candidates from the proteomic and bioinformatic investigations showed up-regulation of Coch mRNA and those of p53, Brn3a and Nrf2, transcription factors linked to stress response and survival. Increased mRNA of Brn3a and Nrf2 has previously been associated with increased expression of cochlin in human glaucomatous trabecular meshwork. Our report strongly suggests that increased level of cochlin is an important etiologic factor leading to the degeneration of cochlear neuroepithelia in the USH1F model. PMID:20097680

RNA sequencing analysis reveals new findings of hyperbaric oxygen treatment on rats with acute carbon monoxide poisoning.

PubMed

Wang, Wenlan; Xue, Li; Li, Ya; Li, Rong; Xie, Xiaoping; Bao, Junxiang; Hai, Chunxu; Li, Jinsheng

2016-01-01

To elucidate the altered gene network in the brains of carbon monoxide (CO) poisoned rats after treatment with hyperbaric oxygen (HBO₂). RNA sequencing (RNA-seq) analysis was performed to examine differentially expressed genes (DEGs) in brain tissue samples from nine male rats: a normal control group; a CO poisoning group; and an HBO₂ treatment group (three rats/group). Reverse transcription polymerase chain reaction (RT-PCR) and real-time quantitative PCR were used for validation of the DEGs in another 18 male rats (six rats/group). RNA-seq revealed that two genes were upregulated (4.18 and 8.76 log to the base 2 fold change) (p⟨0.05) in the CO-poisoned rats relative to the control rats; two genes were upregulated (3.88 and 7.69 log to the base 2 fold change); and 23 genes were downregulated (3.49-15.12 log to the base 2 fold change) (p⟨0.05) in the brains of the HBO₂-treated rats relative to the CO-poisoned rats. Target prediction of DEGs by gene network analysis and analysis of pathways affected suggested that regulation of gene expressions of dopamine metabolism and nitric oxide (NO) synthesis were significantly affected by CO poisoning and HBO₂ treatment. Results of RT-PCR and real-time quantitative PCR indicated that four genes (Pomc, GH-1, Pr1 and Fshβ) associated with hormone secretion in the hypothalamic-pituitary system have potential as markers for prognosis of CO. This study is the first RNA-seq analysis profile of HBO₂ treatment on rats with acute CO poisoning. It concludes that changes of hormone secretion in the hypothalamic-pituitary system, dopamine metabolism and NO synthesis involved in brain damage and behavior abnormalities after CO poisoning and HBO₂ therapy may regulate these changes.

Multiplexed immunohistochemistry, imaging, and quantitation: a review, with an assessment of Tyramide signal amplification, multispectral imaging and multiplex analysis.

PubMed

Stack, Edward C; Wang, Chichung; Roman, Kristin A; Hoyt, Clifford C

2014-11-01

Tissue sections offer the opportunity to understand a patient's condition, to make better prognostic evaluations and to select optimum treatments, as evidenced by the place pathology holds today in clinical practice. Yet, there is a wealth of information locked up in a tissue section that is only partially accessed, due mainly to the limitations of tools and methods. Often tissues are assessed primarily based on visual analysis of one or two proteins, or 2-3 DNA or RNA molecules. Even while analysis is still based on visual perception, image analysis is starting to address the variability of human perception. This is in contrast to measuring characteristics that are substantially out of reach of human perception, such as parameters revealed through co-expression, spatial relationships, heterogeneity, and low abundance molecules. What is not routinely accessed is the information revealed through simultaneous detection of multiple markers, the spatial relationships among cells and tissue in disease, and the heterogeneity now understood to be critical to developing effective therapeutic strategies. Our purpose here is to review and assess methods for multiplexed, quantitative, image analysis based approaches, using new multicolor immunohistochemistry methods, automated multispectral slide imaging, and advanced trainable pattern recognition software. A key aspect of our approach is presenting imagery in a workflow that engages the pathologist to utilize the strengths of human perception and judgment, while significantly expanding the range of metrics collectable from tissue sections and also provide a level of consistency and precision needed to support the complexities of personalized medicine. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Genome-wide Linkage Analysis for Identifying Quantitative Trait Loci Involved in the Regulation of Lipoprotein a (Lpa) Levels

PubMed Central

López, Sonia; Buil, Alfonso; Ordoñez, Jordi; Souto, Juan Carlos; Almasy, Laura; Lathrop, Mark; Blangero, John; Blanco-Vaca, Francisco; Fontcuberta, Jordi; Soria, José Manuel

2009-01-01

Lipoprotein Lp(a) levels are highly heritable and are associated with cardiovascular risk. We performed a genome-wide linkage analysis to delineate the genomic regions that influence the concentration of Lp(a) in families from the Genetic Analysis of Idiopathic Thrombophilia (GAIT) Project. Lp(a) levels were measured in 387 individuals belonging to 21 extended Spanish families. A total of 485 DNA microsatellite markers were genotyped to provide a 7.1 cM genetic map. A variance component linkage method was used to evaluate linkage and to detect quantitative trait loci (QTLs). The main QTL that showed strong evidence of linkage with Lp(a) levels was located at the structural gene for apo(a) on Chromosome 6 (LOD score=13.8). Interestingly, another QTL influencing Lp(a) concentration was located on Chromosome 2 with a LOD score of 2.01. This region contains several candidate genes. One of them is the tissue factor pathway inhibitor (TFPI), which has antithrombotic action and also has the ability to bind lipoproteins. However, quantitative trait association analyses performed with 12 SNPs in TFPI gene revealed no association with Lp(a) levels. Our study confirms previous results on the genetic basis of Lp(a) levels. In addition, we report a new QTL on Chromosome 2 involved in the quantitative variation of Lp(a). These data should serve as the basis for further detection of candidate genes and to elucidate the relationship between the concentration of Lp(a) and cardiovascular risk. PMID:18560444

Systematic review of quantitative clinical gait analysis in patients with dementia.

PubMed

van Iersel, M B; Hoefsloot, W; Munneke, M; Bloem, B R; Olde Rikkert, M G M

2004-02-01

Diminished mobility often accompanies dementia and has a great impact on independence and quality of life. New treatment strategies for dementia are emerging, but the effects on gait remains to be studied objectively. In this review we address the general effects of dementia on gait as revealed by quantitative gait analysis. A systematic literature search with the (MESH) terms: 'dementia' and 'gait disorders' in Medline, CC, Psychlit and CinaHL between 1980-2002. Main inclusion criteria: controlled studies; patients with dementia; quantitative gait data. Seven publications met the inclusion criteria. All compared gait in Alzheimer's Disease (AD) with healthy elderly controls; one also assessed gait in Vascular Dementia (VaD). The methodology used was inconsistent and often had many shortcomings. However, there were several consistent findings: walking velocity decreased in dementia compared to healthy controls and decreased further with progressing severity of dementia. VaD was associated with a significant decrease in walking velocity compared to AD subjects. Dementia was associated with a shortened step length, an increased double support time and step to step variability. Gait in dementia is hardly analyzed in a well-designed manner. Despite this, the literature suggests that quantitative gait analysis can be sufficiently reliable and responsive to measure decline in walking velocity between subjects with and without dementia. More research is required to assess, both on an individual and a group level, how the minimal clinically relevant changes in gait in elderly demented patients should be defined and what would be the most responsive method to measure these changes.

Automated Quantitative Analysis of Retinal Microvasculature in Normal Eyes on Optical Coherence Tomography Angiography.

PubMed

Lupidi, Marco; Coscas, Florence; Cagini, Carlo; Fiore, Tito; Spaccini, Elisa; Fruttini, Daniela; Coscas, Gabriel

2016-09-01

To describe a new automated quantitative technique for displaying and analyzing macular vascular perfusion using optical coherence tomography angiography (OCT-A) and to determine a normative data set, which might be used as reference in identifying progressive changes due to different retinal vascular diseases. Reliability study. A retrospective review of 47 eyes of 47 consecutive healthy subjects imaged with a spectral-domain OCT-A device was performed in a single institution. Full-spectrum amplitude-decorrelation angiography generated OCT angiograms of the retinal superficial and deep capillary plexuses. A fully automated custom-built software was used to provide quantitative data on the foveal avascular zone (FAZ) features and the total vascular and avascular surfaces. A comparative analysis between central macular thickness (and volume) and FAZ metrics was performed. Repeatability and reproducibility were also assessed in order to establish the feasibility and reliability of the method. The comparative analysis between the superficial capillary plexus and the deep capillary plexus revealed a statistically significant difference (P < .05) in terms of FAZ perimeter, surface, and major axis and a not statistically significant difference (P > .05) when considering total vascular and avascular surfaces. A linear correlation was demonstrated between central macular thickness (and volume) and the FAZ surface. Coefficients of repeatability and reproducibility were less than 0.4, thus demonstrating high intraobserver repeatability and interobserver reproducibility for all the examined data. A quantitative approach on retinal vascular perfusion, which is visible on Spectralis OCT angiography, may offer an objective and reliable method for monitoring disease progression in several retinal vascular diseases. Copyright © 2016 Elsevier Inc. All rights reserved.

[Medical habilitation in German-speaking countries : Quantitative assessment of content and elaboration of habilitation guidelines].

PubMed

Weineck, S B; Koelblinger, D; Kiesslich, T

2015-04-01

Habilitation defines the qualification to conduct self-contained university teaching and is the key for access to a professorship at German, Austrian and Swiss universities. Despite all changes implemented in the European higher education systems during the Bologna process, it is the highest qualification level issued through the process of an university examination and remains the core concept of scientific careers in these countries. In the field of medicine, this applies not only to scientific staff at the universities but also to those medical doctors aiming at a clinical career track. To provide a quantitative analysis of the scientific, didactic, and procedural criteria for medical habilitation in German-speaking countries. Based on the guidelines of all 43 medical academic institutions, the criteria which candidates are required to fulfil prior to habilitation as well as formal requirements related to the habilitation procedure itself have been acquired and quantitatively analyzed. Having evaluated all habilitation guidelines by means of 87 items, the quantitative analysis revealed significant differences in terms of number, kind and scale of criteria stated therein. Most habilitation guidelines scarcely define the capabilities applicants have to prove: concerning the scientific qualifications on types of publications for instance, no item was mentioned in more than half of all habilitation guidelines. Based on this data analysis, the authors discuss the related literature and describe five main distinguishing areas of habilitation guidelines in terms of the set of the formal and procedural framework as well as the prequalification and postqualification criteria imposed on habilitation candidates. There are therefore substantial differences in the organization of the habilitation for medicine.

Quantifying the influences of various ecological factors on land surface temperature of urban forests.

PubMed

Ren, Yin; Deng, Lu-Ying; Zuo, Shu-Di; Song, Xiao-Dong; Liao, Yi-Lan; Xu, Cheng-Dong; Chen, Qi; Hua, Li-Zhong; Li, Zheng-Wei

2016-09-01

Identifying factors that influence the land surface temperature (LST) of urban forests can help improve simulations and predictions of spatial patterns of urban cool islands. This requires a quantitative analytical method that combines spatial statistical analysis with multi-source observational data. The purpose of this study was to reveal how human activities and ecological factors jointly influence LST in clustering regions (hot or cool spots) of urban forests. Using Xiamen City, China from 1996 to 2006 as a case study, we explored the interactions between human activities and ecological factors, as well as their influences on urban forest LST. Population density was selected as a proxy for human activity. We integrated multi-source data (forest inventory, digital elevation models (DEM), population, and remote sensing imagery) to develop a database on a unified urban scale. The driving mechanism of urban forest LST was revealed through a combination of multi-source spatial data and spatial statistical analysis of clustering regions. The results showed that the main factors contributing to urban forest LST were dominant tree species and elevation. The interactions between human activity and specific ecological factors linearly or nonlinearly increased LST in urban forests. Strong interactions between elevation and dominant species were generally observed and were prevalent in either hot or cold spots areas in different years. In conclusion, quantitative studies based on spatial statistics and GeogDetector models should be conducted in urban areas to reveal interactions between human activities, ecological factors, and LST. Copyright © 2016 Elsevier Ltd. All rights reserved.

Quantitative Proteomics Analysis Reveals Novel Insights into Mechanisms of Action of Long Noncoding RNA Hox Transcript Antisense Intergenic RNA (HOTAIR) in HeLa Cells*

PubMed Central

Zheng, Peng; Xiong, Qian; Wu, Ying; Chen, Ying; Chen, Zhuo; Fleming, Joy; Gao, Ding; Bi, Lijun; Ge, Feng

2015-01-01

Long noncoding RNAs (lncRNAs), which have emerged in recent years as a new and crucial layer of gene regulators, regulate various biological processes such as carcinogenesis and metastasis. HOTAIR (Hox transcript antisense intergenic RNA), a lncRNA overexpressed in most human cancers, has been shown to be an oncogenic lncRNA. Here, we explored the role of HOTAIR in HeLa cells and searched for proteins regulated by HOTAIR. To understand the mechanism of action of HOTAIR from a systems perspective, we employed a quantitative proteomic strategy to systematically identify potential targets of HOTAIR. The expression of 170 proteins was significantly dys-regulated after inhibition of HOTAIR, implying that they could be potential targets of HOTAIR. Analysis of this data at the systems level revealed major changes in proteins involved in diverse cellular components, including the cytoskeleton and the respiratory chain. Further functional studies on vimentin (VIM), a key protein involved in the cytoskeleton, revealed that HOTAIR exerts its effects on migration and invasion of HeLa cells, at least in part, through the regulation of VIM expression. Inhibition of HOTAIR leads to mitochondrial dysfunction and ultrastructural alterations, suggesting a novel role of HOTAIR in maintaining mitochondrial function in cancer cells. Our results provide novel insights into the mechanisms underlying the function of HOTAIR in cancer cells. We expect that the methods used in this study will become an integral part of functional studies of lncRNAs. PMID:25762744

Trust Measurement using Multimodal Behavioral Analysis and Uncertainty Aware Trust Calibration

DTIC Science & Technology

2018-01-05

to estimate their performance based on their estimation on all prior trials. In the meanwhile via comparing the decisions of participants with the...it is easier compared with situations when more trials have been done. It should be noted that if a participant is good at memorizing the previous...them. The proposed study, being quantitative and explorative, are expected to reveal a number of findings that benefit interaction system design and

Emergence of methadone as a street drug in St. Petersburg, Russia.

PubMed

Heimer, Robert; Lyubimova, Aleksandra; Barbour, Russell; Levina, Olga S

2016-01-01

The syndemic of opioid addiction, HIV, hepatitis, tuberculosis, imprisonment, and overdose in Russia has been worsened by the illegality of opioid substitution therapy. As part of on-going serial studies, we sought to explore the influence of opioid availability on aspects of the syndemic as it has affected the city of St. Petersburg. We employed a sequential approach in which quantitative data collection and statistical analysis were followed by a qualitative phase. Quantitative data were obtained in 2013-2014 from a respondent-driven sample (RDS) of people who inject drugs (PWID). Individuals recruited by RDS were tested for antibodies to HIV and interviewed about drug use and injection practices, sociodemographics, health status, and access to medical care. Subsequently, we collected in-depth qualitative data on methadone use, knowledge, and market availability from PWID recruited at nine different locations within St. Petersburg. Analysis of interview data from the sample revealed the percentage of PWID injecting methadone in the 30 days prior to interview increased from 3.6% in 2010 to 53.3% in 2012-2013. Injection of only methadone, as compared to injecting only heroin or both drugs, was associated with less frequent injection and reduced HIV-related injected risk, especially a lower rate of injecting with a previously used syringe. In-depth questioning of methadone injectors corroborated the finding from serial quantitative surveys of PWID that methadone's black market availability is a recent phenomenon. Spatial analysis revealed widespread methadone availability but no concentration in any specific districts of the city. Despite the prohibition of substitution therapy and demonization of methadone, the drug has emerged to rival heroin as the most commonly available opioid in St. Petersburg. Ironically, its use is associated with reduced injection-related HIV risk even when its use is illegal. Copyright © 2015 Elsevier B.V. All rights reserved.

Emergence of Methadone as a Street Drug in St. Petersburg, Russia

PubMed Central

Heimer, Robert; Lyubimova, Aleksandra; Barbour, Russell; Levina, Olga S.

2015-01-01

Background The syndemic of opioid addiction, HIV, hepatitis, tuberculosis, imprisonment, and overdose in Russia has been worsened by the illegality of opioid substitution therapy. As part of on-going serial studies, we sought to explore the influence of opioid availability on aspects of the syndemic as it has affected the city of St. Petersburg. Methods We employed a sequential approach in which quantitative data collection and statistical analysis were followed by a qualitative phase. Quantitative data were obtained from a respondent-driven sample (RDS) of people who inject drugs (PWID) obtained in 2012–13. Individuals recruited by RDS were tested for antibodies to HIV and interviewed about drug use and injection practices, sociodemographics, health status, and access to medical care. Subsequently, we collected in-depth qualitative data on methadone use, knowledge, and market availability from PWID recruited at nine different locations within St. Petersburg. Results Analysis of interview data from the sample revealed he percentage of PWID injecting methadone in the 30 days prior to interview increased from 3.6% in 2010 to 53.3% in 2012–13. Injection of only methadone, as compared to injecting only heroin or both drugs, was associated with less frequent injection and reduced HIV-related injected risk, especially a lower rate of injecting with a previously used syringe. In-depth questioning of methadone injectors corroborated the finding from serial quantitative surveys of PWID that methadone’s black market availability is a recent phenomenon. Spatial analysis revealed widespread methadone availability but no concentration in any specific districts of the city. Conclusion Despite the prohibition of substitution therapy and demonization of methadone, the drug has emerged to rival heroin as the most commonly available opioid in St. Petersburg. Ironically, its use is associated with reduced injection-related HIV risk even when its use is illegal. PMID:26573380

Functional Genomics Analysis of Big Data Identifies Novel Peroxisome Proliferator-Activated Receptor γ Target Single Nucleotide Polymorphisms Showing Association With Cardiometabolic Outcomes.

PubMed

Richardson, Kris; Schnitzler, Gavin R; Lai, Chao-Qiang; Ordovas, Jose M

2015-12-01

Cardiovascular disease and type 2 diabetes mellitus represent overlapping diseases where a large portion of the variation attributable to genetics remains unexplained. An important player in their pathogenesis is peroxisome proliferator-activated receptor γ (PPARγ) that is involved in lipid and glucose metabolism and maintenance of metabolic homeostasis. We used a functional genomics methodology to interrogate human chromatin immunoprecipitation-sequencing, genome-wide association studies, and expression quantitative trait locus data to inform selection of candidate functional single nucleotide polymorphisms (SNPs) falling in PPARγ motifs. We derived 27 328 chromatin immunoprecipitation-sequencing peaks for PPARγ in human adipocytes through meta-analysis of 3 data sets. The PPARγ consensus motif showed greatest enrichment and mapped to 8637 peaks. We identified 146 SNPs in these motifs. This number was significantly less than would be expected by chance, and Inference of Natural Selection from Interspersed Genomically coHerent elemenTs analysis indicated that these motifs are under weak negative selection. A screen of these SNPs against genome-wide association studies for cardiometabolic traits revealed significant enrichment with 16 SNPs. A screen against the MuTHER expression quantitative trait locus data revealed 8 of these were significantly associated with altered gene expression in human adipose, more than would be expected by chance. Several SNPs fall close, or are linked by expression quantitative trait locus to lipid-metabolism loci including CYP26A1. We demonstrated the use of functional genomics to identify SNPs of potential function. Specifically, that SNPs within PPARγ motifs that bind PPARγ in adipocytes are significantly associated with cardiometabolic disease and with the regulation of transcription in adipose. This method may be used to uncover functional SNPs that do not reach significance thresholds in the agnostic approach of genome-wide association studies. © 2015 American Heart Association, Inc.

The ontogenic expressions of multiple vesicular glutamate transporters during postnatal development of rat pineal gland.

PubMed

Yoshida, S; Ina, A; Konno, J; Wu, T; Shutoh, F; Nogami, H; Hisano, S

2008-03-18

The pineal gland expresses vesicular glutamate transporters 1 and 2 (VGLUT1 and VGLUT2), which are thought to transport glutamate into synaptic-like microvesicles in the pinealocytes. Recently, we reported that the rat pineal gland also expresses VGLUT1v which is a novel variant of VGLUT1 during the perinatal period. To explore the biological significance of these VGLUT expressions in pineal development, we studied the ontogeny of VGLUT in this gland by in situ hybridization, immunohistochemistry and quantitative reverse transcription-polymerase chain reaction (RT-PCR) using rats. Histological analysis revealed that intensities of VGLUT1 hybridization signal and immunostaining drastically increase by postnatal day (P) 7, whereas VGLUT2 expression exhibits high levels of mRNA and protein at birth and decreases gradually from P7 onward. Quantitative RT-PCR analysis supported these histological observations, showing that expressions of VGLUT1 and VGLUT2 exhibit opposite patterns to each other. Coinciding with VGLUT1-upregulation, RT-PCR data showed that expressions of dynamin 1 and endophilin 1, which are factors predictably involved in the endocytotic recovery of VGLUT1-associated vesicle, are also increased by P7. Quantitative RT-PCR analysis of VGLUT1v demonstrated that its mRNA expression is upregulated by P7, kept at the same level until P14, and apparently decreased at P21, suggesting its functional property required for a certain developmental event. Moreover, a comparison of mRNA expressions at daytime and nighttime revealed that neither VGLUT1 nor VGLUT1v shows any difference in both P7 and P21 glands, whereas VGLUT2 is significantly lower at daytime than at nighttime at P21 but not P7, the time point at which the melatonin rhythm is not yet generated. The present study shows that expressions of these VGLUT types are differentially regulated during postnatal pineal development, each presumably participating in physiologically distinct glutamatergic functions.

Development of a Postcolumn Infused-Internal Standard Liquid Chromatography Mass Spectrometry Method for Quantitative Metabolomics Studies.

PubMed

Liao, Hsiao-Wei; Chen, Guan-Yuan; Wu, Ming-Shiang; Liao, Wei-Chih; Lin, Ching-Hung; Kuo, Ching-Hua

2017-02-03

Quantitative metabolomics has become much more important in clinical research in recent years. Individual differences in matrix effects (MEs) and the injection order effect are two major factors that reduce the quantification accuracy in liquid chromatography-electrospray ionization-mass spectrometry-based (LC-ESI-MS) metabolomics studies. This study proposed a postcolumn infused-internal standard (PCI-IS) combined with a matrix normalization factor (MNF) strategy to improve the analytical accuracy of quantitative metabolomics. The PCI-IS combined with the MNF method was applied for a targeted metabolomics study of amino acids (AAs). D8-Phenylalanine was used as the PCI-IS, and it was postcolumn-infused into the ESI interface for calibration purposes. The MNF was used to bridge the AA response in a standard solution with the plasma samples. The MEs caused signal changes that were corrected by dividing the AA signal intensities by the PCI-IS intensities after adjustment with the MNF. After the method validation, we evaluated the method applicability for breast cancer research using 100 plasma samples. The quantification results revealed that the 11 tested AAs exhibit an accuracy between 88.2 and 110.7%. The principal component analysis score plot revealed that the injection order effect can be successfully removed, and most of the within-group variation of the tested AAs decreased after the PCI-IS correction. Finally, targeted metabolomics studies on the AAs showed that tryptophan was expressed more in malignant patients than in the benign group. We anticipate that a similar approach can be applied to other endogenous metabolites to facilitate quantitative metabolomics studies.

Family members' narratives of lifespace: Mapping changes before and after a brain injury causing driving disruption.

PubMed

Liang, Phyllis; Liddle, Jacki; Fleming, Jennifer; Gustafsson, Louise

2016-06-01

Family members of a person with an acquired brain injury often provide transport assistance during driving disruption with potential impacts on their own travel and participation within the community. The geographic area in which people travel and conduct their activities is known as lifespace. This study aimed to describe the quantitative changes in family members' lifespace after brain injury and understand their subjective experiences through interacting with maps during narratives. Mapping was embedded within in-depth semi-structured interviews with 15 family members. Two sets of maps were generated per participant showing the number of travel locations before and after brain injury. In the interviews, participants reflected on the perceived meaning of lifespace change. Qualitative data were analysed using a narrative approach. Quantitative data from the mapping revealed an increase in travel locations for nine participants, a decrease for five, and no change for one participant. Data analysis revealed four typologies which complemented and enriched the quantitative data: (i) I will do everything for him or her; (ii) Trying to fit all in; (iii) We spend all our time together now; (iv) I need to also care for myself. The findings describe the change in family members' lifespace after taking on the driver role following acquired brain injury. This study highlights the importance of understanding both quantitative and qualitative aspects of lifespace. The subjective experiences and consequences of lifespace changes are different from the impact on individuals with health conditions. Mapping in an interview as a tool has potential clinical utility. © 2016 Occupational Therapy Australia.

Development of fluorescent glucose bioprobes and their application on real-time and quantitative monitoring of glucose uptake in living cells.

PubMed

Lee, Hyang Yeon; Lee, Jae Jeong; Park, Jongmin; Park, Seung Bum

2011-01-03

We developed a novel fluorescent glucose bioprobe, GB2-Cy3, for the real-time and quantitative monitoring of glucose uptake in living cells. We synthesized a series of fluorescent glucose analogues by adding Cy3 fluorophores to the α-anomeric position of D-glucose through various linkers. Systematic and quantitative analysis of these Cy3-labeled glucose analogues revealed that GB2-Cy3 was the ideal fluorescent glucose bioprobe. The cellular uptake of this probe competed with the cellular uptake of D-glucose in the media and was mediated by a glucose-specific transport system, and not by passive diffusion. Flow cytometry and fluorescence microscopy analyses revealed that GB2-Cy3 is ten times more sensitive than 2-NBDG, a leading fluorescent glucose bioprobe. GB2-Cy3 can also be utilized for the quantitative flow cytometry monitoring of glucose uptake in metabolically active C2C12 myocytes under various treatment conditions. As opposed to a glucose uptake assay performed by using radioisotope-labeled deoxy-D-glucose and a scintillation counter, GB2-Cy3 allows the real-time monitoring of glucose uptake in living cells under various experimental conditions by using fluorescence microscopy or confocal laser scanning microscopy (CLSM). Therefore, we believe that GB2-Cy3 can be utilized in high-content screening (HCS) for the discovery of novel therapeutic agents and for making significant advances in biomedical studies and diagnosis of various diseases, especially metabolic diseases. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantitative microbiome profiling links gut community variation to microbial load.

PubMed

Vandeputte, Doris; Kathagen, Gunter; D'hoe, Kevin; Vieira-Silva, Sara; Valles-Colomer, Mireia; Sabino, João; Wang, Jun; Tito, Raul Y; De Commer, Lindsey; Darzi, Youssef; Vermeire, Séverine; Falony, Gwen; Raes, Jeroen

2017-11-23

Current sequencing-based analyses of faecal microbiota quantify microbial taxa and metabolic pathways as fractions of the sample sequence library generated by each analysis. Although these relative approaches permit detection of disease-associated microbiome variation, they are limited in their ability to reveal the interplay between microbiota and host health. Comparative analyses of relative microbiome data cannot provide information about the extent or directionality of changes in taxa abundance or metabolic potential. If microbial load varies substantially between samples, relative profiling will hamper attempts to link microbiome features to quantitative data such as physiological parameters or metabolite concentrations. Saliently, relative approaches ignore the possibility that altered overall microbiota abundance itself could be a key identifier of a disease-associated ecosystem configuration. To enable genuine characterization of host-microbiota interactions, microbiome research must exchange ratios for counts. Here we build a workflow for the quantitative microbiome profiling of faecal material, through parallelization of amplicon sequencing and flow cytometric enumeration of microbial cells. We observe up to tenfold differences in the microbial loads of healthy individuals and relate this variation to enterotype differentiation. We show how microbial abundances underpin both microbiota variation between individuals and covariation with host phenotype. Quantitative profiling bypasses compositionality effects in the reconstruction of gut microbiota interaction networks and reveals that the taxonomic trade-off between Bacteroides and Prevotella is an artefact of relative microbiome analyses. Finally, we identify microbial load as a key driver of observed microbiota alterations in a cohort of patients with Crohn's disease, here associated with a low-cell-count Bacteroides enterotype (as defined through relative profiling).

A cytoarchitecture-driven myelin model reveals area-specific signatures in human primary and secondary areas using ultra-high resolution in-vivo brain MRI.

PubMed

Dinse, J; Härtwich, N; Waehnert, M D; Tardif, C L; Schäfer, A; Geyer, S; Preim, B; Turner, R; Bazin, P-L

2015-07-01

This work presents a novel approach for modelling laminar myelin patterns in the human cortex in brain MR images on the basis of known cytoarchitecture. For the first time, it is possible to estimate intracortical contrast visible in quantitative ultra-high resolution MR images in specific primary and secondary cytoarchitectonic areas. The presented technique reveals different area-specific signatures which may help to study the spatial distribution of cortical T1 values and the distribution of cortical myelin in general. It may lead to a new discussion on the concordance of cyto- and myeloarchitectonic boundaries, given the absence of such concordance atlases. The modelled myelin patterns are quantitatively compared with data from human ultra-high resolution in-vivo 7T brain MR images (9 subjects). In the validation, the results are compared to one post-mortem brain sample and its ex-vivo MRI and histological data. Details of the analysis pipeline are provided. In the context of the increasing interest in advanced methods in brain segmentation and cortical architectural studies, the presented model helps to bridge the gap between the microanatomy revealed by classical histology and the macroanatomy visible in MRI. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Quantitative phase analysis and microstructure characterization of magnetite nanocrystals obtained by microwave assisted non-hydrolytic sol–gel synthesis

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

Sciancalepore, Corrado, E-mail: corrado.sciancalepore@unimore.it; Bondioli, Federica; INSTM Consortium, Via G. Giusti 9, 51121 Firenze

2015-02-15

An innovative preparation procedure, based on microwave assisted non-hydrolytic sol–gel synthesis, to obtain spherical magnetite nanoparticles was reported together with a detailed quantitative phase analysis and microstructure characterization of the synthetic products. The nanoparticle growth was analyzed as a function of the synthesis time and was described in terms of crystallization degree employing the Rietveld method on the magnetic nanostructured system for the determination of the amorphous content using hematite as internal standard. Product crystallinity increases as the microwave thermal treatment is increased and reaches very high percentages for synthesis times longer than 1 h. Microstructural evolution of nanocrystals wasmore » followed by the integral breadth methods to obtain information on the crystallite size-strain distribution. The results of diffraction line profile analysis were compared with nanoparticle grain distribution estimated by dimensional analysis of the transmission electron microscopy (TEM) images. A variation both in the average grain size and in the distribution of the coherently diffraction domains is evidenced, allowing to suppose a relationship between the two quantities. The traditional integral breadth methods have proven to be valid for a rapid assessment of the diffraction line broadening effects in the above-mentioned nanostructured systems and the basic assumption for the correct use of these methods are discussed as well. - Highlights: • Fe{sub 3}O{sub 4} nanocrystals were obtained by MW-assisted non-hydrolytic sol–gel synthesis. • Quantitative phase analysis revealed that crystallinity up to 95% was reached. • The strategy of Rietveld refinements was discussed in details. • Dimensional analysis showed nanoparticles ranging from 4 to 8 nm. • Results of integral breadth methods were compared with microscopic analysis.« less

Histopathological image analysis of chemical-induced hepatocellular hypertrophy in mice.

PubMed

Asaoka, Yoshiji; Togashi, Yuko; Mutsuga, Mayu; Imura, Naoko; Miyoshi, Tomoya; Miyamoto, Yohei

2016-04-01

Chemical-induced hepatocellular hypertrophy is frequently observed in rodents, and is mostly caused by the induction of phase I and phase II drug metabolic enzymes and peroxisomal lipid metabolic enzymes. Liver weight is a sensitive and commonly used marker for detecting hepatocellular hypertrophy, but is also increased by a number of other factors. Histopathological observations subjectively detect changes such as hepatocellular hypertrophy based on the size of a hepatocyte. Therefore, quantitative microscopic observations are required to evaluate histopathological alterations objectively. In the present study, we developed a novel quantitative method for an image analysis of hepatocellular hypertrophy using liver sections stained with hematoxylin and eosin, and demonstrated its usefulness for evaluating hepatocellular hypertrophy induced by phenobarbital (a phase I and phase II enzyme inducer) and clofibrate (a peroxisomal enzyme inducer) in mice. The algorithm of this imaging analysis was designed to recognize an individual hepatocyte through a combination of pixel-based and object-based analyses. Hepatocellular nuclei and the surrounding non-hepatocellular cells were recognized by the pixel-based analysis, while the areas of the recognized hepatocellular nuclei were then expanded until they ran against their expanding neighboring hepatocytes and surrounding non-hepatocellular cells by the object-based analysis. The expanded area of each hepatocellular nucleus was regarded as the size of an individual hepatocyte. The results of this imaging analysis showed that changes in the sizes of hepatocytes corresponded with histopathological observations in phenobarbital and clofibrate-treated mice, and revealed a correlation between hepatocyte size and liver weight. In conclusion, our novel image analysis method is very useful for quantitative evaluations of chemical-induced hepatocellular hypertrophy. Copyright © 2015 Elsevier GmbH. All rights reserved.

Using Clinical Data, Hypothesis Generation Tools and PubMed Trends to Discover the Association between Diabetic Retinopathy and Antihypertensive Drugs

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

Senter, Katherine G; Sukumar, Sreenivas R; Patton, Robert M

Diabetic retinopathy (DR) is a leading cause of blindness and common complication of diabetes. Many diabetic patients take antihypertensive drugs to prevent cardiovascular problems, but these drugs may have unintended consequences on eyesight. Six common classes of antihypertensive drug are angiotensin converting enzyme (ACE) inhibitors, alpha blockers, angiotensin receptor blockers (ARBs), -blockers, calcium channel blockers, and diuretics. Analysis of medical history data might indicate which of these drugs provide safe blood pressure control, and a literature review is often used to guide such analyses. Beyond manual reading of relevant publications, we sought to identify quantitative trends in literature from themore » biomedical database PubMed to compare with quantitative trends in the clinical data. By recording and analyzing PubMed search results, we found wide variation in the prevalence of each antihypertensive drug in DR literature. Drug classes developed more recently such as ACE inhibitors and ARBs were most prevalent. We also identified instances of change-over-time in publication patterns. We then compared these literature trends to a dataset of 500 diabetic patients from the UT Hamilton Eye Institute. Data for each patient included class of antihypertensive drug, presence and severity of DR. Graphical comparison revealed that older drug classes such as diuretics, calcium channel blockers, and -blockers were much more prevalent in the clinical data than in the DR and antihypertensive literature. Finally, quantitative analysis of the dataset revealed that patients taking -blockers were statistically more likely to have DR than patients taking other medications, controlling for presence of hypertension and year of diabetes onset. This finding was concerning given the prevalence of -blockers in the clinical data. We determined that clinical use of -blockers should be minimized in diabetic patients to prevent retinal damage.« less

A brief update on physical and optical disector applications and sectioning-staining methods in neuroscience.

PubMed

Yurt, Kıymet Kübra; Kivrak, Elfide Gizem; Altun, Gamze; Mohamed, Hamza; Ali, Fathelrahman; Gasmalla, Hosam Eldeen; Kaplan, Suleyman

2018-02-26

A quantitative description of a three-dimensional (3D) object based on two-dimensional images can be made using stereological methods These methods involve unbiased approaches and provide reliable results with quantitative data. The quantitative morphology of the nervous system has been thoroughly researched in this context. In particular, various novel methods such as design-based stereological approaches have been applied in neuoromorphological studies. The main foundations of these methods are systematic random sampling and a 3D approach to structures such as tissues and organs. One key point in these methods is that selected samples should represent the entire structure. Quantification of neurons, i.e. particles, is important for revealing degrees of neurodegeneration and regeneration in an organ or system. One of the most crucial morphometric parameters in biological studies is thus the "number". The disector counting method introduced by Sterio in 1984 is an efficient and reliable solution for particle number estimation. In order to obtain precise results by means of stereological analysis, counting items should be seen clearly in the tissue. If an item in the tissue cannot be seen, these cannot be analyzed even using unbiased stereological techniques. Staining and sectioning processes therefore play a critical role in stereological analysis. The purpose of this review is to evaluate current neuroscientific studies using optical and physical disector counting methods and to discuss their definitions and methodological characteristics. Although the efficiency of the optical disector method in light microscopic studies has been revealed in recent years, the physical disector method is more easily performed in electron microscopic studies. Also, we offered to readers summaries of some common basic staining and sectioning methods, which can be used for stereological techniques in this review. Copyright © 2018 Elsevier B.V. All rights reserved.

Genome shuffling of Saccharomyces cerevisiae for enhanced glutathione yield and relative gene expression analysis using fluorescent quantitation reverse transcription polymerase chain reaction.

PubMed

Yin, Hua; Ma, Yanlin; Deng, Yang; Xu, Zhenbo; Liu, Junyan; Zhao, Junfeng; Dong, Jianjun; Yu, Junhong; Chang, Zongming

2016-08-01

Genome shuffling is an efficient and promising approach for the rapid improvement of microbial phenotypes. In this study, genome shuffling was applied to enhance the yield of glutathione produced by Saccharomyces cerevisiae YS86. Six isolates with subtle improvements in glutathione yield were obtained from populations generated by ultraviolet (UV) irradiation and nitrosoguanidine (NTG) mutagenesis. These yeast strains were then subjected to recursive pool-wise protoplast fusion. A strain library that was likely to yield positive colonies was created by fusing the lethal protoplasts obtained from both UV irradiation and heat treatments. After two rounds of genome shuffling, a high-yield recombinant YSF2-19 strain that exhibited 3.2- and 3.3-fold increases in glutathione production in shake flask and fermenter respectively was obtained. Comparative analysis of synthetase gene expression was conducted between the initial and shuffled strains using FQ (fluorescent quantitation) RT-PCR (reverse transcription polymerase chain reaction). Delta CT (threshold cycle) relative quantitation analysis revealed that glutathione synthetase gene (GSH-I) expression at the transcriptional level in the YSF2-19 strain was 9.9-fold greater than in the initial YS86. The shuffled yeast strain has a potential application in brewing, other food, and pharmaceutical industries. Simultaneously, the analysis of improved phenotypes will provide more valuable data for inverse metabolic engineering. Copyright © 2016 Elsevier B.V. All rights reserved.

Quantifying the development of user-generated art during 2001–2010

PubMed Central

Yazdani, Mehrdad; Chow, Jay; Manovich, Lev

2017-01-01

One of the main questions in the humanities is how cultures and artistic expressions change over time. While a number of researchers have used quantitative computational methods to study historical changes in literature, music, and cinema, our paper offers the first quantitative analysis of historical changes in visual art created by users of a social online network. We propose a number of computational methods for the analysis of temporal development of art images. We then apply these methods to a sample of 270,000 artworks created between 2001 and 2010 by users of the largest social network for art—DeviantArt (www.deviantart.com). We investigate changes in subjects, techniques, sizes, proportions and also selected visual characteristics of images. Because these artworks are classified by their creators into two general categories—Traditional Art and Digital Art—we are also able to investigate if the use of digital tools has had a significant effect on the content and form of artworks. Our analysis reveals a number of gradual and systematic changes over a ten-year period in artworks belonging to both categories. PMID:28792494

Quantitative semi-automated analysis of morphogenesis with single-cell resolution in complex embryos.

PubMed

Giurumescu, Claudiu A; Kang, Sukryool; Planchon, Thomas A; Betzig, Eric; Bloomekatz, Joshua; Yelon, Deborah; Cosman, Pamela; Chisholm, Andrew D

2012-11-01

A quantitative understanding of tissue morphogenesis requires description of the movements of individual cells in space and over time. In transparent embryos, such as C. elegans, fluorescently labeled nuclei can be imaged in three-dimensional time-lapse (4D) movies and automatically tracked through early cleavage divisions up to ~350 nuclei. A similar analysis of later stages of C. elegans development has been challenging owing to the increased error rates of automated tracking of large numbers of densely packed nuclei. We present Nucleitracker4D, a freely available software solution for tracking nuclei in complex embryos that integrates automated tracking of nuclei in local searches with manual curation. Using these methods, we have been able to track >99% of all nuclei generated in the C. elegans embryo. Our analysis reveals that ventral enclosure of the epidermis is accompanied by complex coordinated migration of the neuronal substrate. We can efficiently track large numbers of migrating nuclei in 4D movies of zebrafish cardiac morphogenesis, suggesting that this approach is generally useful in situations in which the number, packing or dynamics of nuclei present challenges for automated tracking.

Quantifying the development of user-generated art during 2001-2010.

PubMed

Yazdani, Mehrdad; Chow, Jay; Manovich, Lev

2017-01-01

One of the main questions in the humanities is how cultures and artistic expressions change over time. While a number of researchers have used quantitative computational methods to study historical changes in literature, music, and cinema, our paper offers the first quantitative analysis of historical changes in visual art created by users of a social online network. We propose a number of computational methods for the analysis of temporal development of art images. We then apply these methods to a sample of 270,000 artworks created between 2001 and 2010 by users of the largest social network for art-DeviantArt (www.deviantart.com). We investigate changes in subjects, techniques, sizes, proportions and also selected visual characteristics of images. Because these artworks are classified by their creators into two general categories-Traditional Art and Digital Art-we are also able to investigate if the use of digital tools has had a significant effect on the content and form of artworks. Our analysis reveals a number of gradual and systematic changes over a ten-year period in artworks belonging to both categories.

Path analysis of the genetic integration of traits in the sand cricket: a novel use of BLUPs.

PubMed

Roff, D A; Fairbairn, D J

2011-09-01

This study combines path analysis with quantitative genetics to analyse a key life history trade-off in the cricket, Gryllus firmus. We develop a path model connecting five traits associated with the trade-off between flight capability and reproduction and test this model using phenotypic data and estimates of breeding values (best linear unbiased predictors) from a half-sibling experiment. Strong support by both types of data validates our causal model and indicates concordance between the phenotypic and genetic expression of the trade-off. Comparisons of the trade-off between sexes and wing morphs reveal that these discrete phenotypes are not genetically independent and that the evolutionary trajectories of the two wing morphs are more tightly constrained to covary than those of the two sexes. Our results illustrate the benefits of combining a quantitative genetic analysis, which examines statistical correlations between traits, with a path model that focuses upon the causal components of variation. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.

Misinformation on vaccination: A quantitative analysis of YouTube videos.

PubMed

Donzelli, Gabriele; Palomba, Giacomo; Federigi, Ileana; Aquino, Francesco; Cioni, Lorenzo; Verani, Marco; Carducci, Annalaura; Lopalco, Pierluigi

2018-03-19

In Italy, the phenomenon of vaccine hesitancy has increased with time and represents a complex problem that requires a continuous monitoring. Misinformation on media and social media seems to be one of the determinants of the vaccine hesitancy since, for instance, 42.8 percent of Italian citizens used the internet to obtain vaccine information in 2016. This article reports a quantitative analysis of 560 YouTube videos related to the link between vaccines and autism or other serious side effects on children. The analysis revealed that most of the videos were negative in tone and that the annual number of uploaded videos has increased during the considered period, that goes from 27 December 2007 to 31 July 2017, with a peak of 224 videos in the first seven months of 2017. These findings suggest that the public institutions should be more engaged in establishing a web presence in order to provide reliable information, answers, stories, and videos so to respond to questions of the public about vaccination. These actions could be useful to allow citizens to make informed decisions about vaccines so to comply with vaccination regulations.

Quantitative Structure-Activity Relationship Modeling Coupled with Molecular Docking Analysis in Screening of Angiotensin I-Converting Enzyme Inhibitory Peptides from Qula Casein Hydrolysates Obtained by Two-Enzyme Combination Hydrolysis.

PubMed

Lin, Kai; Zhang, Lanwei; Han, Xue; Meng, Zhaoxu; Zhang, Jianming; Wu, Yifan; Cheng, Dayou

2018-03-28

In this study, Qula casein derived from yak milk casein was hydrolyzed using a two-enzyme combination approach, and high angiotensin I-converting enzyme (ACE) inhibitory activity peptides were screened by quantitative structure-activity relationship (QSAR) modeling integrated with molecular docking analysis. Hydrolysates (<3 kDa) derived from combinations of thermolysin + alcalase and thermolysin + proteinase K demonstrated high ACE inhibitory activities. Peptide sequences in hydrolysates derived from these two combinations were identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS). On the basis of the QSAR modeling prediction, a total of 16 peptides were selected for molecular docking analysis. The docking study revealed that four of the peptides (KFPQY, MPFPKYP, MFPPQ, and QWQVL) bound the active site of ACE. These four novel peptides were chemically synthesized, and their IC 50 was determined. Among these peptides, KFPQY showed the highest ACE inhibitory activity (IC 50 = 12.37 ± 0.43 μM). Our study indicated that Qula casein presents an excellent source to produce ACE inhibitory peptides.

Rice Grain Quality and Consumer Preferences: A Case Study of Two Rural Towns in the Philippines

PubMed Central

Velarde, Orlee; Demont, Matty

2016-01-01

Hedonic pricing analysis is conducted to determine the implicit values of various attributes in the market value of a good. In this study, hedonic pricing analysis was applied to measure the contribution of grain quality search and experience attributes to the price of rice in two rural towns in the Philippines. Rice samples from respondents underwent quantitative routine assessments of grain quality. In particular, gelatinization temperature and chalkiness, two parameters that are normally assessed through visual scores, were evaluated by purely quantitative means (differential scanning calorimetry and by digital image analysis). Results indicate that rice consumed by respondents had mainly similar physical and chemical grain quality attributes. The respondents’ revealed preferences were typical of what has been previously reported for Filipino rice consumers. Hedonic regression analyses showed that grain quality characteristics that affected price varied by income class. Some of the traits or socioeconomic factors that affected price were percent broken grains, gel consistency, and household per capita rice consumption. There is an income effect on rice price and the characteristics that affect price vary between income classes. PMID:26982587

Rice Grain Quality and Consumer Preferences: A Case Study of Two Rural Towns in the Philippines.

PubMed

Cuevas, Rosa Paula; Pede, Valerien O; McKinley, Justin; Velarde, Orlee; Demont, Matty

2016-01-01

Hedonic pricing analysis is conducted to determine the implicit values of various attributes in the market value of a good. In this study, hedonic pricing analysis was applied to measure the contribution of grain quality search and experience attributes to the price of rice in two rural towns in the Philippines. Rice samples from respondents underwent quantitative routine assessments of grain quality. In particular, gelatinization temperature and chalkiness, two parameters that are normally assessed through visual scores, were evaluated by purely quantitative means (differential scanning calorimetry and by digital image analysis). Results indicate that rice consumed by respondents had mainly similar physical and chemical grain quality attributes. The respondents' revealed preferences were typical of what has been previously reported for Filipino rice consumers. Hedonic regression analyses showed that grain quality characteristics that affected price varied by income class. Some of the traits or socioeconomic factors that affected price were percent broken grains, gel consistency, and household per capita rice consumption. There is an income effect on rice price and the characteristics that affect price vary between income classes.

Transition metal redox and Mn disproportional reaction in LiMn0.5Fe0.5PO4 electrodes cycled with aqueous electrolyte

NASA Astrophysics Data System (ADS)

Zhuo, Zengqing; Hu, Jiangtao; Duan, Yandong; Yang, Wanli; Pan, Feng

2016-07-01

We performed soft x-ray absorption spectroscopy (sXAS) and a quantitative analysis of the transition metal redox in the LiMn0.5Fe0.5PO4 electrodes upon electrochemical cycling. In order to circumvent the complication of the surface reactions with organic electrolyte at high potential, the LiMn0.5Fe0.5PO4 electrodes are cycled with aqueous electrolyte. The analysis of the transitional metal L-edge spectra allows a quantitative determination of the redox evolution of Mn and Fe during the electrochemical cycling. The sXAS analysis reveals the evolving Mn oxidation states in LiMn0.5Fe0.5PO4. We found that electrochemically inactive Mn2+ is formed on the electrode surface during cycling. Additionally, the signal indicates about 20% concentration of Mn4+ at the charged state, providing a strong experimental evidence of the disproportional reaction of Mn3+ to Mn2+ and Mn4+ on the surface of the charged LiMn0.5Fe0.5PO4 electrodes.

Quantitative Analysis Reveals that Actin and Src-Family Kinases Regulate Nuclear YAP1 and Its Export.

PubMed

Ege, Nil; Dowbaj, Anna M; Jiang, Ming; Howell, Michael; Hooper, Steven; Foster, Charles; Jenkins, Robert P; Sahai, Erik

2018-06-08

The transcriptional regulator YAP1 is critical for the pathological activation of fibroblasts. In normal fibroblasts, YAP1 is located in the cytoplasm, while in activated cancer-associated fibroblasts, it is nuclear and promotes the expression of genes required for pro-tumorigenic functions. Here, we investigate the dynamics of YAP1 shuttling in normal and activated fibroblasts, using EYFP-YAP1, quantitative photobleaching methods, and mathematical modeling. Imaging of migrating fibroblasts reveals the tight temporal coupling of cell shape change and altered YAP1 localization. Both 14-3-3 and TEAD binding modulate YAP1 shuttling, but neither affects nuclear import. Instead, we find that YAP1 nuclear accumulation in activated fibroblasts results from Src and actomyosin-dependent suppression of phosphorylated YAP1 export. Finally, we show that nuclear-constrained YAP1, upon XPO1 depletion, remains sensitive to blockade of actomyosin function. Together, these data place nuclear export at the center of YAP1 regulation and indicate that the cytoskeleton can regulate YAP1 within the nucleus. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Quantitative proteomics analysis reveals the tolerance of Mirabilis jalapa L. to petroleum contamination.

PubMed

Chen, Shuisen; Ma, Hui; Guo, Zhifu; Feng, Yaping; Lin, Jingwei; Zhang, Menghua; Zhong, Ming

2017-03-01

Petroleum is not only an important energy resource but is also a major soil pollutant. To gain better insight into the adaptability mechanism of Mirabilis jalapa to petroleum-contaminated soil, the protein profiles of M. jalapa root were investigated using label-free quantitative proteomics technique. After exposing to petroleum-contaminated soil for 24 h, 34 proteins significantly changed their protein abundance and most of the proteins increased in protein abundance (91.18%). Combined with gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses as well as data from previous studies, our results revealed that M. jalapa enhanced tolerance to petroleum by changing antioxidation and detoxification, cell wall organization, amino acid and carbohydrate metabolism, transportation and protein process, and so on. These metabolism alterations could result in the production and secretion of low molecular carbohydrate, amino acid, and functional protein, which enhanced the bioavailability of petroleum and reducing the toxicity of the petroleum. Taken together, these results provided novel information for better understanding of the tolerance of M. jalapa to petroleum stress.

The Application of SILAC Mouse in Human Body Fluid Proteomics Analysis Reveals Protein Patterns Associated with IgA Nephropathy.

PubMed

Zhao, Shilin; Li, Rongxia; Cai, Xiaofan; Chen, Wanjia; Li, Qingrun; Xing, Tao; Zhu, Wenjie; Chen, Y Eugene; Zeng, Rong; Deng, Yueyi

2013-01-01

Body fluid proteome is the most informative proteome from a medical viewpoint. But the lack of accurate quantitation method for complicated body fluid limited its application in disease research and biomarker discovery. To address this problem, we introduced a novel strategy, in which SILAC-labeled mouse serum was used as internal standard for human serum and urine proteome analysis. The SILAC-labeled mouse serum was mixed with human serum and urine, and multidimensional separation coupled with tandem mass spectrometry (IEF-LC-MS/MS) analysis was performed. The shared peptides between two species were quantified by their SILAC pairs, and the human-only peptides were quantified by mouse peptides with coelution. The comparison for the results from two replicate experiments indicated the high repeatability of our strategy. Then the urine from Immunoglobulin A nephropathy patients treated and untreated was compared by this quantitation strategy. Fifty-three peptides were found to be significantly changed between two groups, including both known diagnostic markers for IgAN and novel candidates, such as Complement C3, Albumin, VDBP, ApoA,1 and IGFBP7. In conclusion, we have developed a practical and accurate quantitation strategy for comparison of complicated human body fluid proteome. The results from such strategy could provide potential disease-related biomarkers for evaluation of treatment.

Do adolescents support early marriage in Bangladesh? Evidence from study.

PubMed

Rahman, M M; Kabir, M

2005-01-01

Adolescence is a critical period for female adolescents as they have to make decisions regarding their marriage, education and work which would influence and determine their future course of life. Although, early marriage has negative consequences, still a proportion of female adolescents favour early marriage because of prevailing cultural norms. This paper attempts to investigate the factors influencing the adolescents' attitude towards early marriage among the married and unmarried female adolescents. This is a quantitative and qualitative study. A multistage cluster sampling technique was used to select the sample. For quantitative results, data on 3362 female adolescents from rural and urban areas irrespective of their marital status were analyzed. To supplement the results found in quantitative analysis, a series of focus group discussions were conducted among the adolescents. Analysis revealed that one fourth (25.9%) of the adolescents were in favour of early marriage. A number of societal factors influenced them towards early marriage, despite the fact that adolescents are aware of the consequences of maternal and child health. Multivariate logistic regression analysis showed that current marital status, years of schooling, work status and parental marital decision are important predictors of early marriage (p < 0.05). The study concluded that female education would be an important determinant of adolescent marriage. Therefore, opportunities and scope of education beyond secondary would helps to bring change in the attitude towards early marriage.

The use of experimental design for the development of a capillary zone electrophoresis method for the quantitation of captopril.

PubMed

Mukozhiwa, S Y; Khamanga, S M M; Walker, R B

2017-09-01

A capillary zone electrophoresis (CZE) method for the quantitation of captopril (CPT) using UV detection was developed. Influence of electrolyte concentration and system variables on electrophoretic separation was evaluated and a central composite design (CCD) was used to optimize the method. Variables investigated were pH, molarity, applied voltage and capillary length. The influence of sodium metabisulphite on the stability of test solutions was also investigated. The use of sodium metabisulphite prevented degradation of CPT over 24 hours. A fused uncoated silica capillary of 67.5cm total and 57.5 cm effective length was used for analysis. The applied voltage and capillary length affected the migration time of CPT significantly. A 20 mM phosphate buffer adjusted to pH 7.0 was used as running buffer and an applied voltage of 23.90 kV was suitable to effect a separation. The optimized electrophoretic conditions produced sharp, well-resolved peaks for CPT and sodium metabisulphite. Linear regression analysis of the response for CPT standards revealed the method was linear (R2 = 0.9995) over the range 5-70 μg/mL. The limits of quantitation and detection were 5 and 1.5 μg/mL. A simple, rapid and reliable CZE method has been developed and successfully applied to the analysis of commercially available CPT products.

Chemical fingerprinting and source tracing of obsidian: the central Mediterranean trade in black gold.

PubMed

Tykot, Robert H

2002-08-01

Chemical fingerprinting using major or trace element composition is used to characterize the Mediterranean island sources of obsidian and can even differentiate as many as nine flows in the Monte Arci region of Sardinia. Analysis of significant numbers of obsidian artifacts from Neolithic sites in the central Mediterranean reveals specific patterns of source exploitation and suggests particular trade mechanisms and routes. The use of techniques such as X-ray fluorescence, the electron microprobe, neutron activation analysis, and laser ablation ICP mass spectrometry are emphasized in order to produce quantitative results while minimizing damage to valuable artifacts.

[Image processing applying in analysis of motion features of cultured cardiac myocyte in rat].

PubMed

Teng, Qizhi; He, Xiaohai; Luo, Daisheng; Wang, Zhengrong; Zhou, Beiyi; Yuan, Zhirun; Tao, Dachang

2007-02-01

Study of mechanism of medicine actions, by quantitative analysis of cultured cardiac myocyte, is one of the cutting edge researches in myocyte dynamics and molecular biology. The characteristics of cardiac myocyte auto-beating without external stimulation make the research sense. Research of the morphology and cardiac myocyte motion using image analysis can reveal the fundamental mechanism of medical actions, increase the accuracy of medicine filtering, and design the optimal formula of medicine for best medical treatments. A system of hardware and software has been built with complete sets of functions including living cardiac myocyte image acquisition, image processing, motion image analysis, and image recognition. In this paper, theories and approaches are introduced for analysis of living cardiac myocyte motion images and implementing quantitative analysis of cardiac myocyte features. A motion estimation algorithm is used for motion vector detection of particular points and amplitude and frequency detection of a cardiac myocyte. Beatings of cardiac myocytes are sometimes very small. In such case, it is difficult to detect the motion vectors from the particular points in a time sequence of images. For this reason, an image correlation theory is employed to detect the beating frequencies. Active contour algorithm in terms of energy function is proposed to approximate the boundary and detect the changes of edge of myocyte.

A synchrotron-based local computed tomography combined with data-constrained modelling approach for quantitative analysis of anthracite coal microstructure

PubMed Central

Chen, Wen Hao; Yang, Sam Y. S.; Xiao, Ti Qiao; Mayo, Sherry C.; Wang, Yu Dan; Wang, Hai Peng

2014-01-01

Quantifying three-dimensional spatial distributions of pores and material compositions in samples is a key materials characterization challenge, particularly in samples where compositions are distributed across a range of length scales, and where such compositions have similar X-ray absorption properties, such as in coal. Consequently, obtaining detailed information within sub-regions of a multi-length-scale sample by conventional approaches may not provide the resolution and level of detail one might desire. Herein, an approach for quantitative high-definition determination of material compositions from X-ray local computed tomography combined with a data-constrained modelling method is proposed. The approach is capable of dramatically improving the spatial resolution and enabling finer details within a region of interest of a sample larger than the field of view to be revealed than by using conventional techniques. A coal sample containing distributions of porosity and several mineral compositions is employed to demonstrate the approach. The optimal experimental parameters are pre-analyzed. The quantitative results demonstrated that the approach can reveal significantly finer details of compositional distributions in the sample region of interest. The elevated spatial resolution is crucial for coal-bed methane reservoir evaluation and understanding the transformation of the minerals during coal processing. The method is generic and can be applied for three-dimensional compositional characterization of other materials. PMID:24763649

Quantitative analysis of professionally trained versus untrained voices.

PubMed

Siupsinskiene, Nora

2003-01-01

The aim of this study was to compare healthy trained and untrained voices as well as healthy and dysphonic trained voices in adults using combined voice range profile and aerodynamic tests, to define the normal range limiting values of quantitative voice parameters and to select the most informative quantitative voice parameters for separation between healthy and dysphonic trained voices. Three groups of persons were evaluated. One hundred eighty six healthy volunteers were divided into two groups according to voice training: non-professional speakers group consisted of 106 untrained voices persons (36 males and 70 females) and professional speakers group--of 80 trained voices persons (21 males and 59 females). Clinical group consisted of 103 dysphonic professional speakers (23 males and 80 females) with various voice disorders. Eighteen quantitative voice parameters from combined voice range profile (VRP) test were analyzed: 8 of voice range profile, 8 of speaking voice, overall vocal dysfunction degree and coefficient of sound, and aerodynamic maximum phonation time. Analysis showed that healthy professional speakers demonstrated expanded vocal abilities in comparison to healthy non-professional speakers. Quantitative voice range profile parameters- pitch range, high frequency limit, area of high frequencies and coefficient of sound differed significantly between healthy professional and non-professional voices, and were more informative than speaking voice or aerodynamic parameters in showing the voice training. Logistic stepwise regression revealed that VRP area in high frequencies was sufficient to discriminate between healthy and dysphonic professional speakers for male subjects (overall discrimination accuracy--81.8%) and combination of three quantitative parameters (VRP high frequency limit, maximum voice intensity and slope of speaking curve) for female subjects (overall model discrimination accuracy--75.4%). We concluded that quantitative voice assessment with selected parameters might be useful for evaluation of voice education for healthy professional speakers as well as for detection of vocal dysfunction and evaluation of rehabilitation effect in dysphonic professionals.

Genetic Variants Associated With Quantitative Glucose Homeostasis Traits Translate to Type 2 Diabetes in Mexican Americans: The GUARDIAN (Genetics Underlying Diabetes in Hispanics) Consortium.

PubMed

Palmer, Nicholette D; Goodarzi, Mark O; Langefeld, Carl D; Wang, Nan; Guo, Xiuqing; Taylor, Kent D; Fingerlin, Tasha E; Norris, Jill M; Buchanan, Thomas A; Xiang, Anny H; Haritunians, Talin; Ziegler, Julie T; Williams, Adrienne H; Stefanovski, Darko; Cui, Jinrui; Mackay, Adrienne W; Henkin, Leora F; Bergman, Richard N; Gao, Xiaoyi; Gauderman, James; Varma, Rohit; Hanis, Craig L; Cox, Nancy J; Highland, Heather M; Below, Jennifer E; Williams, Amy L; Burtt, Noel P; Aguilar-Salinas, Carlos A; Huerta-Chagoya, Alicia; Gonzalez-Villalpando, Clicerio; Orozco, Lorena; Haiman, Christopher A; Tsai, Michael Y; Johnson, W Craig; Yao, Jie; Rasmussen-Torvik, Laura; Pankow, James; Snively, Beverly; Jackson, Rebecca D; Liu, Simin; Nadler, Jerry L; Kandeel, Fouad; Chen, Yii-Der I; Bowden, Donald W; Rich, Stephen S; Raffel, Leslie J; Rotter, Jerome I; Watanabe, Richard M; Wagenknecht, Lynne E

2015-05-01

Insulin sensitivity, insulin secretion, insulin clearance, and glucose effectiveness exhibit strong genetic components, although few studies have examined their genetic architecture or influence on type 2 diabetes (T2D) risk. We hypothesized that loci affecting variation in these quantitative traits influence T2D. We completed a multicohort genome-wide association study to search for loci influencing T2D-related quantitative traits in 4,176 Mexican Americans. Quantitative traits were measured by the frequently sampled intravenous glucose tolerance test (four cohorts) or euglycemic clamp (three cohorts), and random-effects models were used to test the association between loci and quantitative traits, adjusting for age, sex, and admixture proportions (Discovery). Analysis revealed a significant (P < 5.00 × 10(-8)) association at 11q14.3 (MTNR1B) with acute insulin response. Loci with P < 0.0001 among the quantitative traits were examined for translation to T2D risk in 6,463 T2D case and 9,232 control subjects of Mexican ancestry (Translation). Nonparametric meta-analysis of the Discovery and Translation cohorts identified significant associations at 6p24 (SLC35B3/TFAP2A) with glucose effectiveness/T2D, 11p15 (KCNQ1) with disposition index/T2D, and 6p22 (CDKAL1) and 11q14 (MTNR1B) with acute insulin response/T2D. These results suggest that T2D and insulin secretion and sensitivity have both shared and distinct genetic factors, potentially delineating genomic components of these quantitative traits that drive the risk for T2D. © 2015 by the American Diabetes Association. Readers may use this article as long as the work is properly cited, the use is educational and not for profit, and the work is not altered.

A scoring system for appraising mixed methods research, and concomitantly appraising qualitative, quantitative and mixed methods primary studies in Mixed Studies Reviews.

PubMed

Pluye, Pierre; Gagnon, Marie-Pierre; Griffiths, Frances; Johnson-Lafleur, Janique

2009-04-01

A new form of literature review has emerged, Mixed Studies Review (MSR). These reviews include qualitative, quantitative and mixed methods studies. In the present paper, we examine MSRs in health sciences, and provide guidance on processes that should be included and reported. However, there are no valid and usable criteria for concomitantly appraising the methodological quality of the qualitative, quantitative and mixed methods studies. To propose criteria for concomitantly appraising the methodological quality of qualitative, quantitative and mixed methods studies or study components. A three-step critical review was conducted. 2322 references were identified in MEDLINE, and their titles and abstracts were screened; 149 potentially relevant references were selected and the full-text papers were examined; 59 MSRs were retained and scrutinized using a deductive-inductive qualitative thematic data analysis. This revealed three types of MSR: convenience, reproducible, and systematic. Guided by a proposal, we conducted a qualitative thematic data analysis of the quality appraisal procedures used in the 17 systematic MSRs (SMSRs). Of 17 SMSRs, 12 showed clear quality appraisal procedures with explicit criteria but no SMSR used valid checklists to concomitantly appraise qualitative, quantitative and mixed methods studies. In two SMSRs, criteria were developed following a specific procedure. Checklists usually contained more criteria than needed. In four SMSRs, a reliability assessment was described or mentioned. While criteria for quality appraisal were usually based on descriptors that require specific methodological expertise (e.g., appropriateness), no SMSR described the fit between reviewers' expertise and appraised studies. Quality appraisal usually resulted in studies being ranked by methodological quality. A scoring system is proposed for concomitantly appraising the methodological quality of qualitative, quantitative and mixed methods studies for SMSRs. This scoring system may also be used to appraise the methodological quality of qualitative, quantitative and mixed methods components of mixed methods research.

Systematic assessment of survey scan and MS2-based abundance strategies for label-free quantitative proteomics using high-resolution MS data.

PubMed

Tu, Chengjian; Li, Jun; Sheng, Quanhu; Zhang, Ming; Qu, Jun

2014-04-04

Survey-scan-based label-free method have shown no compelling benefit over fragment ion (MS2)-based approaches when low-resolution mass spectrometry (MS) was used, the growing prevalence of high-resolution analyzers may have changed the game. This necessitates an updated, comparative investigation of these approaches for data acquired by high-resolution MS. Here, we compared survey scan-based (ion current, IC) and MS2-based abundance features including spectral-count (SpC) and MS2 total-ion-current (MS2-TIC), for quantitative analysis using various high-resolution LC/MS data sets. Key discoveries include: (i) study with seven different biological data sets revealed only IC achieved high reproducibility for lower-abundance proteins; (ii) evaluation with 5-replicate analyses of a yeast sample showed IC provided much higher quantitative precision and lower missing data; (iii) IC, SpC, and MS2-TIC all showed good quantitative linearity (R(2) > 0.99) over a >1000-fold concentration range; (iv) both MS2-TIC and IC showed good linear response to various protein loading amounts but not SpC; (v) quantification using a well-characterized CPTAC data set showed that IC exhibited markedly higher quantitative accuracy, higher sensitivity, and lower false-positives/false-negatives than both SpC and MS2-TIC. Therefore, IC achieved an overall superior performance than the MS2-based strategies in terms of reproducibility, missing data, quantitative dynamic range, quantitative accuracy, and biomarker discovery.

Systematic Assessment of Survey Scan and MS2-Based Abundance Strategies for Label-Free Quantitative Proteomics Using High-Resolution MS Data

PubMed Central

2015-01-01

Survey-scan-based label-free method have shown no compelling benefit over fragment ion (MS2)-based approaches when low-resolution mass spectrometry (MS) was used, the growing prevalence of high-resolution analyzers may have changed the game. This necessitates an updated, comparative investigation of these approaches for data acquired by high-resolution MS. Here, we compared survey scan-based (ion current, IC) and MS2-based abundance features including spectral-count (SpC) and MS2 total-ion-current (MS2-TIC), for quantitative analysis using various high-resolution LC/MS data sets. Key discoveries include: (i) study with seven different biological data sets revealed only IC achieved high reproducibility for lower-abundance proteins; (ii) evaluation with 5-replicate analyses of a yeast sample showed IC provided much higher quantitative precision and lower missing data; (iii) IC, SpC, and MS2-TIC all showed good quantitative linearity (R2 > 0.99) over a >1000-fold concentration range; (iv) both MS2-TIC and IC showed good linear response to various protein loading amounts but not SpC; (v) quantification using a well-characterized CPTAC data set showed that IC exhibited markedly higher quantitative accuracy, higher sensitivity, and lower false-positives/false-negatives than both SpC and MS2-TIC. Therefore, IC achieved an overall superior performance than the MS2-based strategies in terms of reproducibility, missing data, quantitative dynamic range, quantitative accuracy, and biomarker discovery. PMID:24635752

Detection of titanium in human tissues after craniofacial surgery.

PubMed

Jorgenson, D S; Mayer, M H; Ellenbogen, R G; Centeno, J A; Johnson, F B; Mullick, F G; Manson, P N

1997-04-01

Generally, titanium fixation plates are not removed after osteosynthesis, because they have high biocompatability and high corrosion resistance characteristics. Experiments with laboratory animals, and limited studies of analyses of human tissues, have reported evidence of titanium release into local and distant tissues. This study summarizes our results of the analysis of soft tissues for titanium in four patients with titanium microfixation plates. Energy dispersive x-ray analysis, scanning electron microscopy, and electrothermal atomic absorption spectrophotometry were used to detect trace amounts of titanium in surrounding soft tissues. A single metal inclusion was detected by scanning electron microscopy and energy dispersive x-ray analysis in one patient, whereas, electrothermal atomic absorption spectrophotometry analyses revealed titanium present in three of four specimens in levels ranging from 7.92 to 31.8 micrograms/gm of dry tissue. Results from this study revealed trace amounts of titanium in tissues surrounding craniofacial plates. At the atomic level, electrothermal atomic absorption spectrophotometry appears to be a sensitive tool to quantitatively detect ultra-trace amounts of metal in human tissue.

Proteomic analysis of acquired tamoxifen resistance in MCF-7 cells reveals expression signatures associated with enhanced migration

PubMed Central

2012-01-01

Introduction Acquired tamoxifen resistance involves complex signaling events that are not yet fully understood. Successful therapeutic intervention to delay the onset of hormone resistance depends critically on mechanistic elucidation of viable molecular targets associated with hormone resistance. This study was undertaken to investigate the global proteomic alterations in a tamoxifen resistant MCF-7 breast cancer cell line obtained by long term treatment of the wild type MCF-7 cell line with 4-hydroxytamoxifen (4-OH Tam). Methods We cultured MCF-7 cells with 4-OH Tam over a period of 12 months to obtain the resistant cell line. A gel-free, quantitative proteomic method was used to identify and quantify the proteome of the resistant cell line. Nano-flow high-performance liquid chromatography coupled to high resolution Fourier transform mass spectrometry was used to analyze fractionated peptide mixtures that were isobarically labeled from the resistant and control cell lysates. Real time quantitative PCR and Western blots were used to verify selected proteomic changes. Lentiviral vector transduction was used to generate MCF-7 cells stably expressing S100P. Online pathway analysis was performed to assess proteomic signatures in tamoxifen resistance. Survival analysis was done to evaluate clinical relevance of altered proteomic expressions. Results Quantitative proteomic analysis revealed a wide breadth of signaling events during transition to acquired tamoxifen resistance. A total of 629 proteins were found significantly changed with 364 up-regulated and 265 down-regulated. Collectively, these changes demonstrated the suppressed state of estrogen receptor (ER) and ER-regulated genes, activated survival signaling and increased migratory capacity of the resistant cell line. The protein S100P was found to play a critical role in conferring tamoxifen resistance and enhanced cell motility. Conclusions Our data demonstrate that the adaptive changes in the proteome of tamoxifen resistant breast cancer cells are characterized by down-regulated ER signaling, activation of alternative survival pathways, and enhanced cell motility through regulation of the actin cytoskeleton dynamics. Evidence also emerged that S100P mediates acquired tamoxifen resistance and migration capacity. PMID:22417809

Cloning of quantitative trait genes from rice reveals conservation and divergence of photoperiod flowering pathways in Arabidopsis and rice

PubMed Central

Matsubara, Kazuki; Hori, Kiyosumi; Ogiso-Tanaka, Eri; Yano, Masahiro

2014-01-01

Flowering time in rice (Oryza sativa L.) is determined primarily by daylength (photoperiod), and natural variation in flowering time is due to quantitative trait loci involved in photoperiodic flowering. To date, genetic analysis of natural variants in rice flowering time has resulted in the positional cloning of at least 12 quantitative trait genes (QTGs), including our recently cloned QTGs, Hd17, and Hd16. The QTGs have been assigned to specific photoperiodic flowering pathways. Among them, 9 have homologs in the Arabidopsis genome, whereas it was evident that there are differences in the pathways between rice and Arabidopsis, such that the rice Ghd7–Ehd1–Hd3a/RFT1 pathway modulated by Hd16 is not present in Arabidopsis. In this review, we describe QTGs underlying natural variation in rice flowering time. Additionally, we discuss the implications of the variation in adaptive divergence and its importance in rice breeding. PMID:24860584

Sensomics-Assisted Elucidation of the Tastant Code of Cooked Crustaceans and Taste Reconstruction Experiments.

PubMed

Meyer, Stefanie; Dunkel, Andreas; Hofmann, Thomas

2016-02-10

Sensory-guided fractionation by means of ultrafiltration and cation-exchange chromatography, followed by MS/MS quantitation, and taste re-engineering experiments revealed the key taste molecules coining the characteristic taste profile of the cooked meat of king prawns. Furthermore, quantitative analysis demonstrated that the taste differences between crustaceans are due to quantitative differences in the combinatorial code of tastants, rather than to qualitative differences in the tastant composition. Besides the amino acids glycine, L-proline, and L-alanine, the characteristic seafood-like sweet profile was found to be due to the sweet modulatory action of quaternary ammonium compounds, among which betaine, homarine, stachydrin, and trimethylamine-N-oxide were found as the key contributors on the basis of dose-activity considerations. Knowledge of this combinatorial tastant code provides the foundation for the development of more sophisticated crustacean flavors that are lacking any heavy metal ions and allergenic proteins present when using crustacean extracts for food flavoring.

Untargeted Metabolic Quantitative Trait Loci Analyses Reveal a Relationship between Primary Metabolism and Potato Tuber Quality1[W][OA

PubMed Central

Carreno-Quintero, Natalia; Acharjee, Animesh; Maliepaard, Chris; Bachem, Christian W.B.; Mumm, Roland; Bouwmeester, Harro; Visser, Richard G.F.; Keurentjes, Joost J.B.

2012-01-01

Recent advances in -omics technologies such as transcriptomics, metabolomics, and proteomics along with genotypic profiling have permitted dissection of the genetics of complex traits represented by molecular phenotypes in nonmodel species. To identify the genetic factors underlying variation in primary metabolism in potato (Solanum tuberosum), we have profiled primary metabolite content in a diploid potato mapping population, derived from crosses between S. tuberosum and wild relatives, using gas chromatography-time of flight-mass spectrometry. In total, 139 polar metabolites were detected, of which we identified metabolite quantitative trait loci for approximately 72% of the detected compounds. In order to obtain an insight into the relationships between metabolic traits and classical phenotypic traits, we also analyzed statistical associations between them. The combined analysis of genetic information through quantitative trait locus coincidence and the application of statistical learning methods provide information on putative indicators associated with the alterations in metabolic networks that affect complex phenotypic traits. PMID:22223596

Development and in-house validation of the event-specific qualitative and quantitative PCR detection methods for genetically modified cotton MON15985.

PubMed

Jiang, Lingxi; Yang, Litao; Rao, Jun; Guo, Jinchao; Wang, Shu; Liu, Jia; Lee, Seonghun; Zhang, Dabing

2010-02-01

To implement genetically modified organism (GMO) labeling regulations, an event-specific analysis method based on the junction sequence between exogenous integration and host genomic DNA has become the preferential approach for GMO identification and quantification. In this study, specific primers and TaqMan probes based on the revealed 5'-end junction sequence of GM cotton MON15985 were designed, and qualitative and quantitative polymerase chain reaction (PCR) assays were established employing the designed primers and probes. In the qualitative PCR assay, the limit of detection (LOD) was 0.5 g kg(-1) in 100 ng total cotton genomic DNA, corresponding to about 17 copies of haploid cotton genomic DNA, and the LOD and limit of quantification (LOQ) for quantitative PCR assay were 10 and 17 copies of haploid cotton genomic DNA, respectively. Furthermore, the developed quantitative PCR assays were validated in-house by five different researchers. Also, five practical samples with known GM contents were quantified using the developed PCR assay in in-house validation, and the bias between the true and quantification values ranged from 2.06% to 12.59%. This study shows that the developed qualitative and quantitative PCR methods are applicable for the identification and quantification of GM cotton MON15985 and its derivates.

Quantitative analysis of collagens and fibronectin expression in human right ventricular hypertrophy.

PubMed

Peters, T H; Sharma, H S; Yilmaz, E; Bogers, A J

1999-06-30

One of the main features in human tetralogy of Fallot (TF) is right ventricular hypertrophy (RVH) due to pressure (sub-pulmonary stenosis) and volume overload (ventricular septal defect). Currently, primary correction at a young age is the treatment of choice. To unravel the role of extracellular matrix in RVH, we examined myocardial expression of collagens and fibronectin in TF patients with primary correction (TF1, age 0.7 +/- 0.2 yr.), secondary surgery (TF2, age 36.9 +/- 4.6 yr), and in age-matched control patients. Sirius red staining quantified by video imaging showed significantly increased interstitial staining for collagens in both TF1 and TF2 groups as compared to respective controls. Fibronectin was expressed in extracellular spaces, perivascular regions, and in some cardiomyocytes. Quantitative analysis of fibronectin revealed increased expression in only TF1 group as compared to respective control. Our results indicate an increased amount of myocardial extracellular matrix deposition as a sign of fibrosis during RVH in patients with TF.

Quantitative Analysis of NAD Synthesis-Breakdown Fluxes.

PubMed

Liu, Ling; Su, Xiaoyang; Quinn, William J; Hui, Sheng; Krukenberg, Kristin; Frederick, David W; Redpath, Philip; Zhan, Le; Chellappa, Karthikeyani; White, Eileen; Migaud, Marie; Mitchison, Timothy J; Baur, Joseph A; Rabinowitz, Joshua D

2018-05-01

The redox cofactor nicotinamide adenine dinucleotide (NAD) plays a central role in metabolism and is a substrate for signaling enzymes including poly-ADP-ribose-polymerases (PARPs) and sirtuins. NAD concentration falls during aging, which has triggered intense interest in strategies to boost NAD levels. A limitation in understanding NAD metabolism has been reliance on concentration measurements. Here, we present isotope-tracer methods for NAD flux quantitation. In cell lines, NAD was made from nicotinamide and consumed largely by PARPs and sirtuins. In vivo, NAD was made from tryptophan selectively in the liver, which then excreted nicotinamide. NAD fluxes varied widely across tissues, with high flux in the small intestine and spleen and low flux in the skeletal muscle. Intravenous administration of nicotinamide riboside or mononucleotide delivered intact molecules to multiple tissues, but the same agents given orally were metabolized to nicotinamide in the liver. Thus, flux analysis can reveal tissue-specific NAD metabolism. Copyright © 2018 Elsevier Inc. All rights reserved.

Analysis of the expected density of internal equilibria in random evolutionary multi-player multi-strategy games.

PubMed

Duong, Manh Hong; Han, The Anh

2016-12-01

In this paper, we study the distribution and behaviour of internal equilibria in a d-player n-strategy random evolutionary game where the game payoff matrix is generated from normal distributions. The study of this paper reveals and exploits interesting connections between evolutionary game theory and random polynomial theory. The main contributions of the paper are some qualitative and quantitative results on the expected density, [Formula: see text], and the expected number, E(n, d), of (stable) internal equilibria. Firstly, we show that in multi-player two-strategy games, they behave asymptotically as [Formula: see text] as d is sufficiently large. Secondly, we prove that they are monotone functions of d. We also make a conjecture for games with more than two strategies. Thirdly, we provide numerical simulations for our analytical results and to support the conjecture. As consequences of our analysis, some qualitative and quantitative results on the distribution of zeros of a random Bernstein polynomial are also obtained.

Student nurse-educators' construction of teacher identity from a self-evaluation perspective: A quantitative case study.

PubMed

Mukumbang, Ferdinand C; Alindekane, Leka Marcel

2017-04-01

The aim of this study was to explore the teacher identity formation dynamics of student nurse-educators about the subject matter, pedagogy and didactics. A case study using descriptive quantitative design was employed. Using a cross-sectional approach, data were collected in 2014 using a self-administered questionnaire. Participants were asked to self-evaluate their teaching competencies on the nursing subject matter, pedagogical expertise and didactical expertise. Using descriptive analysis we determined the central tendencies of the constructs. The descriptive analysis revealed a very small variance (0.0011) and standard deviation (0.04) among the means of the three constructs, which indicates a fair balance in the contribution of the subject matter, pedagogy and didactics towards teacher identity formation. Nursing student-educators can achieve a balanced combination of subject matter expert, pedagogical expert and didactical expert combination during the formation of their teacher identity. This could be indicative of how effective the training programme is in helping the students achieve a balanced teacher identity.

Quantitative analysis of autophagic flux by confocal pH-imaging of autophagic intermediates

PubMed Central

Maulucci, Giuseppe; Chiarpotto, Michela; Papi, Massimiliano; Samengo, Daniela; Pani, Giovambattista; De Spirito, Marco

2015-01-01

Although numerous techniques have been developed to monitor autophagy and to probe its cellular functions, these methods cannot evaluate in sufficient detail the autophagy process, and suffer limitations from complex experimental setups and/or systematic errors. Here we developed a method to image, contextually, the number and pH of autophagic intermediates by using the probe mRFP-GFP-LC3B as a ratiometric pH sensor. This information is expressed functionally by AIPD, the pH distribution of the number of autophagic intermediates per cell. AIPD analysis reveals how intermediates are characterized by a continuous pH distribution, in the range 4.5–6.5, and therefore can be described by a more complex set of states rather than the usual biphasic one (autophagosomes and autolysosomes). AIPD shape and amplitude are sensitive to alterations in the autophagy pathway induced by drugs or environmental states, and allow a quantitative estimation of autophagic flux by retrieving the concentrations of autophagic intermediates. PMID:26506895

Odorant Screening and Quantitation of Thiols in Carmenere Red Wine by Gas Chromatography-Olfactometry and Stable Isotope Dilution Assays.

PubMed

Pavez, Carolina; Agosin, Eduardo; Steinhaus, Martin

2016-05-04

The sensory impact of thiols in Vitis vinifera 'Carmenere' red wines was evaluated. For this purpose, aroma extract dilution analysis was applied to the thiols isolated from a Carmenere red wine by affinity chromatography with a mercurated agarose gel. Results revealed the presence of four odorants, identified as 2-furanylmethanethiol, 3-sulfanylhexyl acetate, 3-sulfanyl-1-hexanol, and 2-methyl-3-sulfanyl-1-butanol, with the latter being described here for the first time in Carmenere red wines. Quantitation of the four thiols in the Carmenere wine screened by aroma extract dilution analysis and in three additional Carmenere wines by stable isotope dilution assays resulted in concentrations above the respective orthonasal odor detection threshold values. Triangle tests applied to wine model solutions with and without the addition of the four thiols showed significant differences, thus suggesting that the compounds do have the potential to influence the overall aroma of red wine.

Decoding tumour phenotype by noninvasive imaging using a quantitative radiomics approach

PubMed Central

Aerts, Hugo J. W. L.; Velazquez, Emmanuel Rios; Leijenaar, Ralph T. H.; Parmar, Chintan; Grossmann, Patrick; Cavalho, Sara; Bussink, Johan; Monshouwer, René; Haibe-Kains, Benjamin; Rietveld, Derek; Hoebers, Frank; Rietbergen, Michelle M.; Leemans, C. René; Dekker, Andre; Quackenbush, John; Gillies, Robert J.; Lambin, Philippe

2014-01-01

Human cancers exhibit strong phenotypic differences that can be visualized noninvasively by medical imaging. Radiomics refers to the comprehensive quantification of tumour phenotypes by applying a large number of quantitative image features. Here we present a radiomic analysis of 440 features quantifying tumour image intensity, shape and texture, which are extracted from computed tomography data of 1,019 patients with lung or head-and-neck cancer. We find that a large number of radiomic features have prognostic power in independent data sets of lung and head-and-neck cancer patients, many of which were not identified as significant before. Radiogenomics analysis reveals that a prognostic radiomic signature, capturing intratumour heterogeneity, is associated with underlying gene-expression patterns. These data suggest that radiomics identifies a general prognostic phenotype existing in both lung and head-and-neck cancer. This may have a clinical impact as imaging is routinely used in clinical practice, providing an unprecedented opportunity to improve decision-support in cancer treatment at low cost. PMID:24892406

Exploring G protein-coupled receptor signaling networks using SILAC-based phosphoproteomics

PubMed Central

Williams, Grace R.; Bethard, Jennifer R.; Berkaw, Mary N.; Nagel, Alexis K.; Luttrell, Louis M.; Ball, Lauren E.

2015-01-01

The type 1 parathyroid hormone receptor (PTH1R) is a key regulator of calcium homeostasis and bone turnover. Here, we employed SILAC-based quantitative mass spectrometry combined with bioinformatic pathways analysis to examine global changes in protein phosphorylation following short-term stimulation of endogenously expressed PTH1R in osteoblastic cells in vitro. Following 5 min exposure to the conventional agonist, PTH(1-34), we detected significant changes in the phosphorylation of 224 distinct proteins. Kinase substrate motif enrichment demonstrated that consensus motifs for PKA and CAMK2 were the most heavily upregulated within the phosphoproteome, while consensus motifs for mitogen-activated protein kinases were strongly downregulated. Signaling pathways analysis identified ERK1/2 and AKT as important nodal kinases in the downstream network and revealed strong regulation of small GTPases involved in cytoskeletal rearrangement, cell motility, and focal adhesion complex signaling. Our data illustrate the utility of quantitative mass spectrometry in measuring dynamic changes in protein phosphorylation following GPCR activation. PMID:26160508

Validated reversed phase LC method for quantitative analysis of polymethoxyflavones in citrus peel extracts.

PubMed

Wang, Zhenyu; Li, Shiming; Ferguson, Stephen; Goodnow, Robert; Ho, Chi-Tang

2008-01-01

Polymethoxyflavones (PMFs), which exist exclusively in the citrus genus, have biological activities including anti-inflammatory, anticarcinogenic, and antiatherogenic properties. A validated RPLC method was developed for quantitative analysis of six major PMFs, namely nobiletin, tangeretin, sinensetin, 5,6,7,4'-tetramethoxyflavone, 3,5,6,7,3',4'-hexamethoxyflavone, and 3,5,6,7,8,3',4'-heptamethoxyflavone. The polar embedded LC stationary phase was able to fully resolve the six analogues. The developed method was fully validated in terms of linearity, accuracy, precision, sensitivity, and system suitability. The LOD of the method was calculated as 0.15 microg/mL and the recovery rate was between 97.0 and 105.1%. This analytical method was successfully applied to quantify the individual PMFs in four commercially available citrus peel extracts (CPEs). Each extract shows significant difference in the PMF composition and concentration. This method may provide a simple, rapid, and reliable tool to help reveal the correlation between the bioactivity of the PMF extracts and the individual PMF content.

Exploring the Possibility of Peak Individualism, Humanity's Existential Crisis, and an Emerging Age of Purpose.

PubMed

Grant, Gabriel B

2017-01-01

There is an emerging cultural narrative in the United States that we are entering an age of purpose-that millennials, more than any other generation, are searching for purpose and purposeful work (Sheahan, 2005) and that we are entering an era or economy of purpose (Hurst, 2014). For profit, non-profit, and educational institutions are perceiving and adapting to serve millennials' demand for purpose in life, specifically within the workplace (Klein et al., 2015). Yet, longitudinal studies of purpose do not exist, and millennials are also referred to as GenMe. Existing quantitative research suggests they (we) are increasingly individualistic, materialistic, and narcissistic (Greenfield, 2013). Google's digitization of millions of books and the Ngram Viewer allow for quantified analysis of culture over the past two centuries. This tool was used to quantitatively test the popular notion that there is a rise in demand for purpose. Analysis reveals a growing interest in purpose-in-life and a shift toward collectivistic values emerging over the lifespan of the millennial generation.

Retrieval analysis of different orthodontic brackets: the applicability of electron microprobe techniques for determining material heterogeneities and corrosive potential

PubMed Central

HOLST, Alexandra Ioana; HOLST, Stefan; HIRSCHFELDER, Ursula; von SECKENDORFF, Volker

2012-01-01

Objective The objective of this study was to investigate the applicability of micro-analytical methods with high spatial resolution to the characterization of the composition and corrosion behavior of two bracket systems. Material and methods The surfaces of six nickel-free brackets and six nickel-containing brackets were examined for signs of corrosion and qualitative surface analysis using an electron probe microanalyzer (EPMA), prior to bonding to patient's tooth surfaces and four months after clinical use. The surfaces were characterized qualitatively by secondary electron (SE) images and back scattered electron (BSE) images in both compositional and topographical mode. Qualitative and quantitative wavelength-dispersive analyses were performed for different elements, and by utilizing qualitative analysis the relative concentration of selected elements was mapped two-dimensionally. The absolute concentration of the elements was determined in specially prepared brackets by quantitative analysis using pure element standards for calibration and calculating correction-factors (ZAF). Results Clear differences were observed between the different bracket types. The nickel-containing stainless steel brackets consist of two separate pieces joined by a brazing alloy. Compositional analysis revealed two different alloy compositions, and reaction zones on both sides of the brazing alloy. The nickel-free bracket was a single piece with only slight variation in element concentration, but had a significantly rougher surface. After clinical use, no corrosive phenomena were detectable with the methods applied. Traces of intraoral wear at the contact areas between the bracket slot and the arch wire were verified. Conclusion Electron probe microanalysis is a valuable tool for the characterization of element distribution and quantitative analysis for corrosion studies. PMID:23032212

A Quantitative Analysis of Pulsed Signals Emitted by Wild Bottlenose Dolphins.

PubMed

Luís, Ana Rita; Couchinho, Miguel N; Dos Santos, Manuel E

2016-01-01

Common bottlenose dolphins (Tursiops truncatus), produce a wide variety of vocal emissions for communication and echolocation, of which the pulsed repertoire has been the most difficult to categorize. Packets of high repetition, broadband pulses are still largely reported under a general designation of burst-pulses, and traditional attempts to classify these emissions rely mainly in their aural characteristics and in graphical aspects of spectrograms. Here, we present a quantitative analysis of pulsed signals emitted by wild bottlenose dolphins, in the Sado estuary, Portugal (2011-2014), and test the reliability of a traditional classification approach. Acoustic parameters (minimum frequency, maximum frequency, peak frequency, duration, repetition rate and inter-click-interval) were extracted from 930 pulsed signals, previously categorized using a traditional approach. Discriminant function analysis revealed a high reliability of the traditional classification approach (93.5% of pulsed signals were consistently assigned to their aurally based categories). According to the discriminant function analysis (Wilk's Λ = 0.11, F3, 2.41 = 282.75, P < 0.001), repetition rate is the feature that best enables the discrimination of different pulsed signals (structure coefficient = 0.98). Classification using hierarchical cluster analysis led to a similar categorization pattern: two main signal types with distinct magnitudes of repetition rate were clustered into five groups. The pulsed signals, here described, present significant differences in their time-frequency features, especially repetition rate (P < 0.001), inter-click-interval (P < 0.001) and duration (P < 0.001). We document the occurrence of a distinct signal type-short burst-pulses, and highlight the existence of a diverse repertoire of pulsed vocalizations emitted in graded sequences. The use of quantitative analysis of pulsed signals is essential to improve classifications and to better assess the contexts of emission, geographic variation and the functional significance of pulsed signals.

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

Chuang, Chihpin; Singh, Dileep; Kenesei, Peter

The size and morphology of the graphite particles play a crucial role in determining various mechanical and thermal properties of cast iron. In the present study, we utilized high-energy synchrotron X-ray tomography to perform quantitative 3D-characterization of the distribution of graphite particles in high-strength compacted graphite iron (CGI). The size, shape, and spatial connectivity of graphite were examined. The analysis reveals that the compacted graphite can grow with a coral-tree-like morphology and span several hundred microns in the iron matrix.

Systems cell biology

PubMed Central

Mast, Fred D.; Ratushny, Alexander V.

2014-01-01

Systems cell biology melds high-throughput experimentation with quantitative analysis and modeling to understand many critical processes that contribute to cellular organization and dynamics. Recently, there have been several advances in technology and in the application of modeling approaches that enable the exploration of the dynamic properties of cells. Merging technology and computation offers an opportunity to objectively address unsolved cellular mechanisms, and has revealed emergent properties and helped to gain a more comprehensive and fundamental understanding of cell biology. PMID:25225336

Stromal Gene Expression and Function in Primary Breast Tumors that Metastasize to Bone Cancer

DTIC Science & Technology

2004-07-01

by quantitative RT-QPCR. Further analysis of epithelium from matched spine metastases revealed some genes that were up-regulated further at the...9-fold in matched bone metastases. The expression in spine metastases was verified by in situ hybridisation whilst the expression of stefin Al in...growth in the mammary gland of Balb/c mice. Fresh resected tissue (normal fat pad, primary tumor tissue or the metastatic sites spine , femur and lung) was

Comprehensive Cell-specific Protein Analysis in Early and Late Pollen Development from Diploid Microsporocytes to Pollen Tube Growth*

PubMed Central

Ischebeck, Till; Valledor, Luis; Lyon, David; Gingl, Stephanie; Nagler, Matthias; Meijón, Mónica; Egelhofer, Volker; Weckwerth, Wolfram

2014-01-01

Pollen development in angiosperms is one of the most important processes controlling plant reproduction and thus productivity. At the same time, pollen development is highly sensitive to environmental fluctuations, including temperature, drought, and nutrition. Therefore, pollen biology is a major focus in applied studies and breeding approaches for improving plant productivity in a globally changing climate. The most accessible developmental stages of pollen are the mature pollen and the pollen tubes, and these are thus most frequently analyzed. To reveal a complete quantitative proteome map, we additionally addressed the very early stages, analyzing eight stages of tobacco pollen development: diploid microsporocytes, meiosis, tetrads, microspores, polarized microspores, bipolar pollen, desiccated pollen, and pollen tubes. A protocol for the isolation of the early stages was established. Proteins were extracted and analyzed by means of a new gel LC-MS fractionation protocol. In total, 3817 protein groups were identified. Quantitative analysis was performed based on peptide count. Exceedingly stage-specific differential protein regulation was observed during the conversion from the sporophytic to the gametophytic proteome. A map of highly specialized functionality for the different stages could be revealed from the metabolic activity and pronounced differentiation of proteasomal and ribosomal protein complex composition up to protective mechanisms such as high levels of heat shock proteins in the very early stages of development. PMID:24078888

Comprehensive cell-specific protein analysis in early and late pollen development from diploid microsporocytes to pollen tube growth.

PubMed

Ischebeck, Till; Valledor, Luis; Lyon, David; Gingl, Stephanie; Nagler, Matthias; Meijón, Mónica; Egelhofer, Volker; Weckwerth, Wolfram

2014-01-01

Pollen development in angiosperms is one of the most important processes controlling plant reproduction and thus productivity. At the same time, pollen development is highly sensitive to environmental fluctuations, including temperature, drought, and nutrition. Therefore, pollen biology is a major focus in applied studies and breeding approaches for improving plant productivity in a globally changing climate. The most accessible developmental stages of pollen are the mature pollen and the pollen tubes, and these are thus most frequently analyzed. To reveal a complete quantitative proteome map, we additionally addressed the very early stages, analyzing eight stages of tobacco pollen development: diploid microsporocytes, meiosis, tetrads, microspores, polarized microspores, bipolar pollen, desiccated pollen, and pollen tubes. A protocol for the isolation of the early stages was established. Proteins were extracted and analyzed by means of a new gel LC-MS fractionation protocol. In total, 3817 protein groups were identified. Quantitative analysis was performed based on peptide count. Exceedingly stage-specific differential protein regulation was observed during the conversion from the sporophytic to the gametophytic proteome. A map of highly specialized functionality for the different stages could be revealed from the metabolic activity and pronounced differentiation of proteasomal and ribosomal protein complex composition up to protective mechanisms such as high levels of heat shock proteins in the very early stages of development.

Expression and functional analysis of the lysine decarboxylase and copper amine oxidase genes from the endophytic fungus Colletotrichum gloeosporioides ES026.

PubMed

Zhang, Xiangmei; Wang, Zhangqian; Jan, Saad; Yang, Qian; Wang, Mo

2017-06-05

Huperzine A (HupA) isolated from Huperzia serrata is an important compound used to treat Alzheimer's disease (AD). Recently, HupA was reported in various endophytic fungi, with Colletotrichum gloeosporioides ES026 previously isolated from H. serrata shown to produce HupA. In this study, we performed next-generation sequencing and de novo RNA sequencing of C. gloeosporioides ES026 to elucidate the molecular functions, biological processes, and biochemical pathways of these unique sequences. Gene ontology and Kyoto Encyclopedia of Genes and Genomes assignments allowed annotation of lysine decarboxylase (LDC) and copper amine oxidase (CAO) for their conversion of L-lysine to 5-aminopentanal during HupA biosynthesis. Additionally, we constructed a stable, high-yielding HupA-expression system resulting from the overexpression of CgLDC and CgCAO from the HupA-producing endophytic fungus C. gloeosporioides ES026 in Escherichia coli. Quantitative reverse transcription polymerase chain reaction analysis confirmed CgLDC and CgCAO expression, and quantitative determination of HupA levels was assessed by liquid chromatography high-resolution mass spectrometry, which revealed that elevated expression of CgLDC and CgCAO produced higher yields of HupA than those derived from C. gloeosporioides ES026. These results revealed CgLDC and CgCAO involvement in HupA biosynthesis and their key role in regulating HupA content in C. gloeosporioides ES026.

Quantitative proteomics reveals dynamic responses of Synechocystis sp. PCC 6803 to next-generation biofuel butanol.

PubMed

Tian, Xiaoxu; Chen, Lei; Wang, Jiangxin; Qiao, Jianjun; Zhang, Weiwen

2013-01-14

Butanol is a promising biofuel, and recent metabolic engineering efforts have demonstrated the use of photosynthetic cyanobacterial hosts for its production. However, cyanobacteria have very low tolerance to butanol, limiting the economic viability of butanol production from these renewable producing systems. The existing knowledge of molecular mechanism involved in butanol tolerance in cyanobacteria is very limited. To build a foundation necessary to engineer robust butanol-producing cyanobacterial hosts, in this study, the responses of Synechocystis PCC 6803 to butanol were investigated using a quantitative proteomics approach with iTRAQ - LC-MS/MS technologies. The resulting high-quality dataset consisted of 25,347 peptides corresponding to 1452 unique proteins, a coverage of approximately 40% of the predicted proteins in Synechocystis. Comparative quantification of protein abundances led to the identification of 303 differentially regulated proteins by butanol. Annotation and GO term enrichment analysis showed that multiple biological processes were regulated, suggesting that Synechocystis probably employed multiple and synergistic resistance mechanisms in dealing with butanol stress. Notably, the analysis revealed the induction of heat-shock protein and transporters, along with modification of cell membrane and envelope were the major protection mechanisms against butanol. A conceptual cellular model of Synechocystis PCC 6803 responses to butanol stress was constructed to illustrate the putative molecular mechanisms employed to defend against butanol stress. Copyright © 2012 Elsevier B.V. All rights reserved.

Imaging of size-dependent uptake and identification of novel pathways in mouse Peyer's patches using fluorescent organosilica particles.

PubMed

Awaad, Aziz; Nakamura, Michihiro; Ishimura, Kazunori

2012-07-01

We investigated size-dependent uptake of fluorescent thiol-organosilica particles by Peyer's patches (PPs). We performed an oral single-particle administration (95, 130, 200, 340, 695 and 1050 nm) and a simultaneous dual-particle administration using 2 kinds of particles. Histological imaging and quantitative analysis revealed that particles taken up by the PP subepithelial dome were size dependent, and there was an optimal size range for higher uptake. Quantitative analysis of simultaneous dual-particle administration revealed that the percentage of fluorescence areas for 95, 130, 200, 340, 695 and 1050 nm with respect to 110 nm area was 124.0, 89.1, 73.8, 20.2, 9.2 and 0.5%, respectively. Additionally, imaging using fluorescent thiol-organosilica particles could detect 2 novel pathways through mouse PP epithelium: the transcellular pathway and the paracellular pathway. The uptake of nanoparticles based on an optimal size range and 2 novel pathways could indicate a new approach for vaccine delivery and nanomedicine development. Studying various sizes of fluorescent organosilica particles and their uptake in Peyer's patches, this team of authors determined the optimal size range of administration. Two novel pathways through mouse Peyer's patch epithelium were detected, i.e., the transcellular pathway and the paracellular pathway. This observation may have important applications in future vaccine delivery and nano-drug delivery. Copyright © 2012 Elsevier Inc. All rights reserved.

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

"We are Two of the Lucky Ones": Experiences with Marriage and Wellbeing for Same-Sex Couples.

PubMed

Kennedy, Heather R; Dalla, Rochelle L; Dreesman, Steven

2018-01-01

Happy marriages provide protective health benefits, and social support is a key factor in this association. However, previous research indicates one of the greatest differences between same- and different-sex couples is less social support for same-sex couples. Our goal was to examine the extent to which formal markers of couple status (e.g., marriage) impact wellbeing among same-sex married partners. Using a mixed-methods approach, data were collected from 218 primarily White gay and lesbian individuals in the Midwest. Quantitative analysis revealed individuals in a prior formal union with a different-sex partner reported the lowest levels of sexuality specific social support and acceptance. Qualitative analysis revealed four primary impacts of marriage on support from family, friends, and co-workers: no change, increased support, decreased support, and a synthesis of mixed support. Three mechanisms prompting change in the family were identified and are presented.

Proteomic and N-glycoproteomic quantification reveal aberrant changes in the human saliva of oral ulcer patients.

PubMed

Zhang, Ying; Wang, Xi; Cui, Dan; Zhu, Jun

2016-12-01

Human whole saliva is a vital body fluid for studying the physiology and pathology of the oral cavity. As a powerful technique for biomarker discovery, MS-based proteomic strategies have been introduced for saliva analysis and identified hundreds of proteins and N-glycosylation sites. However, there is still a lack of quantitative analysis, which is necessary for biomarker screening and biological research. In this study, we establish an integrated workflow by the combination of stable isotope dimethyl labeling, HILIC enrichment, and high resolution MS for both quantification of the global proteome and N-glycoproteome of human saliva from oral ulcer patients. With the help of advanced bioinformatics, we comprehensively studied oral ulcers at both protein and glycoprotein scales. Bioinformatics analyses revealed that starch digestion and protein degradation activities are inhibited while the immune response is promoted in oral ulcer saliva. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Proteomics analysis reveals a dynamic diurnal pattern of photosynthesis-related pathways in maize leaves.

PubMed

Feng, Dan; Wang, Yanwei; Lu, Tiegang; Zhang, Zhiguo; Han, Xiao

2017-01-01

Plant leaves exhibit differentiated patterns of photosynthesis rates under diurnal light regulation. Maize leaves show a single-peak pattern without photoinhibition at midday when the light intensity is maximized. This mechanism contributes to highly efficient photosynthesis in maize leaves. To understand the molecular basis of this process, an isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomics analysis was performed to reveal the dynamic pattern of proteins related to photosynthetic reactions. Steady, single-peak and double-peak protein expression patterns were discovered in maize leaves, and antenna proteins in these leaves displayed a steady pattern. In contrast, the photosystem, carbon fixation and citrate pathways were highly controlled by diurnal light intensity. Most enzymes in the limiting steps of these pathways were major sites of regulation. Thus, maize leaves optimize photosynthesis and carbon fixation outside of light harvesting to adapt to the changes in diurnal light intensity at the protein level.

Factors influencing students' perceptions of their quantitative skills

NASA Astrophysics Data System (ADS)

Matthews, Kelly E.; Hodgson, Yvonne; Varsavsky, Cristina

2013-09-01

There is international agreement that quantitative skills (QS) are an essential graduate competence in science. QS refer to the application of mathematical and statistical thinking and reasoning in science. This study reports on the use of the Science Students Skills Inventory to capture final year science students' perceptions of their QS across multiple indicators, at two Australian research-intensive universities. Statistical analysis reveals several variables predicting higher levels of self-rated competence in QS: students' grade point average, students' perceptions of inclusion of QS in the science degree programme, their confidence in QS, and their belief that QS will be useful in the future. The findings are discussed in terms of implications for designing science curricula more effectively to build students' QS throughout science degree programmes. Suggestions for further research are offered.

Figures and First Years: Examining first-year Calculus I student ability to incorporate figures into technical reports

NASA Astrophysics Data System (ADS)

Antonacci, Nathan; Rogers, Michael; Pfaff, Thomas

This three-year study focused on first-year Calculus I students and their abilities to incorporate figures into technical reports. Students were handed guidelines as part of their Multidisciplinary Sustainability Education Module meant to aid them in crafting effective figures. Figure-specific questionnaires were added in the class to gain insight into the quantitative literacy skills students possessed both before starting their course and after its completion. Reviews of the figures in 78 technical reports written by 106 students showed repeated failure to refer to figures in discussion sections and use them in evidence-based arguments. Analysis of quantitative literacy skills revealed that the students could both read and interpret figures, suggesting that issues with literacy were not the main contributor to the sub-par graphs.

Long-Term Efficacy of Maintenance Therapy for Multiple Myeloma: A Quantitative Synthesis of 22 Randomized Controlled Trials.

PubMed

Li, Jie-Li; Fan, Guang-Yu; Liu, Yu-Jie; Zeng, Zi-Hang; Huang, Jing-Juan; Yang, Zong-Ming; Meng, Xiang-Yu

2018-01-01

We aimed to quantitatively synthesize data from randomized controlled trials (RCTs) concerning maintenance for multiple myeloma (MM). We searched electronic literature databases and conference proceedings to identify relevant RCTs. We selected eligible RCTs using predefined selection criteria. We conducted meta-analysis comparing maintenance containing new agents and conventional maintenance, and subgroup analysis by transplantation status and mainstay agent as well. We performed trial sequential analysis (TSA) to determine adequacy of sample size for overall and subgroup meta-analyses. We performed network meta-analysis (NMA) to compare and rank included regimens. A total of 22 RCTs involving 9,968 MM patients and 15 regimens were included, the overall quality of which was adequate. Significant heterogeneity was detected for progression-free survival (PFS) but not overall survival (OS). Meta-analyses showed that maintenance containing new agents significantly improved PFS but not OS [PFS: Hazard Ratio (HR) = 0.59, 95% Confidence Interval (CI) = 0.54 to 0.64; OS: HR = 0.93, 95% CI = 0.87 to 1.00], compared with controls. Subgroup analyses revealed lenalidomide (Len)-based therapies better than thalidomide-based ones (HR = 0.50 and 0.66, respectively; P = 0.001). NMA revealed that most of the maintenance regimens containing new agents were significantly better than simple observation in terms of PFS but not OS. Len single agent was the most effective, considering PFS and OS both. We concluded that conventional maintenance has very limited effect. Maintenance containing new agents is highly effective in improving PFS, but has very limited effect on OS. Maintenance with Len may have the largest survival benefits. Emerging strategies may further change the landscape of maintenance of MM.

Structural Analysis of PTM Hotspots (SAPH-ire) – A Quantitative Informatics Method Enabling the Discovery of Novel Regulatory Elements in Protein Families*

PubMed Central

Dewhurst, Henry M.; Choudhury, Shilpa; Torres, Matthew P.

2015-01-01

Predicting the biological function potential of post-translational modifications (PTMs) is becoming increasingly important in light of the exponential increase in available PTM data from high-throughput proteomics. We developed structural analysis of PTM hotspots (SAPH-ire)—a quantitative PTM ranking method that integrates experimental PTM observations, sequence conservation, protein structure, and interaction data to allow rank order comparisons within or between protein families. Here, we applied SAPH-ire to the study of PTMs in diverse G protein families, a conserved and ubiquitous class of proteins essential for maintenance of intracellular structure (tubulins) and signal transduction (large and small Ras-like G proteins). A total of 1728 experimentally verified PTMs from eight unique G protein families were clustered into 451 unique hotspots, 51 of which have a known and cited biological function or response. Using customized software, the hotspots were analyzed in the context of 598 unique protein structures. By comparing distributions of hotspots with known versus unknown function, we show that SAPH-ire analysis is predictive for PTM biological function. Notably, SAPH-ire revealed high-ranking hotspots for which a functional impact has not yet been determined, including phosphorylation hotspots in the N-terminal tails of G protein gamma subunits—conserved protein structures never before reported as regulators of G protein coupled receptor signaling. To validate this prediction we used the yeast model system for G protein coupled receptor signaling, revealing that gamma subunit–N-terminal tail phosphorylation is activated in response to G protein coupled receptor stimulation and regulates protein stability in vivo. These results demonstrate the utility of integrating protein structural and sequence features into PTM prioritization schemes that can improve the analysis and functional power of modification-specific proteomics data. PMID:26070665

Quantitative Proteomic and Microarray Analysis of the Archaeon Methanosarcina Acetivorans Grown with Acetate Versus Methanol*

PubMed Central

Li, Lingyun; Li, Qingbo; Rohlin, Lars; Kim, UnMi; Salmon, Kirsty; Rejtar, Tomas; Gunsalus, Robert P.; Karger, Barry L.; Ferry, James G.

2008-01-01

Summary Methanosarcina acetivorans strain C2A is an acetate- and methanol-utilizing methane-producing organism for which the genome, the largest yet sequenced among the Archaea, reveals extensive physiological diversity. LC linear ion trap-FTICR mass spectrometry was employed to analyze acetate- vs. methanol-grown cells metabolically labeled with 14N vs. 15N, respectively, to obtain quantitative protein abundance ratios. DNA microarray analyses of acetate- vs. methanol-grown cells was also performed to determine gene expression ratios. The combined approaches were highly complementary, extending the physiological understanding of growth and methanogenesis. Of the 1081 proteins detected, 255 were ≥ 3-fold differentially abundant. DNA microarray analysis revealed 410 genes that were ≥ 2.5-fold differentially expressed of 1972 genes with detected expression. The ratios of differentially abundant proteins were in good agreement with expression ratios of the encoding genes. Taken together, the results suggest several novel roles for electron transport components specific to acetate-grown cells, including two flavodoxins each specific for growth on acetate or methanol. Protein abundance ratios indicated that duplicate CO dehydrogenase/acetyl-CoA complexes function in the conversion of acetate to methane. Surprisingly, the protein abundance and gene expression ratios indicated a general stress response in acetate- vs. methanol-grown cells that included enzymes specific for polyphosphate accumulation and oxidative stress. The microarray analysis identified transcripts of several genes encoding regulatory proteins with identity to the PhoU, MarR, GlnK, and TetR families commonly found in the Bacteria domain. An analysis of neighboring genes suggested roles in controlling phosphate metabolism (PhoU), ammonia assimilation (GlnK), and molybdopterin cofactor biosynthesis (TetR). Finally, the proteomic and microarray results suggested roles for two-component regulatory systems specific for each growth substrate. PMID:17269732

Members of the Dof transcription factor family in Triticum aestivum are associated with light-mediated gene regulation.

PubMed

Shaw, Lindsay M; McIntyre, C Lynne; Gresshoff, Peter M; Xue, Gang-Ping

2009-11-01

DNA binding with One Finger (Dof) protein is a plant-specific transcription factor implicated in the regulation of many important plant-specific processes, including photosynthesis and carbohydrate metabolism. This study has identified 31 Dof genes (TaDof) in bread wheat through extensive analysis of current nucleotide databases. Phylogenetic analysis suggests that the TaDof family can be divided into four clades. Expression analysis of the TaDof family across all major organs using quantitative RT-PCR and searches of the wheat genome array database revealed that the majority of TaDof members were predominately expressed in vegetative organs. A large number of TaDof members were down-regulated by drought and/or were responsive to the light and dark cycle. Further expression analysis revealed that light up-regulated TaDof members were highly correlated in expression with a number of genes that are involved in photosynthesis or sucrose transport. These data suggest that the TaDof family may have an important role in light-mediated gene regulation, including involvement in the photosynthetic process.

Data-Independent Acquisition-Based Quantitative Proteomic Analysis Reveals Potential Biomarkers of Kidney Cancer.

PubMed

Song, Yimeng; Zhong, Lijun; Zhou, Juntuo; Lu, Min; Xing, Tianying; Ma, Lulin; Shen, Jing

2017-12-01

Renal cell carcinoma (RCC) is a malignant and metastatic cancer with 95% mortality, and clear cell RCC (ccRCC) is the most observed among the five major subtypes of RCC. Specific biomarkers that can distinguish cancer tissues from adjacent normal tissues should be developed to diagnose this disease in early stages and conduct a reliable prognostic evaluation. Data-independent acquisition (DIA) strategy has been widely employed in proteomic analysis because of various advantages, including enhanced protein coverage and reliable data acquisition. In this study, a DIA workflow is constructed on a quadrupole-Orbitrap LC-MS platform to reveal dysregulated proteins between ccRCC and adjacent normal tissues. More than 4000 proteins are identified, 436 of these proteins are dysregulated in ccRCC tissues. Bioinformatic analysis reveals that multiple pathways and Gene Ontology items are strongly associated with ccRCC. The expression levels of L-lactate dehydrogenase A chain, annexin A4, nicotinamide N-methyltransferase, and perilipin-2 examined through RT-qPCR, Western blot, and immunohistochemistry confirm the validity of the proteomic analysis results. The proposed DIA workflow yields optimum time efficiency and data reliability and provides a good choice for proteomic analysis in biological and clinical studies, and these dysregulated proteins might be potential biomarkers for ccRCC diagnosis. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Supporting employees' work-family needs improves health care quality: Longitudinal evidence from long-term care.

PubMed

Okechukwu, Cassandra A; Kelly, Erin L; Bacic, Janine; DePasquale, Nicole; Hurtado, David; Kossek, Ellen; Sembajwe, Grace

2016-05-01

We analyzed qualitative and quantitative data from U.S.-based employees in 30 long-term care facilities. Analysis of semi-structured interviews from 154 managers informed quantitative analyses. Quantitative data include 1214 employees' scoring of their supervisors and their organizations on family supportiveness (individual scores and aggregated to facility level), and three outcomes: (1), care quality indicators assessed at facility level (n = 30) and collected monthly for six months after employees' data collection; (2), employees' dichotomous survey response on having additional off-site jobs; and (3), proportion of employees with additional jobs at each facility. Thematic analyses revealed that managers operate within the constraints of an industry that simultaneously: (a) employs low-wage employees with multiple work-family challenges, and (b) has firmly institutionalized goals of prioritizing quality of care and minimizing labor costs. Managers universally described providing work-family support and prioritizing care quality as antithetical to each other. Concerns surfaced that family-supportiveness encouraged employees to work additional jobs off-site, compromising care quality. Multivariable linear regression analysis of facility-level data revealed that higher family-supportive supervision was associated with significant decreases in residents' incidence of all pressure ulcers (-2.62%) and other injuries (-9.79%). Higher family-supportive organizational climate was associated with significant decreases in all falls (-17.94%) and falls with injuries (-7.57%). Managers' concerns about additional jobs were not entirely unwarranted: multivariable logistic regression of employee-level data revealed that among employees with children, having family-supportive supervision was associated with significantly higher likelihood of additional off-site jobs (RR 1.46, 95%CI 1.08-1.99), but family-supportive organizational climate was associated with lower likelihood (RR 0.76, 95%CI 0.59-0.99). However, proportion of workers with additional off-site jobs did not significantly predict care quality at facility levels. Although managers perceived providing work-family support and ensuring high care quality as conflicting goals, results suggest that family-supportiveness is associated with better care quality. Copyright © 2016 Elsevier Ltd. All rights reserved.

Supporting employees’ work-family needs improves health care quality: longitudinal evidence from long-term care

PubMed Central

Okechukwu, Cassandra A.; Kelly, Erin L.; Bacic, Janine; DePasquale, Nicole; Hurtado, David; Kossek, Ellen; Sembajwe, Grace

2016-01-01

We analyzed qualitative and quantitative data from U.S.-based employees in 30 long-term care facilities. Analysis of semi-structured interviews from 154 managers informed quantitative analyses. Quantitative data include 1,214 employees’ scoring of their supervisors and their organizations on family supportiveness (individual scores and aggregated to facility level), and three outcomes: (1), care quality indicators assessed at facility level (n=30) and collected monthly for six months after employees’ data collection; (2), employees’ dichotomous survey response on having additional off-site jobs; and (3), proportion of employees with additional jobs at each facility. Thematic analyses revealed that managers operate within the constraints of an industry that simultaneously: (a) employs low-wage employees with multiple work-family challenges, and (b) has firmly institutionalized goals of prioritizing quality of care and minimizing labor costs. Managers universally described providing work-family support and prioritizing care quality as antithetical to each other. Concerns surfaced that family-supportiveness encouraged employees to work additional jobs off-site, compromising care quality. Multivariable linear regression analysis of facility-level data revealed that higher family-supportive supervision was associated with significant decreases in residents’ incidence of all pressure ulcers (−2.62%) and other injuries (−9.79%). Higher family-supportive organizational climate was associated with significant decreases in all falls (−17.94%) and falls with injuries (−7.57%). Managers’ concerns about additional jobs were not entirely unwarranted: multivariable logistic regression of employee-level data revealed that among employees with children, having family-supportive supervision was associated with significantly higher likelihood of additional off-site jobs (RR 1.46, 95%CI 1.08-1.99), but family-supportive organizational climate was associated with lower likelihood (RR 0.76, 95%CI 0.59-0.99). However, proportion of workers with additional off-site jobs did not significantly predict care quality at facility levels. Although managers perceived providing work-family support and ensuring high care quality as conflicting goals, results suggest that family-supportiveness is associated with better care quality. PMID:27082022

Triple SILAC quantitative proteomic analysis reveals differential abundance of cell signaling proteins between normal and lung cancer-derived exosomes.

PubMed

Clark, David J; Fondrie, William E; Yang, Austin; Mao, Li

2016-02-05

Exosomes are 30-100 nm sized membrane vesicles released by cells into the extracellular space that mediate intercellular communication via transfer of proteins and other biological molecules. To better understand the role of these microvesicles in lung carcinogenesis, we employed a Triple SILAC quantitative proteomic strategy to examine the differential protein abundance between exosomes derived from an immortalized normal bronchial epithelial cell line and two non-small cell lung cancer (NSCLC) cell lines harboring distinct activating mutations in the cell signaling molecules: Kirsten rat sarcoma viral oncogene homolog (KRAS) or epidermal growth factor receptor (EGFR). In total, we were able to quantify 721 exosomal proteins derived from the three cell lines. Proteins associated with signal transduction, including EGFR, GRB2 and SRC, were enriched in NSCLC exosomes, and could actively regulate cell proliferation in recipient cells. This study's investigation of the NSCLC exosomal proteome has identified enriched protein cargo that can contribute to lung cancer progression, which may have potential clinical implications in biomarker development for patients with NSCLC. The high mortality associated with lung cancer is a result of late-stage diagnosis of the disease. Current screening techniques used for early detection of lung cancer lack the specificity for accurate diagnosis. Exosomes are nano-sized extracellular vesicles, and the increased abundance of select protein cargo in exosomes derived from cancer cells may be used for diagnostic purposes. In this paper, we applied quantitative proteomic analysis to elucidate abundance differences in exosomal protein cargo between two NSCLC cell lines with distinctive oncogene mutations and an immortalized normal bronchial epithelial cell line. This study revealed proteins associated with cell adhesion, the extracellular matrix, and a variety of signaling molecules were enriched in NSCLC exosomes. The present data reveals a protein profile associated with NSCLC exosomes that suggests a role these vesicles have in the progression of lung carcinogenesis, as well as identifies several promising candidates that could be utilized as a multi-marker protein panel in a diagnostic platform for NSCLC. Copyright © 2015 Elsevier B.V. All rights reserved.

Semi-quantitative proteomics of mammalian cells upon short-term exposure to non-ionizing electromagnetic fields.

PubMed

Kuzniar, Arnold; Laffeber, Charlie; Eppink, Berina; Bezstarosti, Karel; Dekkers, Dick; Woelders, Henri; Zwamborn, A Peter M; Demmers, Jeroen; Lebbink, Joyce H G; Kanaar, Roland

2017-01-01

The potential effects of non-ionizing electromagnetic fields (EMFs), such as those emitted by power-lines (in extremely low frequency range), mobile cellular systems and wireless networking devices (in radio frequency range) on human health have been intensively researched and debated. However, how exposure to these EMFs may lead to biological changes underlying possible health effects is still unclear. To reveal EMF-induced molecular changes, unbiased experiments (without a priori focusing on specific biological processes) with sensitive readouts are required. We present the first proteome-wide semi-quantitative mass spectrometry analysis of human fibroblasts, osteosarcomas and mouse embryonic stem cells exposed to three types of non-ionizing EMFs (ELF 50 Hz, UMTS 2.1 GHz and WiFi 5.8 GHz). We performed controlled in vitro EMF exposures of metabolically labeled mammalian cells followed by reliable statistical analyses of differential protein- and pathway-level regulations using an array of established bioinformatics methods. Our results indicate that less than 1% of the quantitated human or mouse proteome responds to the EMFs by small changes in protein abundance. Further network-based analysis of the differentially regulated proteins did not detect significantly perturbed cellular processes or pathways in human and mouse cells in response to ELF, UMTS or WiFi exposure. In conclusion, our extensive bioinformatics analyses of semi-quantitative mass spectrometry data do not support the notion that the short-time exposures to non-ionizing EMFs have a consistent biologically significant bearing on mammalian cells in culture.

Design and prediction of new anticoagulants as a selective Factor IXa inhibitor via three-dimensional quantitative structure-property relationships of amidinobenzothiophene derivatives.

PubMed

Gao, Jia-Suo; Tong, Xu-Peng; Chang, Yi-Qun; He, Yu-Xuan; Mei, Yu-Dan; Tan, Pei-Hong; Guo, Jia-Liang; Liao, Guo-Chao; Xiao, Gao-Keng; Chen, Wei-Min; Zhou, Shu-Feng; Sun, Ping-Hua

2015-01-01

Factor IXa (FIXa), a blood coagulation factor, is specifically inhibited at the initiation stage of the coagulation cascade, promising an excellent approach for developing selective and safe anticoagulants. Eighty-four amidinobenzothiophene antithrombotic derivatives targeting FIXa were selected to establish three-dimensional quantitative structure-activity relationship (3D-QSAR) and three-dimensional quantitative structure-selectivity relationship (3D-QSSR) models using comparative molecular field analysis and comparative similarity indices analysis methods. Internal and external cross-validation techniques were investigated as well as region focusing and bootstrapping. The satisfactory q (2) values of 0.753 and 0.770, and r (2) values of 0.940 and 0.965 for 3D-QSAR and 3D-QSSR, respectively, indicated that the models are available to predict both the inhibitory activity and selectivity on FIXa against Factor Xa, the activated status of Factor X. This work revealed that the steric, hydrophobic, and H-bond factors should appropriately be taken into account in future rational design, especially the modifications at the 2'-position of the benzene and the 6-position of the benzothiophene in the R group, providing helpful clues to design more active and selective FIXa inhibitors for the treatment of thrombosis. On the basis of the three-dimensional quantitative structure-property relationships, 16 new potent molecules have been designed and are predicted to be more active and selective than Compound 33, which has the best activity as reported in the literature.

Semi-quantitative proteomics of mammalian cells upon short-term exposure to non-ionizing electromagnetic fields

PubMed Central

Laffeber, Charlie; Eppink, Berina; Bezstarosti, Karel; Dekkers, Dick; Woelders, Henri; Zwamborn, A. Peter M.; Demmers, Jeroen; Lebbink, Joyce H. G.; Kanaar, Roland

2017-01-01

The potential effects of non-ionizing electromagnetic fields (EMFs), such as those emitted by power-lines (in extremely low frequency range), mobile cellular systems and wireless networking devices (in radio frequency range) on human health have been intensively researched and debated. However, how exposure to these EMFs may lead to biological changes underlying possible health effects is still unclear. To reveal EMF-induced molecular changes, unbiased experiments (without a priori focusing on specific biological processes) with sensitive readouts are required. We present the first proteome-wide semi-quantitative mass spectrometry analysis of human fibroblasts, osteosarcomas and mouse embryonic stem cells exposed to three types of non-ionizing EMFs (ELF 50 Hz, UMTS 2.1 GHz and WiFi 5.8 GHz). We performed controlled in vitro EMF exposures of metabolically labeled mammalian cells followed by reliable statistical analyses of differential protein- and pathway-level regulations using an array of established bioinformatics methods. Our results indicate that less than 1% of the quantitated human or mouse proteome responds to the EMFs by small changes in protein abundance. Further network-based analysis of the differentially regulated proteins did not detect significantly perturbed cellular processes or pathways in human and mouse cells in response to ELF, UMTS or WiFi exposure. In conclusion, our extensive bioinformatics analyses of semi-quantitative mass spectrometry data do not support the notion that the short-time exposures to non-ionizing EMFs have a consistent biologically significant bearing on mammalian cells in culture. PMID:28234898

Design and prediction of new anticoagulants as a selective Factor IXa inhibitor via three-dimensional quantitative structure-property relationships of amidinobenzothiophene derivatives

PubMed Central

Gao, Jia-Suo; Tong, Xu-Peng; Chang, Yi-Qun; He, Yu-Xuan; Mei, Yu-Dan; Tan, Pei-Hong; Guo, Jia-Liang; Liao, Guo-Chao; Xiao, Gao-Keng; Chen, Wei-Min; Zhou, Shu-Feng; Sun, Ping-Hua

2015-01-01

Factor IXa (FIXa), a blood coagulation factor, is specifically inhibited at the initiation stage of the coagulation cascade, promising an excellent approach for developing selective and safe anticoagulants. Eighty-four amidinobenzothiophene antithrombotic derivatives targeting FIXa were selected to establish three-dimensional quantitative structure–activity relationship (3D-QSAR) and three-dimensional quantitative structure–selectivity relationship (3D-QSSR) models using comparative molecular field analysis and comparative similarity indices analysis methods. Internal and external cross-validation techniques were investigated as well as region focusing and bootstrapping. The satisfactory q2 values of 0.753 and 0.770, and r2 values of 0.940 and 0.965 for 3D-QSAR and 3D-QSSR, respectively, indicated that the models are available to predict both the inhibitory activity and selectivity on FIXa against Factor Xa, the activated status of Factor X. This work revealed that the steric, hydrophobic, and H-bond factors should appropriately be taken into account in future rational design, especially the modifications at the 2′-position of the benzene and the 6-position of the benzothiophene in the R group, providing helpful clues to design more active and selective FIXa inhibitors for the treatment of thrombosis. On the basis of the three-dimensional quantitative structure–property relationships, 16 new potent molecules have been designed and are predicted to be more active and selective than Compound 33, which has the best activity as reported in the literature. PMID:25848211

The quantitation of buffering action II. Applications of the formal & general approach.

PubMed

Schmitt, Bernhard M

2005-03-16

The paradigm of "buffering" originated in acid-base physiology, but was subsequently extended to other fields and is now used for a wide and diverse set of phenomena. In the preceding article, we have presented a formal and general approach to the quantitation of buffering action. Here, we use that buffering concept for a systematic treatment of selected classical and other buffering phenomena. H+ buffering by weak acids and "self-buffering" in pure water represent "conservative buffered systems" whose analysis reveals buffering properties that contrast in important aspects from classical textbook descriptions. The buffering of organ perfusion in the face of variable perfusion pressure (also termed "autoregulation") can be treated in terms of "non-conservative buffered systems", the general form of the concept. For the analysis of cytoplasmic Ca++ concentration transients (also termed "muffling"), we develop a related unit that is able to faithfully reflect the time-dependent quantitative aspect of buffering during the pre-steady state period. Steady-state buffering is shown to represent the limiting case of time-dependent muffling, namely for infinitely long time intervals and infinitely small perturbations. Finally, our buffering concept provides a stringent definition of "buffering" on the level of systems and control theory, resulting in four absolute ratio scales for control performance that are suited to measure disturbance rejection and setpoint tracking, and both their static and dynamic aspects. Our concept of buffering provides a powerful mathematical tool for the quantitation of buffering action in all its appearances.

Quantitative Proteome Analysis Reveals Increased Content of Basement Membrane Proteins in Arteries From Patients With Type 2 Diabetes Mellitus and Lower Levels Among Metformin Users.

PubMed

Preil, Simone A R; Kristensen, Lars P; Beck, Hans C; Jensen, Pia S; Nielsen, Patricia S; Steiniche, Torben; Bjørling-Poulsen, Marina; Larsen, Martin R; Hansen, Maria L; Rasmussen, Lars M

2015-10-01

The increased risk of cardiovascular diseases in type 2 diabetes mellitus has been extensively documented, but the origins of the association remain largely unknown. We sought to determine changes in protein expressions in arterial tissue from patients with type 2 diabetes mellitus and moreover hypothesized that metformin intake influences the protein composition. We analyzed nonatherosclerotic repair arteries gathered at coronary bypass operations from 30 patients with type 2 diabetes mellitus and from 30 age- and sex-matched nondiabetic individuals. Quantitative proteome analysis was performed by isobaric tag for relative and absolute quantitation-labeling and liquid chromatography-mass spectrometry, tandem mass spectrometry analysis on individual arterial samples. The amounts of the basement membrane components, α1-type IV collagen and α2-type IV collagen, γ1-laminin and β2-laminin, were significantly increased in patients with diabetes mellitus. Moreover, the expressions of basement membrane components and other vascular proteins were significantly lower among metformin users when compared with nonusers. Patients treated with or without metformin had similar levels of hemoglobin A1c, cholesterol, and blood pressure. In addition, quantitative histomorphometry showed increased area fractions of collagen-stainable material in tunica intima and media among patients with diabetes mellitus. The distinct accumulation of arterial basement membrane proteins in type 2 diabetes mellitus discloses a similarity between the diabetic macroangiopathy and microangiopathy and suggests a molecular explanation behind the alterations in vascular remodeling, biomechanical properties, and aneurysm formation described in diabetes mellitus. The lower amounts of basement membrane components in metformin-treated individuals are compatible with the hypothesis of direct beneficial drug effects on the matrix composition in the vasculature. © 2015 American Heart Association, Inc.

Quantitative Analysis of Localized Sources Identified by Focal Impulse and Rotor Modulation Mapping in Atrial Fibrillation

PubMed Central

Benharash, Peyman; Buch, Eric; Frank, Paul; Share, Michael; Tung, Roderick; Shivkumar, Kalyanam; Mandapati, Ravi

2015-01-01

Background New approaches to ablation of atrial fibrillation (AF) include focal impulse and rotor modulation (FIRM) mapping, and initial results reported with this technique have been favorable. We sought to independently evaluate the approach by analyzing quantitative characteristics of atrial electrograms used to identify rotors and describe acute procedural outcomes of FIRM-guided ablation. Methods and Results All FIRM-guided ablation procedures (n=24; 50% paroxysmal) at University of California, Los Angeles Medical Center were included for analysis. During AF, unipolar atrial electrograms collected from a 64-pole basket catheter were used to construct phase maps and identify putative AF sources. These sites were targeted for ablation, in conjunction with pulmonary vein isolation in most patients (n=19; 79%). All patients had rotors identified (mean, 2.3±0.9 per patient; 72% in left atrium). Prespecified acute procedural end point was achieved in 12 of 24 (50%) patients: AF termination (n=1), organization (n=3), or >10% slowing of AF cycle length (n=8). Basket electrodes were within 1 cm of 54% of left atrial surface area, and a mean of 31 electrodes per patient showed interpretable atrial electrograms. Offline analysis revealed no differences between rotor and distant sites in dominant frequency or Shannon entropy. Electroanatomic mapping showed no rotational activation at FIRM-identified rotor sites in 23 of 24 patients (96%). Conclusions FIRM-identified rotor sites did not exhibit quantitative atrial electrogram characteristics expected from rotors and did not differ quantitatively from surrounding tissue. Catheter ablation at these sites, in conjunction with pulmonary vein isolation, resulted in AF termination or organization in a minority of patients (4/24; 17%). Further validation of this approach is necessary. PMID:25873718

Phasegram Analysis of Vocal Fold Vibration Documented With Laryngeal High-speed Video Endoscopy.

PubMed

Herbst, Christian T; Unger, Jakob; Herzel, Hanspeter; Švec, Jan G; Lohscheller, Jörg

2016-11-01

In a recent publication, the phasegram, a bifurcation diagram over time, has been introduced as an intuitive visualization tool for assessing the vibratory states of oscillating systems. Here, this nonlinear dynamics approach is augmented with quantitative analysis parameters, and it is applied to clinical laryngeal high-speed video (HSV) endoscopic recordings of healthy and pathological phonations. HSV data from a total of 73 females diagnosed as healthy (n = 42), or with functional dysphonia (n = 15) or with unilateral vocal fold paralysis (n = 16), were quantitatively analyzed. Glottal area waveforms (GAW) and left and right hemi-GAWs (hGAW) were extracted from the HSV recordings. Based on Poincaré sections through phase space-embedded signals, two novel quantitative parameters were computed: the phasegram entropy (PE) and the phasegram complexity estimate (PCE), inspired by signal entropy and correlation dimension computation, respectively. Both PE and PCE assumed higher average values (suggesting more irregular vibrations) for the pathological as compared with the healthy participants, thus significantly discriminating healthy group from the paralysis group (P = 0.02 for both PE and PCE). Comparisons of individual PE or PCE data for the left and the right hGAW within each subject resulted in asymmetry measures for the regularity of vocal fold vibration. The PCE-based asymmetry measure revealed significant differences between the healthy group and the paralysis group (P = 0.03). Quantitative phasegram analysis of GAW and hGAW data is a promising tool for the automated processing of HSV data in research and in clinical practice. Copyright © 2016 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

Quantitative modelling in cognitive ergonomics: predicting signals passed at danger.

PubMed

Moray, Neville; Groeger, John; Stanton, Neville

2017-02-01

This paper shows how to combine field observations, experimental data and mathematical modelling to produce quantitative explanations and predictions of complex events in human-machine interaction. As an example, we consider a major railway accident. In 1999, a commuter train passed a red signal near Ladbroke Grove, UK, into the path of an express. We use the Public Inquiry Report, 'black box' data, and accident and engineering reports to construct a case history of the accident. We show how to combine field data with mathematical modelling to estimate the probability that the driver observed and identified the state of the signals, and checked their status. Our methodology can explain the SPAD ('Signal Passed At Danger'), generate recommendations about signal design and placement and provide quantitative guidance for the design of safer railway systems' speed limits and the location of signals. Practitioner Summary: Detailed ergonomic analysis of railway signals and rail infrastructure reveals problems of signal identification at this location. A record of driver eye movements measures attention, from which a quantitative model for out signal placement and permitted speeds can be derived. The paper is an example of how to combine field data, basic research and mathematical modelling to solve ergonomic design problems.

Identification of Mature Atherosclerotic Plaque Proteome Signatures Using Data-Independent Acquisition Mass Spectrometry.

PubMed

Hansmeier, Nicole; Buttigieg, Josef; Kumar, Pankaj; Pelle, Shaneen; Choi, Kyoo Yoon; Kopriva, David; Chao, Tzu-Chiao

2018-01-05

Atherosclerosis is a chronic inflammatory disease with complex pathobiology and one of the most common causes of cardiovascular events. The process is characterized by complex vascular remodeling processes that require the actions of numerous proteins. The composition of atherosclerotic plaque is increasingly recognized as a major factor governing the occurrence of cardiovascular or neurological symptoms. To gain deeper insights into the composition of atherosclerotic plaques, we created quantitative proteome profiles of advanced plaque tissues of six male patients undergoing carotid endarterectomy for stroke prevention. Using a quantitative, data-independent proteome approach, we identified 4181 proteins with an average protein coverage of 45%. An analysis of the quantitative composition of the tissue revealed key players of vascular remodeling processes. Moreover, compared with proximal arterial tissue, 20 proteins in mature plaques were enriched, whereas 52 proteins were found in lower quantities. Among the proteins with increased abundance were prominent extracellular matrix proteins such as biglycan and lumican, whereas cytoskeletal markers for contractile smooth muscle cells (SMCs) were decreased. Taken together, this study provides the most comprehensive quantitative assessment of mature human plaque tissue to date, which indicates a central role of SMCs in the structure of advanced atherosclerotic plaques.

Quantitative radiomic profiling of glioblastoma represents transcriptomic expression.

PubMed

Kong, Doo-Sik; Kim, Junhyung; Ryu, Gyuha; You, Hye-Jin; Sung, Joon Kyung; Han, Yong Hee; Shin, Hye-Mi; Lee, In-Hee; Kim, Sung-Tae; Park, Chul-Kee; Choi, Seung Hong; Choi, Jeong Won; Seol, Ho Jun; Lee, Jung-Il; Nam, Do-Hyun

2018-01-19

Quantitative imaging biomarkers have increasingly emerged in the field of research utilizing available imaging modalities. We aimed to identify good surrogate radiomic features that can represent genetic changes of tumors, thereby establishing noninvasive means for predicting treatment outcome. From May 2012 to June 2014, we retrospectively identified 65 patients with treatment-naïve glioblastoma with available clinical information from the Samsung Medical Center data registry. Preoperative MR imaging data were obtained for all 65 patients with primary glioblastoma. A total of 82 imaging features including first-order statistics, volume, and size features, were semi-automatically extracted from structural and physiologic images such as apparent diffusion coefficient and perfusion images. Using commercially available software, NordicICE, we performed quantitative imaging analysis and collected the dataset composed of radiophenotypic parameters. Unsupervised clustering methods revealed that the radiophenotypic dataset was composed of three clusters. Each cluster represented a distinct molecular classification of glioblastoma; classical type, proneural and neural types, and mesenchymal type. These clusters also reflected differential clinical outcomes. We found that extracted imaging signatures does not represent copy number variation and somatic mutation. Quantitative radiomic features provide a potential evidence to predict molecular phenotype and treatment outcome. Radiomic profiles represents transcriptomic phenotypes more well.

Surgical task analysis of simulated laparoscopic cholecystectomy with a navigation system.

PubMed

Sugino, T; Kawahira, H; Nakamura, R

2014-09-01

   Advanced surgical procedures, which have become complex and difficult, increase the burden of surgeons. Quantitative analysis of surgical procedures can improve training, reduce variability, and enable optimization of surgical procedures. To this end, a surgical task analysis system was developed that uses only surgical navigation information.    Division of the surgical procedure, task progress analysis, and task efficiency analysis were done. First, the procedure was divided into five stages. Second, the operating time and progress rate were recorded to document task progress during specific stages, including the dissecting task. Third, the speed of the surgical instrument motion (mean velocity and acceleration), as well as the size and overlap ratio of the approximate ellipse of the location log data distribution, was computed to estimate the task efficiency during each stage. These analysis methods were evaluated based on experimental validation with two groups of surgeons, i.e., skilled and "other" surgeons. The performance metrics and analytical parameters included incidents during the operation, the surgical environment, and the surgeon's skills or habits.    Comparison of groups revealed that skilled surgeons tended to perform the procedure in less time and involved smaller regions; they also manipulated the surgical instruments more gently.    Surgical task analysis developed for quantitative assessment of surgical procedures and surgical performance may provide practical methods and metrics for objective evaluation of surgical expertise.

Novel ionic liquid matrices for qualitative and quantitative detection of carbohydrates by matrix assisted laser desorption/ionization mass spectrometry.

PubMed

Zhao, Xiaoyong; Shen, Shanshan; Wu, Datong; Cai, Pengfei; Pan, Yuanjiang

2017-09-08

Analysis of carbohydrates based on matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is still challenging and researchers have been devoting themselves to efficient matrices discovery. In the present study, the design, synthesis, qualitative and quantitative performance of non-derivative ionic liquid matrices (ILMs) were reported. DHB/N-methylaniline (N-MA) and DHB/N-ethylaniline (N-EA), performing best for carbohydrate detection, have been screened out. The limit of detection for oligosaccharide provided by DHB/N-MA and DHB/N-EA were as low as 10 fmol. DHB/N-MA and DHB/N-EA showed significantly higher ion generation efficiency than DHB. The comparison of capacity to probe polysaccharide between these two ILMs and DHB also revealed their powerful potential. Their outstanding performance were probably due to lower proton affinities and stronger UV absorption at λ = 355 nm. What is more, taking DHB/N-MA as an example, quantitative analysis of fructo-oligosaccharide mixtures extracted and identified from rice noodles has been accomplished sensitively using an internal standard method. Overall, DHB/N-MA and DHB/N-EA exhibited excellent performance and might be significant sources as the carbohydrate matrices. Copyright © 2017 Elsevier B.V. All rights reserved.

Effects of music therapy and music-based interventions in the treatment of substance use disorders: A systematic review

PubMed Central

Hohmann, Louisa; Bradt, Joke; Stegemann, Thomas; Koelsch, Stefan

2017-01-01

Music therapy (MT) and music-based interventions (MBIs) are increasingly used for the treatment of substance use disorders (SUD). Previous reviews on the efficacy of MT emphasized the dearth of research evidence for this topic, although various positive effects were identified. Therefore, we conducted a systematic search on published articles examining effects of music, MT and MBIs and found 34 quantitative and six qualitative studies. There was a clear increase in the number of randomized controlled trials (RCTs) during the past few years. We had planned for a meta-analysis, but due to the diversity of the quantitative studies, effect sizes were not computed. Beneficial effects of MT/ MBI on emotional and motivational outcomes, participation, locus of control, and perceived helpfulness were reported, but results were inconsistent across studies. Furthermore, many RCTs focused on effects of single sessions. No published longitudinal trials could be found. The analysis of the qualitative studies revealed four themes: emotional expression, group interaction, development of skills, and improvement of quality of life. Considering these issues for quantitative research, there is a need to examine social and health variables in future studies. In conclusion, due to the heterogeneity of the studies, the efficacy of MT/ MBI in SUD treatment still remains unclear. PMID:29141012

Garlic (Allium sativum L.) fertility: transcriptome and proteome analyses provide insight into flower and pollen development

PubMed Central

Shemesh-Mayer, Einat; Ben-Michael, Tomer; Rotem, Neta; Rabinowitch, Haim D.; Doron-Faigenboim, Adi; Kosmala, Arkadiusz; Perlikowski, Dawid; Sherman, Amir; Kamenetsky, Rina

2015-01-01

Commercial cultivars of garlic, a popular condiment, are sterile, making genetic studies and breeding of this plant challenging. However, recent fertility restoration has enabled advanced physiological and genetic research and hybridization in this important crop. Morphophysiological studies, combined with transcriptome and proteome analyses and quantitative PCR validation, enabled the identification of genes and specific processes involved in gametogenesis in fertile and male-sterile garlic genotypes. Both genotypes exhibit normal meiosis at early stages of anther development, but in the male-sterile plants, tapetal hypertrophy after microspore release leads to pollen degeneration. Transcriptome analysis and global gene-expression profiling showed that >16,000 genes are differentially expressed in the fertile vs. male-sterile developing flowers. Proteome analysis and quantitative comparison of 2D-gel protein maps revealed 36 significantly different protein spots, 9 of which were present only in the male-sterile genotype. Bioinformatic and quantitative PCR validation of 10 candidate genes exhibited significant expression differences between male-sterile and fertile flowers. A comparison of morphophysiological and molecular traits of fertile and male-sterile garlic flowers suggests that respiratory restrictions and/or non-regulated programmed cell death of the tapetum can lead to energy deficiency and consequent pollen abortion. Potential molecular markers for male fertility and sterility in garlic are proposed. PMID:25972879

Phenotype classification of single cells using SRS microscopy, RNA sequencing, and microfluidics (Conference Presentation)

NASA Astrophysics Data System (ADS)

Streets, Aaron M.; Cao, Chen; Zhang, Xiannian; Huang, Yanyi

2016-03-01

Phenotype classification of single cells reveals biological variation that is masked in ensemble measurement. This heterogeneity is found in gene and protein expression as well as in cell morphology. Many techniques are available to probe phenotypic heterogeneity at the single cell level, for example quantitative imaging and single-cell RNA sequencing, but it is difficult to perform multiple assays on the same single cell. In order to directly track correlation between morphology and gene expression at the single cell level, we developed a microfluidic platform for quantitative coherent Raman imaging and immediate RNA sequencing (RNA-Seq) of single cells. With this device we actively sort and trap cells for analysis with stimulated Raman scattering microscopy (SRS). The cells are then processed in parallel pipelines for lysis, and preparation of cDNA for high-throughput transcriptome sequencing. SRS microscopy offers three-dimensional imaging with chemical specificity for quantitative analysis of protein and lipid distribution in single cells. Meanwhile, the microfluidic platform facilitates single-cell manipulation, minimizes contamination, and furthermore, provides improved RNA-Seq detection sensitivity and measurement precision, which is necessary for differentiating biological variability from technical noise. By combining coherent Raman microscopy with RNA sequencing, we can better understand the relationship between cellular morphology and gene expression at the single-cell level.

A low cost mobile phone dark-field microscope for nanoparticle-based quantitative studies.

PubMed

Sun, Dali; Hu, Tony Y

2018-01-15

Dark-field microscope (DFM) analysis of nanoparticle binding signal is highly useful for a variety of research and biomedical applications, but current applications for nanoparticle quantification rely on expensive DFM systems. The cost, size, limited robustness of these DFMs limits their utility for non-laboratory settings. Most nanoparticle analyses use high-magnification DFM images, which are labor intensive to acquire and subject to operator bias. Low-magnification DFM image capture is faster, but is subject to background from surface artifacts and debris, although image processing can partially compensate for background signal. We thus mated an LED light source, a dark-field condenser and a 20× objective lens with a mobile phone camera to create an inexpensive, portable and robust DFM system suitable for use in non-laboratory conditions. This proof-of-concept mobile DFM device weighs less than 400g and costs less than $2000, but analysis of images captured with this device reveal similar nanoparticle quantitation results to those acquired with a much larger and more expensive desktop DFMM system. Our results suggest that similar devices may be useful for quantification of stable, nanoparticle-based activity and quantitation assays in resource-limited areas where conventional assay approaches are not practical. Copyright © 2017 Elsevier B.V. All rights reserved.

Quantitative analysis of the effect of environmental-scanning electron microscopy on collagenous tissues.

PubMed

Lee, Woowon; Toussaint, Kimani C

2018-05-31

Environmental-scanning electron microscopy (ESEM) is routinely applied to various biological samples due to its ability to maintain a wet environment while imaging; moreover, the technique obviates the need for sample coating. However, there is limited research carried out on electron-beam (e-beam) induced tissue damage resulting from using the ESEM. In this paper, we use quantitative second-harmonic generation (SHG) microscopy to examine the effects of e-beam exposure from the ESEM on collagenous tissue samples prepared as either fixed, frozen, wet or dehydrated. Quantitative SHG analysis of tissues, before and after ESEM e-beam exposure in low-vacuum mode, reveals evidence of cross-linking of collagen fibers, however there are no structural differences observed in fixed tissue. Meanwhile wet-mode ESEM appears to radically alter the structure from a regular fibrous arrangement to a more random fiber orientation. We also confirm that ESEM images of collagenous tissues show higher spatial resolution compared to SHG microscopy, but the relative tradeoff with collagen specificity reduces its effectiveness in quantifying collagen fiber organization. Our work provides insight on both the limitations of the ESEM for tissue imaging, and the potential opportunity to use as a complementary technique when imaging fine features in the non-collagenous regions of tissue samples.

Quantitative characterization of the regressive ecological succession by fractal analysis of plant spatial patterns

USGS Publications Warehouse

Alados, C.L.; Pueyo, Y.; Giner, M.L.; Navarro, T.; Escos, J.; Barroso, F.; Cabezudo, B.; Emlen, J.M.

2003-01-01

We studied the effect of grazing on the degree of regression of successional vegetation dynamic in a semi-arid Mediterranean matorral. We quantified the spatial distribution patterns of the vegetation by fractal analyses, using the fractal information dimension and spatial autocorrelation measured by detrended fluctuation analyses (DFA). It is the first time that fractal analysis of plant spatial patterns has been used to characterize the regressive ecological succession. Plant spatial patterns were compared over a long-term grazing gradient (low, medium and heavy grazing pressure) and on ungrazed sites for two different plant communities: A middle dense matorral of Chamaerops and Periploca at Sabinar-Romeral and a middle dense matorral of Chamaerops, Rhamnus and Ulex at Requena-Montano. The two communities differed also in the microclimatic characteristics (sea oriented at the Sabinar-Romeral site and inland oriented at the Requena-Montano site). The information fractal dimension increased as we moved from a middle dense matorral to discontinuous and scattered matorral and, finally to the late regressive succession, at Stipa steppe stage. At this stage a drastic change in the fractal dimension revealed a change in the vegetation structure, accurately indicating end successional vegetation stages. Long-term correlation analysis (DFA) revealed that an increase in grazing pressure leads to unpredictability (randomness) in species distributions, a reduction in diversity, and an increase in cover of the regressive successional species, e.g. Stipa tenacissima L. These comparisons provide a quantitative characterization of the successional dynamic of plant spatial patterns in response to grazing perturbation gradient. ?? 2002 Elsevier Science B.V. All rights reserved.

Comprehensive Analysis of Proteomic Differences between Escherichia coli K-12 and B Strains Using Multiplexed Isobaric Tandem Mass Tag (TMT) Labeling.

PubMed

Han, Mee-Jung

2017-11-28

The Escherichia coli K-12 and B strains are among the most frequently used bacterial hosts for scientific research and biotechnological applications. However, omics analyses have revealed that E. coli K-12 and B exhibit notably different genotypic and phenotypic attributes, even though they were derived from the same ancestor. In a previous study, we identified a limited number of proteins from the two strains using two-dimensional gel electrophoresis and tandem mass spectrometry (MS/MS). In this study, an in-depth analysis of the physiological behavior of the E. coli K-12 and B strains at the proteomic level was performed using six-plex isobaric tandem mass tag-based quantitative MS. Additionally, the best lysis buffer for increasing the efficiency of protein extraction was selected from three tested buffers prior to the quantitative proteomic analysis. This study identifies the largest number of proteins in the two E. coli strains reported to date and is the first to show the dynamics of these proteins. Notable differences in proteins associated with key cellular properties, including some metabolic pathways, the biosynthesis and degradation of amino acids, membrane integrity, cellular tolerance, and motility, were found between the two representative strains. Compared with previous studies, these proteomic results provide a more holistic view of the overall state of E. coli cells based on a single proteomic study and reveal significant insights into why the two strains show distinct phenotypes. Additionally, the resulting data provide in-depth information that will help fine-tune processes in the future.

[Quantitative surface analysis of Pt-Co, Cu-Au and Cu-Ag alloy films by XPS and AES].

PubMed

Li, Lian-Zhong; Zhuo, Shang-Jun; Shen, Ru-Xiang; Qian, Rong; Gao, Jie

2013-11-01

In order to improve the quantitative analysis accuracy of AES, We associated XPS with AES and studied the method to reduce the error of AES quantitative analysis, selected Pt-Co, Cu-Au and Cu-Ag binary alloy thin-films as the samples, used XPS to correct AES quantitative analysis results by changing the auger sensitivity factors to make their quantitative analysis results more similar. Then we verified the accuracy of the quantitative analysis of AES when using the revised sensitivity factors by other samples with different composition ratio, and the results showed that the corrected relative sensitivity factors can reduce the error in quantitative analysis of AES to less than 10%. Peak defining is difficult in the form of the integral spectrum of AES analysis since choosing the starting point and ending point when determining the characteristic auger peak intensity area with great uncertainty, and to make analysis easier, we also processed data in the form of the differential spectrum, made quantitative analysis on the basis of peak to peak height instead of peak area, corrected the relative sensitivity factors, and verified the accuracy of quantitative analysis by the other samples with different composition ratio. The result showed that the analytical error in quantitative analysis of AES reduced to less than 9%. It showed that the accuracy of AES quantitative analysis can be highly improved by the way of associating XPS with AES to correct the auger sensitivity factors since the matrix effects are taken into account. Good consistency was presented, proving the feasibility of this method.

Response of Ca2+-ATPase to clinorotaion of pea seedlings. O. M. Nedukha and E. L. Kordyum

NASA Astrophysics Data System (ADS)

Nedukha, Olena

2016-07-01

The present study was aimed to reveal of response of Ca2+-ATPase activity of cortex cells in distal elongation zone of Pisum sativum root to slow clinorotation. Pea seedlings were grown on a horizontal clinostat (2 rpm) and in the stationary control for 6 days. The electron-cytochemical method was used to examine the effects of imitated microgravity on the distribution of Ca2+-ATPase in outer layers of root cortex. The quantitative analysis of the density of cytochemical reaction products was measured using the Image J program. Electron microscopy showed the presence of electron-dense lead phosphate precipitated grains, the enzymatic activity reaction products on the plasma membrane, membranes of vesicular structures, endoplasmic reticulum (ER) and on organelles envelope in both of samples of the stationary control and clinorotated seedlings. We revealed the sensitivity of Ca2+-ATPase to clinorotation. The quantitative analysis of the area and density of enzymatic activity reaction products revealed that clinorotation led to the decrease of 3.4 times the density of reaction products on the plasma membrane and the increase of reaction products density on endomembranes and organelles membranes, in particular: in 2.2 times on mitochondria membranes; in 1.3 times - on membranes of ER; in 2.5 times - on tonoplast; by an order of magnitude greater - on contacting membranes of organelles with plasma membrane in comparison with such in cells of control samples. The data analysis can indicate an intensification of calcium pump on endomembranes, on envelopes of cytoplasmic organelles and nucleus. The obtained data suggest that the redistribution of Ca2+-ATPase activity in cells can be mediated by the activation of certain isoforms of enzyme or/and by an activation of Ca2+/H+ antiporter in plasma membrane that helps to maintain optimal calcium balance in plant cells under imitated microgravity.

Quantitative proteomics reveals a role of JAZ7 in plant defense response to Pseudomonas syringae DC3000.

PubMed

Zhang, Tong; Meng, Li; Kong, Wenwen; Yin, Zepeng; Wang, Yang; Schneider, Jacqueline D; Chen, Sixue

2018-03-20

Jasmonate ZIM-domain (JAZ) proteins are key transcriptional repressors regulating various biological processes. Although many studies have studied JAZ proteins by genetic and biochemical analyses, little is known about JAZ7-associated global protein networks and how JAZ7 contributes to bacterial pathogen defense. In this study, we aim to fill this knowledge gap by conducting unbiased large-scale quantitative proteomics using tandem mass tags (TMT). We compared the proteomes of a JAZ7 knock-out line, a JAZ7 overexpression line, as well as the wild type Arabidopsis plants in the presence and absence of Pseudomonas syringae DC3000 infection. Both pairwise comparison and multi-factor analysis of variance reveal that differential proteins are enriched in biological processes such as primary and secondary metabolism, redox regulation, and response to stress. The differential regulation in these pathways may account for the alterations in plant size, redox homeostasis and accumulation of glucosinolates. In addition, possible interplay between genotype and environment is suggested as the abundance of seven proteins is influenced by the interaction of the two factors. Collectively, we demonstrate a role of JAZ7 in pathogen defense and provide a list of proteins that are uniquely responsive to genetic disruption, pathogen infection, or the interaction between genotypes and environmental factors. We report proteomic changes as a result of genetic perturbation of JAZ7, and the contribution of JAZ7 in plant immunity. Specifically, the similarity between the proteomes of a JAZ7 knockout mutant and the wild type plants confirmed the functional redundancy of JAZs. In contrast, JAZ7 overexpression plants were much different, and proteomic analysis of the JAZ7 overexpression plants under Pst DC3000 infection revealed that JAZ7 may regulate plant immunity via ROS modulation, energy balance and glucosinolate biosynthesis. Multiple variate analysis for this two-factor proteomics experiment suggests that protein abundance is determined by genotype, environment and the interaction between them. Copyright © 2018 Elsevier B.V. All rights reserved.

Quantitative Proteomics Reveals the Regulatory Networks of Circular RNA CDR1as in Hepatocellular Carcinoma Cells.

PubMed

Yang, Xue; Xiong, Qian; Wu, Ying; Li, Siting; Ge, Feng

2017-10-06

Circular RNAs (circRNAs), a class of widespread endogenous RNAs, play crucial roles in diverse biological processes and are potential biomarkers in diverse human diseases and cancers. Cerebellar-degeneration-related protein 1 antisense RNA (CDR1as), an oncogenic circRNA, is involved in human tumorigenesis and is dysregulated in hepatocellular carcinoma (HCC). However, the molecular mechanisms underlying CDR1as functions in HCC remain unclear. Here we explored the functions of CDR1as and searched for CDR1as-regulated proteins in HCC cells. A quantitative proteomics strategy was employed to globally identify CDR1as-regulated proteins in HCC cells. In total, we identified 330 differentially expressed proteins (DEPs) upon enhanced CDR1as expression in HepG2 cells, indicating that they could be proteins regulated by CDR1as. Bioinformatic analysis revealed that many DEPs were involved in cell proliferation and the cell cycle. Further functional studies of epidermal growth factor receptor (EGFR) found that CDR1as exerts its effects on cell proliferation at least in part through the regulation of EGFR expression. We further confirmed that CDR1as could inhibit the expression of microRNA-7 (miR-7). EGFR is a validated target of miR-7; therefore, CDR1as may exert its function by regulating EGFR expression via targeting miR-7 in HCC cells. Taken together, we revealed novel functions and underlying mechanisms of CDR1as in HCC cells. This study serves as the first proteome-wide analysis of a circRNA-regulated protein in cells and provides a reliable and highly efficient method for globally identifying circRNA-regulated proteins.

The impact of a scheduling change on ninth grade high school performance on biology benchmark exams and the California Standards Test

NASA Astrophysics Data System (ADS)

Leonardi, Marcelo

The primary purpose of this study was to examine the impact of a scheduling change from a trimester 4x4 block schedule to a modified hybrid schedule on student achievement in ninth grade biology courses. This study examined the impact of the scheduling change on student achievement through teacher created benchmark assessments in Genetics, DNA, and Evolution and on the California Standardized Test in Biology. The secondary purpose of this study examined the ninth grade biology teacher perceptions of ninth grade biology student achievement. Using a mixed methods research approach, data was collected both quantitatively and qualitatively as aligned to research questions. Quantitative methods included gathering data from departmental benchmark exams and California Standardized Test in Biology and conducting multiple analysis of covariance and analysis of covariance to determine significance differences. Qualitative methods include journal entries questions and focus group interviews. The results revealed a statistically significant increase in scores on both the DNA and Evolution benchmark exams. DNA and Evolution benchmark exams showed significant improvements from a change in scheduling format. The scheduling change was responsible for 1.5% of the increase in DNA benchmark scores and 2% of the increase in Evolution benchmark scores. The results revealed a statistically significant decrease in scores on the Genetics Benchmark exam as a result of the scheduling change. The scheduling change was responsible for 1% of the decrease in Genetics benchmark scores. The results also revealed a statistically significant increase in scores on the CST Biology exam. The scheduling change was responsible for .7% of the increase in CST Biology scores. Results of the focus group discussions indicated that all teachers preferred the modified hybrid schedule over the trimester schedule and that it improved student achievement.

Quantitative Proteomic Profiling of Prostate Cancer Reveals a Role for miR-128 in Prostate Cancer*

PubMed Central

Khan, Amjad P.; Poisson, Laila M.; Bhat, Vadiraja B.; Fermin, Damian; Zhao, Rong; Kalyana-Sundaram, Shanker; Michailidis, George; Nesvizhskii, Alexey I.; Omenn, Gilbert S.; Chinnaiyan, Arul M.; Sreekumar, Arun

2010-01-01

Multiple, complex molecular events characterize cancer development and progression. Deciphering the molecular networks that distinguish organ-confined disease from metastatic disease may lead to the identification of biomarkers of cancer invasion and disease aggressiveness. Although alterations in gene expression have been extensively quantified during neoplastic progression, complementary analyses of proteomic changes have been limited. Here we interrogate the proteomic alterations in a cohort of 15 prostate-derived tissues that included five each from adjacent benign prostate, clinically localized prostate cancer, and metastatic disease from distant sites. The experimental strategy couples isobaric tags for relative and absolute quantitation with multidimensional liquid phase peptide fractionation followed by tandem mass spectrometry. Over 1000 proteins were quantified across the specimens and delineated into clinically localized and metastatic prostate cancer-specific signatures. Included in these class-specific profiles were both proteins that were known to be dysregulated during prostate cancer progression and new ones defined by this study. Enrichment analysis of the prostate cancer-specific proteomic signature, to gain insight into the functional consequences of these alterations, revealed involvement of miR-128-a/b regulation during prostate cancer progression. This finding was validated using real time PCR analysis for microRNA transcript levels in an independent set of 15 clinical specimens. miR-128 levels were elevated in benign prostate epithelial cell lines compared with invasive prostate cancer cells. Knockdown of miR-128 induced invasion in benign prostate epithelial cells, whereas its overexpression attenuated invasion in prostate cancer cells. Taken together, our profiles of the proteomic alterations of prostate cancer progression revealed miR-128 as a potentially important negative regulator of prostate cancer cell invasion. PMID:19955085

Quantitative trait loci mapping and gene network analysis implicate protocadherin-15 as a determinant of brain serotonin transporter expression.

PubMed

Ye, R; Carneiro, A M D; Han, Q; Airey, D; Sanders-Bush, E; Zhang, B; Lu, L; Williams, R; Blakely, R D

2014-03-01

Presynaptic serotonin (5-hydroxytryptamine, 5-HT) transporters (SERT) regulate 5-HT signaling via antidepressant-sensitive clearance of released neurotransmitter. Polymorphisms in the human SERT gene (SLC6A4) have been linked to risk for multiple neuropsychiatric disorders, including depression, obsessive-compulsive disorder and autism. Using BXD recombinant inbred mice, a genetic reference population that can support the discovery of novel determinants of complex traits, merging collective trait assessments with bioinformatics approaches, we examine phenotypic and molecular networks associated with SERT gene and protein expression. Correlational analyses revealed a network of genes that significantly associated with SERT mRNA levels. We quantified SERT protein expression levels and identified region- and gender-specific quantitative trait loci (QTLs), one of which associated with male midbrain SERT protein expression, centered on the protocadherin-15 gene (Pcdh15), overlapped with a QTL for midbrain 5-HT levels. Pcdh15 was also the only QTL-associated gene whose midbrain mRNA expression significantly associated with both SERT protein and 5-HT traits, suggesting an unrecognized role of the cell adhesion protein in the development or function of 5-HT neurons. To test this hypothesis, we assessed SERT protein and 5-HT traits in the Pcdh15 functional null line (Pcdh15(av-) (3J) ), studies that revealed a strong, negative influence of Pcdh15 on these phenotypes. Together, our findings illustrate the power of multidimensional profiling of recombinant inbred lines in the analysis of molecular networks that support synaptic signaling, and that, as in the case of Pcdh15, can reveal novel relationships that may underlie risk for mental illness. © 2014 John Wiley & Sons Ltd and International Behavioural and Neural Genetics Society.

Evaluation of the X-Linked High-Grade Myopia Locus (MYP1) with Cone Dysfunction and Color Vision Deficiencies

PubMed Central

Metlapally, Ravikanth; Michaelides, Michel; Bulusu, Anuradha; Li, Yi-Ju; Schwartz, Marianne; Rosenberg, Thomas; Hunt, David M.; Moore, Anthony T.; Züchner, Stephan; Rickman, Catherine Bowes; Young, Terri L.

2014-01-01

Purpose X-linked high myopia with mild cone dysfunction and color vision defects has been mapped to chromosome Xq28 (MYP1 locus). CXorf2/TEX28 is a nested, intercalated gene within the red-green opsin cone pigment gene tandem array on Xq28. The authors investigated whether TEX28 gene alterations were associated with the Xq28-linked myopia phenotype. Genomic DNA from five pedigrees (with high myopia and either protanopia or deuteranopia) that mapped to Xq28 were screened for TEX28 copy number variations (CNVs) and sequence variants. Methods To examine for CNVs, ultra-high resolution array-comparative genomic hybridization (array-CGH) assays were performed comparing the subject genomic DNA with control samples (two pairs from two pedigrees). Opsin or TEX28 gene-targeted quantitative real-time gene expression assays (comparative CT method) were performed to validate the array-CGH findings. All exons of TEX28, including intron/exon boundaries, were amplified and sequenced using standard techniques. Results Array-CGH findings revealed predicted duplications in affected patient samples. Although only three copies of TEX28 were previously reported within the opsin array, quantitative real-time analysis of the TEX28 targeted assay of affected male or carrier female individuals in these pedigrees revealed either fewer (one) or more (four or five) copies than did related and control unaffected individuals. Sequence analysis of TEX28 did not reveal any variants associated with the disease status. Conclusions CNVs have been proposed to play a role in disease inheritance and susceptibility as they affect gene dosage. TEX28 gene CNVs appear to be associated with the MYP1 X-linked myopia phenotypes. PMID:19098318

Methylation analysis of plasma cell-free DNA for breast cancer early detection using bisulfite next-generation sequencing.

PubMed

Li, Zibo; Guo, Xinwu; Tang, Lili; Peng, Limin; Chen, Ming; Luo, Xipeng; Wang, Shouman; Xiao, Zhi; Deng, Zhongping; Dai, Lizhong; Xia, Kun; Wang, Jun

2016-10-01

Circulating cell-free DNA (cfDNA) has been considered as a potential biomarker for non-invasive cancer detection. To evaluate the methylation levels of six candidate genes (EGFR, GREM1, PDGFRB, PPM1E, SOX17, and WRN) in plasma cfDNA as biomarkers for breast cancer early detection, quantitative analysis of the promoter methylation of these genes from 86 breast cancer patients and 67 healthy controls was performed by using microfluidic-PCR-based target enrichment and next-generation bisulfite sequencing technology. The predictive performance of different logistic models based on methylation status of candidate genes was investigated by means of the area under the ROC curve (AUC) and odds ratio (OR) analysis. Results revealed that EGFR, PPM1E, and 8 gene-specific CpG sites showed significantly hypermethylation in cancer patients' plasma and significantly associated with breast cancer (OR ranging from 2.51 to 9.88). The AUC values for these biomarkers were ranging from 0.66 to 0.75. Combinations of multiple hypermethylated genes or CpG sites substantially improved the predictive performance for breast cancer detection. Our study demonstrated the feasibility of quantitative measurement of candidate gene methylation in cfDNA by using microfluidic-PCR-based target enrichment and bisulfite next-generation sequencing, which is worthy of further validation and potentially benefits a broad range of applications in clinical oncology practice. Quantitative analysis of methylation pattern of plasma cfDNA by next-generation sequencing might be a valuable non-invasive tool for early detection of breast cancer.

Recent Advances in Clinical Glycoproteomics of Immunoglobulins (Igs).

PubMed

Plomp, Rosina; Bondt, Albert; de Haan, Noortje; Rombouts, Yoann; Wuhrer, Manfred

2016-07-01

Antibody glycosylation analysis has seen methodological progress resulting in new findings with regard to antibody glycan structure and function in recent years. For example, antigen-specific IgG glycosylation analysis is now applicable for clinical samples because of the increased sensitivity of measurements, and this has led to new insights in the relationship between IgG glycosylation and various diseases. Furthermore, many new methods have been developed for the purification and analysis of IgG Fc glycopeptides, notably multiple reaction monitoring for high-throughput quantitative glycosylation analysis. In addition, new protocols for IgG Fab glycosylation analysis were established revealing autoimmune disease-associated changes. Functional analysis has shown that glycosylation of IgA and IgE is involved in transport across the intestinal epithelium and receptor binding, respectively. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Quantitative PET Imaging with Novel HER3-Targeted Peptides Selected by Phage Display to Predict Androgen-Independent Prostate Cancer Progression

DTIC Science & Technology

2017-12-01

peptide in tumors that was linearly correlated with HER3 levels. Biodistribution analysis revealed low off-target accumulation and rapid clearance...Internal Lab 15-22 Dr. Larimer 5 Stock) Subtask 2: Correlate changes in peptide uptake with protein expression and cell signaling changes ex vivo...signal for each individual tumor was plotted against its corresponding HER3 protein level, the TBR correlated linearly with the amount of protein

A model for sex ratio decline in India.

PubMed

Thukral, A K

1996-01-01

"The sex ratio in India has declined from 972 females per 1,000 males in 1901 to 929 females per 1,000 males in 1991. A model [is] proposed for the quantitative analysis of the problem.... The study reveals that there has been a sex discriminated population growth in India in the twentieth century, although the rate of decline of the female has decreased. If the current trend of population growth continues, there will be a further decline in the [sex ratio]." excerpt

Systems cell biology.

PubMed

Mast, Fred D; Ratushny, Alexander V; Aitchison, John D

2014-09-15

Systems cell biology melds high-throughput experimentation with quantitative analysis and modeling to understand many critical processes that contribute to cellular organization and dynamics. Recently, there have been several advances in technology and in the application of modeling approaches that enable the exploration of the dynamic properties of cells. Merging technology and computation offers an opportunity to objectively address unsolved cellular mechanisms, and has revealed emergent properties and helped to gain a more comprehensive and fundamental understanding of cell biology. © 2014 Mast et al.

Aqueous Sulfate Separation by Sequestration of [(SO 4) 2(H 2O) 4] 4 Clusters within Highly Insoluble Imine-Linked Bis-Guanidinium Crystals

DOE PAGES

Custelcean, Radu; Williams, Neil J.; Seipp, Charles A.; ...

2015-12-18

Quantitative removal of sulfate from seawater was achieved by selective crystallization of the anion with a bis(guanidinium) ligand self-assembled in situ through imine condensation of simple components. The resulting crystalline salt has an exceptionally low aqueous solubility, on a par with BaSO 4. Single-crystal X-ray diffraction analysis revealed pairs of sulfate anions clustered together with four water molecules within the crystals.

[Integral quantitative evaluation of working conditions in the construction industry].

PubMed

Guseĭnov, A A

1993-01-01

Present method evaluating the quality of environment (using MAC and MAL) does not enable to assess completely and objectively the work conditions of building industry due to multiple confounding elements. A solution to this complicated problem including the analysis of various correlating elements of the system "human--work conditions--environment" may be encouraged by social norm of morbidity, which is independent on industrial and natural environment. The complete integral assessment enables to see the whole situation and reveal the points at risk.

Volatilization of oxides during oxidation of some superalloys at 1200 C

NASA Technical Reports Server (NTRS)

Zaplatynsky, I.

1977-01-01

Volatilization of oxides during cyclic oxidation of commercial Nichrome, Inconel 750, Rene 41, Stellite 6B, and GE-1541 was studied at 1200 C in static air. Quantitative analysis of oxide vapor deposits revealed that oxides of tungsten, molybdenum, niobium, manganese, and chromium volatilized preferentially from the oxide scales. Aluminum and silicon were not detected in vapor deposits. For all the alloys except GE-1541 chromium was found to be the main metallic element in the oxide scales.

Volatilization of oxides during oxidation of some superalloys at 1200 C

NASA Technical Reports Server (NTRS)

Zaplatynsky, I.

1977-01-01

Volatilization of oxides during cyclic oxidation of commercial Nichrome, Inconel 750, Rene 41, Stellite 6B, and GE-1541 was studied at 1200 C in static air. Quantitative analysis of oxide vapor deposits revealed that oxides of tungsten, molybdenum, niobium, manganese, and chromium volatilized preferentially from the oxide scales. Aluminum and silicon were not detected in vapor deposits. For all the alloys except GE-1541, chromium was found to be the main metallic element in the oxide scales.

Transgenic plants of Petunia hybrida harboring the CYP2E1 gene efficiently remove benzene and toluene pollutants and improve resistance to formaldehyde

PubMed Central

Zhang, Daoxiang; Xiang, Taihe; Li, Peihan; Bao, Lumin

2011-01-01

The CYP2E1 protein belongs to the P450 enzymes family and plays an important role in the metabolism of small molecular and organic pollutants. In this study we generated CYP2E1 transgenic plants of Petunia using Agrobacterium rhizogenes K599. PCR analysis confirmed that the regenerated plants contained the CYP2E1 transgene and the rolB gene of the Ri plasmid. Southern blotting revealed the presence of multiple copies of CYP2E1 in the genome of transgenic plants. Fluorescent quantitative PCR revealed exogenous CYP2E1 gene expression in CYP2E1 transgenic plants at various levels, whereas no like expression was detected in either GUS transgenic plants or wild-types. The absorption of benzene and toluene by transgenic plants was analyzed through quantitative gas chromatography. Transgenic plants with high CYP2E1 expression showed a significant increase in absorption capacity of environmental benzene and toluene, compared to control GUS transgenic and wild type plants. Furthermore, these plants also presented obvious improved resistance to formaldehyde. This study, besides being the first to reveal that the CYP2E1 gene enhances plant resistance to formaldehyde, also furnishes a new method for reducing pollutants, such as benzene, toluene and formaldehyde, by using transgenic flowering horticultural plants. PMID:22215968

Interactions and reversal-field memory in complex magnetic nanowire arrays

NASA Astrophysics Data System (ADS)

Rotaru, Aurelian; Lim, Jin-Hee; Lenormand, Denny; Diaconu, Andrei; Wiley, John. B.; Postolache, Petronel; Stancu, Alexandru; Spinu, Leonard

2011-10-01

Interactions and magnetization reversal of Ni nanowire arrays have been investigated by the first-order reversal curve (FORC) method. Several series of samples with controlled spatial distribution were considered including simple wires of different lengths and diameters (70 and 110 nm) and complex wires with a single modulated diameter along their length. Subtle features of magnetic interactions are revealed through a quantitative analysis of the local interaction field profile distributions obtained from the FORC method. In addition, the FORC analysis indicates that the nanowire systems with a mean diameter of 70 nm appear to be organized in symmetric clusters indicative of a reversal-field memory effect.

What Is "Good" Research? Revealing the Paradigmatic Tensions in Quantitative Criticalist Work

ERIC Educational Resources Information Center

Hernández, Ebelia

2014-01-01

If quantitative criticalism is thought to be a bridge between positivist epistemologies prevalent in quantitative work and social constructionism often found in critical qualitative work, then this bridge is fraught with challenges and tensions. This chapter examines the methodological issues, questions, and tensions that emerged from a research…

Embedding Quantitative Methods by Stealth in Political Science: Developing a Pedagogy for Psephology

ERIC Educational Resources Information Center

Gunn, Andrew

2017-01-01

Student evaluations of quantitative methods courses in political science often reveal they are characterised by aversion, alienation and anxiety. As a solution to this problem, this paper describes a pedagogic research project with the aim of embedding quantitative methods by stealth into the first-year undergraduate curriculum. This paper…

[Morphologic and AFLP analysis of relationships between tulip species Tulipa biebersteiniana (Liliaceae)].

PubMed

Kutlunina, N A; Polezhaeva, M A; Permiakova, M V

2013-04-01

In populations of four species of tulips, (Tulipa biebersteiniana, T. patens, T. scytica and T. riparia) from the Volgograd, Kurgansk, Orenburg, and Chelyabinsk regions and the Republic of Bashkortostan, genetic diversity was studied by means of morphological and AFLP analysis. A morphological analysis of seven quantitative and two qualitative criteria was carried out. Three selective EcoRI/MseI primer pairs allowed one to genotype 81 individuals from 13 tulip populations with 87 loci. The low level of variability by AFLP loci were revealed in all species, including T. biebersteiniana (P = 20.41%, UH(e) = 0.075), T. patens (26.97%, 0.082), T. scytica (27.53%, 0.086), and T. riparia (27.72%, 0.096). According to the AMOVA results, the variability proportion that characterizes the differences between the four Tulip species was lower (F(CT) = 0.235) than between populations within species (F(ST) = 0.439). Tulipa patens is well differentiated by means of Nei's distances, coordination, and analysis in the STRUCTURE program. An analysis in the STRUCTURE revealed four genetic groups of tulips that are not completely in accordance with the analyzed species. This acknowledges the presence of complicated genetic process in the tulip population.

Quantitative Proteomic Analysis of Duck Ovarian Follicles Infected with Duck Tembusu Virus by Label-Free LC-MS

PubMed Central

Han, Kaikai; Zhao, Dongmin; Liu, Yuzhuo; Liu, Qingtao; Huang, Xinmei; Yang, Jing; An, Fengjiao; Li, Yin

2016-01-01

Duck Tembusu virus (DTMUV) is a newly emerging pathogenic flavivirus that has caused massive economic losses to the duck industry in China. DTMUV infection mainly results in significant decreases in egg production in egg-laying ducks within 1–2 weeks post infection. However, information on the comparative protein expression of host tissues in response to DTMUV infection is limited. In the present study, the cellular protein response to DTMUV infection in duck ovarian follicles was analyzed using nano-flow high-performance liquid chromatography-electrospray tandem mass spectrometry. Quantitative proteomic analysis revealed 131 differentially expressed proteins, among which 53 were up regulated and 78 were down regulated. The identified proteins were involved in the regulation of essential processes such as cellular structure and integrity, RNA processing, protein biosynthesis and modification, vesicle transport, signal transduction, and mitochondrial pathway. Some selected proteins that were found to be regulated in DTMUV-infected tissues were screened by quantitative real-time PCR to examine their regulation at the transcriptional level, western blot analysis was used to validate the changes of some selected proteins on translational level. To our knowledge, this study is the first to analyze the proteomic changes in duck ovarian follicles following DTMUV infection. The protein-related information obtained in this study may be useful to understand the host response to DTMUV infection and the inherent mechanism of DTMUV replication and pathogenicity. PMID:27066001

Quantitative Chemical Imaging and Unsupervised Analysis Using Hyperspectral Coherent Anti-Stokes Raman Scattering Microscopy

PubMed Central

2013-01-01

In this work, we report a method to acquire and analyze hyperspectral coherent anti-Stokes Raman scattering (CARS) microscopy images of organic materials and biological samples resulting in an unbiased quantitative chemical analysis. The method employs singular value decomposition on the square root of the CARS intensity, providing an automatic determination of the components above noise, which are retained. Complex CARS susceptibility spectra, which are linear in the chemical composition, are retrieved from the CARS intensity spectra using the causality of the susceptibility by two methods, and their performance is evaluated by comparison with Raman spectra. We use non-negative matrix factorization applied to the imaginary part and the nonresonant real part of the susceptibility with an additional concentration constraint to obtain absolute susceptibility spectra of independently varying chemical components and their absolute concentration. We demonstrate the ability of the method to provide quantitative chemical analysis on known lipid mixtures. We then show the relevance of the method by imaging lipid-rich stem-cell-derived mouse adipocytes as well as differentiated embryonic stem cells with a low density of lipids. We retrieve and visualize the most significant chemical components with spectra given by water, lipid, and proteins segmenting the image into the cell surrounding, lipid droplets, cytosol, and the nucleus, and we reveal the chemical structure of the cells, with details visualized by the projection of the chemical contrast into a few relevant channels. PMID:24099603

Quantitative analysis of immobilized penicillinase using enzyme-modified AlGaN/GaN field-effect transistors.

PubMed

Müntze, Gesche Mareike; Baur, Barbara; Schäfer, Wladimir; Sasse, Alexander; Howgate, John; Röth, Kai; Eickhoff, Martin

2015-02-15

Penicillinase-modified AlGaN/GaN field-effect transistors (PenFETs) are utilized to systematically investigate the covalently immobilized enzyme penicillinase under different experimental conditions. We demonstrate quantitative evaluation of covalently immobilized penicillinase layers on pH-sensitive field-effect transistors (FETs) using an analytical kinetic PenFET model. This kinetic model is explicitly suited for devices with thin enzyme layers that are not diffusion-limited, as it is the case for the PenFETs discussed here. By means of the kinetic model it was possible to extract the Michaelis constant of covalently immobilized penicillinase as well as relative transport coefficients of the different species associated with the enzymatic reaction which, exempli gratia, give information about the permeability of the enzymatic layer. Based on this analysis we quantify the reproducibility and the stability of the analyzed PenFETs over the course of 33 days as well as the influence of pH and buffer concentration on the properties of the enzymatic layer. Thereby the stability measurements reveal a Michalis constant KM of (67 ± 13)μM while the chronological development of the relative transport coefficients suggests a detachment of physisorbed penicillinase during the first two weeks since production. Our results show that AlGaN/GaN PenFETs prepared by covalent immobilization of a penicillinase enzyme layer present a powerful tool for quantitative analysis of enzyme functionality. Copyright © 2014 Elsevier B.V. All rights reserved.

A quantitative dynamic systems model of health-related quality of life among older adults

PubMed Central

Roppolo, Mattia; Kunnen, E Saskia; van Geert, Paul L; Mulasso, Anna; Rabaglietti, Emanuela

2015-01-01

Health-related quality of life (HRQOL) is a person-centered concept. The analysis of HRQOL is highly relevant in the aged population, which is generally suffering from health decline. Starting from a conceptual dynamic systems model that describes the development of HRQOL in individuals over time, this study aims to develop and test a quantitative dynamic systems model, in order to reveal the possible dynamic trends of HRQOL among older adults. The model is tested in different ways: first, with a calibration procedure to test whether the model produces theoretically plausible results, and second, with a preliminary validation procedure using empirical data of 194 older adults. This first validation tested the prediction that given a particular starting point (first empirical data point), the model will generate dynamic trajectories that lead to the observed endpoint (second empirical data point). The analyses reveal that the quantitative model produces theoretically plausible trajectories, thus providing support for the calibration procedure. Furthermore, the analyses of validation show a good fit between empirical and simulated data. In fact, no differences were found in the comparison between empirical and simulated final data for the same subgroup of participants, whereas the comparison between different subgroups of people resulted in significant differences. These data provide an initial basis of evidence for the dynamic nature of HRQOL during the aging process. Therefore, these data may give new theoretical and applied insights into the study of HRQOL and its development with time in the aging population. PMID:26604722

Resected Brain Tissue, Seizure Onset Zone and Quantitative EEG Measures: Towards Prediction of Post-Surgical Seizure Control

PubMed Central

Andrzejak, Ralph G.; Hauf, Martinus; Pollo, Claudio; Müller, Markus; Weisstanner, Christian; Wiest, Roland; Schindler, Kaspar

2015-01-01

Background Epilepsy surgery is a potentially curative treatment option for pharmacoresistent patients. If non-invasive methods alone do not allow to delineate the epileptogenic brain areas the surgical candidates undergo long-term monitoring with intracranial EEG. Visual EEG analysis is then used to identify the seizure onset zone for targeted resection as a standard procedure. Methods Despite of its great potential to assess the epileptogenicty of brain tissue, quantitative EEG analysis has not yet found its way into routine clinical practice. To demonstrate that quantitative EEG may yield clinically highly relevant information we retrospectively investigated how post-operative seizure control is associated with four selected EEG measures evaluated in the resected brain tissue and the seizure onset zone. Importantly, the exact spatial location of the intracranial electrodes was determined by coregistration of pre-operative MRI and post-implantation CT and coregistration with post-resection MRI was used to delineate the extent of tissue resection. Using data-driven thresholding, quantitative EEG results were separated into normally contributing and salient channels. Results In patients with favorable post-surgical seizure control a significantly larger fraction of salient channels in three of the four quantitative EEG measures was resected than in patients with unfavorable outcome in terms of seizure control (median over the whole peri-ictal recordings). The same statistics revealed no association with post-operative seizure control when EEG channels contributing to the seizure onset zone were studied. Conclusions We conclude that quantitative EEG measures provide clinically relevant and objective markers of target tissue, which may be used to optimize epilepsy surgery. The finding that differentiation between favorable and unfavorable outcome was better for the fraction of salient values in the resected brain tissue than in the seizure onset zone is consistent with growing evidence that spatially extended networks might be more relevant for seizure generation, evolution and termination than a single highly localized brain region (i.e. a “focus”) where seizures start. PMID:26513359

Generation Mechanism of Nonlinear Rayleigh Surface Waves for Randomly Distributed Surface Micro-Cracks.

PubMed

Ding, Xiangyan; Li, Feilong; Zhao, Youxuan; Xu, Yongmei; Hu, Ning; Cao, Peng; Deng, Mingxi

2018-04-23

This paper investigates the propagation of Rayleigh surface waves in structures with randomly distributed surface micro-cracks using numerical simulations. The results revealed a significant ultrasonic nonlinear effect caused by the surface micro-cracks, which is mainly represented by a second harmonic with even more distinct third/quadruple harmonics. Based on statistical analysis from the numerous results of random micro-crack models, it is clearly found that the acoustic nonlinear parameter increases linearly with micro-crack density, the proportion of surface cracks, the size of micro-crack zone, and the excitation frequency. This study theoretically reveals that nonlinear Rayleigh surface waves are feasible for use in quantitatively identifying the physical characteristics of surface micro-cracks in structures.

Elders' Life Stories: Impact on the Next Generation of Health Professionals

PubMed Central

2013-01-01

The purpose of this study was to pilot an enhanced version of the “Share your Life Story” life review writing workshop. The enhanced version included the addition of an intergenerational exchange, based on the content of seniors' writings, with students planning careers in the health sciences. The researcher employed a mixed methods design. Preliminary results using descriptive analysis revealed an increase in positive images of aging and a decrease in negative images of aging among the five student participants. Qualitative results revealed six themes that illuminate the hows and whys of the quantitative results as well as additional program benefits. Feedback from students and seniors helped to refine the intergenerational protocol for a larger scale study. PMID:24027579

Generation Mechanism of Nonlinear Rayleigh Surface Waves for Randomly Distributed Surface Micro-Cracks

PubMed Central

Ding, Xiangyan; Li, Feilong; Xu, Yongmei; Cao, Peng; Deng, Mingxi

2018-01-01

This paper investigates the propagation of Rayleigh surface waves in structures with randomly distributed surface micro-cracks using numerical simulations. The results revealed a significant ultrasonic nonlinear effect caused by the surface micro-cracks, which is mainly represented by a second harmonic with even more distinct third/quadruple harmonics. Based on statistical analysis from the numerous results of random micro-crack models, it is clearly found that the acoustic nonlinear parameter increases linearly with micro-crack density, the proportion of surface cracks, the size of micro-crack zone, and the excitation frequency. This study theoretically reveals that nonlinear Rayleigh surface waves are feasible for use in quantitatively identifying the physical characteristics of surface micro-cracks in structures. PMID:29690580

Analysis of the Expression of Peptide–Major Histocompatibility Complexes Using High Affinity Soluble Divalent T Cell Receptors

PubMed Central

O'Herrin, Sean M.; Lebowitz, Michael S.; Bieler, Joan G.; al-Ramadi, Basel K.; Utz, Ursula; Bothwell, Alfred L.M.; Schneck, Jonathan P.

1997-01-01

Understanding the regulation of cell surface expression of specific peptide–major histocompatibility complex (MHC) complexes is hindered by the lack of direct quantitative analyses of specific peptide–MHC complexes. We have developed a direct quantitative biochemical approach by engineering soluble divalent T cell receptor analogues (TCR–Ig) that have high affinity for their cognate peptide–MHC ligands. The generality of this approach was demonstrated by specific staining of peptide-pulsed cells with two different TCR–Ig complexes: one specific for the murine alloantigen 2C, and one specific for a viral peptide from human T lymphocyte virus–1 presented by human histocompatibility leukocyte antigens–A2. Further, using 2C TCR– Ig, a more detailed analysis of the interaction with cognate peptide–MHC complexes revealed several interesting findings. Soluble divalent 2C TCR–Ig detected significant changes in the level of specific antigenic–peptide MHC cell surface expression in cells treated with γ-interferon (γ-IFN). Interestingly, the effects of γ-IFN on expression of specific peptide–MHC complexes recognized by 2C TCR–Ig were distinct from its effects on total H-2 Ld expression; thus, lower doses of γ-IFN were required to increase expression of cell surface class I MHC complexes than were required for upregulation of expression of specific peptide–MHC complexes. Analysis of the binding of 2C TCR–Ig for specific peptide–MHC ligands unexpectedly revealed that the affinity of the 2C TCR–Ig for the naturally occurring alloreactive, putatively, negatively selecting, complex, dEV-8–H-2 Kbm3, is very low, weaker than 71 μM. The affinity of the 2C TCR for the other naturally occurring, negatively selecting, alloreactive complex, p2Ca–H-2 Ld, is ∼1000-fold higher. Thus, negatively selecting peptide–MHC complexes do not necessarily have intrinsically high affinity for cognate TCR. These results, uniquely revealed by this analysis, indicate the importance of using high affinity biologically relevant cognates, such as soluble divalent TCR, in furthering our understanding of immune responses. PMID:9334373

Comprehensive assay of kinase catalytic activity reveals features of kinase inhibitor selectivity

PubMed Central

Anastassiadis, Theonie; Deacon, Sean W.; Devarajan, Karthik; Ma, Haiching; Peterson, Jeffrey R.

2011-01-01

Small-molecule protein kinase inhibitors are central tools for elucidating cellular signaling pathways and are promising therapeutic agents. Due to evolutionary conservation of the ATP-binding site, most kinase inhibitors that target this site promiscuously inhibit multiple kinases. Interpretation of experiments utilizing these compounds is confounded by a lack of data on the comprehensive kinase selectivity of most inhibitors. Here we profiled the activity of 178 commercially available kinase inhibitors against a panel of 300 recombinant protein kinases using a functional assay. Quantitative analysis revealed complex and often unexpected kinase-inhibitor interactions, with a wide spectrum of promiscuity. Many off-target interactions occur with seemingly unrelated kinases, revealing how large-scale profiling can be used to identify multi-targeted inhibitors of specific, diverse kinases. The results have significant implications for drug development and provide a resource for selecting compounds to elucidate kinase function and for interpreting the results of experiments that use them. PMID:22037377

Direct visualization reveals kinetics of meiotic chromosome synapsis

DOE PAGES

Rog, Ofer; Dernburg, Abby  F.

2015-03-17

The synaptonemal complex (SC) is a conserved protein complex that stabilizes interactions along homologous chromosomes (homologs) during meiosis. The SC regulates genetic exchanges between homologs, thereby enabling reductional division and the production of haploid gametes. Here, we directly observe SC assembly (synapsis) by optimizing methods for long-term fluorescence recording in C. elegans. We report that synapsis initiates independently on each chromosome pair at or near pairing centers—specialized regions required for homolog associations. Once initiated, the SC extends rapidly and mostly irreversibly to chromosome ends. Quantitation of SC initiation frequencies and extension rates reveals that initiation is a rate-limiting step inmore » homolog interactions. Eliminating the dynein-driven chromosome movements that accompany synapsis severely retards SC extension, revealing a new role for these conserved motions. This work provides the first opportunity to directly observe and quantify key aspects of meiotic chromosome interactions and will enable future in vivo analysis of germline processes.« less

Stereoselective Degradation and Molecular Ecological Mechanism of Chiral Pesticides Beta-Cypermethrin in Soils with Different pH Values.

PubMed

Yang, Zhong-Hua; Ji, Guo-Dong

2015-12-15

For decades, pesticides have been widely used for agricultural activities around the world, and the environmental problems caused by these compounds have raised widespread concern. However, the different enantioselective behaviors of chiral pesticide enantiomers are often ignored. Here, the selective degradation patterns and mechanisms of chiral pesticide enantiomers were successfully investigated for the first time in the soils of three cultivation areas with different pH values. Beta-cypermethrin was chosen as the target analyte. We found that the degradation rates of the four isomers of beta-cypermethrin were different. We used stepwise regression equations between degradation rates and functional genes to quantitatively study their relationships. Quantitative response analysis revealed that different isomers have different equations even under identical conditions. The results of path analysis showed that a single functional gene can make different direct and indirect contributions to the degradation of different isomers. Finally, the high-throughput technology was used to analysis the genome of the three tested soils and then compared the main microbial communities in them. We have successfully devised a method to investigate the molecular biological mechanisms of the selective degradation behavior of chiral compounds, thus enabling us to better understand these mechanisms.

Quantitative semi-automated analysis of morphogenesis with single-cell resolution in complex embryos

PubMed Central

Giurumescu, Claudiu A.; Kang, Sukryool; Planchon, Thomas A.; Betzig, Eric; Bloomekatz, Joshua; Yelon, Deborah; Cosman, Pamela; Chisholm, Andrew D.

2012-01-01

A quantitative understanding of tissue morphogenesis requires description of the movements of individual cells in space and over time. In transparent embryos, such as C. elegans, fluorescently labeled nuclei can be imaged in three-dimensional time-lapse (4D) movies and automatically tracked through early cleavage divisions up to ~350 nuclei. A similar analysis of later stages of C. elegans development has been challenging owing to the increased error rates of automated tracking of large numbers of densely packed nuclei. We present Nucleitracker4D, a freely available software solution for tracking nuclei in complex embryos that integrates automated tracking of nuclei in local searches with manual curation. Using these methods, we have been able to track >99% of all nuclei generated in the C. elegans embryo. Our analysis reveals that ventral enclosure of the epidermis is accompanied by complex coordinated migration of the neuronal substrate. We can efficiently track large numbers of migrating nuclei in 4D movies of zebrafish cardiac morphogenesis, suggesting that this approach is generally useful in situations in which the number, packing or dynamics of nuclei present challenges for automated tracking. PMID:23052905

Development of short Indonesian lesson plan to improve teacher performance

NASA Astrophysics Data System (ADS)

Yulianto, B.; Kamidjan; Ahmadi, A.; Asteria, P. V.

2018-01-01

The developmental research was motivated by the results of preliminary study through interviews, which revealed almost all of the teachers did not create lesson plan themselves. As a result of this load, the performance of the real learning in the classroom becomes inadequate. Moreover, when lesson plan was not made by teachers themselves, the learning process becomes ineffective. Therefore, this study designed to develop a prototype of the short lesson plan, in particular, Indonesian language teaching, and to investigate its effectiveness. The participants in the study were teachers who were trained through lesson study group to design short model’s lesson plan. Questionnaires and open-ended questions were used, and the quantitative and qualitative data obtained were analyzed accordingly. The analysis of the quantitative data, aided with SPSS, were frequency, percentage, and means, whereas the qualitative data were analyzed descriptively. The results showed that the teachers liked the model, and they were willing to design their own lesson plan. The observation data revealed that the classroom learning process became more interactive, and classroom atmosphere was more engaging and natural because the teachers did not stick to the lesson plan made by other teachers.

Phosphoproteomics reveals ALK promote cell progress via RAS/ JNK pathway in neuroblastoma.

PubMed

Chen, Kai; Lv, Fan; Xu, Guofeng; Zhang, Min; Wu, Yeming; Wu, Zhixiang

2016-11-15

Emerging evidence suggests receptor tyrosine kinase ALK as a promising therapeutic target in neuroblastoma. However, clinical trials reveal that a limited proportion of ALK-positive neuroblastoma patients experience clinical benefits from Crizotinib, a clinically approved specific inhibitor of ALK. The precise molecular mechanisms of aberrant ALK activity in neuroblastoma remain elusive, limiting the clinical application of ALK as a therapeutic target in neuroblastoma. Here, we describe a deep quantitative phosphoproteomic approach in which Crizotinib-treated neuroblastoma cell lines bearing aberrant ALK are used to investigate downstream regulated phosphoproteins. We identified more than 19,500-and quantitatively analyzed approximately 10,000-phosphorylation sites from each cell line, ultimately detecting 450-790 significantly-regulated phosphorylation sites. Multiple layers of bioinformatic analysis of the significantly-regulated phosphoproteins identified RAS/JNK as a downstream signaling pathway of ALK, independent of the ALK variant present. Further experiments demonstrated that ALK/JNK signaling could be inactivated by either ALK- or JNK-specific inhibitors, resulting in cell growth inhibition by induction of cell cycle arrest and cell apoptosis. Our study broadly defines the phosphoproteome in response to ALK inhibition and provides a resource for further clinical investigation of ALK as therapeutic target for the treatment of neuroblastoma.

Transforming attitudes and lives: Liberating African-American elementary and middle school students in out-of-school time STEM education

NASA Astrophysics Data System (ADS)

Smith, Charisse F.

Statistically, African-Americans, women, and the disabled are underrepresented in the fields of Science, Technology, Engineering, and Math (STEM). Historically, these underrepresented students, are described as being unrecognized and underdeveloped in the American STEM circuit. Many experience deficient and inadequate educational resources, are not encouraged to pursue STEM education and careers, and are confronted with copious obstructions. In this quantitative study, the researcher collected pretest and posttest survey data from a group of 4th, 5th, and 6th-grade African-American students in Title I funded schools. The reseacher used quantitative analysis to determine any significant differences in the science related attitudes between and within groups who participated in Out of School-Time Science, Technology, Engineering, and Mathematics programs and those who did not. Results revealed no significant differences in the science related attitudes between the groups of the students who participated in the Out of School Time-Science, Technology, Engineering, and Mathematics programs and those who did not. Results also revealed no significant differences in the science related attitudes within the groups of students who participated in the Out of School Time-Science, Technology, Engineering, and Mathematics programs and those who did not.

Pre- and post-remediation characterization of acid-generating fluvial tailings material

USGS Publications Warehouse

Smith, Kathleen S.; Walton-Day, Katherine; Hoal, Karin O.; Driscoll, Rhonda L.; Pietersen, K.

2012-01-01

The upper Arkansas River south of Leadville, Colorado, USA, contains deposits of fluvial tailings from historical mining operations in the Leadville area. These deposits are potential non-point sources of acid and metal contamination to surface- and groundwater systems. We are investigating a site that recently underwent in situ remediation treatment with lime, fertilizer, and compost. Pre- and post-remediation fluvial tailings material was collected from a variety of depths to examine changes in mineralogy, acid generation, and extractable nutrients. Results indicate sufficient nutrient availability in the post-remediation near-surface material, but pyrite and acid generation persist below the depth of lime and fertilizer addition. Mineralogical characterization performed using semi-quantitative X-ray diffraction and quantitative SEM-based micro-mineralogy (Mineral Liberation Analysis, MLA) reveal formation of gypsum, jarosite, and complex coatings surrounding mineral grains in post-remediation samples.

Quantitative Description of Crystal Nucleation and Growth from in Situ Liquid Scanning Transmission Electron Microscopy.

PubMed

Ievlev, Anton V; Jesse, Stephen; Cochell, Thomas J; Unocic, Raymond R; Protopopescu, Vladimir A; Kalinin, Sergei V

2015-12-22

Recent advances in liquid cell (scanning) transmission electron microscopy (S)TEM has enabled in situ nanoscale investigations of controlled nanocrystal growth mechanisms. Here, we experimentally and quantitatively investigated the nucleation and growth mechanisms of Pt nanostructures from an aqueous solution of K2PtCl6. Averaged statistical, network, and local approaches have been used for the data analysis and the description of both collective particles dynamics and local growth features. In particular, interaction between neighboring particles has been revealed and attributed to reduction of the platinum concentration in the vicinity of the particle boundary. The local approach for solving the inverse problem showed that particles dynamics can be simulated by a stationary diffusional model. The obtained results are important for understanding nanocrystal formation and growth processes and for optimization of synthesis conditions.

Oxalic Acid from Lentinula edodes Culture Filtrate: Antimicrobial Activity on Phytopathogenic Bacteria and Qualitative and Quantitative Analyses

PubMed Central

Kwak, A-Min; Lee, In-Kyoung; Lee, Sang-Yeop

2016-01-01

The culture filtrate of Lentinula edodes shows potent antimicrobial activity against the plant pathogenic bacteria Ralstonia solanacearum. Bioassay-guided fractionation was conducted using Diaion HP-20 column chromatography, and the insoluble active compound was not adsorbed on the resin. Further fractionation by high-performance liquid chromatography (HPLC) suggested that the active compounds were organic acids. Nine organic acids were detected in the culture filtrate of L. edodes; oxalic acid was the major component and exhibited antibacterial activity against nine different phytopathogenic bacteria. Quantitative analysis by HPLC revealed that the content of oxalic acid was higher in the water extract from spent mushroom substrate than in liquid culture. This suggests that the water extract of spent L. edodes substrate is an eco-friendly control agent for plant diseases. PMID:28154495

Systematic analysis of Ca2+ homeostasis in Saccharomyces cerevisiae based on chemical-genetic interaction profiles

PubMed Central

Ghanegolmohammadi, Farzan; Yoshida, Mitsunori; Ohnuki, Shinsuke; Sukegawa, Yuko; Okada, Hiroki; Obara, Keisuke; Kihara, Akio; Suzuki, Kuninori; Kojima, Tetsuya; Yachie, Nozomu; Hirata, Dai; Ohya, Yoshikazu

2017-01-01

We investigated the global landscape of Ca2+ homeostasis in budding yeast based on high-dimensional chemical-genetic interaction profiles. The morphological responses of 62 Ca2+-sensitive (cls) mutants were quantitatively analyzed with the image processing program CalMorph after exposure to a high concentration of Ca2+. After a generalized linear model was applied, an analysis of covariance model was used to detect significant Ca2+–cls interactions. We found that high-dimensional, morphological Ca2+–cls interactions were mixed with positive (86%) and negative (14%) chemical-genetic interactions, whereas one-dimensional fitness Ca2+–cls interactions were all negative in principle. Clustering analysis with the interaction profiles revealed nine distinct gene groups, six of which were functionally associated. In addition, characterization of Ca2+–cls interactions revealed that morphology-based negative interactions are unique signatures of sensitized cellular processes and pathways. Principal component analysis was used to discriminate between suppression and enhancement of the Ca2+-sensitive phenotypes triggered by inactivation of calcineurin, a Ca2+-dependent phosphatase. Finally, similarity of the interaction profiles was used to reveal a connected network among the Ca2+ homeostasis units acting in different cellular compartments. Our analyses of high-dimensional chemical-genetic interaction profiles provide novel insights into the intracellular network of yeast Ca2+ homeostasis. PMID:28566553

Transcriptional profiling of CD31(+) cells isolated from murine embryonic stem cells.

PubMed

Mariappan, Devi; Winkler, Johannes; Chen, Shuhua; Schulz, Herbert; Hescheler, Jürgen; Sachinidis, Agapios

2009-02-01

Identification of genes involved in endothelial differentiation is of great interest for the understanding of the cellular and molecular mechanisms involved in the development of new blood vessels. Mouse embryonic stem (mES) cells serve as a potential source of endothelial cells for transcriptomic analysis. We isolated endothelial cells from 8-days old embryoid bodies by immuno-magnetic separation using platelet endothelial cell adhesion molecule-1 (also known as CD31) expressed on both early and mature endothelial cells. CD31(+) cells exhibit endothelial-like behavior by being able to incorporate DiI-labeled acetylated low-density lipoprotein as well as form tubular structures on matrigel. Quantitative and semi-quantitative PCR analysis further demonstrated the increased expression of endothelial transcripts. To ascertain the specific transcriptomic identity of the CD31(+) cells, large-scale microarray analysis was carried out. Comparative bioinformatic analysis reveals an enrichment of the gene ontology categories angiogenesis, blood vessel morphogenesis, vasculogenesis and blood coagulation in the CD31(+) cell population. Based on the transcriptomic signatures of the CD31(+) cells, we conclude that this ES cell-derived population contains endothelial-like cells expressing a mesodermal marker BMP2 and possess an angiogenic potential. The transcriptomic characterization of CD31(+) cells enables an in vitro functional genomic model to identify genes required for angiogenesis.

The Impact of Polio Eradication on Routine Immunization and Primary Health Care: A Mixed-Methods Study

PubMed Central

Closser, Svea; Cox, Kelly; Parris, Thomas M.; Landis, R. Matthew; Justice, Judith; Gopinath, Ranjani; Maes, Kenneth; Banteyerga Amaha, Hailom; Mohammed, Ismaila Zango; Dukku, Aminu Mohammed; Omidian, Patricia A.; Varley, Emma; Tedoff, Pauley; Koon, Adam D.; Nyirazinyoye, Laetitia; Luck, Matthew A.; Pont, W. Frank; Neergheen, Vanessa; Rosenthal, Anat; Nsubuga, Peter; Thacker, Naveen; Jooma, Rashid; Nuttall, Elizabeth

2014-01-01

Background. After 2 decades of focused efforts to eradicate polio, the impact of eradication activities on health systems continues to be controversial. This study evaluated the impact of polio eradication activities on routine immunization (RI) and primary healthcare (PHC). Methods. Quantitative analysis assessed the effects of polio eradication campaigns on RI and maternal healthcare coverage. A systematic qualitative analysis in 7 countries in South Asia and sub-Saharan Africa assessed impacts of polio eradication activities on key health system functions, using data from interviews, participant observation, and document review. Results. Our quantitative analysis did not find compelling evidence of widespread and significant effects of polio eradication campaigns, either positive or negative, on measures of RI and maternal healthcare. Our qualitative analysis revealed context-specific positive impacts of polio eradication activities in many of our case studies, particularly disease surveillance and cold chain strengthening. These impacts were dependent on the initiative of policy makers. Negative impacts, including service interruption and public dissatisfaction, were observed primarily in districts with many campaigns per year. Conclusions. Polio eradication activities can provide support for RI and PHC, but many opportunities to do so remain missed. Increased commitment to scaling up best practices could lead to significant positive impacts. PMID:24690667

Gene silencing reveals multiple functions of Na+/K+-ATPase in the salmon louse (Lepeophtheirus salmonis).

PubMed

Komisarczuk, Anna Z; Kongshaug, Heidi; Nilsen, Frank

2018-02-01

Na + /K + -ATPase has a key function in a variety of physiological processes including membrane excitability, osmoregulation, regulation of cell volume, and transport of nutrients. While knowledge about Na + /K + -ATPase function in osmoregulation in crustaceans is extensive, the role of this enzyme in other physiological and developmental processes is scarce. Here, we report characterization, transcriptional distribution and likely functions of the newly identified L. salmonis Na + /K + -ATPase (LsalNa + /K + -ATPase) α subunit in various developmental stages. The complete mRNA sequence was identified, with 3003 bp open reading frame encoding a putative protein of 1001 amino acids. Putative protein sequence of LsalNa + /K + -ATPase revealed all typical features of Na + /K + -ATPase and demonstrated high sequence identity to other invertebrate and vertebrate species. Quantitative RT-PCR analysis revealed higher LsalNa + /K + -ATPase transcript level in free-living stages in comparison to parasitic stages. In situ hybridization analysis of copepodids and adult lice revealed LsalNa + /K + -ATPase transcript localization in a wide variety of tissues such as nervous system, intestine, reproductive system, and subcuticular and glandular tissue. RNAi mediated knock-down of LsalNa + /K + -ATPase caused locomotion impairment, and affected reproduction and feeding. Morphological analysis of dsRNA treated animals revealed muscle degeneration in larval stages, severe changes in the oocyte formation and maturation in females and abnormalities in tegmental glands. Thus, the study represents an important foundation for further functional investigation and identification of physiological pathways in which Na + /K + -ATPase is directly or indirectly involved. Copyright © 2018 Elsevier Inc. All rights reserved.

The Development of Mathematical Knowledge for Teaching for Quantitative Reasoning Using Video-Based Instruction

NASA Astrophysics Data System (ADS)

Walters, Charles David

Quantitative reasoning (P. W. Thompson, 1990, 1994) is a powerful mathematical tool that enables students to engage in rich problem solving across the curriculum. One way to support students' quantitative reasoning is to develop prospective secondary teachers' (PSTs) mathematical knowledge for teaching (MKT; Ball, Thames, & Phelps, 2008) related to quantitative reasoning. However, this may prove challenging, as prior to entering the classroom, PSTs often have few opportunities to develop MKT by examining and reflecting on students' thinking. Videos offer one avenue through which such opportunities are possible. In this study, I report on the design of a mini-course for PSTs that featured a series of videos created as part of a proof-of-concept NSF-funded project. These MathTalk videos highlight the ways in which the quantitative reasoning of two high school students developed over time. Using a mixed approach to grounded theory, I analyzed pre- and postinterviews using an extant coding scheme based on the Silverman and Thompson (2008) framework for the development of MKT. This analysis revealed a shift in participants' affect as well as three distinct shifts in their MKT around quantitative reasoning with distances, including shifts in: (a) quantitative reasoning; (b) point of view (decentering); and (c) orientation toward problem solving. Using the four-part focusing framework (Lobato, Hohensee, & Rhodehamel, 2013), I analyzed classroom data to account for how participants' noticing was linked with the shifts in MKT. Notably, their increased noticing of aspects of MKT around quantitative reasoning with distances, which features prominently in the MathTalk videos, seemed to contribute to the emergence of the shifts in MKT. Results from this study link elements of the learning environment to the development of specific facets of MKT around quantitative reasoning with distances. These connections suggest that vicarious experiences with two students' quantitative reasoning over time was critical for participants' development of MKT.

Clusters of Insomnia Disorder: An Exploratory Cluster Analysis of Objective Sleep Parameters Reveals Differences in Neurocognitive Functioning, Quantitative EEG, and Heart Rate Variability.

PubMed

Miller, Christopher B; Bartlett, Delwyn J; Mullins, Anna E; Dodds, Kirsty L; Gordon, Christopher J; Kyle, Simon D; Kim, Jong Won; D'Rozario, Angela L; Lee, Rico S C; Comas, Maria; Marshall, Nathaniel S; Yee, Brendon J; Espie, Colin A; Grunstein, Ronald R

2016-11-01

To empirically derive and evaluate potential clusters of Insomnia Disorder through cluster analysis from polysomnography (PSG). We hypothesized that clusters would differ on neurocognitive performance, sleep-onset measures of quantitative ( q )-EEG and heart rate variability (HRV). Research volunteers with Insomnia Disorder (DSM-5) completed a neurocognitive assessment and overnight PSG measures of total sleep time (TST), wake time after sleep onset (WASO), and sleep onset latency (SOL) were used to determine clusters. From 96 volunteers with Insomnia Disorder, cluster analysis derived at least two clusters from objective sleep parameters: Insomnia with normal objective sleep duration (I-NSD: n = 53) and Insomnia with short sleep duration (I-SSD: n = 43). At sleep onset, differences in HRV between I-NSD and I-SSD clusters suggest attenuated parasympathetic activity in I-SSD (P < 0.05). Preliminary work suggested three clusters by retaining the I-NSD and splitting the I-SSD cluster into two: I-SSD A (n = 29): defined by high WASO and I-SSD B (n = 14): a second I-SSD cluster with high SOL and medium WASO. The I-SSD B cluster performed worse than I-SSD A and I-NSD for sustained attention (P ≤ 0.05). In an exploratory analysis, q -EEG revealed reduced spectral power also in I-SSD B before (Delta, Alpha, Beta-1) and after sleep-onset (Beta-2) compared to I-SSD A and I-NSD (P ≤ 0.05). Two insomnia clusters derived from cluster analysis differ in sleep onset HRV. Preliminary data suggest evidence for three clusters in insomnia with differences for sustained attention and sleep-onset q -EEG. Insomnia 100 sleep study: Australia New Zealand Clinical Trials Registry (ANZCTR) identification number 12612000049875. URL: https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=347742. © 2016 Associated Professional Sleep Societies, LLC.

Statistical analysis of electroconvection near an ion-selective membrane in the highly chaotic regime

NASA Astrophysics Data System (ADS)

Druzgalski, Clara; Mani, Ali

2016-11-01

We investigate electroconvection and its impact on ion transport in a model system comprised of an ion-selective membrane, an aqueous electrolyte, and an external electric field applied normal to the membrane. We develop a direct numerical simulation code to solve the governing Poisson-Nernst-Planck and Navier-Stokes equations in three dimensions using a specialized parallel numerical algorithm and sufficient resolution to capture the high frequency and high wavenumber physics. We show a comprehensive statistical analysis of the transport phenomena in the highly chaotic regime. Qualitative and quantitative comparisons of two-dimensional (2D) and 3D simulations include prediction of the mean concentration fields as well as the spectra of concentration, charge density, and velocity signals. Our analyses reveal a significant quantitative difference between 2D and 3D electroconvection. Furthermore, we show that high-intensity yet short-lived current density hot spots appear randomly on the membrane surface, contributing significantly to the mean current density. By examining cross correlations between current density on the membrane and other field quantities we explore the physical mechanisms leading to current hot spots. We also present analysis of transport fluxes in the context of ensemble-averaged equations. Our analysis reveals that in the highly chaotic regime the mixing layer (ML), which spans the majority of the domain extent, is governed by advective fluctuations. Furthermore, we show that in the ML the mean electromigration fluxes cancel out for positive and negative ions, indicating that the mean transport of total salt content within the ML can be represented via the electroneutral approximation. Finally, we present an assessment of the importance of different length scales in enhancing transport by computing the cross covariance of concentration and velocity fluctuations in the wavenumber space. Our analysis indicates that in the majority of the domain the large scales contribute most significantly to transport, while the effects of small scales become more appreciable in regions very near the membrane.

Molecular cloning and characterization of a steroidogenic enzyme, 17β-hydroxysteroid dehydrogenase type 14, from the stony coral Euphyllia ancora (Cnidaria, Anthozoa).

PubMed

Shikina, Shinya; Chung, Yi-Jou; Chiu, Yi-Ling; Huang, Yi-Jie; Lee, Yan-Horn; Chang, Ching-Fong

2016-03-01

Sex steroids play a fundamental role not only in reproduction but also in various other biological processes in vertebrates. Although the presence of sex steroids has been confirmed in cnidarians (e.g., coral, sea anemone, jellyfish, and hydra), which are basal metazoans, only a few studies to date have characterized steroidogenesis-related genes in cnidarians. Based on a transcriptomic analysis of the stony coral Euphyllia ancora, we identified the steroidogenic enzyme 17β-hydroxysteroid dehydrogenase type 14 (17beta-hsd 14), an oxidative enzyme that catalyzes the NAD(+)-dependent inactivation of estrogen/androgen (estradiol to estrone and testosterone to androstenedione) in mammals. Phylogenetic analysis showed that E. ancora 17beta-Hsd 14 (Ea17beta-Hsd 14) clusters with other animal 17beta-HSD 14s but not with other members of the 17beta-HSD family. Subsequent quantitative RT-PCR analysis revealed a lack of correlation of Ea17beta-hsd 14 transcript levels with the coral's reproductive cycle. In addition, Ea17beta-hsd 14 transcript and protein were detected in all tissues examined, such as the tentacles, mesenterial filaments, and gonads, at similar levels in both sexes, as determined by quantitative RT-PCR analysis and Western blotting with an anti-Ea17beta-Hsd 14 antibody. Immunohistochemical analysis revealed that Ea17beta-Hsd 14 is mainly distributed in the endodermal regions of the polyps, but the protein was also observed in all tissues examined. These results suggest that Ea17beta-Hsd 14 is involved in important functions that commonly occur in endodermal cells or has multiple functions in different tissues. Our data provide information for comparison with advanced animals as well as insight into the evolution of steroidogenesis-related genes in metazoans. Copyright © 2016 Elsevier Inc. All rights reserved.

Genome-wide identification and expression profile analysis of the NAC transcription factor family during abiotic and biotic stress in woodland strawberry

PubMed Central

Qi, Yanxiang; Liu, Xiaomei; Pu, Jinji

2018-01-01

The NAC transcription factors involved plant development and response to various stress stimuli. However, little information is available concerning the NAC family in the woodland strawberry. Herein, 37 NAC genes were identified from the woodland strawberry genome and were classified into 13 groups based on phylogenetic analysis. And further analyses of gene structure and conserved motifs showed closer relationship of them in every subgroup. Quantitative real-time PCR evaluation different tissues revealed distinct spatial expression profiles of the FvNAC genes. The comprehensive expression of FvNAC genes revealed under abiotic stress (cold, heat, drought, salt), signal molecule treatments (H2O2, ABA, melatonin, rapamycin), biotic stress (Colletotrichum gloeosporioides and Ralstonia solanacearum). Expression profiles derived from quantitative real-time PCR suggested that 5 FvNAC genes responded dramatically to the various abiotic and biotic stresses, indicating their contribution to abiotic and biotic stresses resistance in woodland strawberry. Interestingly, FvNAC genes showed greater extent responded to the cold treatment than other abiotic stress, and H2O2 exhibited a greater response than ABA, melatonin, and rapamycin. For biotic stresses, 3 FvNAC genes were up-regulated during infection with C. gloeosporioides, while 6 FvNAC genes were down-regulated during infection with R. solanacearum. In conclusion, this study identified candidate FvNAC genes to be used for the genetic improvement of abiotic and biotic stress tolerance in woodland strawberry. PMID:29897926

NMR-based metabonomic and quantitative real-time PCR in the profiling of metabolic changes in carbon tetrachloride-induced rat liver injury.

PubMed

Li, Xiaowei; Zhang, Fusheng; Wang, Dongqin; Li, Zhenyu; Qin, Xuemei; Du, Guanhua

2014-02-01

Carbon tetrachloride (CCl4) is commonly used as a model toxicant to induce chronic and acute liver injuries. In this study, metabolite profiling and gene expression analysis of liver tissues were performed by nuclear magnetic resonance and quantitative real-time polymerase chain reaction to understand the responses of acute liver injury system in rats to CCl4. Acute liver injury was successfully induced by CCl4 as revealed by histopathological results and significant increase in alanine aminotransferase and serum aspartate aminotransferase. We found that CCl4 caused a significant increase in lactate, succinate, citrate, dimethylgycine, choline and taurine. CCl4 also caused a decrease in some of the amino acids such as leucine/isoleucine, glutamine/glutathione and betaine. Gene function analysis revealed that 10 relevant enzyme genes exhibited changes in expressions in the acute liver injury model. In conclusion, the metabolic pathways, including tricarboxylic acid cycle, antioxidant defense systems, fatty acid β-oxidation, glycolysis and choline and mevalonate metabolisms were impaired in CCl4-treated rat livers. These findings provided an overview of the biochemical consequences of CCl4 exposure and comprehensive insights into the metabolic aspects of CCl4-induced hepatotoxicity in rats. These findings may also provide reference of the mechanisms of acute liver injury that could be used to study the changes in functional genes and metabolites. Copyright © 2013 Elsevier B.V. All rights reserved.

iTRAQ-based quantitative proteomic analysis reveals potential factors associated with the enhancement of phenazine-1-carboxamide production in Pseudomonas chlororaphis P3

PubMed Central

Jin, Xue-Jie; Peng, Hua-Song; Hu, Hong-Bo; Huang, Xian-Qing; Wang, Wei; Zhang, Xue-Hong

2016-01-01

Phenazine-1-carboxamide (PCN), a phenazine derivative, is strongly antagonistic to fungal phytopathogens. Pseudomonas chlororaphis HT66 is a PCN-producing, non-pathogenic biocontrol strain, and we obtained the mutant P. chlororaphis P3, which produces 4.7 times more PCN than the wild-type HT66 strain. To reveal the cause of PCN production enhancement in P3 and find potential factors related to PCN biosynthesis, an iTRAQ-based quantitative proteomic analysis was used to study the expression changes between the two strains. Of the 452 differentially expressed proteins, most were functionally mapped into PCN biosynthesis pathway or other related metabolisms. The upregulation of proteins, including PhzA/B, PhzD, PhzF, PhzG, and PhzH, involved in PCN biosynthesis was in agreement with the efficient production of PCN in P3. A number of proteins that function primarily in energy production, amino acid metabolism, and secondary metabolism played important roles in PCN biosynthesis. Notably, proteins involved in the uptake and conversion of phosphate, inorganic nitrogen sources, and iron improved the PCN production. Furthermore, the type VI secretion system may participate in the secretion or/and indirect biosynthetic regulation of PCN in P. chlororaphis. This study provides valuable clues to better understand the biosynthesis, excretion and regulation of PCN in Pseudomonas and also provides potential gene targets for further engineering high-yield strains. PMID:27273243

Altered Expression of Ganglioside Metabolizing Enzymes Results in GM3 Ganglioside Accumulation in Cerebellar Cells of a Mouse Model of Juvenile Neuronal Ceroid Lipofuscinosis.

PubMed

Somogyi, Aleksandra; Petcherski, Anton; Beckert, Benedikt; Huebecker, Mylene; Priestman, David A; Banning, Antje; Cotman, Susan L; Platt, Frances M; Ruonala, Mika O; Tikkanen, Ritva

2018-02-22

Juvenile neuronal ceroid lipofuscinosis (JNCL) is caused by mutations in the CLN3 gene. Most JNCL patients exhibit a 1.02 kb genomic deletion removing exons 7 and 8 of this gene, which results in a truncated CLN3 protein carrying an aberrant C-terminus. A genetically accurate mouse model ( Cln3 Δex7/8 mice) for this deletion has been generated. Using cerebellar precursor cell lines generated from wildtype and Cln3 Δex7/8 mice, we have here analyzed the consequences of the CLN3 deletion on levels of cellular gangliosides, particularly GM3, GM2, GM1a and GD1a. The levels of GM1a and GD1a were found to be significantly reduced by both biochemical and cytochemical methods. However, quantitative high-performance liquid chromatography analysis revealed a highly significant increase in GM3, suggesting a metabolic blockade in the conversion of GM3 to more complex gangliosides. Quantitative real-time PCR analysis revealed a significant reduction in the transcripts of the interconverting enzymes, especially of β-1,4- N -acetyl-galactosaminyl transferase 1 (GM2 synthase), which is the enzyme converting GM3 to GM2. Thus, our data suggest that the complex a-series gangliosides are reduced in Cln3 Δex7/8 mouse cerebellar precursor cells due to impaired transcription of the genes responsible for their synthesis.

Altered Expression of Ganglioside Metabolizing Enzymes Results in GM3 Ganglioside Accumulation in Cerebellar Cells of a Mouse Model of Juvenile Neuronal Ceroid Lipofuscinosis

PubMed Central

Somogyi, Aleksandra; Petcherski, Anton; Beckert, Benedikt; Huebecker, Mylene; Priestman, David A.; Banning, Antje; Cotman, Susan L.; Platt, Frances M.; Ruonala, Mika O.

2018-01-01

Juvenile neuronal ceroid lipofuscinosis (JNCL) is caused by mutations in the CLN3 gene. Most JNCL patients exhibit a 1.02 kb genomic deletion removing exons 7 and 8 of this gene, which results in a truncated CLN3 protein carrying an aberrant C-terminus. A genetically accurate mouse model (Cln3Δex7/8 mice) for this deletion has been generated. Using cerebellar precursor cell lines generated from wildtype and Cln3Δex7/8 mice, we have here analyzed the consequences of the CLN3 deletion on levels of cellular gangliosides, particularly GM3, GM2, GM1a and GD1a. The levels of GM1a and GD1a were found to be significantly reduced by both biochemical and cytochemical methods. However, quantitative high-performance liquid chromatography analysis revealed a highly significant increase in GM3, suggesting a metabolic blockade in the conversion of GM3 to more complex gangliosides. Quantitative real-time PCR analysis revealed a significant reduction in the transcripts of the interconverting enzymes, especially of β-1,4-N-acetyl-galactosaminyl transferase 1 (GM2 synthase), which is the enzyme converting GM3 to GM2. Thus, our data suggest that the complex a-series gangliosides are reduced in Cln3Δex7/8 mouse cerebellar precursor cells due to impaired transcription of the genes responsible for their synthesis. PMID:29470438

Molecular cytogenetic characterization of an inv dup(15) chromosome presenting as a small supernumerary marker chromosome associated with the inv dup(15) syndrome.

PubMed

Chen, Chih-Ping; Lin, Shuan-Pei; Chern, Schu-Rern; Wu, Peih-Shan; Chen, Yen-Ni; Chen, Shin-Wen; Lee, Chen-Chi; Town, Dai-Dyi; Yang, Chien-Wen; Wang, Wayseen

2016-10-01

To present molecular cytogenetic characterization of an inverted duplication of proximal chromosome 15 [inv dup(15)] presenting as a small supernumerary marker chromosome (sSMC) associated with the inv dup(15) syndrome. A 35-year-old woman underwent amniocentesis because of advanced maternal age at 27 weeks of gestation, which revealed an sSMC that was confirmed by fluorescence in situ hybridization (FISH) to be derived from chromosome 15. Prenatal ultrasound findings were unremarkable. A 3434-g male baby was delivered at term with no phenotypic abnormalities. The cord blood analysis revealed a bisatellited dicentric inv dup(15). When followed up at 21 years of age, the proband manifested hypotonia, ataxic gait, developmental delay, intellectual disability, epilepsy, poor speech, and autism consistent with the inv dup(15) syndrome. Array comparative genomic hybridization of the peripheral blood revealed arr 15q11.1q13.2 (20,686,219-30,390,043) × 4, 15q13.2q13.3 (30,390,043-32,445,226) × 3. Conventional cytogenetic analysis of the peripheral blood revealed a karyotype of 47,XY,+inv dup(15)(pter→q13::q13→pter). Quantitative fluorescent polymerase chain reaction analysis showed a maternal origin of the inv dup(15) chromosome. FISH analysis confirmed an inv dup(15) chromosome. Molecular cytogenetic techniques are useful for rapid diagnosis of an inv dup(15) chromosome associated with the inv dup(15) syndrome. Copyright © 2016. Published by Elsevier B.V.

Quantitative evaluation of haze formation of koji and progression of internal haze by drying of koji during koji making.

PubMed

Ito, Kazunari; Gomi, Katsuya; Kariyama, Masahiro; Miyake, Tsuyoshi

2017-07-01

The construction of an experimental system that can mimic koji making in the manufacturing setting of a sake brewery is initially required for the quantitative evaluation of mycelia grown on/in koji pellets (haze formation). Koji making with rice was investigated with a solid-state fermentation (SSF) system using a non-airflow box (NAB), which produced uniform conditions in the culture substrate with high reproducibility and allowed for the control of favorable conditions in the substrate during culture. The SSF system using NAB accurately reproduced koji making in a manufacturing setting. To evaluate haze formation during koji making, surfaces and cross sections of koji pellets obtained from koji making tests were observed using a digital microscope. Image analysis was used to distinguish between haze and non-haze sections of koji pellets, enabling the evaluation of haze formation in a batch by measuring the haze rate of a specific number of koji pellets. This method allowed us to obtain continuous and quantitative data on the time course of haze formation. Moreover, drying koji during the late stage of koji making was revealed to cause further penetration of mycelia into koji pellets (internal haze). The koji making test with the SSF system using NAB and quantitative evaluation of haze formation in a batch by image analysis is a useful method for understanding the relations between haze formation and koji making conditions. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Structural evaluation of InAsP/InGaAsP strained-layer superlattices with dislocations as grown by metal-organic molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Nakashima, Kiichi; Sugiura, Hideo

1997-08-01

The relaxation process in InAsP/InGaAsP strained-layer superlattices (SLSs) with interfacial misfit dislocations has been investigated systematically by transmission electron microscopy (TEM) and x-ray analyses. The TEM analysis reveals that dislocations locate a little inside the buffer layer near the interface between the buffer and first well layer in the SLS. The x-ray analysis of (400) azimuthal angle dependence indicates the buffer layer has a large macroscopic tilt. Using a curve fitting analysis of various (hkl) x-ray profiles and reciprocal lattice mapping measurements, residual strain was determined quantitatively, i.e., Δa∥ and Δa⊥, in the SLS and buffer layer. These results reveal that the dislocations mainly cause lattice distortion of the buffer layer rather than relaxation of the SLS layer. The most remarkable result is that the change of a∥ is not equal to that of a⊥ in the buffer layer. This phenomenon strongly suggests that microplastic domains are generated in the buffer layer.

[Automated morphometric evaluation of the chromatin structure of liver cell nuclei after vagotomy].

PubMed

Butusova, N N; Zhukotskiĭ, A V; Sherbo, I V; Gribkov, E N; Dubovaia, T K

1989-05-01

The morphometric analysis of the interphase chromatine structure of the hepatic cells nuclei was carried out on the automated TV installation for the quantitative analysis of images "IBAS-2" (by the OPTON firm, the FRG) according to 50 optical and geometric parameters during various periods (1.2 and 4 weeks) after the vagotomy operation. It is determined that upper-molecular organisation of chromatine undergoes the biggest changes one week after operation, and changes of granular component are more informative than changes of the nongranular component (with the difference 15-20%). It was also revealed that chromatine components differ in tinctorial properties, which are evidently dependent on physicochemical characteristics of the chromatine under various functional conditions of the cell. As a result of the correlation analysis the group of morphometric indices of chromatine structure was revealed, which are highly correlated with level of transcription activity of chromatine during various terms after denervation. The correlation quotient of these parameters is 0.85-0.97. The summing up: vagus denervation of the liver causes changes in the morphofunctional organisation of the chromatine.

Quantitative proteomic analysis reveals proteins involved in the neurotoxicity of marine medaka Oryzias melastigma chronically exposed to inorganic mercury.

PubMed

Wang, Yuyu; Wang, Dazhi; Lin, Lin; Wang, Minghua

2015-01-01

Mercury is a ubiquitous environmental contaminant which exerts neurotoxicity upon animals. Nevertheless, the molecular mechanisms involved in inorganic mercury neurotoxicity are unknown. We investigated protein profiles of marine medaka, chronically exposed to mercuric chloride using two-dimensional difference gel electrophoresis (2D-DIGE) and matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry (MALDI-TOF-TOF MS) analysis. The mercury accumulation and ultrastructure were also examined in the brain. The results showed that mercury was significantly accumulated in the treated brain, and subsequently caused a noticeable damage. The comparison of 2D-DIGE protein profiles between the control and treatment revealed that 16 protein spots were remarkably altered in abundance, which were further submitted for MALDI-TOF-TOF MS analysis. The identified proteins indicated that inorganic mercury may cause neurotoxicity through the induction of oxidative stress, cytoskeletal assembly dysfunction and metabolic disorders. Thus, this study provided a basis for a better understanding of the molecular mechanisms involved in mercury neurotoxicity. Copyright © 2014 Elsevier Ltd. All rights reserved.

[Quantitative mineralogical analyzes of kidney stones and diagnosing metabolic disorders in female patients with calcium oxalate urolithiasis].

PubMed

Kustov, A V; Moryganov, M A; Strel'nikov, A I; Zhuravleva, N I; Airapetyan, A O

2016-02-01

To conduct a complex examination of female patients with calcium oxalate urolithiasis to detect metabolic disorders, leading to stone formation. The study was carried out using complex physical and chemical methods, including quantitative X-ray phase analysis of urinary stones, pH measurement, volumetry, urine and blood spectrophotometry. Quantitative mineralogical composition of stones, daily urine pH profile, daily urinary excretion of ions of calcium, magnesium, oxalate, phosphate, citrate and uric acid were determined in 20 female patients with calcium oxalate stones. We have shown that most of the stones comprised calcium oxalate monohydrate or mixtures of calcium oxalate dihydrate and hydroxyapatite. Among the identified abnormalities, the most frequent were hypocitraturia and hypercalciuria - 90 and 45%, respectively. Our findings revealed that the daily secretion of citrate and oxalate in patients older than 50 years was significantly lower than in younger patients. In conclusion, daily urinary citrate excretion should be measured in female patients with calcium oxalate stones. This is necessary both to determine the causes of stone formation, and to monitor the effectiveness of citrate therapy.

Determination of Grayanotoxins from Rhododendron brachycarpum in Dietary Supplements and Homemade Wine by Liquid Chromatography-Quadrupole Time-of-Flight-Mass Spectrometry and Liquid Chromatography-Tandem Mass Spectrometry.

PubMed

Hwang, Taeik; Noh, Eunyoung; Jeong, Ji Hye; Park, Sung-Kwan; Shin, Dongwoo; Kang, Hoil

2018-02-28

A sensitive and specific high-performance liquid chromatography-quadrupole time-of-flight-mass spectrometry (LC-QTOF-MS) method combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS) was developed for the determination of grayanotoxins I and III in dietary supplements and homemade wine. Grayanotoxins I and III were successfully extracted using solid-phase extraction cartridges, characterized by LC-QTOF-MS, and quantitated by LC-MS/MS. The LC-MS/MS calibration curves were linear over concentrations of 10-100 ng/mL (grayanotoxin I) and 20-400 ng/mL (grayanotoxin III). Grayanotoxins I and III were found in 51 foodstuffs, with quantitative determinations revealing total toxin concentrations of 18.4-101 000 ng/mL (grayanotoxin I) and 15.3-56 000 ng/mL (grayanotoxin III). The potential of the validated method was demonstrated by successful quantitative analysis of grayanotoxins I and III in dietary supplements and homemade wine; the method appears suitable for the routine detection of grayanotoxins I and III from Rhododendron brachycarpum.

Why are there race/ethnic differences in adult body mass index–adiposity relationships? A quantitative critical review

PubMed Central

Heymsfield, S. B.; Peterson, C. M.; Thomas, D. M.; Heo, M.; Schuna, J. M.

2016-01-01

Summary Body mass index (BMI) is now the most widely used measure of adiposity on a global scale. Nevertheless, intense discussion centers on the appropriateness of BMI as a phenotypic marker of adiposity across populations differing in race and ethnicity. BMI-adiposity relations appear to vary significantly across race/ethnic groups, but a collective critical analysis of these effects establishing their magnitude and underlying body shape/composition basis is lacking. Accordingly, we systematically review the magnitude of these race-ethnic differences across non-Hispanic (NH) white, NH black and Mexican American adults, their anatomic body composition basis and potential biologically linked mechanisms, using both earlier publications and new analyses from the US National Health and Nutrition Examination Survey. Our collective observations provide a new framework for critically evaluating the quantitative relations between BMI and adiposity across groups differing in race and ethnicity; reveal new insights into BMI as a measure of adiposity across the adult age-span; identify knowledge gaps that can form the basis of future research and create a quantitative foundation for developing BMI-related public health recommendations. PMID:26663309

Transcriptome-wide identification of salt-responsive members of the WRKY gene family in Gossypium aridum.

PubMed

Fan, Xinqi; Guo, Qi; Xu, Peng; Gong, YuanYong; Shu, Hongmei; Yang, Yang; Ni, Wanchao; Zhang, Xianggui; Shen, Xinlian

2015-01-01

WRKY transcription factors are plant-specific, zinc finger-type transcription factors. The WRKY superfamily is involved in abiotic stress responses in many crops including cotton, a major fiber crop that is widely cultivated and consumed throughout the world. Salinity is an important abiotic stress that results in considerable yield losses. In this study, we identified 109 WRKY genes (GarWRKYs) in a salt-tolerant wild cotton species Gossypium aridum from transcriptome sequencing data to elucidate the roles of these factors in cotton salt tolerance. According to their structural features, the predicted members were divided into three groups (Groups I-III), as previously described for Arabidopsis. Furthermore, 28 salt-responsive GarWRKY genes were identified from digital gene expression data and subjected to real-time quantitative RT-PCR analysis. The expression patterns of most GarWRKY genes revealed by this analysis are in good agreement with those revealed by RNA-Seq analysis. RT-PCR analysis revealed that 27 GarWRKY genes were expressed in roots and one was exclusively expressed in roots. Analysis of gene orthology and motif compositions indicated that WRKY members from Arabidopsis, rice and soybean generally shared the similar motifs within the same subgroup, suggesting they have the similar function. Overexpression-GarWRKY17 and -GarWRKY104 in Arabidopsis revealed that they could positively regulate salt tolerance of transgenic Arabidopsis during different development stages. The comprehensive data generated in this study provide a platform for elucidating the functions of WRKY transcription factors in salt tolerance of G. aridum. In addition, GarWRKYs related to salt tolerance identified in this study will be potential candidates for genetic improvement of cultivated cotton salt stress tolerance.

Australia’s first national level quantitative environmental justice assessment of industrial air pollution

NASA Astrophysics Data System (ADS)

Chakraborty, Jayajit; Green, Donna

2014-04-01

This study presents the first national level quantitative environmental justice assessment of industrial air pollution in Australia. Specifically, our analysis links the spatial distribution of sites and emissions associated with industrial pollution sources derived from the National Pollution Inventory, to Indigenous status and social disadvantage characteristics of communities derived from Australian Bureau of Statistics indicators. Our results reveal a clear national pattern of environmental injustice based on the locations of industrial pollution sources, as well as volume, and toxicity of air pollution released at these locations. Communities with the highest number of polluting sites, emission volume, and toxicity-weighted air emissions indicate significantly greater proportions of Indigenous population and higher levels of socio-economic disadvantage. The quantities and toxicities of industrial air pollution are particularly higher in communities with the lowest levels of educational attainment and occupational status. These findings emphasize the need for more detailed analysis in specific regions and communities where socially disadvantaged groups are disproportionately impacted by industrial air pollution. Our empirical findings also underscore the growing necessity to incorporate environmental justice considerations in environmental planning and policy-making in Australia.

Potential involvement of N-terminal acetylation in the quantitative regulation of the ε subunit of chloroplast ATP synthase under drought stress.

PubMed

Hoshiyasu, Saki; Kohzuma, Kaori; Yoshida, Kazuo; Fujiwara, Masayuki; Fukao, Yoichiro; Yokota, Akiho; Akashi, Kinya

2013-01-01

In plants, modulation of photosynthetic energy conversion in varying environments is often accompanied by adjustment of the abundance of photosynthetic components. In wild watermelon (Citrullus lanatus L.), proteome analysis revealed that the ε subunit of chloroplast ATP synthase occurs as two distinct isoforms with largely-different isoelectric points, although encoded by a single gene. Mass spectrometry (MS) analysis of the ε isoforms indicated that the structural difference between the ε isoforms lies in the presence or absence of an acetyl group at the N-terminus. The protein level of the non-acetylated ε isoform preferentially decreased in drought, whereas the abundance of the acetylated ε isoform was unchanged. Moreover, metalloprotease activity that decomposed the ε subunit was detected in a leaf extract from drought-stressed plants. Furthermore, in vitro assay suggested that the non-acetylated ε subunit was more susceptible to degradation by metalloaminopeptidase. We propose a model in which quantitative regulation of the ε subunit involves N-terminal acetylation and stress-induced proteases.

Automatic detection of cone photoreceptors in split detector adaptive optics scanning light ophthalmoscope images.

PubMed

Cunefare, David; Cooper, Robert F; Higgins, Brian; Katz, David F; Dubra, Alfredo; Carroll, Joseph; Farsiu, Sina

2016-05-01

Quantitative analysis of the cone photoreceptor mosaic in the living retina is potentially useful for early diagnosis and prognosis of many ocular diseases. Non-confocal split detector based adaptive optics scanning light ophthalmoscope (AOSLO) imaging reveals the cone photoreceptor inner segment mosaics often not visualized on confocal AOSLO imaging. Despite recent advances in automated cone segmentation algorithms for confocal AOSLO imagery, quantitative analysis of split detector AOSLO images is currently a time-consuming manual process. In this paper, we present the fully automatic adaptive filtering and local detection (AFLD) method for detecting cones in split detector AOSLO images. We validated our algorithm on 80 images from 10 subjects, showing an overall mean Dice's coefficient of 0.95 (standard deviation 0.03), when comparing our AFLD algorithm to an expert grader. This is comparable to the inter-observer Dice's coefficient of 0.94 (standard deviation 0.04). To the best of our knowledge, this is the first validated, fully-automated segmentation method which has been applied to split detector AOSLO images.

Insights into the Key Compounds of Durian (Durio zibethinus L. 'Monthong') Pulp Odor by Odorant Quantitation and Aroma Simulation Experiments.

PubMed

Li, Jia-Xiao; Schieberle, Peter; Steinhaus, Martin

2017-01-25

Sixteen compounds, previously identified as potent odorants by application of an aroma extract dilution analysis and the gas chromatography-olfactometry analysis of static headspace samples, were quantitated in the pulp of durians, variety Monthong, and odor activity values (OAVs) were calculated by dividing the concentrations obtained by the odor thresholds of the compounds in water. In combination with data recently reported for hydrogen sulfide and short-chain alkanethiols, OAVs > 1 were obtained for 19 compounds, among which ethyl (2S)-2-methylbutanoate (fruity; OAV 1700000), ethanethiol (rotten onion; OAV 480000), and 1-(ethylsulfanyl)ethane-1-thiol (roasted onion; OAV 250000) were the most potent, followed by methanethiol (rotten, cabbage; OAV 45000), ethane-1,1-dithiol (sulfury, durian; OAV 23000), and ethyl 2-methylpropanoate (fruity; OAV 22000). Aroma simulation and omission experiments revealed that the overall odor of durian pulp could be mimicked by only two compounds, namely, ethyl (2S)-2-methylbutanoate and 1-(ethylsulfanyl)ethane-1-thiol, when combined in their natural concentrations.

Quantitative analysis of a reconstruction method for fully three-dimensional PET.

PubMed

Suckling, J; Ott, R J; Deehan, B J

1992-03-01

The major advantage of positron emission tomography (PET) using large area planar detectors over scintillator-based commercial ring systems is the potentially larger (by a factor of two or three) axial field-of-view (FOV). However, to achieve the space invariance of the point spread function necessary for Fourier filtering a polar angle rejection criterion is applied to the data during backprojection resulting in a trade-off between FOV size and sensitivity. A new algorithm due to Defrise and co-workers developed for list-mode data overcomes this problem with a solution involving the division of the image into several subregions. A comparison between the existing backprojection-then-filter algorithm and the new method (with three subregions) has been made using both simulated and real data collected from the MUP-PET positron camera. Signal-to-noise analysis reveals that improvements of up to a factor of 1.4 are possible resulting from an increased data usage of up to a factor of 2.5 depending on the axial extent of the imaged object. Quantitation is also improved.

Exploring the Possibility of Peak Individualism, Humanity's Existential Crisis, and an Emerging Age of Purpose

PubMed Central

Grant, Gabriel B.

2017-01-01

There is an emerging cultural narrative in the United States that we are entering an age of purpose—that millennials, more than any other generation, are searching for purpose and purposeful work (Sheahan, 2005) and that we are entering an era or economy of purpose (Hurst, 2014). For profit, non-profit, and educational institutions are perceiving and adapting to serve millennials' demand for purpose in life, specifically within the workplace (Klein et al., 2015). Yet, longitudinal studies of purpose do not exist, and millennials are also referred to as GenMe. Existing quantitative research suggests they (we) are increasingly individualistic, materialistic, and narcissistic (Greenfield, 2013). Google's digitization of millions of books and the Ngram Viewer allow for quantified analysis of culture over the past two centuries. This tool was used to quantitatively test the popular notion that there is a rise in demand for purpose. Analysis reveals a growing interest in purpose-in-life and a shift toward collectivistic values emerging over the lifespan of the millennial generation. PMID:28928689

Precision of dehydroascorbic acid quantitation with the use of the subtraction method--validation of HPLC-DAD method for determination of total vitamin C in food.

PubMed

Mazurek, Artur; Jamroz, Jerzy

2015-04-15

In food analysis, a method for determination of vitamin C should enable measuring of total content of ascorbic acid (AA) and dehydroascorbic acid (DHAA) because both chemical forms exhibit biological activity. The aim of the work was to confirm applicability of HPLC-DAD method for analysis of total content of vitamin C (TC) and ascorbic acid in various types of food by determination of validation parameters such as: selectivity, precision, accuracy, linearity and limits of detection and quantitation. The results showed that the method applied for determination of TC and AA was selective, linear and precise. Precision of DHAA determination by the subtraction method was also evaluated. It was revealed that the results of DHAA determination obtained by the subtraction method were not precise which resulted directly from the assumption of this method and the principles of uncertainty propagation. The proposed chromatographic method should be recommended for routine determinations of total vitamin C in various food. Copyright © 2014 Elsevier Ltd. All rights reserved.

An interactive tool for semi-automatic feature extraction of hyperspectral data

NASA Astrophysics Data System (ADS)

Kovács, Zoltán; Szabó, Szilárd

2016-09-01

The spectral reflectance of the surface provides valuable information about the environment, which can be used to identify objects (e.g. land cover classification) or to estimate quantities of substances (e.g. biomass). We aimed to develop an MS Excel add-in - Hyperspectral Data Analyst (HypDA) - for a multipurpose quantitative analysis of spectral data in VBA programming language. HypDA was designed to calculate spectral indices from spectral data with user defined formulas (in all possible combinations involving a maximum of 4 bands) and to find the best correlations between the quantitative attribute data of the same object. Different types of regression models reveal the relationships, and the best results are saved in a worksheet. Qualitative variables can also be involved in the analysis carried out with separability and hypothesis testing; i.e. to find the wavelengths responsible for separating data into predefined groups. HypDA can be used both with hyperspectral imagery and spectrometer measurements. This bivariate approach requires significantly fewer observations than popular multivariate methods; it can therefore be applied to a wide range of research areas.

Quantitative proteomics of synaptic and nonsynaptic mitochondria: insights for synaptic mitochondrial vulnerability.

PubMed

Stauch, Kelly L; Purnell, Phillip R; Fox, Howard S

2014-05-02

Synaptic mitochondria are essential for maintaining calcium homeostasis and producing ATP, processes vital for neuronal integrity and synaptic transmission. Synaptic mitochondria exhibit increased oxidative damage during aging and are more vulnerable to calcium insult than nonsynaptic mitochondria. Why synaptic mitochondria are specifically more susceptible to cumulative damage remains to be determined. In this study, the generation of a super-SILAC mix that served as an appropriate internal standard for mouse brain mitochondria mass spectrometry based analysis allowed for the quantification of the proteomic differences between synaptic and nonsynaptic mitochondria isolated from 10-month-old mice. We identified a total of 2260 common proteins between synaptic and nonsynaptic mitochondria of which 1629 were annotated as mitochondrial. Quantitative proteomic analysis of the proteins common between synaptic and nonsynaptic mitochondria revealed significant differential expression of 522 proteins involved in several pathways including oxidative phosphorylation, mitochondrial fission/fusion, calcium transport, and mitochondrial DNA replication and maintenance. In comparison to nonsynaptic mitochondria, synaptic mitochondria exhibited increased age-associated mitochondrial DNA deletions and decreased bioenergetic function. These findings provide insights into synaptic mitochondrial susceptibility to damage.

Quantitative Proteomics of Synaptic and Nonsynaptic Mitochondria: Insights for Synaptic Mitochondrial Vulnerability

PubMed Central

2015-01-01

Synaptic mitochondria are essential for maintaining calcium homeostasis and producing ATP, processes vital for neuronal integrity and synaptic transmission. Synaptic mitochondria exhibit increased oxidative damage during aging and are more vulnerable to calcium insult than nonsynaptic mitochondria. Why synaptic mitochondria are specifically more susceptible to cumulative damage remains to be determined. In this study, the generation of a super-SILAC mix that served as an appropriate internal standard for mouse brain mitochondria mass spectrometry based analysis allowed for the quantification of the proteomic differences between synaptic and nonsynaptic mitochondria isolated from 10-month-old mice. We identified a total of 2260 common proteins between synaptic and nonsynaptic mitochondria of which 1629 were annotated as mitochondrial. Quantitative proteomic analysis of the proteins common between synaptic and nonsynaptic mitochondria revealed significant differential expression of 522 proteins involved in several pathways including oxidative phosphorylation, mitochondrial fission/fusion, calcium transport, and mitochondrial DNA replication and maintenance. In comparison to nonsynaptic mitochondria, synaptic mitochondria exhibited increased age-associated mitochondrial DNA deletions and decreased bioenergetic function. These findings provide insights into synaptic mitochondrial susceptibility to damage. PMID:24708184

The value of fame: preadolescent perceptions of popular media and their relationship to future aspirations.

PubMed

Uhls, Yalda T; Greenfield, Patricia M

2012-03-01

In line with Greenfield's (2009) theory of social change and human development, current popular preadolescent TV shows suggest that fame, an individualistic goal, is an important and achievable aspiration (Uhls & Greenfield, 2011). Such messages may be particularly salient for preadolescents, ages 10-12. This study used focus groups and mixed analytic methods (qualitative and quantitative) to examine how popular media, passive and interactive, are interpreted by preadolescents and how their interpretations relate to their media practices and future goals. Quantitative analysis revealed that fame was the number one value, selected as the most important value for participants' future goals significantly more frequently than expected by chance. Qualitative analysis of focus group discourse suggested that (a) youth absorb messages in their media environment regarding fame as a future goal and (b) their interpretations of these messages highlight the importance and value of public recognition. Enacting the value of fame, the majority of preadolescent participants use online video sharing sites (e.g., YouTube) to seek an audience beyond their immediate community. PsycINFO Database Record (c) 2012 APA, all rights reserved.

Quantitative Assessment of Free Flap Viability with CEUS Using an Integrated Perfusion Software.

PubMed

Geis, S; Klein, S; Prantl, L; Dolderer, J; Lamby, P; Jung, E-M

2015-12-01

New treatment strategies in oncology and trauma surgery lead to an increasing demand for soft tissue reconstruction with free tissue transfer. In previous studies, CEUS was proven to detect early flap failure. The aim of this study was to detect and quantify vascular disturbances after free flap transplantation using a fast integrated perfusion software tool. From 2011 to 2013, 33 patients were examined by one experienced radiologist using CEUS after a bolus injection of 1-2.4 ml of SonoVue(®). Flap perfusion was analysed qualitatively regarding contrast defects or delayed wash-in. Additionally, an integrated semi-quantitative analysis using time-intensity curve analysis (TIC) was performed. TIC analysis of the transplant was conducted on a centimetre-by-centimetre basis up to a penetration depth of 4 cm. The 2 perfusion parameters "Time to PEAK" and "Area under the Curve" were compared in patients without complications vs. patients with minor complications or complete flap loss to figure out significant differences. TtoPk is given in seconds (s) and Area is given in relative units (rU) Results: A regular postoperative process was observed in 26 (79%) patients. In contrast, 5 (15%) patients with partial superficial flap necrosis, 1 patient (3%) with complete flap loss and 1 patient (3%) with haematoma were observed. TtoPk revealed no significant differences, whereas Area revealed significantly lower perfusion values in the corresponding areas in patients with complications. The critical threshold for sufficient flap perfusion was set below 150 rU. In conclusion, CEUS is a mobile and cost-effective opportunity to quantify tissue perfusion and can even be used almost without any restrictions in multi-morbid patients with renal and hepatic failure. © Georg Thieme Verlag KG Stuttgart · New York.

SILAC-based quantitative proteomic analysis reveals widespread molecular alterations in human skin keratinocytes upon chronic arsenic exposure.

PubMed

Mir, Sartaj Ahmad; Pinto, Sneha M; Paul, Somnath; Raja, Remya; Nanjappa, Vishalakshi; Syed, Nazia; Advani, Jayshree; Renuse, Santosh; Sahasrabuddhe, Nandini A; Prasad, T S Keshava; Giri, Ashok K; Gowda, Harsha; Chatterjee, Aditi

2017-03-01

Chronic exposure to arsenic is associated with dermatological and nondermatological disorders. Consumption of arsenic-contaminated drinking water results in accumulation of arsenic in liver, spleen, kidneys, lungs, and gastrointestinal tract. Although arsenic is cleared from these sites, a substantial amount of residual arsenic is left in keratin-rich tissues including skin. Epidemiological studies suggest the association of skin cancer upon arsenic exposure, however, the mechanism of arsenic-induced carcinogenesis is not completely understood. We developed a cell line based model to understand the molecular mechanisms involved in arsenic-mediated toxicity and carcinogenicity. Human skin keratinocyte cell line, HaCaT, was chronically exposed to 100 nM sodium arsenite over a period of 6 months. We observed an increase in basal ROS levels in arsenic-exposed cells. SILAC-based quantitative proteomics approach resulted in identification of 2111 proteins of which 42 proteins were found to be overexpressed and 54 downregulated (twofold) upon chronic arsenic exposure. Our analysis revealed arsenic-induced overexpression of aldo-keto reductase family 1 member C2 (AKR1C2), aldo-keto reductase family 1 member C3 (AKR1C3), glutamate-cysteine ligase catalytic subunit (GCLC), and NAD(P)H dehydrogenase [quinone] 1 (NQO1) among others. We observed downregulation of several members of the plakin family including periplakin (PPL), envoplakin (EVPL), and involucrin (IVL) that are essential for terminal differentiation of keratinocytes. MRM and Western blot analysis confirmed differential expression of several candidate proteins. Our study provides insights into molecular alterations upon chronic arsenic exposure on skin. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantitative analysis of the anti-inflammatory activity of orengedokuto II: berberine is responsible for the inhibition of NO production.

PubMed

Oshima, Naohiro; Shimizu, Tomofumi; Narukawa, Yuji; Hada, Noriyasu; Kiuchi, Fumiyuki

2018-06-01

Orengedokuto is a Kampo formula that has been used for removing "heat" and "poison" to treat inflammation, hypertension, gastrointestinal disorders, and liver and cerebrovascular diseases. We report here our analysis of the anti-inflammatory effect of the component crude drugs of orengedokuto and their constituents using the inhibition of nitric oxide (NO) production in the murine macrophage-like cell line J774.1. An initial comparison of NO production inhibitory activities of the extracts of the component crude drugs and their combinations revealed that the activity could be attributed to Phellodendron Bark and Coptis Rhizome. Berberine (1), the major constituent of these crude drugs, showed potent activity (IC 50 4.73 ± 1.46 μM). Quantitative analysis of 1 in the extracts of all combinations of component crude drugs revealed that the amount of 1 in each extract of the combination of Scutellaria Root with either Phellodendron Bark and/or Coptis Rhizome was lower than that in the corresponding mixtures of the extracts of the individual crude drugs and that 1 was present in the precipitates formed during the decoction process. To the contrary, the differences in the amounts of 1 were smaller in the extracts containing Gardenia Fruit. These results indicated that the constituents of Scutellaria Root precipitated with 1 and that the constituents of Gardenia Fruit dissolved the precipitates. To identify the constituents affecting the solubility of 1, we fractionated the hot-water extracts of Scutellaria Root based on solubility tests of 1 to give baicalin (2), wogonin (3) and oroxyloside (4), which formed precipitates with 1.

Differential protein-coding gene and long noncoding RNA expression in smoking-related lung squamous cell carcinoma.

PubMed

Li, Shicheng; Sun, Xiao; Miao, Shuncheng; Liu, Jia; Jiao, Wenjie

2017-11-01

Cigarette smoking is one of the greatest preventable risk factors for developing cancer, and most cases of lung squamous cell carcinoma (lung SCC) are associated with smoking. The pathogenesis mechanism of tumor progress is unclear. This study aimed to identify biomarkers in smoking-related lung cancer, including protein-coding gene, long noncoding RNA, and transcription factors. We selected and obtained messenger RNA microarray datasets and clinical data from the Gene Expression Omnibus database to identify gene expression altered by cigarette smoking. Integrated bioinformatic analysis was used to clarify biological functions of the identified genes, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, the construction of a protein-protein interaction network, transcription factor, and statistical analyses. Subsequent quantitative real-time PCR was utilized to verify these bioinformatic analyses. Five hundred and ninety-eight differentially expressed genes and 21 long noncoding RNA were identified in smoking-related lung SCC. GO and KEGG pathway analysis showed that identified genes were enriched in the cancer-related functions and pathways. The protein-protein interaction network revealed seven hub genes identified in lung SCC. Several transcription factors and their binding sites were predicted. The results of real-time quantitative PCR revealed that AURKA and BIRC5 were significantly upregulated and LINC00094 was downregulated in the tumor tissues of smoking patients. Further statistical analysis indicated that dysregulation of AURKA, BIRC5, and LINC00094 indicated poor prognosis in lung SCC. Protein-coding genes AURKA, BIRC5, and LINC00094 could be biomarkers or therapeutic targets for smoking-related lung SCC. © 2017 The Authors. Thoracic Cancer published by China Lung Oncology Group and John Wiley & Sons Australia, Ltd.

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

Guo, Lei; Xiao, Yongsheng; Wang, Yinsheng, E-mail: yinsheng.wang@ucr.edu

Human exposure to arsenic in drinking water is a widespread public health concern, and such exposure is known to be associated with many human diseases. The detailed molecular mechanisms about how arsenic species contribute to the adverse human health effects, however, remain incompletely understood. Monomethylarsonous acid [MMA(III)] is a highly toxic and stable metabolite of inorganic arsenic. To exploit the mechanisms through which MMA(III) exerts its cytotoxic effect, we adopted a quantitative proteomic approach, by coupling stable isotope labeling by amino acids in cell culture (SILAC) with LC-MS/MS analysis, to examine the variation in the entire proteome of GM00637 humanmore » skin fibroblasts following acute MMA(III) exposure. Among the ∼ 6500 unique proteins quantified, ∼ 300 displayed significant changes in expression after exposure with 2 μM MMA(III) for 24 h. Subsequent analysis revealed the perturbation of de novo cholesterol biosynthesis, selenoprotein synthesis and Nrf2 pathways evoked by MMA(III) exposure. Particularly, MMA(III) treatment resulted in considerable down-regulation of several enzymes involved in cholesterol biosynthesis. In addition, real-time PCR analysis showed reduced mRNA levels of select genes in this pathway. Furthermore, MMA(III) exposure contributed to a distinct decline in cellular cholesterol content and significant growth inhibition of multiple cell lines, both of which could be restored by supplementation of cholesterol to the culture media. Collectively, the present study demonstrated that the cytotoxicity of MMA(III) may arise, at least in part, from the down-regulation of cholesterol biosynthesis enzymes and the resultant decrease of cellular cholesterol content. - Highlights: • MMA(III)-induced perturbation of the entire proteome of GM00637 cells is studied. • Quantitative proteomic approach revealed alterations of multiple cellular pathways. • MMA(III) inhibits de novo cholesterol biosynthesis. • MMA(III) perturbs Nrf2 pathway and selenoprotein synthesis.« less

Bacterial and archaeal symbionts in the South China Sea sponge Phakellia fusca: community structure, relative abundance, and ammonia-oxidizing populations.

PubMed

Han, Minqi; Liu, Fang; Zhang, Fengli; Li, Zhiyong; Lin, Houwen

2012-12-01

Many biologically active natural products have been isolated from Phakellia fusca, an indigenous sponge in the South China Sea; however, the microbial symbionts of Phakellia fusca remain unknown. The present investigations on sponge microbial community are mainly based on qualitative analysis, while quantitative analysis, e.g., relative abundance, is rarely carried out, and little is known about the roles of microbial symbionts. In this study, the community structure and relative abundance of bacteria, actinobacteria, and archaea associated with Phakellia fusca were revealed by 16S rRNA gene library-based sequencing and quantitative real time PCR (qRT-PCR). The ammonia-oxidizing populations were investigated based on amoA gene and anammox-specific 16S rRNA gene libraries. As a result, it was found that bacterial symbionts of sponge Phakellia fusca consist of Proteobacteria including Gamma-, Alpha-, and Delta-proteobacteria, Cyanobacteria with Gamma-proteobacteria as the predominant components. In particular, the diversity of actinobacterial symbionts in Phakellia fusca is high, which is composed of Corynebacterineae, Acidimicrobidae, Frankineae, Micrococcineae, and Streptosporangineae. All the observed archaea in sponge Phakellia fusca belong to Crenarchaeota, and the detected ammonia-oxidizing populations are ammonia-oxidizing archaea, suggesting the nitrification function of sponge archaeal symbionts. According to qRT-PCR analysis, bacterial symbionts dominated the microbial community, while archaea represented the second predominant symbionts, followed by actinobacteria. The revealed diverse prokaryotic symbionts of Phakellia fusca are valuable for the understanding and in-depth utilization of Phakellia fusca microbial symbionts. This study extends our knowledge of the community, especially the relative abundance of microbial symbionts in sponges.

iTRAQ Protein Profile Differential Analysis of Dormant and Germinated Grassbur Twin Seeds Reveals that Ribosomal Synthesis and Carbohydrate Metabolism Promote Germination Possibly Through the PI3K Pathway.

PubMed

Zhang, Guo-Liang; Zhu, Yue; Fu, Wei-Dong; Wang, Peng; Zhang, Rui-Hai; Zhang, Yan-Lei; Song, Zhen; Xia, Gui-Xian; Wu, Jia-He

2016-06-01

Grassbur is a destructive and invasive weed in pastures, and its burs can cause gastric damage to animals. The strong adaptability and reproductive potential of grassbur are partly due to a unique germination mechanism whereby twin seeds develop in a single bur: one seed germinates, but the other remains dormant. To investigate the molecular mechanism of seed germination in twin seeds, we used isobaric tags for relative and absolute quantitation (iTRAQ) to perform a dynamic proteomic analysis of germination and dormancy. A total of 1,984 proteins were identified, 161 of which were considered to be differentially accumulated. The differentially accumulated proteins comprised 102 up-regulated and 59 down-regulated proteins. These proteins were grouped into seven functional categories, ribosomal proteins being the predominant group. The authenticity and accuracy of the results were confirmed by enzyme-linked immunosorbent assay (ELISA) and quantitative real-time reverse transcription-PCR (qPCR). A dynamic proteomic analysis revealed that ribosome synthesis and carbohydrate metabolism affect seed germination possibly through the phosphoinositide 3-kinase (PI3K) pathway. As the PI3K pathway is generally activated by insulin, analyses of seeds treated with exogenous insulin by qPCR, ELISA and iTRAQ confirmed that the PI3K pathway can be activated, which suppresses dormancy and promotes germination in twin grassbur seeds. Together, these results show that the PI3K pathway may play roles in stimulating seed germination in grassbur by modulating ribosomal synthesis and carbohydrate metabolism. © The Author 2016. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Mapping Adipose and Muscle Tissue Expression Quantitative Trait Loci in African Americans to Identify Genes for Type 2 Diabetes and Obesity

PubMed Central

Sajuthi, Satria P.; Sharma, Neeraj K.; Chou, Jeff W.; Palmer, Nicholette D.; McWilliams, David R.; Beal, John; Comeau, Mary E.; Ma, Lijun; Calles-Escandon, Jorge; Demons, Jamehl; Rogers, Samantha; Cherry, Kristina; Menon, Lata; Kouba, Ethel; Davis, Donna; Burris, Marcie; Byerly, Sara J.; Ng, Maggie C.Y.; Maruthur, Nisa M.; Patel, Sanjay R.; Bielak, Lawrence F.; Lange, Leslie; Guo, Xiuqing; Sale, Michèle M.; Chan, Kei Hang; Monda, Keri L.; Chen, Gary K.; Taylor, Kira; Palmer, Cameron; Edwards, Todd L; North, Kari E.; Haiman, Christopher A.; Bowden, Donald W.; Freedman, Barry I.; Langefeld, Carl D.; Das, Swapan K.

2016-01-01

Relative to European Americans, type 2 diabetes (T2D) is more prevalent in African Americans (AAs). Genetic variation may modulate transcript abundance in insulin-responsive tissues and contribute to risk; yet published studies identifying expression quantitative trait loci (eQTLs) in African ancestry populations are restricted to blood cells. This study aims to develop a map of genetically regulated transcripts expressed in tissues important for glucose homeostasis in AAs, critical for identifying the genetic etiology of T2D and related traits. Quantitative measures of adipose and muscle gene expression, and genotypic data were integrated in 260 non-diabetic AAs to identify expression regulatory variants. Their roles in genetic susceptibility to T2D, and related metabolic phenotypes were evaluated by mining GWAS datasets. eQTL analysis identified 1,971 and 2,078 cis-eGenes in adipose and muscle, respectively. Cis-eQTLs for 885 transcripts including top cis-eGenes CHURC1, USMG5, and ERAP2, were identified in both tissues. 62.1% of top cis-eSNPs were within ±50kb of transcription start sites and cis-eGenes were enriched for mitochondrial transcripts. Mining GWAS databases revealed association of cis-eSNPs for more than 50 genes with T2D (e.g. PIK3C2A, RBMS1, UFSP1), gluco-metabolic phenotypes, (e.g. INPP5E, SNX17, ERAP2, FN3KRP), and obesity (e.g. POMC, CPEB4). Integration of GWAS meta-analysis data from AA cohorts revealed the most significant association for cis-eSNPs of ATP5SL and MCCC1 genes, with T2D and BMI, respectively. This study developed the first comprehensive map of adipose and muscle tissue eQTLs in AAs (publically accessible at https://mdsetaa.phs.wakehealth.edu) and identified genetically-regulated transcripts for delineating genetic causes of T2D, and related metabolic phenotypes. PMID:27193597

A mixed‐method systematic review and meta‐analysis of mental health professionals' attitudes toward smoking and smoking cessation among people with mental illnesses

PubMed Central

Sheals, Kate; Tombor, Ildiko; McNeill, Ann

2016-01-01

Abstract Background and aims People with mental illnesses and substance abuse disorders are important targets for smoking cessation interventions. Mental health professionals (MHPs) are ideally placed to deliver interventions, but their attitudes may prevent this. This systematic review therefore aimed to identify and estimate quantitatively MHPs attitudes towards smoking and main barriers for providing smoking cessation support and to explore these attitudes in‐depth through qualitative synthesis. Methods The online databases AMED, EMBASE, Medline, PsychINFO, HMIC and CINAHL were searched in March 2015 using terms relating to three concepts: ‘attitudes’, ‘mental health professionals’ and ‘smoking cessation’. Quantitative or qualitative studies of any type were included. Proportions of MHPs' attitudes towards smoking and smoking cessation were pooled across studies using random effects meta‐analysis. Qualitative findings were evaluated using thematic synthesis. Results Thirty‐eight studies including 16 369 participants were eligible for inclusion. Pooled proportions revealed that 42.2% [95% confidence interval (CI) = 35.7–48.8] of MHPs reported perceived barriers to smoking cessation interventions, 40.5% (95% CI = 30.4–51.0) negative attitudes towards smoking cessation and 45.0% (95% CI = 31.9–58.4) permissive attitudes towards smoking. The most commonly held beliefs were that patients are not interested in quitting (51.4%, 95% CI = 33.4–69.2) and that quitting smoking is too much for patients to take on (38%, 95% CI = 16.4–62.6). Qualitative findings were consistent with quantitative results, revealing a culture of smoking as ‘the norm’ and a perception of cigarettes as a useful tool for patients and staff. Conclusions A significant proportion of mental health professionals hold attitudes and misconceptions that may undermine the delivery of smoking cessation interventions; many report a lack of time, training and confidence as main barriers to addressing smoking in their patients. PMID:27003925

A mixed-method systematic review and meta-analysis of mental health professionals' attitudes toward smoking and smoking cessation among people with mental illnesses.

PubMed

Sheals, Kate; Tombor, Ildiko; McNeill, Ann; Shahab, Lion

2016-09-01

People with mental illnesses and substance abuse disorders are important targets for smoking cessation interventions. Mental health professionals (MHPs) are ideally placed to deliver interventions, but their attitudes may prevent this. This systematic review therefore aimed to identify and estimate quantitatively MHPs attitudes towards smoking and main barriers for providing smoking cessation support and to explore these attitudes in-depth through qualitative synthesis. The online databases AMED, EMBASE, Medline, PsychINFO, HMIC and CINAHL were searched in March 2015 using terms relating to three concepts: 'attitudes', 'mental health professionals' and 'smoking cessation'. Quantitative or qualitative studies of any type were included. Proportions of MHPs' attitudes towards smoking and smoking cessation were pooled across studies using random effects meta-analysis. Qualitative findings were evaluated using thematic synthesis. Thirty-eight studies including 16 369 participants were eligible for inclusion. Pooled proportions revealed that 42.2% [95% confidence interval (CI) = 35.7-48.8] of MHPs reported perceived barriers to smoking cessation interventions, 40.5% (95% CI = 30.4-51.0) negative attitudes towards smoking cessation and 45.0% (95% CI = 31.9-58.4) permissive attitudes towards smoking. The most commonly held beliefs were that patients are not interested in quitting (51.4%, 95% CI = 33.4-69.2) and that quitting smoking is too much for patients to take on (38%, 95% CI = 16.4-62.6). Qualitative findings were consistent with quantitative results, revealing a culture of smoking as 'the norm' and a perception of cigarettes as a useful tool for patients and staff. A significant proportion of mental health professionals hold attitudes and misconceptions that may undermine the delivery of smoking cessation interventions; many report a lack of time, training and confidence as main barriers to addressing smoking in their patients. © 2016 The Authors. Addiction published by John Wiley & Sons Ltd on behalf of Society for the Study of Addiction.

Intraoperative microscope-mounted spectral domain optical coherence tomography for evaluation of retinal anatomy during macular surgery.

PubMed

Ray, Robin; Barañano, David E; Fortun, Jorge A; Schwent, Bryan J; Cribbs, Blaine E; Bergstrom, Chris S; Hubbard, G Baker; Srivastava, Sunil K

2011-11-01

To evaluate the use of microscope mounted spectral domain optical coherence tomography (SD-OCT) to detect changes in retinal anatomy during macular surgery. Retrospective, observational case series. We included 25 eyes of 24 consecutive patients who underwent SD-OCT during macular surgery. A retrospective review of operative techniques, outcomes, and imaging for all patients who underwent intraoperative microscope mounted SD-OCT during surgery for macular hole or epiretinal membrane (ERM) from April 2009 to April 2010 was performed. Qualitative and quantitative characteristics of intraoperative and postoperative changes in retinal anatomy were studied. Intraoperative change in macular hole dimensions and retinal thickness in patients with ERM owing to surgical manipulation measured using SD-OCT. Intraoperative SD-OCT from 13 eyes of 13 patients undergoing surgery for macular hole was reviewed. Two cases had images of suboptimal quality and were excluded. The remaining 11 eyes were subjected to quantitative analysis, which revealed stability of macular hole height and central hole diameter after internal limiting membrane (ILM) peeling, but an increase in the diameter of subretinal fluid under the macula in ten of 11 eyes (average 87% wider). Intraoperative imaging from 12 eyes of 11 patients undergoing surgery for ERM was analyzed. Quantitative analysis revealed an average increase of retinal thickness after ILM peel of <2%. Ten of 12 eyes developed a new subretinal hyporeflectance, which likely represents shallow detachment of the macula, after uncomplicated membrane peel. Use of intraoperative SD-OCT has provided new insight into the changes to retinal anatomy during macular surgery and may prove to be a useful tool for vitreoretinal surgery. Further study is warranted to determine whether intraoperative changes such as the creation of shallow retinal detachments during uncomplicated macular surgery affects visual recovery. Proprietary or commercial disclosure may be found after the references. Copyright © 2011 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.

Quantitative and Qualitative Analysis of Phenolic and Flavonoid Content in Moringa oleifera Lam and Ocimum tenuiflorum L.

PubMed Central

Sankhalkar, Sangeeta; Vernekar, Vrunda

2016-01-01

Background: Number of secondary compounds is produced by plants as natural antioxidants. Moringa oleifera Lam. and Ocimum tenuiflorum L. are known for their wide applications in food and pharmaceutical industry. Objective: To compare phenolic and flavonoid content in M. oleifera Lam and O. tenuiflorum L. by quantitative and qualitative analysis. Materials and Methods: Phenolic and flavonoid content were studied spectrophotometrically and by paper chromatography in M. oleifera Lam. and O. tenuiflorum L. Results: Higher phenolic and flavonoid content were observed in Moringa leaf and flower. Ocimum flower showed higher phenolic content and low flavonoid in comparison to Moringa. Flavonoids such as biflavonyl, flavones, glycosylflavones, and kaempferol were identified by paper chromatography. Phytochemical analysis for flavonoid, tannins, saponins, alkaloids, reducing sugars, and anthraquinones were tested positive for Moringa and Ocimum leaf as well as flower. Conclusions: In the present study higher phenolic and flavonoid content, indicated the natural antioxidant nature of Moringa and Ocimum signifying their medicinal importance. SUMMARY Moringa oleifera Lam. and Ocimum tenuiflorum L. are widly grown in India and are known for their medicinal properties. Number of secondary metabolites like phenolics and flavonoids are known to be present in both the plants. The present study was conducted with an objective to qualitatively and quantitatively compare the phenolics and flavanoids in these two medicinally important plants.Quantitation of total phenolics and flavanoids was done by spectrophotometrically while qualitative analysis was perfomed by paper chromatography and by phytochemical tests. Our results have shown higher phenolics and flavanoid content in Moringa leaf and flower. However, higher phenolic content was absent in Ocimum flower compared to that of Moringa. Phytochemical analysis of various metabolites such as flavonoids, tanins, sapponins, alkaloids, anthraquinones revealed that both the plant extracts were rich sources of secondary metabolites and thus tested positive for the above tests. Various flavanoids and Phenolics were identified by paper chromatography based on their Rf values and significant colors. From the above study we conclude that Moringa and Ocimum are rich in natural antioxidants hence are potent source in pharmaceutical industry. PMID:26941531

Quantitative and Qualitative Analysis of Phenolic and Flavonoid Content in Moringa oleifera Lam and Ocimum tenuiflorum L.

PubMed

Sankhalkar, Sangeeta; Vernekar, Vrunda

2016-01-01

Number of secondary compounds is produced by plants as natural antioxidants. Moringa oleifera Lam. and Ocimum tenuiflorum L. are known for their wide applications in food and pharmaceutical industry. To compare phenolic and flavonoid content in M. oleifera Lam and O. tenuiflorum L. by quantitative and qualitative analysis. Phenolic and flavonoid content were studied spectrophotometrically and by paper chromatography in M. oleifera Lam. and O. tenuiflorum L. Higher phenolic and flavonoid content were observed in Moringa leaf and flower. Ocimum flower showed higher phenolic content and low flavonoid in comparison to Moringa. Flavonoids such as biflavonyl, flavones, glycosylflavones, and kaempferol were identified by paper chromatography. Phytochemical analysis for flavonoid, tannins, saponins, alkaloids, reducing sugars, and anthraquinones were tested positive for Moringa and Ocimum leaf as well as flower. In the present study higher phenolic and flavonoid content, indicated the natural antioxidant nature of Moringa and Ocimum signifying their medicinal importance. Moringa oleifera Lam. and Ocimum tenuiflorum L. are widly grown in India and are known for their medicinal properties. Number of secondary metabolites like phenolics and flavonoids are known to be present in both the plants. The present study was conducted with an objective to qualitatively and quantitatively compare the phenolics and flavanoids in these two medicinally important plants.Quantitation of total phenolics and flavanoids was done by spectrophotometrically while qualitative analysis was perfomed by paper chromatography and by phytochemical tests. Our results have shown higher phenolics and flavanoid content in Moringa leaf and flower. However, higher phenolic content was absent in Ocimum flower compared to that of Moringa. Phytochemical analysis of various metabolites such as flavonoids, tanins, sapponins, alkaloids, anthraquinones revealed that both the plant extracts were rich sources of secondary metabolites and thus tested positive for the above tests. Various flavanoids and Phenolics were identified by paper chromatography based on their Rf values and significant colors. From the above study we conclude that Moringa and Ocimum are rich in natural antioxidants hence are potent source in pharmaceutical industry.

Two Carrier Analysis of Persistent Photoconductivity in Modulation-Doped Structures

NASA Technical Reports Server (NTRS)

Schacham, S. E.; Mena, R. A.; Haugland, E. J.; Alterovitz, S. A.

1995-01-01

A simultaneous fit of Hall and conductivity data gives quantitative results on the carrier concentration and mobility in both the quantum well and the parallel conduction channel. In this study this method was applied to reveal several new findings on the effect of persistent photoconductivity (PPC) on free-carrier concentrations and mobilities. The increase in the two-dimensional electron-gas (2DEG) concentration is significantly smaller than the apparent one derived from single carrier analysis of the Hall coefficient. In the two types of structures investigated, delta doped and continuously doped barrier, the apparent concentration almost doubles following illumination, while analysis reveals an increase of about 20% in the 2DEG. The effect of PPC on mobility depends on the structure. For the sample with a continuously doped barrier the mobility in the quantum well more than doubles. This increase is attributed to the effective screening of the ionized donors by the large electron concentration in the barrier. In the delta doped barrier sample the mobility is reduced by almost a factor of 2. This decrease is probably caused by strong coupling between the two wells, as is demonstrated by self-consistent analysis.

Gene expression analysis reveals schizophrenia-associated dysregulation of immune pathways in peripheral blood mononuclear cells.

PubMed

Gardiner, Erin J; Cairns, Murray J; Liu, Bing; Beveridge, Natalie J; Carr, Vaughan; Kelly, Brian; Scott, Rodney J; Tooney, Paul A

2013-04-01

Peripheral blood mononuclear cells (PBMCs) represent an accessible tissue source for gene expression profiling in schizophrenia that could provide insight into the molecular basis of the disorder. This study used the Illumina HT_12 microarray platform and quantitative real time PCR (QPCR) to perform mRNA expression profiling on 114 patients with schizophrenia or schizoaffective disorder and 80 non-psychiatric controls from the Australian Schizophrenia Research Bank (ASRB). Differential expression analysis revealed altered expression of 164 genes (59 up-regulated and 105 down-regulated) in the PBMCs from patients with schizophrenia compared to controls. Bioinformatic analysis indicated significant enrichment of differentially expressed genes known to be involved or associated with immune function and regulating the immune response. The differential expression of 6 genes, EIF2C2 (Ago 2), MEF2D, EVL, PI3, S100A12 and DEFA4 was confirmed by QPCR. Genome-wide expression analysis of PBMCs from individuals with schizophrenia was characterized by the alteration of genes with immune system function, supporting the hypothesis that the disorder has a significant immunological component in its etiology. Copyright © 2012 Elsevier Ltd. All rights reserved.

Comparing GWAS Results of Complex Traits Using Full Genetic Model and Additive Models for Revealing Genetic Architecture

PubMed Central

Monir, Md. Mamun; Zhu, Jun

2017-01-01

Most of the genome-wide association studies (GWASs) for human complex diseases have ignored dominance, epistasis and ethnic interactions. We conducted comparative GWASs for total cholesterol using full model and additive models, which illustrate the impacts of the ignoring genetic variants on analysis results and demonstrate how genetic effects of multiple loci could differ across different ethnic groups. There were 15 quantitative trait loci with 13 individual loci and 3 pairs of epistasis loci identified by full model, whereas only 14 loci (9 common loci and 5 different loci) identified by multi-loci additive model. Again, 4 full model detected loci were not detected using multi-loci additive model. PLINK-analysis identified two loci and GCTA-analysis detected only one locus with genome-wide significance. Full model identified three previously reported genes as well as several new genes. Bioinformatics analysis showed some new genes are related with cholesterol related chemicals and/or diseases. Analyses of cholesterol data and simulation studies revealed that the full model performs were better than the additive-model performs in terms of detecting power and unbiased estimations of genetic variants of complex traits. PMID:28079101

Kinetics of Forming Aldehydes in Frying Oils and Their Distribution in French Fries Revealed by LC-MS-Based Chemometrics.

PubMed

Wang, Lei; Csallany, A Saari; Kerr, Brian J; Shurson, Gerald C; Chen, Chi

2016-05-18

In this study, the kinetics of aldehyde formation in heated frying oils was characterized by 2-hydrazinoquinoline derivatization, liquid chromatography-mass spectrometry (LC-MS) analysis, principal component analysis (PCA), and hierarchical cluster analysis (HCA). The aldehydes contributing to time-dependent separation of heated soybean oil (HSO) in a PCA model were grouped by the HCA into three clusters (A1, A2, and B) on the basis of their kinetics and fatty acid precursors. The increases of 4-hydroxynonenal (4-HNE) and the A2-to-B ratio in HSO were well-correlated with the duration of thermal stress. Chemometric and quantitative analysis of three frying oils (soybean, corn, and canola oils) and French fry extracts further supported the associations between aldehyde profiles and fatty acid precursors and also revealed that the concentrations of pentanal, hexanal, acrolein, and the A2-to-B ratio in French fry extracts were more comparable to their values in the frying oils than other unsaturated aldehydes. All of these results suggest the roles of specific aldehydes or aldehyde clusters as novel markers of the lipid oxidation status for frying oils or fried foods.

Multi-Resolution Analysis of LiDAR data for Characterizing a Stabilized Aeolian Landscape in South Texas

NASA Astrophysics Data System (ADS)

Barrineau, C. P.; Dobreva, I. D.; Bishop, M. P.; Houser, C.

2014-12-01

Aeolian systems are ideal natural laboratories for examining self-organization in patterned landscapes, as certain wind regimes generate certain morphologies. Topographic information and scale dependent analysis offer the opportunity to study such systems and characterize process-form relationships. A statistically based methodology for differentiating aeolian features would enable the quantitative association of certain surface characteristics with certain morphodynamic regimes. We conducted a multi-resolution analysis of LiDAR elevation data to assess scale-dependent morphometric variations in an aeolian landscape in South Texas. For each pixel, mean elevation values are calculated along concentric circles moving outward at 100-meter intervals (i.e. 500 m, 600 m, 700 m from pixel). The calculated average elevation values plotted against distance from the pixel of interest as curves are used to differentiate multi-scalar variations in elevation across the landscape. In this case, it is hypothesized these curves may be used to quantitatively differentiate certain morphometries from others like a spectral signature may be used to classify paved surfaces from natural vegetation, for example. After generating multi-resolution curves for all the pixels in a selected area of interest (AOI), a Principal Components Analysis is used to highlight commonalities and singularities between generated curves from pixels across the AOI. Our findings suggest that the resulting components could be used for identification of discrete aeolian features like open sands, trailing ridges and active dune crests, and, in particular, zones of deflation. This new approach to landscape characterization not only works to mitigate bias introduced when researchers must select training pixels for morphometric investigations, but can also reveal patterning in aeolian landscapes that would not be as obvious without quantitative characterization.

Quantitative statistical analysis of cis-regulatory sequences in ABA/VP1- and CBF/DREB1-regulated genes of Arabidopsis.

PubMed

Suzuki, Masaharu; Ketterling, Matthew G; McCarty, Donald R

2005-09-01

We have developed a simple quantitative computational approach for objective analysis of cis-regulatory sequences in promoters of coregulated genes. The program, designated MotifFinder, identifies oligo sequences that are overrepresented in promoters of coregulated genes. We used this approach to analyze promoter sequences of Viviparous1 (VP1)/abscisic acid (ABA)-regulated genes and cold-regulated genes, respectively, of Arabidopsis (Arabidopsis thaliana). We detected significantly enriched sequences in up-regulated genes but not in down-regulated genes. This result suggests that gene activation but not repression is mediated by specific and common sequence elements in promoters. The enriched motifs include several known cis-regulatory sequences as well as previously unidentified motifs. With respect to known cis-elements, we dissected the flanking nucleotides of the core sequences of Sph element, ABA response elements (ABREs), and the C repeat/dehydration-responsive element. This analysis identified the motif variants that may correlate with qualitative and quantitative differences in gene expression. While both VP1 and cold responses are mediated in part by ABA signaling via ABREs, these responses correlate with unique ABRE variants distinguished by nucleotides flanking the ACGT core. ABRE and Sph motifs are tightly associated uniquely in the coregulated set of genes showing a strict dependence on VP1 and ABA signaling. Finally, analysis of distribution of the enriched sequences revealed a striking concentration of enriched motifs in a proximal 200-base region of VP1/ABA and cold-regulated promoters. Overall, each class of coregulated genes possesses a discrete set of the enriched motifs with unique distributions in their promoters that may account for the specificity of gene regulation.

Qualitative and quantitative interpretation of computed tomography of the lungs in healthy neonatal foals.

PubMed

Lascola, Kara M; O'Brien, Robert T; Wilkins, Pamela A; Clark-Price, Stuart C; Hartman, Susan K; Mitchell, Mark A

2013-09-01

To qualitatively describe lung CT images obtained from sedated healthy equine neonates (≤ 14 days of age), use quantitative analysis of CT images to characterize attenuation and distribution of gas and tissue volumes within the lungs, and identify differences between lung characteristics of foals ≤ 7 days of age and foals > 7 days of age. 10 Standardbred foals between 2.5 and 13 days of age. Foals were sedated with butorphanol, midazolam, and propofol and positioned in sternal recumbency for thoracic CT. Image analysis software was used to exclude lung from nonlung structures. Lung attenuation was measured in Hounsfield units (HU) for analysis of whole lung and regional changes in attenuation and lung gas and tissue components. Degree of lung attenuation was classified as follows: hyperinflated or emphysema, -1,000 to -901 HU; well aerated, -900 to -501 HU; poorly aerated, -500 to -101 HU; and nonaerated, > -100 HU. Qualitative evidence of an increase in lung attenuation and patchy alveolar patterns in the ventral lung region were more pronounced in foals ≤ 7 days of age than in older foals. Quantitative analysis revealed that mean ± SD lung attenuation was greater in foals ≤ 7 days of age (-442 ± 28 HU) than in foals > 7 days of age (-521 ± 24 HU). Lung aeration and gas volumes were lower than in other regions ventrally and in the mid lung region caudal to the heart. CONCLUSIONS AND CLINICAL RELEVANCE-Identified radiographic patterns and changes in attenuation were most consistent with atelectasis and appeared more severe in foals ≤ 7 days of age than in older neonatal foals. Recognition of these changes may have implications for accurate CT interpretation in sedated neonatal foals with pulmonary disease.

Relationship between self-reported upper limb disability and quantitative tests in hand-arm vibration syndrome.

PubMed

Poole, Kerry; Mason, Howard

2007-03-15

To establish the relationship between quantitative tests of hand function and upper limb disability, as measured by the Disability of the Arm, Shoulder and Hand (DASH) questionnaire, in hand-arm vibration syndrome (HAVS). A total of 228 individuals with HAVS were included in this study. Each had undergone a full HAVS assessment by an experienced physician, including quantitative tests of vibrotactile and thermal perception thresholds, maximal hand-grip strength (HG) and the Purdue pegboard (PP) test. Individuals were also asked to complete a DASH questionnaire. PP and HG of the quantitative tests gave the best and statistically significant individual correlations with the DASH disability score (r2 = 0.168 and 0.096). Stepwise linear regression analysis revealed that only PP and HG measurements were statistically significant predictors of upper limb disability (r2 = 0.178). Overall a combination of the PP and HG measurements, rather than each alone, gave slightly better discrimination, although not statistically significant, between normal and abnormal DASH scores with a sensitivity of 73.1% and specificity of 64.3%. Measurements of manual dexterity and hand-grip strength using PP and HG may be useful in helping to confirm lack of upper limb function and 'perceived' disability in HAVS.

Stereotype Threat? Male and Female Students in Advanced High School Courses

NASA Astrophysics Data System (ADS)

Corra, Mamadi

Propositions of stereotype threat theory imply that the social consequences of academic distinction in advanced quantitative areas (such as math and the physical sciences) for women may promote the under representation of female students in advanced quantitative academic courses. The hypothesis that female students will be underrepresented in advanced quantitative (honors and advanced placement math and physical science) courses is tested using academic performance and enrollment data for high school students in a "Student/Parent Informed Choice" (open registration) school district in North Carolina. Results show female students to be overrepresented in both advanced verbal/writing intensive (honors and advanced placement English, foreign language, and social science) and advanced quantitative (honors and advanced placement math and physical science) courses compared to their proportion of the student body. More surprisingly, results also indicate female students (compared to male students) to be overrepresented in advanced courses compared to their proportion of high-performing students. Furthermore, as with patterns observed at the district level, additional analysis of enrollment data for the entire state reveals similar results. Taken together, the findings call into question the prevailing presumption that female students continue to be underrepresented in math and physical science courses. Instead, the changing social context within which females and males experience schooling may provide an explanation for the findings.

Response of Human Osteoblast to n-HA/PEEK—Quantitative Proteomic Study of Bio-effects of Nano-Hydroxyapatite Composite

NASA Astrophysics Data System (ADS)

Zhao, Minzhi; Li, Haiyun; Liu, Xiaochen; Wei, Jie; Ji, Jianguo; Yang, Shu; Hu, Zhiyuan; Wei, Shicheng

2016-03-01

Nano-sized hydroxyapatite (n-HA) is considered as a bio-active material, which is often mixed into bone implant material, polyetheretherketone (PEEK). To reveal the global protein expression modulations of osteoblast in response to direct contact with the PEEK composite containing high level (40%) nano-sized hydroxyapatite (n-HA/PEEK) and explain its comprehensive bio-effects, quantitative proteomic analysis was conducted on human osteoblast-like cells MG-63 cultured on n-HA/PEEK in comparison with pure PEEK. Results from quantitative proteomic analysis showed that the most enriched categories in the up-regulated proteins were related to calcium ion processes and associated functions while the most enriched categories in the down-regulated proteins were related to RNA process. This enhanced our understanding to the molecular mechanism of the promotion of the cell adhesion and differentiation with the inhibition of the cell proliferation on n-HA/PEEK composite. It also exhibited that although the calcium ion level of incubate environment hadn’t increased, merely the calcium fixed on the surface of material had influence to intracellular calcium related processes, which was also reflect by the higher intracellular Ca2+ concentration of n-HA/PEEK. This study could lead to more comprehensive cognition to the versatile biocompatibility of composite materials. It further proves that proteomics is useful in new bio-effect discovery.

Quantitative iTRAQ secretome analysis of Aspergillus niger reveals novel hydrolytic enzymes.

PubMed

Adav, Sunil S; Li, An A; Manavalan, Arulmani; Punt, Peter; Sze, Siu Kwan

2010-08-06

The natural lifestyle of Aspergillus niger made them more effective secretors of hydrolytic proteins and becomes critical when this species were exploited as hosts for the commercial secretion of heterologous proteins. The protein secretion profile of A. niger and its mutant at different pH was explored using iTRAQ-based quantitative proteomics approach coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS). This study characterized 102 highly confident unique proteins in the secretome with zero false discovery rate based on decoy strategy. The iTRAQ technique identified and relatively quantified many hydrolyzing enzymes such as cellulases, hemicellulases, glycoside hydrolases, proteases, peroxidases, and protein translocating transporter proteins during fermentation. The enzymes have potential application in lignocellulosic biomass hydrolysis for biofuel production, for example, the cellulolytic and hemicellulolytic enzymes glucan 1,4-alpha-glucosidase, alpha-glucosidase C, endoglucanase, alpha l-arabinofuranosidase, beta-mannosidase, glycosyl hydrolase; proteases such as tripeptidyl-peptidase, aspergillopepsin, and other enzymes including cytochrome c oxidase, cytochrome c oxidase, glucose oxidase were highly expressed in A. niger and its mutant secretion. In addition, specific enzyme production can be stimulated by controlling pH of the culture medium. Our results showed comprehensive unique secretory protein profile of A. niger, its regulation at different pH, and the potential application of iTRAQ-based quantitative proteomics for the microbial secretome analysis.

Quantitative microscopy uncovers ploidy changes during mitosis in live Drosophila embryos and their effect on nuclear size.

PubMed

Puah, Wee Choo; Chinta, Rambabu; Wasser, Martin

2017-03-15

Time-lapse microscopy is a powerful tool to investigate cellular and developmental dynamics. In Drosophila melanogaster , it can be used to study division cycles in embryogenesis. To obtain quantitative information from 3D time-lapse data and track proliferating nuclei from the syncytial stage until gastrulation, we developed an image analysis pipeline consisting of nuclear segmentation, tracking, annotation and quantification. Image analysis of maternal-haploid ( mh ) embryos revealed that a fraction of haploid syncytial nuclei fused to give rise to nuclei of higher ploidy (2n, 3n, 4n). Moreover, nuclear densities in mh embryos at the mid-blastula transition varied over threefold. By tracking synchronized nuclei of different karyotypes side-by-side, we show that DNA content determines nuclear growth rate and size in early interphase, while the nuclear to cytoplasmic ratio constrains nuclear growth during late interphase. mh encodes the Drosophila ortholog of human Spartan, a protein involved in DNA damage tolerance. To explore the link between mh and chromosome instability, we fluorescently tagged Mh protein to study its subcellular localization. We show Mh-mKO2 localizes to nuclear speckles that increase in numbers as nuclei expand in interphase. In summary, quantitative microscopy can provide new insights into well-studied genes and biological processes. © 2017. Published by The Company of Biologists Ltd.

TECHNOLOGICAL INNOVATION IN NEUROSURGERY: A QUANTITATIVE STUDY

PubMed Central

Marcus, Hani J; Hughes-Hallett, Archie; Kwasnicki, Richard M; Darzi, Ara; Yang, Guang-Zhong; Nandi, Dipankar

2015-01-01

Object Technological innovation within healthcare may be defined as the introduction of a new technology that initiates a change in clinical practice. Neurosurgery is a particularly technologically intensive surgical discipline, and new technologies have preceded many of the major advances in operative neurosurgical technique. The aim of the present study was to quantitatively evaluate technological innovation in neurosurgery using patents and peer-reviewed publications as metrics of technology development and clinical translation respectively. Methods A patent database was searched between 1960 and 2010 using the search terms “neurosurgeon” OR “neurosurgical” OR “neurosurgery”. The top 50 performing patent codes were then grouped into technology clusters. Patent and publication growth curves were then generated for these technology clusters. A top performing technology cluster was then selected as an exemplar for more detailed analysis of individual patents. Results In all, 11,672 patents and 208,203 publications relating to neurosurgery were identified. The top performing technology clusters over the 50 years were: image guidance devices, clinical neurophysiology devices, neuromodulation devices, operating microscopes and endoscopes. Image guidance and neuromodulation devices demonstrated a highly correlated rapid rise in patents and publications, suggesting they are areas of technology expansion. In-depth analysis of neuromodulation patents revealed that the majority of high performing patents were related to Deep Brain Stimulation (DBS). Conclusions Patent and publication data may be used to quantitatively evaluate technological innovation in neurosurgery. PMID:25699414

A quantitative PCR assay for aerobic, vinyl chloride- and ethene-assimilating microorganisms in groundwater.

PubMed

Jin, Yang Oh; Mattes, Timothy E

2010-12-01

Vinyl chloride (VC) is a known human carcinogen that is primarily formed in groundwater via incomplete anaerobic dechlorination of chloroethenes. Aerobic, ethene-degrading bacteria (etheneotrophs), which are capable of both fortuitous and growth-linked VC oxidation, could be important in natural attenuation of VC plumes that escape anaerobic treatment. In this work, we developed a quantitative, real-time PCR (qPCR) assay for etheneotrophs in groundwater. We designed and tested degenerate qPCR primers for two functional genes involved in aerobic, growth-coupled VC- and ethene-oxidation (etnC and etnE). Primer specificity to these target genes was tested by comparison to nucleotide sequence databases, PCR analysis of template DNA extracted from isolates and environmental samples, and sequencing of qPCR products obtained from VC-contaminated groundwater. The assay was made quantitative by constructing standard curves (threshold cycle vs log gene copy number) with DNA amplified from Mycobacterium strain JS60, an etheneotrophic isolate. Analysis of groundwater samples from three different VC-contaminated sites revealed that etnC abundance ranged from 1.6 × 10(3) - 1.0 × 10(5) copies/L groundwater while etnE abundance ranged from 4.3 × 10(3) - 6.3 × 10(5) copies/L groundwater. Our data suggest this novel environmental measurement method will be useful for supporting VC bioremediation strategies, assisting in site closure, and conducting microbial ecology studies involving etheneotrophs.

Response of Human Osteoblast to n-HA/PEEK--Quantitative Proteomic Study of Bio-effects of Nano-Hydroxyapatite Composite.

PubMed

Zhao, Minzhi; Li, Haiyun; Liu, Xiaochen; Wei, Jie; Ji, Jianguo; Yang, Shu; Hu, Zhiyuan; Wei, Shicheng

2016-03-09

Nano-sized hydroxyapatite (n-HA) is considered as a bio-active material, which is often mixed into bone implant material, polyetheretherketone (PEEK). To reveal the global protein expression modulations of osteoblast in response to direct contact with the PEEK composite containing high level (40%) nano-sized hydroxyapatite (n-HA/PEEK) and explain its comprehensive bio-effects, quantitative proteomic analysis was conducted on human osteoblast-like cells MG-63 cultured on n-HA/PEEK in comparison with pure PEEK. Results from quantitative proteomic analysis showed that the most enriched categories in the up-regulated proteins were related to calcium ion processes and associated functions while the most enriched categories in the down-regulated proteins were related to RNA process. This enhanced our understanding to the molecular mechanism of the promotion of the cell adhesion and differentiation with the inhibition of the cell proliferation on n-HA/PEEK composite. It also exhibited that although the calcium ion level of incubate environment hadn't increased, merely the calcium fixed on the surface of material had influence to intracellular calcium related processes, which was also reflect by the higher intracellular Ca(2+) concentration of n-HA/PEEK. This study could lead to more comprehensive cognition to the versatile biocompatibility of composite materials. It further proves that proteomics is useful in new bio-effect discovery.

Quantitative Trait Loci Mapping in Brassica rapa Revealed the Structural and Functional Conservation of Genetic Loci Governing Morphological and Yield Component Traits in the A, B, and C Subgenomes of Brassica Species

PubMed Central

Li, Xiaonan; Ramchiary, Nirala; Dhandapani, Vignesh; Choi, Su Ryun; Hur, Yoonkang; Nou, Ill-Sup; Yoon, Moo Kyoung; Lim, Yong Pyo

2013-01-01

Brassica rapa is an important crop species that produces vegetables, oilseed, and fodder. Although many studies reported quantitative trait loci (QTL) mapping, the genes governing most of its economically important traits are still unknown. In this study, we report QTL mapping for morphological and yield component traits in B. rapa and comparative map alignment between B. rapa, B. napus, B. juncea, and Arabidopsis thaliana to identify candidate genes and conserved QTL blocks between them. A total of 95 QTL were identified in different crucifer blocks of the B. rapa genome. Through synteny analysis with A. thaliana, B. rapa candidate genes and intronic and exonic single nucleotide polymorphisms in the parental lines were detected from whole genome resequenced data, a few of which were validated by mapping them to the QTL regions. Semi-quantitative reverse transcriptase PCR analysis showed differences in the expression levels of a few genes in parental lines. Comparative mapping identified five key major evolutionarily conserved crucifer blocks (R, J, F, E, and W) harbouring QTL for morphological and yield components traits between the A, B, and C subgenomes of B. rapa, B. juncea, and B. napus. The information of the identified candidate genes could be used for breeding B. rapa and other related Brassica species. PMID:23223793

Severity of pulmonary emphysema and lung cancer: analysis using quantitative lobar emphysema scoring.

PubMed

Bae, Kyungsoo; Jeon, Kyung Nyeo; Lee, Seung Jun; Kim, Ho Cheol; Ha, Ji Young; Park, Sung Eun; Baek, Hye Jin; Choi, Bo Hwa; Cho, Soo Buem; Moon, Jin Il

2016-11-01

The aim of this study was to determine the relationship between lobar severity of emphysema and lung cancer using automated lobe segmentation and emphysema quantification methods.This study included 78 patients (74 males and 4 females; mean age of 72 years) with the following conditions: pathologically proven lung cancer, available chest computed tomographic (CT) scans for lobe segmentation, and quantitative scoring of emphysema. The relationship between emphysema and lung cancer was analyzed using quantitative emphysema scoring of each pulmonary lobe.The most common location of cancer was the left upper lobe (LUL) (n = 28), followed by the right upper lobe (RUL) (n = 27), left lower lobe (LLL) (n = 13), right lower lobe (RLL) (n = 9), and right middle lobe (RML) (n = 1). Emphysema ratio was the highest in LUL, followed by that in RUL, LLL, RML, and RLL. Multivariate logistic regression analysis revealed that upper lobes (odds ratio: 1.77; 95% confidence interval: 1.01-3.11, P = 0.048) and lobes with emphysema ratio ranked the 1st or the 2nd (odds ratio: 2.48; 95% confidence interval: 1.48-4.15, P < 0.001) were significantly and independently associated with lung cancer development.In emphysema patients, lung cancer has a tendency to develop in lobes with more severe emphysema.

Severity of pulmonary emphysema and lung cancer: analysis using quantitative lobar emphysema scoring

PubMed Central

Bae, Kyungsoo; Jeon, Kyung Nyeo; Lee, Seung Jun; Kim, Ho Cheol; Ha, Ji Young; Park, Sung Eun; Baek, Hye Jin; Choi, Bo Hwa; Cho, Soo Buem; Moon, Jin Il

2016-01-01

Abstract The aim of this study was to determine the relationship between lobar severity of emphysema and lung cancer using automated lobe segmentation and emphysema quantification methods. This study included 78 patients (74 males and 4 females; mean age of 72 years) with the following conditions: pathologically proven lung cancer, available chest computed tomographic (CT) scans for lobe segmentation, and quantitative scoring of emphysema. The relationship between emphysema and lung cancer was analyzed using quantitative emphysema scoring of each pulmonary lobe. The most common location of cancer was the left upper lobe (LUL) (n = 28), followed by the right upper lobe (RUL) (n = 27), left lower lobe (LLL) (n = 13), right lower lobe (RLL) (n = 9), and right middle lobe (RML) (n = 1). Emphysema ratio was the highest in LUL, followed by that in RUL, LLL, RML, and RLL. Multivariate logistic regression analysis revealed that upper lobes (odds ratio: 1.77; 95% confidence interval: 1.01–3.11, P = 0.048) and lobes with emphysema ratio ranked the 1st or the 2nd (odds ratio: 2.48; 95% confidence interval: 1.48–4.15, P < 0.001) were significantly and independently associated with lung cancer development. In emphysema patients, lung cancer has a tendency to develop in lobes with more severe emphysema. PMID:27902611

Genetic divergence in northern Benin sorghum (Sorghum bicolor L. Moench) landraces as revealed by agromorphological traits and selection of candidate genotypes.

PubMed

Dossou-Aminon, Innocent; Loko, Laura Yêyinou; Adjatin, Arlette; Ewédjè, Eben-Ezer B K; Dansi, Alexandre; Rakshit, Sujay; Cissé, Ndiaga; Patil, Jagannath Vishnu; Agbangla, Clément; Sanni, Ambaliou; Akoègninou, Akpovi; Akpagana, Koffi

2015-01-01

Sorghum [Sorghum bicolor (L.) Moench] is an important staple food crop in northern Benin. In order to assess its diversity in Benin, 142 accessions of landraces collected from Northern Benin were grown in Central Benin and characterised using 10 qualitative and 14 quantitative agromorphological traits. High variability among both qualitative and quantitative traits was observed. Grain yield (0.72-10.57 tons/ha), panicle weight (15-215.95 g), days to 50% flowering (57-200 days), and plant height (153.27-636.5 cm) were among traits that exhibited broader variability. Correlations between quantitative traits were determined. Grain yield for instance exhibited highly positive association with panicle weight (r = 0.901, P = 0.000) and 100 seed weight (r = 0.247, P = 0.000). UPGMA cluster analysis classified the 142 accessions into 89 morphotypes. Based on multivariate analysis, twenty promising sorghum genotypes were selected. Among them, AT41, AT14, and AT29 showed early maturity (57 to 66 days to 50% flowering), high grain yields (4.85 to 7.85 tons/ha), and shorter plant height (153.27 to 180.37 cm). The results obtained will help enhancing sorghum production and diversity and developing new varieties that will be better adapted to the current soil and climate conditions in Benin.

Programmed death-ligand 1 expression by digital image analysis advances thyroid cancer diagnosis among encapsulated follicular lesions.

PubMed

Hsieh, Anne M-Y; Polyakova, Olena; Fu, Guodong; Chazen, Ronald S; MacMillan, Christina; Witterick, Ian J; Ralhan, Ranju; Walfish, Paul G

2018-04-13

Recognition of noninvasive follicular thyroid neoplasms with papillary-like nuclear features (NIFTP) that distinguishes them from invasive malignant encapsulated follicular variant of papillary thyroid carcinoma (EFVPTC) can prevent overtreatment of NIFTP patients. We and others have previously reported that programmed death-ligand 1 (PD-L1) is a useful biomarker in thyroid tumors; however, all reports to date have relied on manual scoring that is time consuming as well as subject to individual bias. Consequently, we developed a digital image analysis (DIA) protocol for cytoplasmic and membranous stain quantitation (ThyApp) and evaluated three tumor sampling methods [Systemic Uniform Random Sampling, hotspot nucleus, and hotspot nucleus/3,3'-Diaminobenzidine (DAB)]. A patient cohort of 153 cases consisting of 48 NIFTP, 44 EFVPTC, 26 benign nodules and 35 encapsulated follicular lesions/neoplasms with lymphocytic thyroiditis (LT) was studied. ThyApp quantitation of PD-L1 expression revealed a significant difference between invasive EFVPTC and NIFTP; but none between NIFTP and benign nodules. ThyApp integrated with hotspot nucleus tumor sampling method demonstrated to be most clinically relevant, consumed least processing time, and eliminated interobserver variance. In conclusion, the fully automatic DIA algorithm developed using a histomorphological approach objectively quantitated PD-L1 expression in encapsulated thyroid neoplasms and outperformed manual scoring in reproducibility and higher efficiency.

Improvement of Insulin Secretion and Pancreatic β-cell Function in Streptozotocin-induced Diabetic Rats Treated with Aloe vera Extract

PubMed Central

Noor, Ayesha; Gunasekaran, S.; Vijayalakshmi, M. A.

2017-01-01

Background: Diabetes mellitus is a metabolic disorder characterized by chronic hyperglycemia. Plant extracts and their products are being used as an alternative system of medicine for the treatment of diabetes. Aloe vera has been traditionally used to treat several diseases and it exhibits antioxidant, anti-inflammatory, and wound-healing effects. Streptozotocin (STZ)-induced Wistar diabetic rats were used in this study to understand the potential protective effect of A. vera extract on the pancreatic islets. Objective: The aim of the present study was to evaluate the A. vera extract on improvement of insulin secretion and pancreatic β-cell function by morphometric analysis of pancreatic islets in STZ-induced diabetic Wistar rats. Materials and Methods: After acclimatization, male Wistar rats, maintained as per the Committee for the Purpose of Control and Supervision of Experiments on Animals guidelines, were randomly divided into four groups of six rats each. Fasting plasma glucose and insulin levels were assessed. The effect of A. vera extract in STZ-induced diabetic rats on the pancreatic islets by morphometric analysis was evaluated. Results: Oral administration of A. vera extract (300 mg/kg) daily to diabetic rats for 3 weeks showed restoration of blood glucose levels to normal levels with a concomitant increase in insulin levels upon feeding with A. vera extract in STZ-induced diabetic rats. Morphometric analysis of pancreatic sections revealed quantitative and qualitative gain in terms of number, diameter, volume, and area of the pancreatic islets of diabetic rats treated with A. vera extract when compared to the untreated diabetic rats. Conclusion: A. vera extract exerts antidiabetic effects by improving insulin secretion and pancreatic β-cell function by restoring pancreatic islet mass in STZ-induced diabetic Wistar rats. SUMMARY Fasting plasma glucose (FPG) and insulin levels were restored to normal levels in diabetic rats treated with Aloe vera extractIslets of pancreas were qualitatively and quantitatively restored to normalcy leading to restoration of FPG and insulin levels of diabetic rats treated with Aloe vera extractMorphometric analysis of pancreatic sections revealed quantitative and qualitative gain in terms of number, diameter, volume, and area of the pancreatic islets of diabetic rats treated with Aloe vera extract when compared to the untreated diabetic rats. Abbreviations Used: A. vera, FPG: Fasting plasma glucose, STZ: Streptozotocin, BW: Body weight PMID:29333050

Proteomics analysis of human placenta reveals glutathione metabolism dysfunction as the underlying pathogenesis for preeclampsia.

PubMed

Jin, Xiaohan; Xu, Zhongwei; Cao, Jin; Shao, Ping; Zhou, Maobin; Qin, Zhe; Liu, Yan; Yu, Fang; Zhou, Xin; Ji, Wenjie; Cai, Wei; Ma, Yongqiang; Wang, Chengyan; Shan, Nana; Yang, Ning; Chen, Xu; Li, Yuming

2017-09-01

Hypertensive disorder in pregnancy (HDP) refers to a series of diseases that cause the hypertension during pregnancy, including HDP, preeclampsia (PE) and eclampsia. This study screens differentially expressed proteins of placenta tissues in PE cases using 2D LC-MS/MS quantitative proteomics strategy. A total of 2281 proteins are quantified, of these, 145 altering expression proteins are successfully screened between PE and control cases (p<0.05). Bioinformatics analysis suggests that these proteins are mainly involved in many biological processes, such as oxidation reduction, mitochondrion organization, and acute inflammatory response. Especially, the glutamine metabolic process related molecules, GPX1, GPX3, SMS, GGCT, GSTK1, NFκB, GSTT2, SOD1 and GCLM, are involved in the switching process from oxidized glutathione (GSSG) conversion to the reduced glutathione (GSH) by glutathione, mercapturic acid and arginine metabolism process. Results of this study revealed that glutathione metabolism disorder of placenta tissues may contribute to the occurrence of PE disease. Copyright © 2017. Published by Elsevier B.V.