Quantitative analyses and modelling to support achievement of the 2020 goals for nine neglected tropical diseases.

PubMed

Hollingsworth, T Déirdre; Adams, Emily R; Anderson, Roy M; Atkins, Katherine; Bartsch, Sarah; Basáñez, María-Gloria; Behrend, Matthew; Blok, David J; Chapman, Lloyd A C; Coffeng, Luc; Courtenay, Orin; Crump, Ron E; de Vlas, Sake J; Dobson, Andy; Dyson, Louise; Farkas, Hajnal; Galvani, Alison P; Gambhir, Manoj; Gurarie, David; Irvine, Michael A; Jervis, Sarah; Keeling, Matt J; Kelly-Hope, Louise; King, Charles; Lee, Bruce Y; Le Rutte, Epke A; Lietman, Thomas M; Ndeffo-Mbah, Martial; Medley, Graham F; Michael, Edwin; Pandey, Abhishek; Peterson, Jennifer K; Pinsent, Amy; Porco, Travis C; Richardus, Jan Hendrik; Reimer, Lisa; Rock, Kat S; Singh, Brajendra K; Stolk, Wilma; Swaminathan, Subramanian; Torr, Steve J; Townsend, Jeffrey; Truscott, James; Walker, Martin; Zoueva, Alexandra

2015-12-09

Quantitative analysis and mathematical models are useful tools in informing strategies to control or eliminate disease. Currently, there is an urgent need to develop these tools to inform policy to achieve the 2020 goals for neglected tropical diseases (NTDs). In this paper we give an overview of a collection of novel model-based analyses which aim to address key questions on the dynamics of transmission and control of nine NTDs: Chagas disease, visceral leishmaniasis, human African trypanosomiasis, leprosy, soil-transmitted helminths, schistosomiasis, lymphatic filariasis, onchocerciasis and trachoma. Several common themes resonate throughout these analyses, including: the importance of epidemiological setting on the success of interventions; targeting groups who are at highest risk of infection or re-infection; and reaching populations who are not accessing interventions and may act as a reservoir for infection,. The results also highlight the challenge of maintaining elimination 'as a public health problem' when true elimination is not reached. The models elucidate the factors that may be contributing most to persistence of disease and discuss the requirements for eventually achieving true elimination, if that is possible. Overall this collection presents new analyses to inform current control initiatives. These papers form a base from which further development of the models and more rigorous validation against a variety of datasets can help to give more detailed advice. At the moment, the models' predictions are being considered as the world prepares for a final push towards control or elimination of neglected tropical diseases by 2020.

Study Quality in SLA: An Assessment of Designs, Analyses, and Reporting Practices in Quantitative L2 Research

ERIC Educational Resources Information Center

Plonsky, Luke

2013-01-01

This study assesses research and reporting practices in quantitative second language (L2) research. A sample of 606 primary studies, published from 1990 to 2010 in "Language Learning and Studies in Second Language Acquisition," was collected and coded for designs, statistical analyses, reporting practices, and outcomes (i.e., effect…

Quantitative aspects of inductively coupled plasma mass spectrometry

PubMed Central

Wagner, Barbara

2016-01-01

Accurate determination of elements in various kinds of samples is essential for many areas, including environmental science, medicine, as well as industry. Inductively coupled plasma mass spectrometry (ICP-MS) is a powerful tool enabling multi-elemental analysis of numerous matrices with high sensitivity and good precision. Various calibration approaches can be used to perform accurate quantitative measurements by ICP-MS. They include the use of pure standards, matrix-matched standards, or relevant certified reference materials, assuring traceability of the reported results. This review critically evaluates the advantages and limitations of different calibration approaches, which are used in quantitative analyses by ICP-MS. Examples of such analyses are provided. This article is part of the themed issue ‘Quantitative mass spectrometry’. PMID:27644971

Stability Test and Quantitative and Qualitative Analyses of the Amino Acids in Pharmacopuncture Extracted from Scolopendra subspinipes mutilans

PubMed Central

Cho, GyeYoon; Han, KyuChul; Yoon, JinYoung

2015-01-01

Objectives: Scolopendra subspinipes mutilans (S. subspinipes mutilans) is known as a traditional medicine and includes various amino acids, peptides and proteins. The amino acids in the pharmacopuncture extracted from S. subspinipes mutilans by using derivatization methods were analyzed quantitatively and qualitatively by using high performance liquid chromatography (HPLC) over a 12 month period to confirm its stability. Methods: Amino acids of pharmacopuncture extracted from S. subspinipes mutilans were derived by using O-phthaldialdehyde (OPA) & 9-fluorenyl methoxy carbonyl chloride (FMOC) reagent and were analyzed using HPLC. The amino acids were detected by using a diode array detector (DAD) and a fluorescence detector (FLD) to compare a mixed amino acid standard (STD) to the pharmacopuncture from centipedes. The stability tests on the pharmacopuncture from centipedes were done using HPLC for three conditions: a room temperature test chamber, an acceleration test chamber, and a cold test chamber. Results: The pharmacopuncture from centipedes was prepared by using the method of the Korean Pharmacopuncture Institute (KPI) and through quantitative analyses was shown to contain 9 amino acids of the 16 amino acids in the mixed amino acid STD. The amounts of the amino acids in the pharmacopuncture from centipedes were 34.37 ppm of aspartate, 123.72 ppm of arginine, 170.63 ppm of alanine, 59.55 ppm of leucine and 57 ppm of lysine. The relative standard deviation (RSD %) results for the pharmacopuncture from centipedes had a maximum value of 14.95% and minimum value of 1.795% on the room temperature test chamber, the acceleration test chamber and the cold test chamber stability tests. Conclusion: Stability tests on and quantitative and qualitative analyses of the amino acids in the pharmacopuncture extracted from centipedes by using derivatization methods were performed by using HPLC. Through research, we hope to determine the relationship between time and the

Pulmonary nodule characterization, including computer analysis and quantitative features.

PubMed

Bartholmai, Brian J; Koo, Chi Wan; Johnson, Geoffrey B; White, Darin B; Raghunath, Sushravya M; Rajagopalan, Srinivasan; Moynagh, Michael R; Lindell, Rebecca M; Hartman, Thomas E

2015-03-01

Pulmonary nodules are commonly detected in computed tomography (CT) chest screening of a high-risk population. The specific visual or quantitative features on CT or other modalities can be used to characterize the likelihood that a nodule is benign or malignant. Visual features on CT such as size, attenuation, location, morphology, edge characteristics, and other distinctive "signs" can be highly suggestive of a specific diagnosis and, in general, be used to determine the probability that a specific nodule is benign or malignant. Change in size, attenuation, and morphology on serial follow-up CT, or features on other modalities such as nuclear medicine studies or MRI, can also contribute to the characterization of lung nodules. Imaging analytics can objectively and reproducibly quantify nodule features on CT, nuclear medicine, and magnetic resonance imaging. Some quantitative techniques show great promise in helping to differentiate benign from malignant lesions or to stratify the risk of aggressive versus indolent neoplasm. In this article, we (1) summarize the visual characteristics, descriptors, and signs that may be helpful in management of nodules identified on screening CT, (2) discuss current quantitative and multimodality techniques that aid in the differentiation of nodules, and (3) highlight the power, pitfalls, and limitations of these various techniques.

Qualitative and quantitative analyses of flavonoids in Spirodela polyrrhiza by high-performance liquid chromatography coupled with mass spectrometry.

PubMed

Qiao, Xue; He, Wen-ni; Xiang, Cheng; Han, Jian; Wu, Li-jun; Guo, De-an; Ye, Min

2011-01-01

Spirodela polyrrhiza (L.) Schleid. is a traditional Chinese herbal medicine for the treatment of influenza. Despite its wide use in Chinese medicine, no report on quality control of this herb is available so far. To establish qualitative and quantitative analytical methods by high-performance liquid chromatography (HPLC) coupled with mass spectrometry (MS) for the quality control of S. polyrrhiza. The methanol extract of S. polyrrhiza was analysed by HPLC/ESI-MS(n). Flavonoids were identified by comparing with reference standards or according to their MS(n) (n = 2-4) fragmentation behaviours. Based on LC/MS data, a standardised HPLC fingerprint was established by analysing 15 batches of commercial herbal samples. Furthermore, quantitative analysis was conducted by determining five major flavonoids, namely luteolin 8-C-glucoside, apigenin 8-C-glucoside, luteolin 7-O-glucoside, apigenin 7-O-glucoside and luteolin. A total of 18 flavonoids were identified by LC/MS, and 14 of them were reported from this herb for the first time. The HPLC fingerprints contained 10 common peaks, and could differentiate good quality batches from counterfeits. The total contents of five major flavonoids in S. polyrrhiza varied significantly from 4.28 to 19.87 mg/g. Qualitative LC/MS and quantitative HPLC analytical methods were established for the comprehensive quality control of S. polyrrhiza. Copyright © 2011 John Wiley & Sons, Ltd.

Quantitative Analyse und Visualisierung der Herzfunktionen

NASA Astrophysics Data System (ADS)

Sauer, Anne; Schwarz, Tobias; Engel, Nicole; Seitel, Mathias; Kenngott, Hannes; Mohrhardt, Carsten; Loßnitzer, Dirk; Giannitsis, Evangelos; Katus, Hugo A.; Meinzer, Hans-Peter

Die computergestützte bildbasierte Analyse der Herzfunktionen ist mittlerweile Standard in der Kardiologie. Die verfügbaren Produkte erfordern meist ein hohes Maß an Benutzerinteraktion und somit einen erhöhten Zeitaufwand. In dieser Arbeit wird ein Ansatz vorgestellt, der dem Kardiologen eine größtenteils automatische Analyse der Herzfunktionen mittels MRT-Bilddaten ermöglicht und damit Zeitersparnis schafft. Hierbei werden alle relevanten herzphysiologsichen Parameter berechnet und mithilfe von Diagrammen und Graphen visualisiert. Diese Berechnungen werden evaluiert, indem die ermittelten Werte mit manuell vermessenen verglichen werden. Der hierbei berechnete mittlere Fehler liegt mit 2,85 mm für die Wanddicke und 1,61 mm für die Wanddickenzunahme immer noch im Bereich einer Pixelgrösse der verwendeten Bilder.

A quantitative image cytometry technique for time series or population analyses of signaling networks.

PubMed

Ozaki, Yu-ichi; Uda, Shinsuke; Saito, Takeshi H; Chung, Jaehoon; Kubota, Hiroyuki; Kuroda, Shinya

2010-04-01

Modeling of cellular functions on the basis of experimental observation is increasingly common in the field of cellular signaling. However, such modeling requires a large amount of quantitative data of signaling events with high spatio-temporal resolution. A novel technique which allows us to obtain such data is needed for systems biology of cellular signaling. We developed a fully automatable assay technique, termed quantitative image cytometry (QIC), which integrates a quantitative immunostaining technique and a high precision image-processing algorithm for cell identification. With the aid of an automated sample preparation system, this device can quantify protein expression, phosphorylation and localization with subcellular resolution at one-minute intervals. The signaling activities quantified by the assay system showed good correlation with, as well as comparable reproducibility to, western blot analysis. Taking advantage of the high spatio-temporal resolution, we investigated the signaling dynamics of the ERK pathway in PC12 cells. The QIC technique appears as a highly quantitative and versatile technique, which can be a convenient replacement for the most conventional techniques including western blot, flow cytometry and live cell imaging. Thus, the QIC technique can be a powerful tool for investigating the systems biology of cellular signaling.

Improving Short Term Instability for Quantitative Analyses with Portable Electronic Noses

PubMed Central

Macías, Miguel Macías; Agudo, J. Enrique; Manso, Antonio García; Orellana, Carlos Javier García; Velasco, Horacio Manuel González; Caballero, Ramón Gallardo

2014-01-01

One of the main problems when working with electronic noses is the lack of reproducibility or repeatability of the sensor response, so that, if this problem is not properly considered, electronic noses can be useless, especially for quantitative analyses. On the other hand, irreproducibility is increased with portable and low cost electronic noses where laboratory equipment like gas zero generators cannot be used. In this work, we study the reproducibility of two portable electronic noses, the PEN3 (commercial) and CAPINose (a proprietary design) by using synthetic wine samples. We show that in both cases short term instability associated to the sensors' response to the same sample and under the same conditions represents a major problem and we propose an internal normalization technique that, in both cases, reduces the variability of the sensors' response. Finally, we show that the normalization proposed seems to be more effective in the CAPINose case, reducing, for example, the variability associated to the TGS2602 sensor from 12.19% to 2.2%. PMID:24932869

Quantitative and comparative liquid chromatography-electrospray ionization-mass spectrometry analyses of hydrogen sulfide and thiol metabolites derivaitized with 2-iodoacetanilide isotopologues.

PubMed

Lee, Der-Yen; Huang, Wei-Chieh; Gu, Ting-Jia; Chang, Geen-Dong

2018-06-01

Hydrogen sulfide (H 2 S), previously known as a toxic gas, is now recognized as a gasotransmitter along with nitric oxide and carbon monoxide. However, only few methods are available for quantitative determination of H 2 S in biological samples. 2-Iodoacetanilide (2-IAN), a thiol-reacting agent, has been used to tag the reduced cysteine residues of proteins for quantitative proteomics and for detection of cysteine oxidation modification. In this article, we proposed a new method for quantitative analyses of H 2 S and thiol metabolites using the procedure of pre-column 2-IAN derivatization coupled with liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS). 13 C 6 -Labeled and label-free 2-IAN efficiently react with H 2 S and thiol compounds at pH 9.5 and 65 °C. The derivatives exhibit excellent stability at alkaline conditions, high resolution on reverse phase liquid chromatography and great sensitivity for ESI-MS detection. The measurement of H 2 S, l-cysteine, glutathione, and DL-homocysteine derivatives was validated using 13 C 6 -labeled standard in LC-ESI-MS analyses and exhibited 10 nM-1 μM linear ranges for DL-homocysteine and glutathione and 1 nM-1 μM linear ranges for l-cysteine and H 2 S. In addition, the sequence of derivatization and extraction of metabolites is important in the quantification of thiol metabolites suggesting the presence of matrix effects. Most importantly, labeling with 2-IAN and 13 C 6 -2-IAN isotopologues could achieve quantitative and matched sample comparative analyses with minimal bias using our extraction and labeling procedures before LC-MS analysis. Copyright © 2018 Elsevier B.V. All rights reserved.

Transcriptomic and Quantitative Proteomic Analyses Provide Insights Into the Phagocytic Killing of Hemocytes in the Oyster Crassostrea gigas

PubMed Central

Jiang, Shuai; Qiu, Limei; Wang, Lingling; Jia, Zhihao; Lv, Zhao; Wang, Mengqiang; Liu, Conghui; Xu, Jiachao; Song, Linsheng

2018-01-01

As invertebrates lack an adaptive immune system, they depend to a large extent on their innate immune system to recognize and clear invading pathogens. Although phagocytes play pivotal roles in invertebrate innate immunity, the molecular mechanisms underlying this killing remain unclear. Cells of this type from the Pacific oyster Crassostrea gigas were classified efficiently in this study via fluorescence-activated cell sorting (FACS) based on their phagocytosis of FITC-labeled latex beads. Transcriptomic and quantitative proteomic analyses revealed a series of differentially expressed genes (DEGs) and proteins present in phagocytes; of the 352 significantly high expressed proteins identified here within the phagocyte proteome, 262 corresponding genes were similarly high expressed in the transcriptome, while 140 of 205 significantly low expressed proteins within the proteome were transcriptionally low expressed. A pathway crosstalk network analysis of these significantly high expressed proteins revealed that phagocytes were highly activated in a number of antimicrobial-related biological processes, including oxidation–reduction and lysosomal proteolysis processes. A number of DEGs, including oxidase, lysosomal protease, and immune receptors, were also validated in this study using quantitative PCR, while seven lysosomal cysteine proteases, referred to as cathepsin Ls, were significantly high expressed in phagocytes. Results show that the expression level of cathepsin L protein in phagocytes [mean fluorescence intensity (MFI): 327 ± 51] was significantly higher (p < 0.01) than that in non-phagocytic hemocytes (MFI: 83 ± 26), while the cathepsin L protein was colocalized with the phagocytosed Vibrio splendidus in oyster hemocytes during this process. The results of this study collectively suggest that oyster phagocytes possess both potent oxidative killing and microbial disintegration capacities; these findings provide important insights into hemocyte

Practicable methods for histological section thickness measurement in quantitative stereological analyses.

PubMed

Matenaers, Cyrill; Popper, Bastian; Rieger, Alexandra; Wanke, Rüdiger; Blutke, Andreas

2018-01-01

The accuracy of quantitative stereological analysis tools such as the (physical) disector method substantially depends on the precise determination of the thickness of the analyzed histological sections. One conventional method for measurement of histological section thickness is to re-embed the section of interest vertically to its original section plane. The section thickness is then measured in a subsequently prepared histological section of this orthogonally re-embedded sample. However, the orthogonal re-embedding (ORE) technique is quite work- and time-intensive and may produce inaccurate section thickness measurement values due to unintentional slightly oblique (non-orthogonal) positioning of the re-embedded sample-section. Here, an improved ORE method is presented, allowing for determination of the factual section plane angle of the re-embedded section, and correction of measured section thickness values for oblique (non-orthogonal) sectioning. For this, the analyzed section is mounted flat on a foil of known thickness (calibration foil) and both the section and the calibration foil are then vertically (re-)embedded. The section angle of the re-embedded section is then calculated from the deviation of the measured section thickness of the calibration foil and its factual thickness, using basic geometry. To find a practicable, fast, and accurate alternative to ORE, the suitability of spectral reflectance (SR) measurement for determination of plastic section thicknesses was evaluated. Using a commercially available optical reflectometer (F20, Filmetrics®, USA), the thicknesses of 0.5 μm thick semi-thin Epon (glycid ether)-sections and of 1-3 μm thick plastic sections (glycolmethacrylate/ methylmethacrylate, GMA/MMA), as regularly used in physical disector analyses, could precisely be measured within few seconds. Compared to the measured section thicknesses determined by ORE, SR measures displayed less than 1% deviation. Our results prove the applicability

Practicable methods for histological section thickness measurement in quantitative stereological analyses

PubMed Central

Matenaers, Cyrill; Popper, Bastian; Rieger, Alexandra; Wanke, Rüdiger

2018-01-01

The accuracy of quantitative stereological analysis tools such as the (physical) disector method substantially depends on the precise determination of the thickness of the analyzed histological sections. One conventional method for measurement of histological section thickness is to re-embed the section of interest vertically to its original section plane. The section thickness is then measured in a subsequently prepared histological section of this orthogonally re-embedded sample. However, the orthogonal re-embedding (ORE) technique is quite work- and time-intensive and may produce inaccurate section thickness measurement values due to unintentional slightly oblique (non-orthogonal) positioning of the re-embedded sample-section. Here, an improved ORE method is presented, allowing for determination of the factual section plane angle of the re-embedded section, and correction of measured section thickness values for oblique (non-orthogonal) sectioning. For this, the analyzed section is mounted flat on a foil of known thickness (calibration foil) and both the section and the calibration foil are then vertically (re-)embedded. The section angle of the re-embedded section is then calculated from the deviation of the measured section thickness of the calibration foil and its factual thickness, using basic geometry. To find a practicable, fast, and accurate alternative to ORE, the suitability of spectral reflectance (SR) measurement for determination of plastic section thicknesses was evaluated. Using a commercially available optical reflectometer (F20, Filmetrics®, USA), the thicknesses of 0.5 μm thick semi-thin Epon (glycid ether)-sections and of 1–3 μm thick plastic sections (glycolmethacrylate/ methylmethacrylate, GMA/MMA), as regularly used in physical disector analyses, could precisely be measured within few seconds. Compared to the measured section thicknesses determined by ORE, SR measures displayed less than 1% deviation. Our results prove the applicability

Grey literature in meta-analyses.

PubMed

Conn, Vicki S; Valentine, Jeffrey C; Cooper, Harris M; Rantz, Marilyn J

2003-01-01

In meta-analysis, researchers combine the results of individual studies to arrive at cumulative conclusions. Meta-analysts sometimes include "grey literature" in their evidential base, which includes unpublished studies and studies published outside widely available journals. Because grey literature is a source of data that might not employ peer review, critics have questioned the validity of its data and the results of meta-analyses that include it. To examine evidence regarding whether grey literature should be included in meta-analyses and strategies to manage grey literature in quantitative synthesis. This article reviews evidence on whether the results of studies published in peer-reviewed journals are representative of results from broader samplings of research on a topic as a rationale for inclusion of grey literature. Strategies to enhance access to grey literature are addressed. The most consistent and robust difference between published and grey literature is that published research is more likely to contain results that are statistically significant. Effect size estimates of published research are about one-third larger than those of unpublished studies. Unfunded and small sample studies are less likely to be published. Yet, importantly, methodological rigor does not differ between published and grey literature. Meta-analyses that exclude grey literature likely (a) over-represent studies with statistically significant findings, (b) inflate effect size estimates, and (c) provide less precise effect size estimates than meta-analyses including grey literature. Meta-analyses should include grey literature to fully reflect the existing evidential base and should assess the impact of methodological variations through moderator analysis.

Zebrafish Caudal Fin Angiogenesis Assay—Advanced Quantitative Assessment Including 3-Way Correlative Microscopy

PubMed Central

Correa Shokiche, Carlos; Schaad, Laura; Triet, Ramona; Jazwinska, Anna; Tschanz, Stefan A.; Djonov, Valentin

2016-01-01

Background Researchers evaluating angiomodulating compounds as a part of scientific projects or pre-clinical studies are often confronted with limitations of applied animal models. The rough and insufficient early-stage compound assessment without reliable quantification of the vascular response counts, at least partially, to the low transition rate to clinics. Objective To establish an advanced, rapid and cost-effective angiogenesis assay for the precise and sensitive assessment of angiomodulating compounds using zebrafish caudal fin regeneration. It should provide information regarding the angiogenic mechanisms involved and should include qualitative and quantitative data of drug effects in a non-biased and time-efficient way. Approach & Results Basic vascular parameters (total regenerated area, vascular projection area, contour length, vessel area density) were extracted from in vivo fluorescence microscopy images using a stereological approach. Skeletonization of the vasculature by our custom-made software Skelios provided additional parameters including “graph energy” and “distance to farthest node”. The latter gave important insights into the complexity, connectivity and maturation status of the regenerating vascular network. The employment of a reference point (vascular parameters prior amputation) is unique for the model and crucial for a proper assessment. Additionally, the assay provides exceptional possibilities for correlative microscopy by combining in vivo-imaging and morphological investigation of the area of interest. The 3-way correlative microscopy links the dynamic changes in vivo with their structural substrate at the subcellular level. Conclusions The improved zebrafish fin regeneration model with advanced quantitative analysis and optional 3-way correlative morphology is a promising in vivo angiogenesis assay, well-suitable for basic research and preclinical investigations. PMID:26950851

Quantitative three-dimensional microtextural analyses of tooth wear as a tool for dietary discrimination in fishes

PubMed Central

Purnell, Mark; Seehausen, Ole; Galis, Frietson

2012-01-01

Resource polymorphisms and competition for resources are significant factors in speciation. Many examples come from fishes, and cichlids are of particular importance because of their role as model organisms at the interface of ecology, development, genetics and evolution. However, analysis of trophic resource use in fishes can be difficult and time-consuming, and for fossil fish species it is particularly problematic. Here, we present evidence from cichlids that analysis of tooth microwear based on high-resolution (sub-micrometre scale) three-dimensional data and new ISO standards for quantification of surface textures provides a powerful tool for dietary discrimination and investigation of trophic resource exploitation. Our results suggest that three-dimensional approaches to analysis offer significant advantages over two-dimensional operator-scored methods of microwear analysis, including applicability to rough tooth surfaces that lack distinct scratches and pits. Tooth microwear textures develop over a longer period of time than is represented by stomach contents, and analyses based on textures are less prone to biases introduced by opportunistic feeding. They are more sensitive to subtle dietary differences than isotopic analysis. Quantitative textural analysis of tooth microwear has a useful role to play, complementing existing approaches, in trophic analysis of fishes—both extant and extinct. PMID:22491979

Quantitative measures for redox signaling.

PubMed

Pillay, Ché S; Eagling, Beatrice D; Driscoll, Scott R E; Rohwer, Johann M

2016-07-01

Redox signaling is now recognized as an important regulatory mechanism for a number of cellular processes including the antioxidant response, phosphokinase signal transduction and redox metabolism. While there has been considerable progress in identifying the cellular machinery involved in redox signaling, quantitative measures of redox signals have been lacking, limiting efforts aimed at understanding and comparing redox signaling under normoxic and pathogenic conditions. Here we have outlined some of the accepted principles for redox signaling, including the description of hydrogen peroxide as a signaling molecule and the role of kinetics in conferring specificity to these signaling events. Based on these principles, we then develop a working definition for redox signaling and review a number of quantitative methods that have been employed to describe signaling in other systems. Using computational modeling and published data, we show how time- and concentration- dependent analyses, in particular, could be used to quantitatively describe redox signaling and therefore provide important insights into the functional organization of redox networks. Finally, we consider some of the key challenges with implementing these methods. Copyright © 2016 Elsevier Inc. All rights reserved.

Shedding quantitative fluorescence light on novel regulatory mechanisms in skeletal biomedicine and biodentistry.

PubMed

Lee, Ji-Won; Iimura, Tadahiro

2017-02-01

Digitalized fluorescence images contain numerical information such as color (wavelength), fluorescence intensity and spatial position. However, quantitative analyses of acquired data and their validation remained to be established. Our research group has applied quantitative fluorescence imaging on tissue sections and uncovered novel findings in skeletal biomedicine and biodentistry. This review paper includes a brief background of quantitative fluorescence imaging and discusses practical applications by introducing our previous research. Finally, the future perspectives of quantitative fluorescence imaging are discussed.

Cloning, characterisation, and comparative quantitative expression analyses of receptor for advanced glycation end products (RAGE) transcript forms.

PubMed

Sterenczak, Katharina A; Willenbrock, Saskia; Barann, Matthias; Klemke, Markus; Soller, Jan T; Eberle, Nina; Nolte, Ingo; Bullerdiek, Jörn; Murua Escobar, Hugo

2009-04-01

RAGE is a member of the immunoglobulin superfamily of cell surface molecules playing key roles in pathophysiological processes, e.g. immune/inflammatory disorders, Alzheimer's disease, diabetic arteriosclerosis and tumourigenesis. In humans 19 naturally occurring RAGE splicing variants resulting in either N-terminally or C-terminally truncated proteins were identified and are lately discussed as mechanisms for receptor regulation. Accordingly, deregulation of sRAGE levels has been associated with several diseases e.g. Alzheimer's disease, Type 1 diabetes, and rheumatoid arthritis. Administration of recombinant sRAGE to animal models of cancer blocked tumour growth successfully. In spite of its obvious relationship to cancer and metastasis data focusing sRAGE deregulation and tumours is rare. In this study we screened a set of tumours, healthy tissues and various cancer cell lines for RAGE splicing variants and analysed their structure. Additionally, we analysed the ratio of the mainly found transcript variants using quantitative Real-Time PCR. In total we characterised 24 previously not described canine and 4 human RAGE splicing variants, analysed their structure, classified their characteristics, and derived their respective protein forms. Interestingly, the healthy and the neoplastic tissue samples showed in majority RAGE transcripts coding for the complete receptor and transcripts showing insertions of intron 1.

Underutilisation of routinely collected data in the HIV programme in Zambia: a review of quantitatively analysed peer-reviewed articles.

PubMed

Munthali, Tendai; Musonda, Patrick; Mee, Paul; Gumede, Sehlulekile; Schaap, Ab; Mwinga, Alwyn; Phiri, Caroline; Kapata, Nathan; Michelo, Charles; Todd, Jim

2017-06-13

The extent to which routinely collected HIV data from Zambia has been used in peer-reviewed published articles remains unexplored. This paper is an analysis of peer-reviewed articles that utilised routinely collected HIV data from Zambia within six programme areas from 2004 to 2014. Articles on HIV, published in English, listed in the Directory of open access journals, African Journals Online, Google scholar, and PubMed were reviewed. Only articles from peer-reviewed journals, that utilised routinely collected data and included quantitative data analysis methods were included. Multi-country studies involving Zambia and another country, where the specific results for Zambia were not reported, as well as clinical trials and intervention studies that did not take place under routine care conditions were excluded, although community trials which referred patients to the routine clinics were included. Independent extraction was conducted using a predesigned data collection form. Pooled analysis was not possible due to diversity in topics reviewed. A total of 69 articles were extracted for review. Of these, 7 were excluded. From the 62 articles reviewed, 39 focused on HIV treatment and retention in care, 15 addressed prevention of mother-to-child transmission, 4 assessed social behavioural change, and 4 reported on voluntary counselling and testing. In our search, no articles were found on condom programming or voluntary male medical circumcision. The most common outcome measures reported were CD4+ count, clinical failure or mortality. The population analysed was children in 13 articles, women in 16 articles, and both adult men and women in 33 articles. During the 10 year period of review, only 62 articles were published analysing routinely collected HIV data in Zambia. Serious consideration needs to be made to maximise the utility of routinely collected data, and to benefit from the funds and efforts to collect these data. This could be achieved with government support

Quantitative DNA Methylation Profiling in Cancer.

PubMed

Ammerpohl, Ole; Haake, Andrea; Kolarova, Julia; Siebert, Reiner

2016-01-01

Epigenetic mechanisms including DNA methylation are fundamental for the regulation of gene expression. Epigenetic alterations can lead to the development and the evolution of malignant tumors as well as the emergence of phenotypically different cancer cells or metastasis from one single tumor cell. Here we describe bisulfite pyrosequencing, a technology to perform quantitative DNA methylation analyses, to detect aberrant DNA methylation in malignant tumors.

QTest: Quantitative Testing of Theories of Binary Choice.

PubMed

Regenwetter, Michel; Davis-Stober, Clintin P; Lim, Shiau Hong; Guo, Ying; Popova, Anna; Zwilling, Chris; Cha, Yun-Shil; Messner, William

2014-01-01

The goal of this paper is to make modeling and quantitative testing accessible to behavioral decision researchers interested in substantive questions. We provide a novel, rigorous, yet very general, quantitative diagnostic framework for testing theories of binary choice. This permits the nontechnical scholar to proceed far beyond traditionally rather superficial methods of analysis, and it permits the quantitatively savvy scholar to triage theoretical proposals before investing effort into complex and specialized quantitative analyses. Our theoretical framework links static algebraic decision theory with observed variability in behavioral binary choice data. The paper is supplemented with a custom-designed public-domain statistical analysis package, the QTest software. We illustrate our approach with a quantitative analysis using published laboratory data, including tests of novel versions of "Random Cumulative Prospect Theory." A major asset of the approach is the potential to distinguish decision makers who have a fixed preference and commit errors in observed choices from decision makers who waver in their preferences.

QTest: Quantitative Testing of Theories of Binary Choice

PubMed Central

Regenwetter, Michel; Davis-Stober, Clintin P.; Lim, Shiau Hong; Guo, Ying; Popova, Anna; Zwilling, Chris; Cha, Yun-Shil; Messner, William

2014-01-01

The goal of this paper is to make modeling and quantitative testing accessible to behavioral decision researchers interested in substantive questions. We provide a novel, rigorous, yet very general, quantitative diagnostic framework for testing theories of binary choice. This permits the nontechnical scholar to proceed far beyond traditionally rather superficial methods of analysis, and it permits the quantitatively savvy scholar to triage theoretical proposals before investing effort into complex and specialized quantitative analyses. Our theoretical framework links static algebraic decision theory with observed variability in behavioral binary choice data. The paper is supplemented with a custom-designed public-domain statistical analysis package, the QTest software. We illustrate our approach with a quantitative analysis using published laboratory data, including tests of novel versions of “Random Cumulative Prospect Theory.” A major asset of the approach is the potential to distinguish decision makers who have a fixed preference and commit errors in observed choices from decision makers who waver in their preferences. PMID:24999495

Quantitative Residual Strain Analyses on Strain Hardened Nickel Based Alloy

NASA Astrophysics Data System (ADS)

Yonezawa, Toshio; Maeguchi, Takaharu; Goto, Toru; Juan, Hou

Many papers have reported about the effects of strain hardening by cold rolling, grinding, welding, etc. on stress corrosion cracking susceptibility of nickel based alloys and austenitic stainless steels for LWR pipings and components. But, the residual strain value due to cold rolling, grinding, welding, etc. is not so quantitatively evaluated.

A bottom-up approach in estimating the measurement uncertainty and other important considerations for quantitative analyses in drug testing for horses.

PubMed

Leung, Gary N W; Ho, Emmie N M; Kwok, W Him; Leung, David K K; Tang, Francis P W; Wan, Terence S M; Wong, April S Y; Wong, Colton H F; Wong, Jenny K Y; Yu, Nola H

2007-09-07

Quantitative determination, particularly for threshold substances in biological samples, is much more demanding than qualitative identification. A proper assessment of any quantitative determination is the measurement uncertainty (MU) associated with the determined value. The International Standard ISO/IEC 17025, "General requirements for the competence of testing and calibration laboratories", has more prescriptive requirements on the MU than its superseded document, ISO/IEC Guide 25. Under the 2005 or 1999 versions of the new standard, an estimation of the MU is mandatory for all quantitative determinations. To comply with the new requirement, a protocol was established in the authors' laboratory in 2001. The protocol has since evolved based on our practical experience, and a refined version was adopted in 2004. This paper describes our approach in establishing the MU, as well as some other important considerations, for the quantification of threshold substances in biological samples as applied in the area of doping control for horses. The testing of threshold substances can be viewed as a compliance test (or testing to a specified limit). As such, it should only be necessary to establish the MU at the threshold level. The steps in a "Bottom-Up" approach adopted by us are similar to those described in the EURACHEM/CITAC guide, "Quantifying Uncertainty in Analytical Measurement". They involve first specifying the measurand, including the relationship between the measurand and the input quantities upon which it depends. This is followed by identifying all applicable uncertainty contributions using a "cause and effect" diagram. The magnitude of each uncertainty component is then calculated and converted to a standard uncertainty. A recovery study is also conducted to determine if the method bias is significant and whether a recovery (or correction) factor needs to be applied. All standard uncertainties with values greater than 30% of the largest one are then used to

Targeted Quantitation of Proteins by Mass Spectrometry

PubMed Central

2013-01-01

Quantitative measurement of proteins is one of the most fundamental analytical tasks in a biochemistry laboratory, but widely used immunochemical methods often have limited specificity and high measurement variation. In this review, we discuss applications of multiple-reaction monitoring (MRM) mass spectrometry, which allows sensitive, precise quantitative analyses of peptides and the proteins from which they are derived. Systematic development of MRM assays is permitted by databases of peptide mass spectra and sequences, software tools for analysis design and data analysis, and rapid evolution of tandem mass spectrometer technology. Key advantages of MRM assays are the ability to target specific peptide sequences, including variants and modified forms, and the capacity for multiplexing that allows analysis of dozens to hundreds of peptides. Different quantitative standardization methods provide options that balance precision, sensitivity, and assay cost. Targeted protein quantitation by MRM and related mass spectrometry methods can advance biochemistry by transforming approaches to protein measurement. PMID:23517332

Targeted quantitation of proteins by mass spectrometry.

PubMed

Liebler, Daniel C; Zimmerman, Lisa J

2013-06-04

Quantitative measurement of proteins is one of the most fundamental analytical tasks in a biochemistry laboratory, but widely used immunochemical methods often have limited specificity and high measurement variation. In this review, we discuss applications of multiple-reaction monitoring (MRM) mass spectrometry, which allows sensitive, precise quantitative analyses of peptides and the proteins from which they are derived. Systematic development of MRM assays is permitted by databases of peptide mass spectra and sequences, software tools for analysis design and data analysis, and rapid evolution of tandem mass spectrometer technology. Key advantages of MRM assays are the ability to target specific peptide sequences, including variants and modified forms, and the capacity for multiplexing that allows analysis of dozens to hundreds of peptides. Different quantitative standardization methods provide options that balance precision, sensitivity, and assay cost. Targeted protein quantitation by MRM and related mass spectrometry methods can advance biochemistry by transforming approaches to protein measurement.

Quantitative research.

PubMed

Watson, Roger

2015-04-01

This article describes the basic tenets of quantitative research. The concepts of dependent and independent variables are addressed and the concept of measurement and its associated issues, such as error, reliability and validity, are explored. Experiments and surveys – the principal research designs in quantitative research – are described and key features explained. The importance of the double-blind randomised controlled trial is emphasised, alongside the importance of longitudinal surveys, as opposed to cross-sectional surveys. Essential features of data storage are covered, with an emphasis on safe, anonymous storage. Finally, the article explores the analysis of quantitative data, considering what may be analysed and the main uses of statistics in analysis.

Using Qualitative Metasummary to Synthesize Qualitative and Quantitative Descriptive Findings

PubMed Central

Sandelowski, Margarete; Barroso, Julie; Voils, Corrine I.

2008-01-01

The new imperative in the health disciplines to be more methodologically inclusive has generated a growing interest in mixed research synthesis, or the integration of qualitative and quantitative research findings. Qualitative metasummary is a quantitatively oriented aggregation of qualitative findings originally developed to accommodate the distinctive features of qualitative surveys. Yet these findings are similar in form and mode of production to the descriptive findings researchers often present in addition to the results of bivariate and multivariable analyses. Qualitative metasummary, which includes the extraction, grouping, and formatting of findings, and the calculation of frequency and intensity effect sizes, can be used to produce mixed research syntheses and to conduct a posteriori analyses of the relationship between reports and findings. PMID:17243111

Analyses and descriptions of geochemical samples from the Rich Mountain Roadless Area, Fannin and Gilmer counties, Georgia

USGS Publications Warehouse

Sears, C.M.; Foose, M.P.; Day, G.W.; Ericksen, M.S.

1983-01-01

Semi-quantitative spectrographic analyses for 31 elements on rock, soil, fine-grained stream sediment, bulk stream sediment, and panned stream sediment samples collected in the Rich Mountain Roadless Area, Fannin and Gilmer Counties, Georgia, are reported here. Atomic absorption analyses for gold and fluorometric analyses for uranium are also reported. Brief descriptions of all rock samples analyzed are included.

Multiplexed and Microparticle-based Analyses: Quantitative Tools for the Large-Scale Analysis of Biological Systems

PubMed Central

Nolan, John P.; Mandy, Francis

2008-01-01

While the term flow cytometry refers to the measurement of cells, the approach of making sensitive multiparameter optical measurements in a flowing sample stream is a very general analytical approach. The past few years have seen an explosion in the application of flow cytometry technology for molecular analysis and measurements using micro-particles as solid supports. While microsphere-based molecular analyses using flow cytometry date back three decades, the need for highly parallel quantitative molecular measurements that has arisen from various genomic and proteomic advances has driven the development in particle encoding technology to enable highly multiplexed assays. Multiplexed particle-based immunoassays are now common place, and new assays to study genes, protein function, and molecular assembly. Numerous efforts are underway to extend the multiplexing capabilities of microparticle-based assays through new approaches to particle encoding and analyte reporting. The impact of these developments will be seen in the basic research and clinical laboratories, as well as in drug development. PMID:16604537

Dynamic Analyses Including Joints Of Truss Structures

NASA Technical Reports Server (NTRS)

Belvin, W. Keith

1991-01-01

Method for mathematically modeling joints to assess influences of joints on dynamic response of truss structures developed in study. Only structures with low-frequency oscillations considered; only Coulomb friction and viscous damping included in analysis. Focus of effort to obtain finite-element mathematical models of joints exhibiting load-vs.-deflection behavior similar to measured load-vs.-deflection behavior of real joints. Experiments performed to determine stiffness and damping nonlinearities typical of joint hardware. Algorithm for computing coefficients of analytical joint models based on test data developed to enable study of linear and nonlinear effects of joints on global structural response. Besides intended application to large space structures, applications in nonaerospace community include ground-based antennas and earthquake-resistant steel-framed buildings.

Combined metabonomic and quantitative real-time PCR analyses reveal systems metabolic changes in Jurkat T-cells treated with HIV-1 Tat protein.

PubMed

Liao, Wenting; Tan, Guangguo; Zhu, Zhenyu; Chen, Qiuli; Lou, Ziyang; Dong, Xin; Zhang, Wei; Pan, Wei; Chai, Yifeng

2012-11-02

HIV-1 Tat protein is released by infected cells and can affect bystander uninfected T cells and induce numerous biological responses which contribute to its pathogenesis. To elucidate the complex pathogenic mechanism, we conducted a comprehensive investigation on Tat protein-related extracellular and intracellular metabolic changes in Jurkat T-cells using combined gas chromatography-mass spectrometry (GC-MS), reversed-phase liquid chromatography-mass spectrometry (RPLC-MS) and a hydrophilic interaction liquid chromatography-mass spectrometry (HILIC-MS)-based metabonomics approach. Quantitative real-time PCR (qRT-PCR) analyses were further employed to measure expressions of several relevant enzymes together with perturbed metabolic pathways. Combined metabonomic and qRT-PCR analyses revealed that HIV-1 Tat caused significant and comprehensive metabolic changes, as represented by significant changes of 37 metabolites and 10 relevant enzymes in HIV-1 Tat-treated cells. Using MetaboAnalyst 2.0, it was found that 11 pathways (Impact-value >0.10) among the regulated pathways were acutely perturbed, including sphingolipid metabolism, glycine, serine and threonine metabolism, pyruvate metabolism, inositol phosphate metabolism, arginine and proline metabolism, citrate cycle, phenylalanine metabolism, tryptophan metabolism, pentose phosphate pathway, glycerophospholipid metabolism, glycolysis or gluconeogenesis. These results provide metabolic evidence of the complex pathogenic mechanism of HIV-1 Tat protein as a "viral toxin", and would help obligate Tat protein as "an important target" for therapeutic intervention and vaccine development.

Quantitative genetics

USDA-ARS?s Scientific Manuscript database

The majority of economically important traits targeted for cotton improvement are quantitatively inherited. In this chapter, the current state of cotton quantitative genetics is described and separated into four components. These components include: 1) traditional quantitative inheritance analysis, ...

Sensitivity analyses of exposure estimates from a quantitative job-exposure matrix (SYN-JEM) for use in community-based studies.

PubMed

Peters, Susan; Kromhout, Hans; Portengen, Lützen; Olsson, Ann; Kendzia, Benjamin; Vincent, Raymond; Savary, Barbara; Lavoué, Jérôme; Cavallo, Domenico; Cattaneo, Andrea; Mirabelli, Dario; Plato, Nils; Fevotte, Joelle; Pesch, Beate; Brüning, Thomas; Straif, Kurt; Vermeulen, Roel

2013-01-01

We describe the elaboration and sensitivity analyses of a quantitative job-exposure matrix (SYN-JEM) for respirable crystalline silica (RCS). The aim was to gain insight into the robustness of the SYN-JEM RCS estimates based on critical decisions taken in the elaboration process. SYN-JEM for RCS exposure consists of three axes (job, region, and year) based on estimates derived from a previously developed statistical model. To elaborate SYN-JEM, several decisions were taken: i.e. the application of (i) a single time trend; (ii) region-specific adjustments in RCS exposure; and (iii) a prior job-specific exposure level (by the semi-quantitative DOM-JEM), with an override of 0 mg/m(3) for jobs a priori defined as non-exposed. Furthermore, we assumed that exposure levels reached a ceiling in 1960 and remained constant prior to this date. We applied SYN-JEM to the occupational histories of subjects from a large international pooled community-based case-control study. Cumulative exposure levels derived with SYN-JEM were compared with those from alternative models, described by Pearson correlation ((Rp)) and differences in unit of exposure (mg/m(3)-year). Alternative models concerned changes in application of job- and region-specific estimates and exposure ceiling, and omitting the a priori exposure ranking. Cumulative exposure levels for the study subjects ranged from 0.01 to 60 mg/m(3)-years, with a median of 1.76 mg/m(3)-years. Exposure levels derived from SYN-JEM and alternative models were overall highly correlated (R(p) > 0.90), although somewhat lower when omitting the region estimate ((Rp) = 0.80) or not taking into account the assigned semi-quantitative exposure level (R(p) = 0.65). Modification of the time trend (i.e. exposure ceiling at 1950 or 1970, or assuming a decline before 1960) caused the largest changes in absolute exposure levels (26-33% difference), but without changing the relative ranking ((Rp) = 0.99). Exposure estimates derived from SYN

Effects of detector dead-time on quantitative analyses involving boron and multi-hit detection events in atom probe tomography.

PubMed

Meisenkothen, Frederick; Steel, Eric B; Prosa, Ty J; Henry, Karen T; Prakash Kolli, R

2015-12-01

In atom probe tomography (APT), some elements tend to field evaporate preferentially in multi-hit detection events. Boron (B) is one such element. It is thought that a large fraction of the B signal may be lost during data acquisition and is not reported in the mass spectrum or in the 3-D APT reconstruction. Understanding the relationship between the field evaporation behavior of B and the limitations for detecting multi-hit events can provide insight into the signal loss mechanism for B and may suggest ways to improve B detection accuracy. The present work reports data for nominally pure B and for B-implanted silicon (Si) (NIST-SRM2137) at dose levels two-orders of magnitude lower than previously studied by Da Costa, et al. in 2012. Boron concentration profiles collected from SRM2137 specimens qualitatively confirmed a signal loss mechanism is at work in laser pulsed atom probe measurements of B in Si. Ion correlation analysis was used to graphically demonstrate that the detector dead-time results in few same isotope, same charge-state (SISCS) ion pairs being properly recorded in the multi-hit data, explaining why B is consistently under-represented in quantitative analyses. Given the important role of detector dead-time as a signal loss mechanism, the results from three different methods of estimating the detector dead-time are presented. The findings of this study apply to all quantitative analyses that involve multi-hit data, but the dead-time will have the greatest effect on the elements that have a significant quantity of ions detected in multi-hit events. Published by Elsevier B.V.

A new high-resolution 3-D quantitative method for analysing small morphological features: an example using a Cambrian trilobite.

PubMed

Esteve, Jorge; Zhao, Yuan-Long; Maté-González, Miguel Ángel; Gómez-Heras, Miguel; Peng, Jin

2018-02-12

Taphonomic processes play an important role in the preservation of small morphological features such as granulation or pits. However, the assessment of these features may face the issue of the small size of the specimens and, sometimes, the destructiveness of these analyses, which makes impossible carrying them out in singular specimen, such as holotypes or lectotypes. This paper takes a new approach to analysing small-morphological features, by using an optical surface roughness (OSR) meter to create a high-resolution three-dimensional digital-elevation model (DEM). This non-destructive technique allows analysing quantitatively the DEM using geometric morphometric methods (GMM). We created a number of DEMs from three populations putatively belonging to the same species of trilobite (Oryctocephalus indicus) that present the same cranidial outline, but differ in the presence or absence of the second and third transglabellar furrows. Profile analysis of the DEMs demonstrate that all three populations show similar preservation variation in the glabellar furrows and lobes. The GMM shows that all populations exhibit the same range of variation. Differences in preservation are a consequence of different degrees of cementation and rates of dissolution. Fast cementation enhances the preservation of glabellar furrows and lobes, while fast dissolution hampers preservation of the same structures.

Performing statistical analyses on quantitative data in Taverna workflows: an example using R and maxdBrowse to identify differentially-expressed genes from microarray data.

PubMed

Li, Peter; Castrillo, Juan I; Velarde, Giles; Wassink, Ingo; Soiland-Reyes, Stian; Owen, Stuart; Withers, David; Oinn, Tom; Pocock, Matthew R; Goble, Carole A; Oliver, Stephen G; Kell, Douglas B

2008-08-07

There has been a dramatic increase in the amount of quantitative data derived from the measurement of changes at different levels of biological complexity during the post-genomic era. However, there are a number of issues associated with the use of computational tools employed for the analysis of such data. For example, computational tools such as R and MATLAB require prior knowledge of their programming languages in order to implement statistical analyses on data. Combining two or more tools in an analysis may also be problematic since data may have to be manually copied and pasted between separate user interfaces for each tool. Furthermore, this transfer of data may require a reconciliation step in order for there to be interoperability between computational tools. Developments in the Taverna workflow system have enabled pipelines to be constructed and enacted for generic and ad hoc analyses of quantitative data. Here, we present an example of such a workflow involving the statistical identification of differentially-expressed genes from microarray data followed by the annotation of their relationships to cellular processes. This workflow makes use of customised maxdBrowse web services, a system that allows Taverna to query and retrieve gene expression data from the maxdLoad2 microarray database. These data are then analysed by R to identify differentially-expressed genes using the Taverna RShell processor which has been developed for invoking this tool when it has been deployed as a service using the RServe library. In addition, the workflow uses Beanshell scripts to reconcile mismatches of data between services as well as to implement a form of user interaction for selecting subsets of microarray data for analysis as part of the workflow execution. A new plugin system in the Taverna software architecture is demonstrated by the use of renderers for displaying PDF files and CSV formatted data within the Taverna workbench. Taverna can be used by data analysis

Performing statistical analyses on quantitative data in Taverna workflows: An example using R and maxdBrowse to identify differentially-expressed genes from microarray data

PubMed Central

Li, Peter; Castrillo, Juan I; Velarde, Giles; Wassink, Ingo; Soiland-Reyes, Stian; Owen, Stuart; Withers, David; Oinn, Tom; Pocock, Matthew R; Goble, Carole A; Oliver, Stephen G; Kell, Douglas B

2008-01-01

Background There has been a dramatic increase in the amount of quantitative data derived from the measurement of changes at different levels of biological complexity during the post-genomic era. However, there are a number of issues associated with the use of computational tools employed for the analysis of such data. For example, computational tools such as R and MATLAB require prior knowledge of their programming languages in order to implement statistical analyses on data. Combining two or more tools in an analysis may also be problematic since data may have to be manually copied and pasted between separate user interfaces for each tool. Furthermore, this transfer of data may require a reconciliation step in order for there to be interoperability between computational tools. Results Developments in the Taverna workflow system have enabled pipelines to be constructed and enacted for generic and ad hoc analyses of quantitative data. Here, we present an example of such a workflow involving the statistical identification of differentially-expressed genes from microarray data followed by the annotation of their relationships to cellular processes. This workflow makes use of customised maxdBrowse web services, a system that allows Taverna to query and retrieve gene expression data from the maxdLoad2 microarray database. These data are then analysed by R to identify differentially-expressed genes using the Taverna RShell processor which has been developed for invoking this tool when it has been deployed as a service using the RServe library. In addition, the workflow uses Beanshell scripts to reconcile mismatches of data between services as well as to implement a form of user interaction for selecting subsets of microarray data for analysis as part of the workflow execution. A new plugin system in the Taverna software architecture is demonstrated by the use of renderers for displaying PDF files and CSV formatted data within the Taverna workbench. Conclusion Taverna can

Quantitative and qualitative analyses of subacromial impingement by kinematic open MRI.

PubMed

Tasaki, Atsushi; Nimura, Akimoto; Nozaki, Taiki; Yamakawa, Akira; Niitsu, Mamoru; Morita, Wataru; Hoshikawa, Yoshimitsu; Akita, Keiichi

2015-05-01

Quantitative and qualitative kinematic analyses of subacromial impingement by 1.2T open MRI were performed to determine the location of impingement and the involvement of the acromioclavicular joint. In 20 healthy shoulders, 10 sequential images in the scapular plane were taken in a 10-s pause at equal intervals from 30° to maximum abduction in neutral and internal rotation. The distances between the rotator cuff (RC) and the acromion and the acromioclavicular joint were measured. To comprehend the positional relationships, cadaveric specimens were also observed. Although asymptomatic, the RC came into contact with the acromion and the acromioclavicular joint in six and five cases, respectively. The superior RC acted as a depressor for the humeral head against the acromion as the shoulder elevated. The mean elevation angle and distance at the closest position between the RC and the acromion in neutral rotation were 93.5° and 1.6 mm, respectively, while those between the RC and the acromioclavicular joint were 86.7° and 2.0 mm. When comparing this distance and angle, there was no significant difference between the RC to the acromion and to the acromioclavicular joint. The minimum distance between the RC and the acromion was significantly shorter than that between the greater tuberosity and the acromion. The location of RC closest to the acromion and the acromioclavicular joint differed significantly. Although asymptomatic, contact was found between the RC and the acromion and the acromioclavicular joint. The important role of the RC to prevent impingement was observed, and hence, dysfunction of the RC could lead to impingement that could result in a RC lesion. The RC lesions may differ when they are caused by impingement from either the acromion or the acromioclavicular joint.

The APOSTEL recommendations for reporting quantitative optical coherence tomography studies.

PubMed

Cruz-Herranz, Andrés; Balk, Lisanne J; Oberwahrenbrock, Timm; Saidha, Shiv; Martinez-Lapiscina, Elena H; Lagreze, Wolf A; Schuman, Joel S; Villoslada, Pablo; Calabresi, Peter; Balcer, Laura; Petzold, Axel; Green, Ari J; Paul, Friedemann; Brandt, Alexander U; Albrecht, Philipp

2016-06-14

To develop consensus recommendations for reporting of quantitative optical coherence tomography (OCT) study results. A panel of experienced OCT researchers (including 11 neurologists, 2 ophthalmologists, and 2 neuroscientists) discussed requirements for performing and reporting quantitative analyses of retinal morphology and developed a list of initial recommendations based on experience and previous studies. The list of recommendations was subsequently revised during several meetings of the coordinating group. We provide a 9-point checklist encompassing aspects deemed relevant when reporting quantitative OCT studies. The areas covered are study protocol, acquisition device, acquisition settings, scanning protocol, funduscopic imaging, postacquisition data selection, postacquisition data analysis, recommended nomenclature, and statistical analysis. The Advised Protocol for OCT Study Terminology and Elements recommendations include core items to standardize and improve quality of reporting in quantitative OCT studies. The recommendations will make reporting of quantitative OCT studies more consistent and in line with existing standards for reporting research in other biomedical areas. The recommendations originated from expert consensus and thus represent Class IV evidence. They will need to be regularly adjusted according to new insights and practices. © 2016 American Academy of Neurology.

Quantitative characterization of colloidal assembly of graphene oxide-silver nanoparticle hybrids using aerosol differential mobility-coupled mass analyses.

PubMed

Nguyen, Thai Phuong; Chang, Wei-Chang; Lai, Yen-Chih; Hsiao, Ta-Chih; Tsai, De-Hao

2017-10-01

In this work, we develop an aerosol-based, time-resolved ion mobility-coupled mass characterization method to investigate colloidal assembly of graphene oxide (GO)-silver nanoparticle (AgNP) hybrid nanostructure on a quantitative basis. Transmission electron microscopy (TEM) and zeta potential (ZP) analysis were used to provide visual information and elemental-based particle size distributions, respectively. Results clearly show a successful controlled assembly of GO-AgNP by electrostatic-directed heterogeneous aggregation between GO and bovine serum albumin (BSA)-functionalized AgNP under an acidic environment. Additionally, physical size, mass, and conformation (i.e., number of AgNP per nanohybrid) of GO-AgNP were shown to be proportional to the number concentration ratio of AgNP to GO (R) and the selected electrical mobility diameter. An analysis of colloidal stability of GO-AgNP indicates that the stability increased with its absolute ZP, which was dependent on R and environmental pH. The work presented here provides a proof of concept for systematically synthesizing hybrid colloidal nanomaterials through the tuning of surface chemistry in aqueous phase with the ability in quantitative characterization. Graphical Abstract Colloidal assembly of graphene oxide-silver nanoparticle hybrids characterized by aerosol differential mobility-coupled mass analyses.

A Second-Generation Device for Automated Training and Quantitative Behavior Analyses of Molecularly-Tractable Model Organisms

PubMed Central

Blackiston, Douglas; Shomrat, Tal; Nicolas, Cindy L.; Granata, Christopher; Levin, Michael

2010-01-01

A deep understanding of cognitive processes requires functional, quantitative analyses of the steps leading from genetics and the development of nervous system structure to behavior. Molecularly-tractable model systems such as Xenopus laevis and planaria offer an unprecedented opportunity to dissect the mechanisms determining the complex structure of the brain and CNS. A standardized platform that facilitated quantitative analysis of behavior would make a significant impact on evolutionary ethology, neuropharmacology, and cognitive science. While some animal tracking systems exist, the available systems do not allow automated training (feedback to individual subjects in real time, which is necessary for operant conditioning assays). The lack of standardization in the field, and the numerous technical challenges that face the development of a versatile system with the necessary capabilities, comprise a significant barrier keeping molecular developmental biology labs from integrating behavior analysis endpoints into their pharmacological and genetic perturbations. Here we report the development of a second-generation system that is a highly flexible, powerful machine vision and environmental control platform. In order to enable multidisciplinary studies aimed at understanding the roles of genes in brain function and behavior, and aid other laboratories that do not have the facilities to undergo complex engineering development, we describe the device and the problems that it overcomes. We also present sample data using frog tadpoles and flatworms to illustrate its use. Having solved significant engineering challenges in its construction, the resulting design is a relatively inexpensive instrument of wide relevance for several fields, and will accelerate interdisciplinary discovery in pharmacology, neurobiology, regenerative medicine, and cognitive science. PMID:21179424

Multivariate Quantitative Chemical Analysis

NASA Technical Reports Server (NTRS)

Kinchen, David G.; Capezza, Mary

1995-01-01

Technique of multivariate quantitative chemical analysis devised for use in determining relative proportions of two components mixed and sprayed together onto object to form thermally insulating foam. Potentially adaptable to other materials, especially in process-monitoring applications in which necessary to know and control critical properties of products via quantitative chemical analyses of products. In addition to chemical composition, also used to determine such physical properties as densities and strengths.

Application of Mixed-Methods Approaches to Higher Education and Intersectional Analyses

ERIC Educational Resources Information Center

Griffin, Kimberly A.; Museus, Samuel D.

2011-01-01

In this article, the authors discuss the utility of combining quantitative and qualitative methods in conducting intersectional analyses. First, they discuss some of the paradigmatic underpinnings of qualitative and quantitative research, and how these methods can be used in intersectional analyses. They then consider how paradigmatic pragmatism…

Analyzing the impacts of global trade and investment on non-communicable diseases and risk factors: a critical review of methodological approaches used in quantitative analyses.

PubMed

Cowling, Krycia; Thow, Anne Marie; Pollack Porter, Keshia

2018-05-24

A key mechanism through which globalization has impacted health is the liberalization of trade and investment, yet relatively few studies to date have used quantitative methods to investigate the impacts of global trade and investment policies on non-communicable diseases and risk factors. Recent reviews of this literature have found heterogeneity in results and a range of quality across studies, which may be in part attributable to a lack of conceptual clarity and methodological inconsistencies. This study is a critical review of methodological approaches used in the quantitative literature on global trade and investment and diet, tobacco, alcohol, and related health outcomes, with the objective of developing recommendations and providing resources to guide future robust, policy relevant research. A review of reviews, expert review, and reference tracing were employed to identify relevant studies, which were evaluated using a novel quality assessment tool designed for this research. Eight review articles and 34 quantitative studies were identified for inclusion. Important ways to improve this literature were identified and discussed: clearly defining exposures of interest and not conflating trade and investment; exploring mechanisms of broader relationships; increasing the use of individual-level data; ensuring consensus and consistency in key confounding variables; utilizing more sector-specific versus economy-wide trade and investment indicators; testing and adequately adjusting for autocorrelation and endogeneity when using longitudinal data; and presenting results from alternative statistical models and sensitivity analyses. To guide the development of future analyses, recommendations for international data sources for selected trade and investment indicators, as well as key gaps in the literature, are presented. More methodologically rigorous and consistent approaches in future quantitative studies on the impacts of global trade and investment policies on non

78 FR 26847 - Including Specific Pavement Types in Federal-aid Highway Traffic Noise Analyses

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-08

... traffic noise analyses. Current highway traffic noise analyses rely on data from three pavement types: dense-graded asphaltic concrete (DGAC), open-graded asphaltic concrete (OGAC), and Portland cement... noise analyses provide data for decisionmakers to make informed decisions on project alternatives and...

Assessing the reporting of categorised quantitative variables in observational epidemiological studies.

PubMed

Mabikwa, Onkabetse V; Greenwood, Darren C; Baxter, Paul D; Fleming, Sarah J

2017-03-14

One aspect to consider when reporting results of observational studies in epidemiology is how quantitative risk factors are analysed. The STROBE (Strengthening the Reporting of Observational Studies in Epidemiology) guidelines recommend that researchers describe how they handle quantitative variables when analysing data. For categorised quantitative variables, the authors are required to provide reasons and justifications informing their practice. We investigated and assessed the practices and reporting of categorised quantitative variables in epidemiology. The assessment was based on five medical journals that publish epidemiological research. Observational studies published between April and June 2015 and investigating the relationships between quantitative exposures (or risk factors) and the outcomes were considered for assessment. A standard form was used to collect the data, and the reporting patterns amongst eligible studies were quantified and described. Out of 61 articles assessed for eligibility, 23 observational studies were included in the assessment. Categorisation of quantitative exposures occurred in 61% of these studies and reasons informing the practice were rarely provided. Only one article explained the choice of categorisation in the analysis. Transformation of quantitative exposures into four or five groups was common and dominant amongst studies using equally spaced categories. Dichotomisation was not popular; the practice featured in one article. Overall, the majority (86%) of the studies preferred ordered or arbitrary group categories. Other criterions used to decide categorical boundaries were based on established guidelines such as consensus statements and WHO standards. Categorisation of continuous variables remains a dominant practice in epidemiological studies. The reasons informing the practice of categorisation within published work are limited and remain unknown in most articles. The existing STROBE guidelines could provide stronger

Comparative chloroplast genomics: Analyses including new sequencesfrom the angiosperms Nuphar advena and Ranunculus macranthus

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

Raubeso, Linda A.; Peery, Rhiannon; Chumley, Timothy W.

2007-03-01

The number of completely sequenced plastid genomes available is growing rapidly. This new array of sequences presents new opportunities to perform comparative analyses. In comparative studies, it is most useful to compare across wide phylogenetic spans and, within angiosperms, to include representatives from basally diverging lineages such as the new genomes reported here: Nuphar advena (from a basal-most lineage) and Ranunculus macranthus (from the basal group of eudicots). We report these two new plastid genome sequences and make comparisons (within angiosperms, seed plants, or all photosynthetic lineages) to evaluate features such as the status of ycf15 and ycf68 as proteinmore » coding genes, the distribution of simple sequence repeats (SSRs) and longer dispersed repeats (SDR), and patterns of nucleotide composition.« less

Quantitative analyses of tartaric acid based on terahertz time domain spectroscopy

NASA Astrophysics Data System (ADS)

Cao, Binghua; Fan, Mengbao

2010-10-01

Terahertz wave is the electromagnetic spectrum situated between microwave and infrared wave. Quantitative analysis based on terahertz spectroscopy is very important for the application of terahertz techniques. But how to realize it is still under study. L-tartaric acid is widely used as acidulant in beverage, and other food, such as soft drinks, wine, candy, bread and some colloidal sweetmeats. In this paper, terahertz time-domain spectroscopy is applied to quantify the tartaric acid. Two methods are employed to process the terahertz spectra of different samples with different content of tartaric acid. The first one is linear regression combining correlation analysis. The second is partial least square (PLS), in which the absorption spectra in the 0.8-1.4THz region are used to quantify the tartaric acid. To compare the performance of these two principles, the relative error of the two methods is analyzed. For this experiment, the first method does better than the second one. But the first method is suitable for the quantitative analysis of materials which has obvious terahertz absorption peaks, while for material which has no obvious terahertz absorption peaks, the second one is more appropriate.

Diagnostic Performance and Utility of Quantitative EEG Analyses in Delirium: Confirmatory Results From a Large Retrospective Case-Control Study.

PubMed

Fleischmann, Robert; Tränkner, Steffi; Bathe-Peters, Rouven; Rönnefarth, Maria; Schmidt, Sein; Schreiber, Stephan J; Brandt, Stephan A

2018-03-01

The lack of objective disease markers is a major cause of misdiagnosis and nonstandardized approaches in delirium. Recent studies conducted in well-selected patients and confined study environments suggest that quantitative electroencephalography (qEEG) can provide such markers. We hypothesize that qEEG helps remedy diagnostic uncertainty not only in well-defined study cohorts but also in a heterogeneous hospital population. In this retrospective case-control study, EEG power spectra of delirious patients and age-/gender-matched controls (n = 31 and n = 345, respectively) were fitted in a linear model to test their performance as binary classifiers. We subsequently evaluated the diagnostic performance of the best classifiers in control samples with normal EEGs (n = 534) and real-world samples including pathologic findings (n = 4294). Test reliability was estimated through split-half analyses. We found that the combination of spectral power at F3-P4 at 2 Hz (area under the curve [AUC] = .994) and C3-O1 at 19 Hz (AUC = .993) provided a sensitivity of 100% and a specificity of 99% to identify delirious patients among normal controls. These classifiers also yielded a false positive rate as low as 5% and increased the pretest probability of being delirious by 57% in an unselected real-world sample. Split-half reliabilities were .98 and .99, respectively. This retrospective study yielded preliminary evidence that qEEG provides excellent diagnostic performance to identify delirious patients even outside confined study environments. It furthermore revealed reduced beta power as a novel specific finding in delirium and that a normal EEG excludes delirium. Prospective studies including parameters of pretest probability and delirium severity are required to elaborate on these promising findings.

A high seroprevalence of antibodies to pertussis toxin among Japanese adults: Qualitative and quantitative analyses

PubMed Central

Moriuchi, Takumi; Otsuka, Nao; Hiramatsu, Yukihiro; Shibayama, Keigo

2017-01-01

In 2013, national serosurveillance detected a high seroprevalence of antibodies to pertussis toxin (PT) from Bordetella pertussis among Japanese adults. Thus, we aimed to determine the cause(s) of this high seroprevalence, and analyzed the titers of antibodies to PT and filamentous hemagglutinin (FHA) among adults (35–44 years old), young children (4–7 years old), and older children (10–14 years old). Our quantitative analyses revealed that adults had higher seroprevalences of anti-PT IgG and PT-neutralizing antibodies, and similar titers of anti-FHA IgG, compared to the young and older children. Positive correlations were observed between the titers of PT-neutralizing antibodies and anti-PT IgG in all age groups (rs values of 0.326–0.522), although the correlation tended to decrease with age. The ratio of PT-neutralizing antibodies to anti-PT IgG was significantly different when we compared the serum and purified IgG fractions among adults (p = 0.016), although this result was not observed among young and older children. Thus, it appears that some adults had non-IgG immunoglobulins to PT. Our analyses also revealed that adults had high-avidity anti-PT IgG (avidity index: 63.5%, similar results were observed among the children); however, the adults had lower-avidity anti-FHA IgG (37.9%, p < 0.05). It is possible that low-avidity anti-FHA IgG is related to infection with other respiratory pathogens (e.g., Bordetella parapertussis, Haemophilus influenzae, or Mycoplasma pneumoniae), which produces antibodies to FHA-like proteins. Our observations suggest that these adults had been infected with B. pertussis and other pathogen(s) during their adulthood. PMID:28700751

Classical evolution and quantum generation in generalized gravity theories including string corrections and tachyons: Unified analyses

NASA Astrophysics Data System (ADS)

Hwang, Jai-Chan; Noh, Hyerim

2005-03-01

We present cosmological perturbation theory based on generalized gravity theories including string theory correction terms and a tachyonic complication. The classical evolution as well as the quantum generation processes in these varieties of gravity theories are presented in unified forms. These apply both to the scalar- and tensor-type perturbations. Analyses are made based on the curvature variable in two different gauge conditions often used in the literature in Einstein’s gravity; these are the curvature variables in the comoving (or uniform-field) gauge and the zero-shear gauge. Applications to generalized slow-roll inflation and its consequent power spectra are derived in unified forms which include a wide range of inflationary scenarios based on Einstein’s gravity and others.

Meta-synthesis of health behavior change meta-analyses.

PubMed

Johnson, Blair T; Scott-Sheldon, Lori A J; Carey, Michael P

2010-11-01

We integrated and compared meta-analytic findings across diverse behavioral interventions to characterize how well they have achieved change in health behavior. Outcomes from 62 meta-analyses of interventions for change in health behavior were quantitatively synthesized, including 1011 primary-level investigations with 599,559 participants. Content coding suggested 6 behavioral domains: eating and physical activity, sexual behavior, addictive behaviors, stress management, female-specific screening and intervention behaviors, and behaviors involving use of health services. Behavior change interventions were efficacious (mean effect sizes = 0.08-0.45). Behavior change was more evident in more recent meta-analyses; those that sampled older interventions and literatures or sampled more published articles; those that included studies that relied on self-report, used briefer interventions, or sampled fewer, older, or female participants; and in some domains (e.g., stress management) more than others (e.g., sexual behaviors). Interventions improved health-related behaviors; however, efficacy varied as a function of participant and intervention characteristics. This meta-synthesis provides information about the efficacy of behavioral change interventions across health domains and populations; this knowledge can inform the design and development of public health interventions and future meta-analyses of these studies.

Quantitative characterisation of sedimentary grains

NASA Astrophysics Data System (ADS)

Tunwal, Mohit; Mulchrone, Kieran F.; Meere, Patrick A.

2016-04-01

Analysis of sedimentary texture helps in determining the formation, transportation and deposition processes of sedimentary rocks. Grain size analysis is traditionally quantitative, whereas grain shape analysis is largely qualitative. A semi-automated approach to quantitatively analyse shape and size of sand sized sedimentary grains is presented. Grain boundaries are manually traced from thin section microphotographs in the case of lithified samples and are automatically identified in the case of loose sediments. Shape and size paramters can then be estimated using a software package written on the Mathematica platform. While automated methodology already exists for loose sediment analysis, the available techniques for the case of lithified samples are limited to cases of high definition thin section microphotographs showing clear contrast between framework grains and matrix. Along with the size of grain, shape parameters such as roundness, angularity, circularity, irregularity and fractal dimension are measured. A new grain shape parameter developed using Fourier descriptors has also been developed. To test this new approach theoretical examples were analysed and produce high quality results supporting the accuracy of the algorithm. Furthermore sandstone samples from known aeolian and fluvial environments from the Dingle Basin, County Kerry, Ireland were collected and analysed. Modern loose sediments from glacial till from County Cork, Ireland and aeolian sediments from Rajasthan, India have also been collected and analysed. A graphical summary of the data is presented and allows for quantitative distinction between samples extracted from different sedimentary environments.

The ACCE method: an approach for obtaining quantitative or qualitative estimates of residual confounding that includes unmeasured confounding

PubMed Central

Smith, Eric G.

2015-01-01

Background:  Nonrandomized studies typically cannot account for confounding from unmeasured factors.  Method:  A method is presented that exploits the recently-identified phenomenon of  “confounding amplification” to produce, in principle, a quantitative estimate of total residual confounding resulting from both measured and unmeasured factors.  Two nested propensity score models are constructed that differ only in the deliberate introduction of an additional variable(s) that substantially predicts treatment exposure.  Residual confounding is then estimated by dividing the change in treatment effect estimate between models by the degree of confounding amplification estimated to occur, adjusting for any association between the additional variable(s) and outcome. Results:  Several hypothetical examples are provided to illustrate how the method produces a quantitative estimate of residual confounding if the method’s requirements and assumptions are met.  Previously published data is used to illustrate that, whether or not the method routinely provides precise quantitative estimates of residual confounding, the method appears to produce a valuable qualitative estimate of the likely direction and general size of residual confounding. Limitations:  Uncertainties exist, including identifying the best approaches for: 1) predicting the amount of confounding amplification, 2) minimizing changes between the nested models unrelated to confounding amplification, 3) adjusting for the association of the introduced variable(s) with outcome, and 4) deriving confidence intervals for the method’s estimates (although bootstrapping is one plausible approach). Conclusions:  To this author’s knowledge, it has not been previously suggested that the phenomenon of confounding amplification, if such amplification is as predictable as suggested by a recent simulation, provides a logical basis for estimating total residual confounding. The method's basic approach is

Quantitative X-ray Map Analyser (Q-XRMA): A new GIS-based statistical approach to Mineral Image Analysis

NASA Astrophysics Data System (ADS)

Ortolano, Gaetano; Visalli, Roberto; Godard, Gaston; Cirrincione, Rosolino

2018-06-01

We present a new ArcGIS®-based tool developed in the Python programming language for calibrating EDS/WDS X-ray element maps, with the aim of acquiring quantitative information of petrological interest. The calibration procedure is based on a multiple linear regression technique that takes into account interdependence among elements and is constrained by the stoichiometry of minerals. The procedure requires an appropriate number of spot analyses for use as internal standards and provides several test indexes for a rapid check of calibration accuracy. The code is based on an earlier image-processing tool designed primarily for classifying minerals in X-ray element maps; the original Python code has now been enhanced to yield calibrated maps of mineral end-members or the chemical parameters of each classified mineral. The semi-automated procedure can be used to extract a dataset that is automatically stored within queryable tables. As a case study, the software was applied to an amphibolite-facies garnet-bearing micaschist. The calibrated images obtained for both anhydrous (i.e., garnet and plagioclase) and hydrous (i.e., biotite) phases show a good fit with corresponding electron microprobe analyses. This new GIS-based tool package can thus find useful application in petrology and materials science research. Moreover, the huge quantity of data extracted opens new opportunities for the development of a thin-section microchemical database that, using a GIS platform, can be linked with other major global geoscience databases.

Good practices for quantitative bias analysis.

PubMed

Lash, Timothy L; Fox, Matthew P; MacLehose, Richard F; Maldonado, George; McCandless, Lawrence C; Greenland, Sander

2014-12-01

Quantitative bias analysis serves several objectives in epidemiological research. First, it provides a quantitative estimate of the direction, magnitude and uncertainty arising from systematic errors. Second, the acts of identifying sources of systematic error, writing down models to quantify them, assigning values to the bias parameters and interpreting the results combat the human tendency towards overconfidence in research results, syntheses and critiques and the inferences that rest upon them. Finally, by suggesting aspects that dominate uncertainty in a particular research result or topic area, bias analysis can guide efficient allocation of sparse research resources. The fundamental methods of bias analyses have been known for decades, and there have been calls for more widespread use for nearly as long. There was a time when some believed that bias analyses were rarely undertaken because the methods were not widely known and because automated computing tools were not readily available to implement the methods. These shortcomings have been largely resolved. We must, therefore, contemplate other barriers to implementation. One possibility is that practitioners avoid the analyses because they lack confidence in the practice of bias analysis. The purpose of this paper is therefore to describe what we view as good practices for applying quantitative bias analysis to epidemiological data, directed towards those familiar with the methods. We focus on answering questions often posed to those of us who advocate incorporation of bias analysis methods into teaching and research. These include the following. When is bias analysis practical and productive? How does one select the biases that ought to be addressed? How does one select a method to model biases? How does one assign values to the parameters of a bias model? How does one present and interpret a bias analysis?. We hope that our guide to good practices for conducting and presenting bias analyses will encourage

A New Material Mapping Procedure for Quantitative Computed Tomography-Based, Continuum Finite Element Analyses of the Vertebra

PubMed Central

Unnikrishnan, Ginu U.; Morgan, Elise F.

2011-01-01

Inaccuracies in the estimation of material properties and errors in the assignment of these properties into finite element models limit the reliability, accuracy, and precision of quantitative computed tomography (QCT)-based finite element analyses of the vertebra. In this work, a new mesh-independent, material mapping procedure was developed to improve the quality of predictions of vertebral mechanical behavior from QCT-based finite element models. In this procedure, an intermediate step, called the material block model, was introduced to determine the distribution of material properties based on bone mineral density, and these properties were then mapped onto the finite element mesh. A sensitivity study was first conducted on a calibration phantom to understand the influence of the size of the material blocks on the computed bone mineral density. It was observed that varying the material block size produced only marginal changes in the predictions of mineral density. Finite element (FE) analyses were then conducted on a square column-shaped region of the vertebra and also on the entire vertebra in order to study the effect of material block size on the FE-derived outcomes. The predicted values of stiffness for the column and the vertebra decreased with decreasing block size. When these results were compared to those of a mesh convergence analysis, it was found that the influence of element size on vertebral stiffness was less than that of the material block size. This mapping procedure allows the material properties in a finite element study to be determined based on the block size required for an accurate representation of the material field, while the size of the finite elements can be selected independently and based on the required numerical accuracy of the finite element solution. The mesh-independent, material mapping procedure developed in this study could be particularly helpful in improving the accuracy of finite element analyses of

Portable gas chromatograph mass spectrometer for on-site chemical analyses

DOEpatents

Haas, Jeffrey S.; Bushman, John F.; Howard, Douglas E.; Wong, James L.; Eckels, Joel D.

2002-01-01

A portable, lightweight (approximately 25 kg) gas chromatograph mass spectrometer, including the entire vacuum system, can perform qualitative and quantitative analyses of all sample types in the field. The GC/MS has a conveniently configured layout of components for ease of serviceability and maintenance. The GC/MS system can be transported under operating or near-operating conditions (i.e., under vacuum and at elevated temperature) to reduce the downtime before samples can be analyzed on-site.

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.

Using Inequality Measures to Incorporate Environmental Justice into Regulatory Analyses

EPA Science Inventory

Abstract: Formally evaluating how specific policy measures influence environmental justice is challenging, especially in the context of regulatory analyses in which quantitative comparisons are the norm. However, there is a large literature on developing and applying quantitative...

Beyond nutrient-based food indices: a data mining approach to search for a quantitative holistic index reflecting the degree of food processing and including physicochemical properties.

PubMed

Fardet, Anthony; Lakhssassi, Sanaé; Briffaz, Aurélien

2018-01-24

Processing has major impacts on both the structure and composition of food and hence on nutritional value. In particular, high consumption of ultra-processed foods (UPFs) is associated with increased risks of obesity and diabetes. Unfortunately, existing food indices only focus on food nutritional content while failing to consider either food structure or the degree of processing. The objectives of this study were thus to link non-nutrient food characteristics (texture, water activity (a w ), glycemic and satiety potentials (FF), and shelf life) to the degree of processing; search for associations between these characteristics with nutritional composition; search for a holistic quantitative technological index; and determine quantitative rules for a food to be defined as UPF using data mining. Among the 280 most widely consumed foods by the elderly in France, 139 solid/semi-solid foods were selected for textural and a w measurements, and classified according to three degrees of processing. Our results showed that minimally-processed foods were less hyperglycemic, more satiating, had better nutrient profile, higher a w , shorter shelf life, lower maximum stress, and higher energy at break than UPFs. Based on 72 food variables, multivariate analyses differentiated foods according to their degree of processing. Then technological indices including food nutritional composition, a w , FF and textural parameters were tested against technological groups. Finally, a LIM score (nutrients to limit) ≥8 per 100 kcal and a number of ingredients/additives >4 are relevant, but not sufficient, rules to define UPFs. We therefore suggest that food health potential should be first defined by its degree of processing.

Quantitative DNA Analyses for Airborne Birch Pollen

PubMed Central

Müller-Germann, Isabell; Vogel, Bernhard; Vogel, Heike; Pauling, Andreas; Fröhlich-Nowoisky, Janine; Pöschl, Ulrich; Després, Viviane R.

2015-01-01

Birch trees produce large amounts of highly allergenic pollen grains that are distributed by wind and impact human health by causing seasonal hay fever, pollen-related asthma, and other allergic diseases. Traditionally, pollen forecasts are based on conventional microscopic counting techniques that are labor-intensive and limited in the reliable identification of species. Molecular biological techniques provide an alternative approach that is less labor-intensive and enables identification of any species by its genetic fingerprint. A particularly promising method is quantitative Real-Time polymerase chain reaction (qPCR), which can be used to determine the number of DNA copies and thus pollen grains in air filter samples. During the birch pollination season in 2010 in Mainz, Germany, we collected air filter samples of fine (<3 μm) and coarse air particulate matter. These were analyzed by qPCR using two different primer pairs: one for a single-copy gene (BP8) and the other for a multi-copy gene (ITS). The BP8 gene was better suitable for reliable qPCR results, and the qPCR results obtained for coarse particulate matter were well correlated with the birch pollen forecasting results of the regional air quality model COSMO-ART. As expected due to the size of birch pollen grains (~23 μm), the concentration of DNA in fine particulate matter was lower than in the coarse particle fraction. For the ITS region the factor was 64, while for the single-copy gene BP8 only 51. The possible presence of so-called sub-pollen particles in the fine particle fraction is, however, interesting even in low concentrations. These particles are known to be highly allergenic, reach deep into airways and cause often severe health problems. In conclusion, the results of this exploratory study open up the possibility of predicting and quantifying the pollen concentration in the atmosphere more precisely in the future. PMID:26492534

Enhancement of a virtual reality wheelchair simulator to include qualitative and quantitative performance metrics.

PubMed

Harrison, C S; Grant, P M; Conway, B A

2010-01-01

The increasing importance of inclusive design and in particular accessibility guidelines established in the U.K. 1996 Disability Discrimination Act (DDA) has been a prime motivation for the work on wheelchair access, a subset of the DDA guidelines, described in this article. The development of these guidelines mirrors the long-standing provisions developed in the U.S. In order to raise awareness of these guidelines and in particular to give architects, building designers, and users a physical sensation of how a planned development could be experienced, a wheelchair virtual reality system was developed. This compares with conventional methods of measuring against drawings and comparing dimensions against building regulations, established in the U.K. under British standards. Features of this approach include the marriage of an electromechanical force-feedback system with high-quality immersive graphics as well as the potential ability to generate a physiological rating of buildings that do not yet exist. The provision of this sense of "feel" augments immersion within the virtual reality environment and also provides the basis from which both qualitative and quantitative measures of a building's access performance can be gained.

Role Of Social Networks In Resilience Of Naval Recruits: A Quantitative Analysis

DTIC Science & Technology

2016-06-01

comprises 1,297 total surveys from a total of eight divisions of recruits at two different time periods. Quantitative analyses using surveys and network... surveys from a total of eight divisions of recruits at two different time periods. Quantitative analyses using surveys and network data examine the effects...NETWORKS IN RESILIENCE OF NAVAL RECRUITS: A QUANTITATIVE ANALYSIS by Andrea M. Watling June 2016 Thesis Advisor: Edward H. Powley Co

Proteomic Analyses of the Effects of Drugs of Abuse on Monocyte-Derived Mature Dendritic Cells

PubMed Central

Reynolds, Jessica L.; Mahajan, Supriya D.; Aalinkeel, Ravikunar; Nair, B.; Sykes, Donald E.; Schwartz, Stanley A.

2010-01-01

Drug abuse has become a global health concern. Understanding how drug abuse modulates the immune system and how the immune system responds to pathogens associated with drug abuse, such hepatitis C virus (HCV) and human immunodeficiency virus (HIV-1), can be assessed by an integrated approach comparing proteomic analyses and quantitation of gene expression. Two-dimensional (2D) difference gel electrophoresis was used to determine the molecular mechanisms underlying the proteomic changes that alter normal biological processes when monocyte-derived mature dendritic cells were treated with cocaine or methamphetamine. Both drugs differentially regulated the expression of several functional classes of proteins including those that modulate apoptosis, protein folding, protein kinase activity, and metabolism and proteins that function as intracellular signal transduction molecules. Proteomic data were validated using a combination of quantitative, real-time PCR and Western blot analyses. These studies will help to identify the molecular mechanisms, including the expression of several functionally important classes of proteins that have emerged as potential mediators of pathogenesis. These proteins may predispose immunocompetent cells, including dendritic cells, to infection with viruses such as HCV and HIV-1, which are associated with drug abuse. PMID:19811410

Simultaneous Qualitative and Quantitative Analyses of Triterpenoids in Ilex pubescens by Ultra-High-Performance Liquid Chromatography Coupled with Quadrupole Time-of-Flight Mass Spectrometry.

PubMed

Cao, Di; Wang, Qing; Jin, Jing; Qiu, Maosong; Zhou, Lian; Zhou, Xinghong; Li, Hui; Zhao, Zhongxiang

2018-03-01

Ilex pubescens Hook et Arn mainly contains triterpenoids that possess antithrombotic, anti-inflammatory and analgesic effects. Quantitative and qualitative analyses of the triterpenoids in I. pubescens can be useful for determining the authenticity and quality of raw materials and guiding its clinical preparation. To establish a method for rapid and comprehensive analysis of triterpenoids in I. pubescens using ultra-high-performance liquid chromatography coupled to electrospray ionisation and quadrupole time-of-flight-mass spectrometry (UPLC-ESI-QTOF-MS), which will also be applied to evaluate the contents of nine triterpenoids among root, root heartwood and root bark of I. pubescens to judge the value of the root bark to avoid wastage. UPLC-ESI-QTOF-MS data from the extracts of I. pubescens in negative mode were analysed using Peakview and Masterview software that provided molecular weight, mass errors, isotope pattern fit and MS/MS fragments for the identification of triterpenoids. The quantification of nine investigated compounds of I. pubescens was accomplished using MultiQuant software. A total of 33 triterpenoids, five phenolic acids, two lignans and a flavonol were characterised in only 14 min. The total content of the nine compounds in the root bark was generally slightly higher than that of the root and root heartwood, which has not been reported before. The developed UPLC-ESI-QTOF-MS method was proven to be rapid and comprehensive for simultaneous qualitative and quantitative analyses of the characteristic triterpenoids in I. pubescens. The results may provide a basis for holistic quality control and metabolic studies of I. pubescens, as well as serve as a reference for the analysis of other Ilex plants. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Quantitative Analyses of Core Promoters Enable Precise Engineering of Regulated Gene Expression in Mammalian Cells.

PubMed

Ede, Christopher; Chen, Ximin; Lin, Meng-Yin; Chen, Yvonne Y

2016-05-20

Inducible transcription systems play a crucial role in a wide array of synthetic biology circuits. However, the majority of inducible promoters are constructed from a limited set of tried-and-true promoter parts, which are susceptible to common shortcomings such as high basal expression levels (i.e., leakiness). To expand the toolbox for regulated mammalian gene expression and facilitate the construction of mammalian genetic circuits with precise functionality, we quantitatively characterized a panel of eight core promoters, including sequences with mammalian, viral, and synthetic origins. We demonstrate that this selection of core promoters can provide a wide range of basal gene expression levels and achieve a gradient of fold-inductions spanning 2 orders of magnitude. Furthermore, commonly used parts such as minimal CMV and minimal SV40 promoters were shown to achieve robust gene expression upon induction, but also suffer from high levels of leakiness. In contrast, a synthetic promoter, YB_TATA, was shown to combine low basal expression with high transcription rate in the induced state to achieve significantly higher fold-induction ratios compared to all other promoters tested. These behaviors remain consistent when the promoters are coupled to different genetic outputs and different response elements, as well as across different host-cell types and DNA copy numbers. We apply this quantitative understanding of core promoter properties to the successful engineering of human T cells that respond to antigen stimulation via chimeric antigen receptor signaling specifically under hypoxic environments. Results presented in this study can facilitate the design and calibration of future mammalian synthetic biology systems capable of precisely programmed functionality.

Linear Quantitative Profiling Method Fast Monitors Alkaloids of Sophora Flavescens That Was Verified by Tri-Marker Analyses.

PubMed

Hou, Zhifei; Sun, Guoxiang; Guo, Yong

2016-01-01

The present study demonstrated the use of the Linear Quantitative Profiling Method (LQPM) to evaluate the quality of Alkaloids of Sophora flavescens (ASF) based on chromatographic fingerprints in an accurate, economical and fast way. Both linear qualitative and quantitative similarities were calculated in order to monitor the consistency of the samples. The results indicate that the linear qualitative similarity (LQLS) is not sufficiently discriminating due to the predominant presence of three alkaloid compounds (matrine, sophoridine and oxymatrine) in the test samples; however, the linear quantitative similarity (LQTS) was shown to be able to obviously identify the samples based on the difference in the quantitative content of all the chemical components. In addition, the fingerprint analysis was also supported by the quantitative analysis of three marker compounds. The LQTS was found to be highly correlated to the contents of the marker compounds, indicating that quantitative analysis of the marker compounds may be substituted with the LQPM based on the chromatographic fingerprints for the purpose of quantifying all chemicals of a complex sample system. Furthermore, once reference fingerprint (RFP) developed from a standard preparation in an immediate detection way and the composition similarities calculated out, LQPM could employ the classical mathematical model to effectively quantify the multiple components of ASF samples without any chemical standard.

Linear Quantitative Profiling Method Fast Monitors Alkaloids of Sophora Flavescens That Was Verified by Tri-Marker Analyses

PubMed Central

Hou, Zhifei; Sun, Guoxiang; Guo, Yong

2016-01-01

The present study demonstrated the use of the Linear Quantitative Profiling Method (LQPM) to evaluate the quality of Alkaloids of Sophora flavescens (ASF) based on chromatographic fingerprints in an accurate, economical and fast way. Both linear qualitative and quantitative similarities were calculated in order to monitor the consistency of the samples. The results indicate that the linear qualitative similarity (LQLS) is not sufficiently discriminating due to the predominant presence of three alkaloid compounds (matrine, sophoridine and oxymatrine) in the test samples; however, the linear quantitative similarity (LQTS) was shown to be able to obviously identify the samples based on the difference in the quantitative content of all the chemical components. In addition, the fingerprint analysis was also supported by the quantitative analysis of three marker compounds. The LQTS was found to be highly correlated to the contents of the marker compounds, indicating that quantitative analysis of the marker compounds may be substituted with the LQPM based on the chromatographic fingerprints for the purpose of quantifying all chemicals of a complex sample system. Furthermore, once reference fingerprint (RFP) developed from a standard preparation in an immediate detection way and the composition similarities calculated out, LQPM could employ the classical mathematical model to effectively quantify the multiple components of ASF samples without any chemical standard. PMID:27529425

Leadership and Culture-Building in Schools: Quantitative and Qualitative Understandings.

ERIC Educational Resources Information Center

Sashkin, Marshall; Sashkin, Molly G.

Understanding effective school leadership as a function of culture building through quantitative and qualitative analyses is the purpose of this paper. The two-part quantitative phase of the research focused on statistical measures of culture and leadership behavior directed toward culture building in the school. The first quantitative part…

Tissue microarrays and quantitative tissue-based image analysis as a tool for oncology biomarker and diagnostic development.

PubMed

Dolled-Filhart, Marisa P; Gustavson, Mark D

2012-11-01

Translational oncology has been improved by using tissue microarrays (TMAs), which facilitate biomarker analysis of large cohorts on a single slide. This has allowed for rapid analysis and validation of potential biomarkers for prognostic and predictive value, as well as for evaluation of biomarker prevalence. Coupled with quantitative analysis of immunohistochemical (IHC) staining, objective and standardized biomarker data from tumor samples can further advance companion diagnostic approaches for the identification of drug-responsive or resistant patient subpopulations. This review covers the advantages, disadvantages and applications of TMAs for biomarker research. Research literature and reviews of TMAs and quantitative image analysis methodology have been surveyed for this review (with an AQUA® analysis focus). Applications such as multi-marker diagnostic development and pathway-based biomarker subpopulation analyses are described. Tissue microarrays are a useful tool for biomarker analyses including prevalence surveys, disease progression assessment and addressing potential prognostic or predictive value. By combining quantitative image analysis with TMAs, analyses will be more objective and reproducible, allowing for more robust IHC-based diagnostic test development. Quantitative multi-biomarker IHC diagnostic tests that can predict drug response will allow for greater success of clinical trials for targeted therapies and provide more personalized clinical decision making.

Quantitative in vivo Analyses Reveal Calcium-dependent Phosphorylation Sites and Identifies a Novel Component of the Toxoplasma Invasion Motor Complex

PubMed Central

Nebl, Thomas; Prieto, Judith Helena; Kapp, Eugene; Smith, Brian J.; Williams, Melanie J.; Yates, John R.; Cowman, Alan F.; Tonkin, Christopher J.

2011-01-01

Apicomplexan parasites depend on the invasion of host cells for survival and proliferation. Calcium-dependent signaling pathways appear to be essential for micronemal release and gliding motility, yet the target of activated kinases remains largely unknown. We have characterized calcium-dependent phosphorylation events during Toxoplasma host cell invasion. Stimulation of live tachyzoites with Ca2+-mobilizing drugs leads to phosphorylation of numerous parasite proteins, as shown by differential 2-DE display of 32[P]-labeled protein extracts. Multi-dimensional Protein Identification Technology (MudPIT) identified ∼546 phosphorylation sites on over 300 Toxoplasma proteins, including 10 sites on the actomyosin invasion motor. Using a Stable Isotope of Amino Acids in Culture (SILAC)-based quantitative LC-MS/MS analyses we monitored changes in the abundance and phosphorylation of the invasion motor complex and defined Ca2+-dependent phosphorylation patterns on three of its components - GAP45, MLC1 and MyoA. Furthermore, calcium-dependent phosphorylation of six residues across GAP45, MLC1 and MyoA is correlated with invasion motor activity. By analyzing proteins that appear to associate more strongly with the invasion motor upon calcium stimulation we have also identified a novel 15-kDa Calmodulin-like protein that likely represents the MyoA Essential Light Chain of the Toxoplasma invasion motor. This suggests that invasion motor activity could be regulated not only by phosphorylation but also by the direct binding of calcium ions to this new component. PMID:21980283

Comparative and quantitative proteomic analysis of normal and degenerated human annulus fibrosus cells.

PubMed

Ye, Dongping; Liang, Weiguo; Dai, Libing; Zhou, Longqiang; Yao, Yicun; Zhong, Xin; Chen, Honghui; Xu, Jiake

2015-05-01

Degeneration of the intervertebral disc (IVD) is a major chronic medical condition associated with back pain. To better understand the pathogenesis of IVD degeneration, we performed comparative and quantitative proteomic analyses of normal and degenerated human annulus fibrosus (AF) cells and identified proteins that are differentially expressed between them. Annulus fibrosus cells were isolated and cultured from patients with lumbar disc herniation (the experimental group, degenerated AF cells) and scoliosis patients who underwent orthopaedic surgery (the control group, normal AF cells). Comparative proteomic analyses of normal and degenerated cultured AF cells were carried out using 2-D electrophoresis, mass spectrometric analyses, and database searching. Quantitative analyses of silver-stained 2-D electrophoresis gels of normal and degenerated cultured AF cells identified 10 protein spots that showed the most altered differential expression levels between the two groups. Among these, three proteins were decreased, including heat shock cognate 71-kDa protein, glucose-6-phosphate 1-dehydrogenase, and protocadherin-23, whereas seven proteins were increased, including guanine nucleotide-binding protein G(i) subunit α-2, superoxide dismutase, transmembrane protein 51, adenosine receptor A3, 26S protease regulatory subunit 8, lipid phosphate phosphatase-related protein, and fatty acyl-crotonic acid reductase 1. These differentially expressed proteins might be involved in the pathophysiological process of IVD degeneration and have potential values as biomarkers of the degeneration of IVD. © 2015 Wiley Publishing Asia Pty Ltd.

Teaching Children How to Include the Inversion Principle in Their Reasoning about Quantitative Relations

ERIC Educational Resources Information Center

Nunes, Terezinha; Bryant, Peter; Evans, Deborah; Bell, Daniel; Barros, Rossana

2012-01-01

The basis of this intervention study is a distinction between numerical calculus and relational calculus. The former refers to numerical calculations and the latter to the analysis of the quantitative relations in mathematical problems. The inverse relation between addition and subtraction is relevant to both kinds of calculus, but so far research…

Diagnostic performance of semi-quantitative and quantitative stress CMR perfusion analysis: a meta-analysis.

PubMed

van Dijk, R; van Assen, M; Vliegenthart, R; de Bock, G H; van der Harst, P; Oudkerk, M

2017-11-27

Stress cardiovascular magnetic resonance (CMR) perfusion imaging is a promising modality for the evaluation of coronary artery disease (CAD) due to high spatial resolution and absence of radiation. Semi-quantitative and quantitative analysis of CMR perfusion are based on signal-intensity curves produced during the first-pass of gadolinium contrast. Multiple semi-quantitative and quantitative parameters have been introduced. Diagnostic performance of these parameters varies extensively among studies and standardized protocols are lacking. This study aims to determine the diagnostic accuracy of semi- quantitative and quantitative CMR perfusion parameters, compared to multiple reference standards. Pubmed, WebOfScience, and Embase were systematically searched using predefined criteria (3272 articles). A check for duplicates was performed (1967 articles). Eligibility and relevance of the articles was determined by two reviewers using pre-defined criteria. The primary data extraction was performed independently by two researchers with the use of a predefined template. Differences in extracted data were resolved by discussion between the two researchers. The quality of the included studies was assessed using the 'Quality Assessment of Diagnostic Accuracy Studies Tool' (QUADAS-2). True positives, false positives, true negatives, and false negatives were subtracted/calculated from the articles. The principal summary measures used to assess diagnostic accuracy were sensitivity, specificity, andarea under the receiver operating curve (AUC). Data was pooled according to analysis territory, reference standard and perfusion parameter. Twenty-two articles were eligible based on the predefined study eligibility criteria. The pooled diagnostic accuracy for segment-, territory- and patient-based analyses showed good diagnostic performance with sensitivity of 0.88, 0.82, and 0.83, specificity of 0.72, 0.83, and 0.76 and AUC of 0.90, 0.84, and 0.87, respectively. In per territory

Quantitation and Identification of Intact Major Milk Proteins for High-Throughput LC-ESI-Q-TOF MS Analyses

PubMed Central

Vincent, Delphine; Elkins, Aaron; Condina, Mark R.; Ezernieks, Vilnis; Rochfort, Simone

2016-01-01

Cow’s milk is an important source of proteins in human nutrition. On average, cow’s milk contains 3.5% protein. The most abundant proteins in bovine milk are caseins and some of the whey proteins, namely beta-lactoglobulin, alpha-lactalbumin, and serum albumin. A number of allelic variants and post-translationally modified forms of these proteins have been identified. Their occurrence varies with breed, individuality, stage of lactation, and health and nutritional status of the animal. It is therefore essential to have reliable methods of detection and quantitation of these proteins. Traditionally, major milk proteins are quantified using liquid chromatography (LC) and ultra violet detection method. However, as these protein variants co-elute to some degree, another dimension of separation is beneficial to accurately measure their amounts. Mass spectrometry (MS) offers such a tool. In this study, we tested several RP-HPLC and MS parameters to optimise the analysis of intact bovine proteins from milk. From our tests, we developed an optimum method that includes a 20-28-40% phase B gradient with 0.02% TFA in both mobile phases, at 0.2 mL/min flow rate, using 75°C for the C8 column temperature, scanning every 3 sec over a 600–3000 m/z window. The optimisations were performed using external standards commercially purchased for which ionisation efficiency, linearity of calibration, LOD, LOQ, sensitivity, selectivity, precision, reproducibility, and mass accuracy were demonstrated. From the MS analysis, we can use extracted ion chromatograms (EICs) of specific ion series of known proteins and integrate peaks at defined retention time (RT) window for quantitation purposes. This optimum quantitative method was successfully applied to two bulk milk samples from different breeds, Holstein-Friesian and Jersey, to assess differences in protein variant levels. PMID:27749892

Quantitation and Identification of Intact Major Milk Proteins for High-Throughput LC-ESI-Q-TOF MS Analyses.

PubMed

Vincent, Delphine; Elkins, Aaron; Condina, Mark R; Ezernieks, Vilnis; Rochfort, Simone

2016-01-01

Cow's milk is an important source of proteins in human nutrition. On average, cow's milk contains 3.5% protein. The most abundant proteins in bovine milk are caseins and some of the whey proteins, namely beta-lactoglobulin, alpha-lactalbumin, and serum albumin. A number of allelic variants and post-translationally modified forms of these proteins have been identified. Their occurrence varies with breed, individuality, stage of lactation, and health and nutritional status of the animal. It is therefore essential to have reliable methods of detection and quantitation of these proteins. Traditionally, major milk proteins are quantified using liquid chromatography (LC) and ultra violet detection method. However, as these protein variants co-elute to some degree, another dimension of separation is beneficial to accurately measure their amounts. Mass spectrometry (MS) offers such a tool. In this study, we tested several RP-HPLC and MS parameters to optimise the analysis of intact bovine proteins from milk. From our tests, we developed an optimum method that includes a 20-28-40% phase B gradient with 0.02% TFA in both mobile phases, at 0.2 mL/min flow rate, using 75°C for the C8 column temperature, scanning every 3 sec over a 600-3000 m/z window. The optimisations were performed using external standards commercially purchased for which ionisation efficiency, linearity of calibration, LOD, LOQ, sensitivity, selectivity, precision, reproducibility, and mass accuracy were demonstrated. From the MS analysis, we can use extracted ion chromatograms (EICs) of specific ion series of known proteins and integrate peaks at defined retention time (RT) window for quantitation purposes. This optimum quantitative method was successfully applied to two bulk milk samples from different breeds, Holstein-Friesian and Jersey, to assess differences in protein variant levels.

Toward Quantitative Small Animal Pinhole SPECT: Assessment of Quantitation Accuracy Prior to Image Compensations

PubMed Central

Chen, Chia-Lin; Wang, Yuchuan; Lee, Jason J. S.; Tsui, Benjamin M. W.

2011-01-01

Purpose We assessed the quantitation accuracy of small animal pinhole single photon emission computed tomography (SPECT) under the current preclinical settings, where image compensations are not routinely applied. Procedures The effects of several common image-degrading factors and imaging parameters on quantitation accuracy were evaluated using Monte-Carlo simulation methods. Typical preclinical imaging configurations were modeled, and quantitative analyses were performed based on image reconstructions without compensating for attenuation, scatter, and limited system resolution. Results Using mouse-sized phantom studies as examples, attenuation effects alone degraded quantitation accuracy by up to −18% (Tc-99m or In-111) or −41% (I-125). The inclusion of scatter effects changed the above numbers to −12% (Tc-99m or In-111) and −21% (I-125), respectively, indicating the significance of scatter in quantitative I-125 imaging. Region-of-interest (ROI) definitions have greater impacts on regional quantitation accuracy for small sphere sources as compared to attenuation and scatter effects. For the same ROI, SPECT acquisitions using pinhole apertures of different sizes could significantly affect the outcome, whereas the use of different radii-of-rotation yielded negligible differences in quantitation accuracy for the imaging configurations simulated. Conclusions We have systematically quantified the influence of several factors affecting the quantitation accuracy of small animal pinhole SPECT. In order to consistently achieve accurate quantitation within 5% of the truth, comprehensive image compensation methods are needed. PMID:19048346

Elastic fibers in human skin: quantitation of elastic fibers by computerized digital image analyses and determination of elastin by radioimmunoassay of desmosine.

PubMed

Uitto, J; Paul, J L; Brockley, K; Pearce, R H; Clark, J G

1983-10-01

The elastic fibers in the skin and other organs can be affected in several disease processes. In this study, we have developed morphometric techniques that allow accurate quantitation of the elastic fibers in punch biopsy specimens of skin. In this procedure, the elastic fibers, visualized by elastin-specific stains, are examined through a camera unit attached to the microscope. The black and white images sensing various gray levels are then converted to binary images after selecting a threshold with an analog threshold selection device. The binary images are digitized and the data analyzed by a computer program designed to express the properties of the image, thus allowing determination of the volume fraction occupied by the elastic fibers. As an independent measure of the elastic fibers, alternate tissue sections were used for assay of desmosine, an elastin-specific cross-link compound, by a radioimmunoassay. The clinical applicability of the computerized morphometric analyses was tested by examining the elastic fibers in the skin of five patients with pseudoxanthoma elasticum or Buschke-Ollendorff syndrome. In the skin of 10 healthy control subjects, the elastic fibers occupied 2.1 +/- 1.1% (mean +/- SD) of the dermis. The volume fractions occupied by the elastic fibers in the lesions of pseudoxanthoma elasticum or Buschke-Ollendorff syndrome were increased as much as 6-fold, whereas the values in the unaffected areas of the skin in the same patients were within normal limits. A significant correlation between the volume fraction of elastic fibers, determined by computerized morphometric analyses, and the concentration of desmosine, quantitated by radioimmunoassay, was noted in the total material. These results demonstrate that computerized morphometric techniques are helpful in characterizing disease processes affecting skin. This methodology should also be applicable to other tissues that contain elastic fibers and that are affected in various heritable and

A two-factor error model for quantitative steganalysis

NASA Astrophysics Data System (ADS)

Böhme, Rainer; Ker, Andrew D.

2006-02-01

Quantitative steganalysis refers to the exercise not only of detecting the presence of hidden stego messages in carrier objects, but also of estimating the secret message length. This problem is well studied, with many detectors proposed but only a sparse analysis of errors in the estimators. A deep understanding of the error model, however, is a fundamental requirement for the assessment and comparison of different detection methods. This paper presents a rationale for a two-factor model for sources of error in quantitative steganalysis, and shows evidence from a dedicated large-scale nested experimental set-up with a total of more than 200 million attacks. Apart from general findings about the distribution functions found in both classes of errors, their respective weight is determined, and implications for statistical hypothesis tests in benchmarking scenarios or regression analyses are demonstrated. The results are based on a rigorous comparison of five different detection methods under many different external conditions, such as size of the carrier, previous JPEG compression, and colour channel selection. We include analyses demonstrating the effects of local variance and cover saturation on the different sources of error, as well as presenting the case for a relative bias model for between-image error.

A thioacidolysis method tailored for higher‐throughput quantitative analysis of lignin monomers

PubMed Central

Foster, Cliff; Happs, Renee M.; Doeppke, Crissa; Meunier, Kristoffer; Gehan, Jackson; Yue, Fengxia; Lu, Fachuang; Davis, Mark F.

2016-01-01

Abstract Thioacidolysis is a method used to measure the relative content of lignin monomers bound by β‐O‐4 linkages. Current thioacidolysis methods are low‐throughput as they require tedious steps for reaction product concentration prior to analysis using standard GC methods. A quantitative thioacidolysis method that is accessible with general laboratory equipment and uses a non‐chlorinated organic solvent and is tailored for higher‐throughput analysis is reported. The method utilizes lignin arylglycerol monomer standards for calibration, requires 1–2 mg of biomass per assay and has been quantified using fast‐GC techniques including a Low Thermal Mass Modular Accelerated Column Heater (LTM MACH). Cumbersome steps, including standard purification, sample concentrating and drying have been eliminated to help aid in consecutive day‐to‐day analyses needed to sustain a high sample throughput for large screening experiments without the loss of quantitation accuracy. The method reported in this manuscript has been quantitatively validated against a commonly used thioacidolysis method and across two different research sites with three common biomass varieties to represent hardwoods, softwoods, and grasses. PMID:27534715

MULTI-DIMENSIONAL MASS SPECTROMETRY-BASED SHOTGUN LIPIDOMICS AND NOVEL STRATEGIES FOR LIPIDOMIC ANALYSES

PubMed Central

Han, Xianlin; Yang, Kui; Gross, Richard W.

2011-01-01

Since our last comprehensive review on multi-dimensional mass spectrometry-based shotgun lipidomics (Mass Spectrom. Rev. 24 (2005), 367), many new developments in the field of lipidomics have occurred. These developments include new strategies and refinements for shotgun lipidomic approaches that use direct infusion, including novel fragmentation strategies, identification of multiple new informative dimensions for mass spectrometric interrogation, and the development of new bioinformatic approaches for enhanced identification and quantitation of the individual molecular constituents that comprise each cell’s lipidome. Concurrently, advances in liquid chromatography-based platforms and novel strategies for quantitative matrix-assisted laser desorption/ionization mass spectrometry for lipidomic analyses have been developed. Through the synergistic use of this repertoire of new mass spectrometric approaches, the power and scope of lipidomics has been greatly expanded to accelerate progress toward the comprehensive understanding of the pleiotropic roles of lipids in biological systems. PMID:21755525

Light scattering application for quantitative estimation of apoptosis

NASA Astrophysics Data System (ADS)

Bilyy, Rostyslav O.; Stoika, Rostyslav S.; Getman, Vasyl B.; Bilyi, Olexander I.

2004-05-01

Estimation of cell proliferation and apoptosis are in focus of instrumental methods used in modern biomedical sciences. Present study concerns monitoring of functional state of cells, specifically the development of their programmed death or apoptosis. The available methods for such purpose are either very expensive, or require time-consuming operations. Their specificity and sensitivity are frequently not sufficient for making conclusions which could be used in diagnostics or treatment monitoring. We propose a novel method for apoptosis measurement based on quantitative determination of cellular functional state taking into account their physical characteristics. This method uses the patented device -- laser microparticle analyser PRM-6 -- for analyzing light scattering by the microparticles, including cells. The method gives an opportunity for quick, quantitative, simple (without complicated preliminary cell processing) and relatively cheap measurement of apoptosis in cellular population. The elaborated method was used for studying apoptosis expression in murine leukemia cells of L1210 line and human lymphoblastic leukemia cells of K562 line. The results obtained by the proposed method permitted measuring cell number in tested sample, detecting and quantitative characterization of functional state of cells, particularly measuring the ratio of the apoptotic cells in suspension.

Quantitative proteomics in biological research.

PubMed

Wilm, Matthias

2009-10-01

Proteomics has enabled the direct investigation of biological material, at first through the analysis of individual proteins, then of lysates from cell cultures, and finally of extracts from tissues and biopsies from entire organisms. Its latest manifestation - quantitative proteomics - allows deeper insight into biological systems. This article reviews the different methods used to extract quantitative information from mass spectra. It follows the technical developments aimed toward global proteomics, the attempt to characterize every expressed protein in a cell by at least one peptide. When applications of the technology are discussed, the focus is placed on yeast biology. In particular, differential quantitative proteomics, the comparison between an experiment and its control, is very discriminating for proteins involved in the process being studied. When trying to understand biological processes on a molecular level, differential quantitative proteomics tends to give a clearer picture than global transcription analyses. As a result, MS has become an even more indispensable tool for biochemically motivated biological research.

Reinventing the ames test as a quantitative lab that connects classical and molecular genetics.

PubMed

Goodson-Gregg, Nathan; De Stasio, Elizabeth A

2009-01-01

While many institutions use a version of the Ames test in the undergraduate genetics laboratory, students typically are not exposed to techniques or procedures beyond qualitative analysis of phenotypic reversion, thereby seriously limiting the scope of learning. We have extended the Ames test to include both quantitative analysis of reversion frequency and molecular analysis of revertant gene sequences. By giving students a role in designing their quantitative methods and analyses, students practice and apply quantitative skills. To help students connect classical and molecular genetic concepts and techniques, we report here procedures for characterizing the molecular lesions that confer a revertant phenotype. We suggest undertaking reversion of both missense and frameshift mutants to allow a more sophisticated molecular genetic analysis. These modifications and additions broaden the educational content of the traditional Ames test teaching laboratory, while simultaneously enhancing students' skills in experimental design, quantitative analysis, and data interpretation.

A High-Density Genetic Map with Array-Based Markers Facilitates Structural and Quantitative Trait Locus Analyses of the Common Wheat Genome

PubMed Central

Iehisa, Julio Cesar Masaru; Ohno, Ryoko; Kimura, Tatsuro; Enoki, Hiroyuki; Nishimura, Satoru; Okamoto, Yuki; Nasuda, Shuhei; Takumi, Shigeo

2014-01-01

The large genome and allohexaploidy of common wheat have complicated construction of a high-density genetic map. Although improvements in the throughput of next-generation sequencing (NGS) technologies have made it possible to obtain a large amount of genotyping data for an entire mapping population by direct sequencing, including hexaploid wheat, a significant number of missing data points are often apparent due to the low coverage of sequencing. In the present study, a microarray-based polymorphism detection system was developed using NGS data obtained from complexity-reduced genomic DNA of two common wheat cultivars, Chinese Spring (CS) and Mironovskaya 808. After design and selection of polymorphic probes, 13,056 new markers were added to the linkage map of a recombinant inbred mapping population between CS and Mironovskaya 808. On average, 2.49 missing data points per marker were observed in the 201 recombinant inbred lines, with a maximum of 42. Around 40% of the new markers were derived from genic regions and 11% from repetitive regions. The low number of retroelements indicated that the new polymorphic markers were mainly derived from the less repetitive region of the wheat genome. Around 25% of the mapped sequences were useful for alignment with the physical map of barley. Quantitative trait locus (QTL) analyses of 14 agronomically important traits related to flowering, spikes, and seeds demonstrated that the new high-density map showed improved QTL detection, resolution, and accuracy over the original simple sequence repeat map. PMID:24972598

Using Inequality Measures to Incorporate Environmental Justice into Regulatory Analyses

PubMed Central

Harper, Sam; Ruder, Eric; Roman, Henry A.; Geggel, Amelia; Nweke, Onyemaechi; Payne-Sturges, Devon; Levy, Jonathan I.

2013-01-01

Formally evaluating how specific policy measures influence environmental justice is challenging, especially in the context of regulatory analyses in which quantitative comparisons are the norm. However, there is a large literature on developing and applying quantitative measures of health inequality in other settings, and these measures may be applicable to environmental regulatory analyses. In this paper, we provide information to assist policy decision makers in determining the viability of using measures of health inequality in the context of environmental regulatory analyses. We conclude that quantification of the distribution of inequalities in health outcomes across social groups of concern, considering both within-group and between-group comparisons, would be consistent with both the structure of regulatory analysis and the core definition of environmental justice. Appropriate application of inequality indicators requires thorough characterization of the baseline distribution of exposures and risks, leveraging data generally available within regulatory analyses. Multiple inequality indicators may be applicable to regulatory analyses, and the choice among indicators should be based on explicit value judgments regarding the dimensions of environmental justice of greatest interest. PMID:23999551

The relationship between international trade and non-nutritional health outcomes: A systematic review of quantitative studies.

PubMed

Burns, Darren K; Jones, Andrew P; Suhrcke, Marc

2016-03-01

Markets throughout the world have been reducing barriers to international trade and investment in recent years. The resulting increases in levels of international trade and investment have subsequently generated research interest into the potential population health impact. We present a systematic review of quantitative studies investigating the relationship between international trade, foreign direct investment and non-nutritional health outcomes. Articles were systematically collected from the SCOPUS, PubMed, EconLit and Web of Science databases. Due to the heterogeneous nature of the evidence considered, the 16 included articles were subdivided into individual level data analyses, selected country analyses and international panel analyses. Articles were then quality assessed using a tool developed as part of the project. Nine of the studies were assessed to be high quality, six as medium quality, and one as low quality. The evidence from the quantitative literature suggests that overall, there appears to be a beneficial association between international trade and population health. There was also evidence of the importance of foreign direct investment, yet a lack of research considering the direction of causality. Taken together, quantitative research into the relationship between trade and non-nutritional health indicates trade to be beneficial, yet this body of research is still in its infancy. Future quantitative studies based on this foundation will provide a stronger basis on which to inform relevant national and international institutions about the health consequences of trade policies. Copyright © 2016 Elsevier Ltd. All rights reserved.

Analyses of Mobilization Manpower Supply and Demand.

DTIC Science & Technology

1982-03-01

7AD-AI30 148 ANALYSES OF MOBIL ZATION MANPOWER SUPPLY AND DEMAND U) l1 . ADMINISTRATIVE SCIENCES CORP SPRINOFIELD VA BREAU EAL MAR82 ASCR134...79-C-0527 for use in identifying and quantifying issues in the CPAM process, and to employ the model for selected quantitative ard qualitative analyses...nurses and corpsmen) to operate on a Commander FX Microcomputer, to be used by 2 the Bureau of Medicine and Surgery to develop inputs for Navy-wide

Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast

PubMed Central

Jeffares, Daniel C.; Jolly, Clemency; Hoti, Mimoza; Speed, Doug; Shaw, Liam; Rallis, Charalampos; Balloux, Francois; Dessimoz, Christophe; Bähler, Jürg; Sedlazeck, Fritz J.

2017-01-01

Large structural variations (SVs) within genomes are more challenging to identify than smaller genetic variants but may substantially contribute to phenotypic diversity and evolution. We analyse the effects of SVs on gene expression, quantitative traits and intrinsic reproductive isolation in the yeast Schizosaccharomyces pombe. We establish a high-quality curated catalogue of SVs in the genomes of a worldwide library of S. pombe strains, including duplications, deletions, inversions and translocations. We show that copy number variants (CNVs) show a variety of genetic signals consistent with rapid turnover. These transient CNVs produce stoichiometric effects on gene expression both within and outside the duplicated regions. CNVs make substantial contributions to quantitative traits, most notably intracellular amino acid concentrations, growth under stress and sugar utilization in winemaking, whereas rearrangements are strongly associated with reproductive isolation. Collectively, these findings have broad implications for evolution and for our understanding of quantitative traits including complex human diseases. PMID:28117401

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

Molecular genetic analyses in familial and sporadic congenital primary erythrocytosis.

PubMed

Rives, Susana; Pahl, Heike L; Florensa, Lourdes; Bellosillo, Beatriz; Neusuess, Andrea; Estella, Jesus; Debatin, Klaus-Michael; Kohne, Elisabeth; Schwarz, Klaus; Cario, Holger

2007-05-01

Dominant mutations in the erythropoietin receptor (EPOR) gene account for only about 15% of cases of primary congenital erythrocytosis. To search for molecular alterations in patients with this disorder. Sixteen patients with Epo <10 mU/mL were studied, 3 were related. Analyses included EPOR and JAK2 gene sequencing, quantitative PRV-1 RT-PCR, and erythroid colony assays. A novel sporadic EPOR 1453G->A (Trp439Stop) mutation was detected. All familial cases, varied in phenotype, presented the EPOR 1414C->G (Tyr426Stop) mutation. JAK2 mutations are not involved in the pathogenesis of primary congenital erythrocytosis.

USING MICROSOFT OFFICE EXCEL® 2007 TO CONDUCT GENERALIZED MATCHING ANALYSES

PubMed Central

Reed, Derek D

2009-01-01

The generalized matching equation is a robust and empirically supported means of analyzing relations between reinforcement and behavior. Unfortunately, no simple task analysis is available to behavior analysts interested in using the matching equation to evaluate data in clinical or applied settings. This technical article presents a task analysis for the use of Microsoft Excel to analyze and plot the generalized matching equation. Using a data-based case example and a step-by-step guide for completing the analysis, these instructions are intended to promote the use of quantitative analyses by researchers with little to no experience in quantitative analyses or the matching law. PMID:20514196

Using Microsoft Office Excel 2007 to conduct generalized matching analyses.

PubMed

Reed, Derek D

2009-01-01

The generalized matching equation is a robust and empirically supported means of analyzing relations between reinforcement and behavior. Unfortunately, no simple task analysis is available to behavior analysts interested in using the matching equation to evaluate data in clinical or applied settings. This technical article presents a task analysis for the use of Microsoft Excel to analyze and plot the generalized matching equation. Using a data-based case example and a step-by-step guide for completing the analysis, these instructions are intended to promote the use of quantitative analyses by researchers with little to no experience in quantitative analyses or the matching law.

Accuracy of quantitative visual soil assessment

NASA Astrophysics Data System (ADS)

van Leeuwen, Maricke; Heuvelink, Gerard; Stoorvogel, Jetse; Wallinga, Jakob; de Boer, Imke; van Dam, Jos; van Essen, Everhard; Moolenaar, Simon; Verhoeven, Frank; Stoof, Cathelijne

2016-04-01

farmers carried out quantitative visual observations all independently from each other. All observers assessed five sites, having a sand, peat or clay soil. For almost all quantitative visual observations the spread of observed values was low (coefficient of variation < 1.0), except for the number of biopores and gley mottles. Furthermore, farmers' observed mean values were significantly higher than soil scientists' mean values, for soil structure, amount of gley mottles and compaction. This study showed that VSA could be a valuable tool to assess soil quality. Subjectivity, due to the background of the observer, might influence the outcome of visual assessment of some soil properties. In countries where soil analyses can easily be carried out, VSA might be a good replenishment to available soil chemical analyses, and in countries where it is not feasible to carry out soil analyses, VSA might be a good start to assess soil quality.

General quantitative genetic methods for comparative biology: phylogenies, taxonomies and multi-trait models for continuous and categorical characters.

PubMed

Hadfield, J D; Nakagawa, S

2010-03-01

Although many of the statistical techniques used in comparative biology were originally developed in quantitative genetics, subsequent development of comparative techniques has progressed in relative isolation. Consequently, many of the new and planned developments in comparative analysis already have well-tested solutions in quantitative genetics. In this paper, we take three recent publications that develop phylogenetic meta-analysis, either implicitly or explicitly, and show how they can be considered as quantitative genetic models. We highlight some of the difficulties with the proposed solutions, and demonstrate that standard quantitative genetic theory and software offer solutions. We also show how results from Bayesian quantitative genetics can be used to create efficient Markov chain Monte Carlo algorithms for phylogenetic mixed models, thereby extending their generality to non-Gaussian data. Of particular utility is the development of multinomial models for analysing the evolution of discrete traits, and the development of multi-trait models in which traits can follow different distributions. Meta-analyses often include a nonrandom collection of species for which the full phylogenetic tree has only been partly resolved. Using missing data theory, we show how the presented models can be used to correct for nonrandom sampling and show how taxonomies and phylogenies can be combined to give a flexible framework with which to model dependence.

Quantitative Research Methods in Chaos and Complexity: From Probability to Post Hoc Regression Analyses

ERIC Educational Resources Information Center

Gilstrap, Donald L.

2013-01-01

In addition to qualitative methods presented in chaos and complexity theories in educational research, this article addresses quantitative methods that may show potential for future research studies. Although much in the social and behavioral sciences literature has focused on computer simulations, this article explores current chaos and…

[Clinical research XXIII. From clinical judgment to meta-analyses].

PubMed

Rivas-Ruiz, Rodolfo; Castelán-Martínez, Osvaldo D; Pérez-Rodríguez, Marcela; Palacios-Cruz, Lino; Noyola-Castillo, Maura E; Talavera, Juan O

2014-01-01

Systematic reviews (SR) are studies made in order to ask clinical questions based on original articles. Meta-analysis (MTA) is the mathematical analysis of SR. These analyses are divided in two groups, those which evaluate the measured results of quantitative variables (for example, the body mass index -BMI-) and those which evaluate qualitative variables (for example, if a patient is alive or dead, or if he is healing or not). Quantitative variables generally use the mean difference analysis and qualitative variables can be performed using several calculations: odds ratio (OR), relative risk (RR), absolute risk reduction (ARR) and hazard ratio (HR). These analyses are represented through forest plots which allow the evaluation of each individual study, as well as the heterogeneity between studies and the overall effect of the intervention. These analyses are mainly based on Student's t test and chi-squared. To take appropriate decisions based on the MTA, it is important to understand the characteristics of statistical methods in order to avoid misinterpretations.

Impact of vaccine herd-protection effects in cost-effectiveness analyses of childhood vaccinations. A quantitative comparative analysis.

PubMed

Holubar, Marisa; Stavroulakis, Maria Christina; Maldonado, Yvonne; Ioannidis, John P A; Contopoulos-Ioannidis, Despina

2017-01-01

Inclusion of vaccine herd-protection effects in cost-effectiveness analyses (CEAs) can impact the CEAs-conclusions. However, empirical epidemiologic data on the size of herd-protection effects from original studies are limited. We performed a quantitative comparative analysis of the impact of herd-protection effects in CEAs for four childhood vaccinations (pneumococcal, meningococcal, rotavirus and influenza). We considered CEAs reporting incremental-cost-effectiveness-ratios (ICERs) (per quality-adjusted-life-years [QALY] gained; per life-years [LY] gained or per disability-adjusted-life-years [DALY] avoided), both with and without herd protection, while keeping all other model parameters stable. We calculated the size of the ICER-differences without vs with-herd-protection and estimated how often inclusion of herd-protection led to crossing of the cost-effectiveness threshold (of an assumed societal-willingness-to-pay) of $50,000 for more-developed countries or X3GDP/capita (WHO-threshold) for less-developed countries. We identified 35 CEA studies (20 pneumococcal, 4 meningococcal, 8 rotavirus and 3 influenza vaccines) with 99 ICER-analyses (55 per-QALY, 27 per-LY and 17 per-DALY). The median ICER-absolute differences per QALY, LY and DALY (without minus with herd-protection) were $15,620 (IQR: $877 to $48,376); $54,871 (IQR: $787 to $115,026) and $49 (IQR: $15 to $1,636) respectively. When the target-vaccination strategy was not cost-saving without herd-protection, inclusion of herd-protection always resulted in more favorable results. In CEAs that had ICERs above the cost-effectiveness threshold without herd-protection, inclusion of herd-protection led to crossing of that threshold in 45% of the cases. This impacted only CEAs for more developed countries, as all but one CEAs for less developed countries had ICERs below the WHO-cost-effectiveness threshold even without herd-protection. In several analyses, recommendation for the adoption of the target

Impact of vaccine herd-protection effects in cost-effectiveness analyses of childhood vaccinations. A quantitative comparative analysis

PubMed Central

Maldonado, Yvonne; Ioannidis, John P. A.; Contopoulos-Ioannidis, Despina

2017-01-01

Background Inclusion of vaccine herd-protection effects in cost-effectiveness analyses (CEAs) can impact the CEAs-conclusions. However, empirical epidemiologic data on the size of herd-protection effects from original studies are limited. Methods We performed a quantitative comparative analysis of the impact of herd-protection effects in CEAs for four childhood vaccinations (pneumococcal, meningococcal, rotavirus and influenza). We considered CEAs reporting incremental-cost-effectiveness-ratios (ICERs) (per quality-adjusted-life-years [QALY] gained; per life-years [LY] gained or per disability-adjusted-life-years [DALY] avoided), both with and without herd protection, while keeping all other model parameters stable. We calculated the size of the ICER-differences without vs with-herd-protection and estimated how often inclusion of herd-protection led to crossing of the cost-effectiveness threshold (of an assumed societal-willingness-to-pay) of $50,000 for more-developed countries or X3GDP/capita (WHO-threshold) for less-developed countries. Results We identified 35 CEA studies (20 pneumococcal, 4 meningococcal, 8 rotavirus and 3 influenza vaccines) with 99 ICER-analyses (55 per-QALY, 27 per-LY and 17 per-DALY). The median ICER-absolute differences per QALY, LY and DALY (without minus with herd-protection) were $15,620 (IQR: $877 to $48,376); $54,871 (IQR: $787 to $115,026) and $49 (IQR: $15 to $1,636) respectively. When the target-vaccination strategy was not cost-saving without herd-protection, inclusion of herd-protection always resulted in more favorable results. In CEAs that had ICERs above the cost-effectiveness threshold without herd-protection, inclusion of herd-protection led to crossing of that threshold in 45% of the cases. This impacted only CEAs for more developed countries, as all but one CEAs for less developed countries had ICERs below the WHO-cost-effectiveness threshold even without herd-protection. In several analyses, recommendation for the

Quantitative solid-state 13C nuclear magnetic resonance spectrometric analyses of wood xylen: effect of increasing carbohydrate content

USGS Publications Warehouse

Bates, A.L.; Hatcher, P.G.

1992-01-01

Isolated lignin with a low carbohydrate content was spiked with increasing amounts of alpha-cellulose, and then analysed by solid-state 13C nuclear magnetic resonance (NMR) using cross-polarization with magic angle spinning (CPMAS) and dipolar dephasing methods in order to assess the quantitative reliability of CPMAS measurement of carbohydrate content and to determine how increasingly intense resonances for carbohydrate carbons affect calculations of the degree of lignin's aromatic ring substitution and methoxyl carbon content. Comparisons were made of the carbohydrate content calculated by NMR with carbohydrate concentrations obtained by phenol-sulfuric acid assay and by the calculation from the known amounts of cellulose added. The NMR methods used in this study yield overestimates for carbohydrate carbons due to resonance area overlap from the aliphatic side chain carbons of lignin. When corrections are made for these overlapping resonance areas, the NMR results agree very well with results obtained by other methods. Neither the calculated methoxyl carbon content nor the degree of aromatic ring substitution in lignin, both calculated from dipolar dephasing spectra, change with cellulose content. Likewise, lignin methoxyl content does not correlate with cellulose abundance when measured by integration of CPMAS spectra. ?? 1992.

Quantitative analyses of the behavior of exogenously added bacteria during an acidulocomposting process.

PubMed

Suematsu, Takatoshi; Yamashita, Satoshi; Hemmi, Hisashi; Yoshinari, Ayaka; Shimoyama, Takefumi; Nakayama, Toru; Nishino, Tokuzo

2012-07-01

The behavior of adventitious bacteria during an acidulocomposting process was quantitatively analyzed in garbage-free trials. The numbers of the added Bacillus subtilis and Pseudomonas putida cells diminished in a first-order manner with t(1/2) values of 0.45d and 0.79d, respectively, consistent with the observed stability of the acidulocomposting function. Copyright © 2012 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Quantitative proteomic analyses of the microbial degradation of estrone under various background nitrogen and carbon conditions.

PubMed

Du, Zhe; Chen, Yinguang; Li, Xu

2017-10-15

Microbial degradation of estrogenic compounds can be affected by the nitrogen source and background carbon in the environment. However, the underlying mechanisms are not well understood. The objective of this study was to elucidate the molecular mechanisms of estrone (E1) biodegradation at the protein level under various background nitrogen (nitrate or ammonium) and carbon conditions (no background carbon, acetic acid, or humic acid as background carbon) by a newly isolated bacterial strain. The E1 degrading bacterial strain, Hydrogenophaga atypica ZD1, was isolated from river sediments and its proteome was characterized under various experimental conditions using quantitative proteomics. Results show that the E1 degradation rate was faster when ammonium was used as the nitrogen source than with nitrate. The degradation rate was also faster when either acetic acid or humic acid was present in the background. Proteomics analyses suggested that the E1 biodegradation products enter the tyrosine metabolism pathway. Compared to nitrate, ammonium likely promoted E1 degradation by increasing the activities of the branched-chain-amino-acid aminotransferase (IlvE) and enzymes involved in the glutamine synthetase-glutamine oxoglutarate aminotransferase (GS-GOGAT) pathway. The increased E1 degradation rate with acetic acid or humic acid in the background can also be attributed to the up-regulation of IlvE. Results from this study can help predict and explain E1 biodegradation kinetics under various environmental conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Does the inclusion of grey literature influence estimates of intervention effectiveness reported in meta-analyses?

PubMed

McAuley, L; Pham, B; Tugwell, P; Moher, D

2000-10-07

The inclusion of only a subset of all available evidence in a meta-analysis may introduce biases and threaten its validity; this is particularly likely if the subset of included studies differ from those not included, which may be the case for published and grey literature (unpublished studies, with limited distribution). We set out to examine whether exclusion of grey literature, compared with its inclusion in meta-analysis, provides different estimates of the effectiveness of interventions assessed in randomised trials. From a random sample of 135 meta-analyses, we identified and retrieved 33 publications that included both grey and published primary studies. The 33 publications contributed 41 separate meta-analyses from several disease areas. General characteristics of the meta-analyses and associated studies and outcome data at the trial level were collected. We explored the effects of the inclusion of grey literature on the quantitative results using logistic-regression analyses. 33% of the meta-analyses were found to include some form of grey literature. The grey literature, when included, accounts for between 4.5% and 75% of the studies in a meta-analysis. On average, published work, compared with grey literature, yielded significantly larger estimates of the intervention effect by 15% (ratio of odds ratios=1.15 [95% CI 1.04-1.28]). Excluding abstracts from the analysis further compounded the exaggeration (1.33 [1.10-1.60]). The exclusion of grey literature from meta-analyses can lead to exaggerated estimates of intervention effectiveness. In general, meta-analysts should attempt to identify, retrieve, and include all reports, grey and published, that meet predefined inclusion criteria.

Analyser-based phase contrast image reconstruction using geometrical optics.

PubMed

Kitchen, M J; Pavlov, K M; Siu, K K W; Menk, R H; Tromba, G; Lewis, R A

2007-07-21

Analyser-based phase contrast imaging can provide radiographs of exceptional contrast at high resolution (<100 microm), whilst quantitative phase and attenuation information can be extracted using just two images when the approximations of geometrical optics are satisfied. Analytical phase retrieval can be performed by fitting the analyser rocking curve with a symmetric Pearson type VII function. The Pearson VII function provided at least a 10% better fit to experimentally measured rocking curves than linear or Gaussian functions. A test phantom, a hollow nylon cylinder, was imaged at 20 keV using a Si(1 1 1) analyser at the ELETTRA synchrotron radiation facility. Our phase retrieval method yielded a more accurate object reconstruction than methods based on a linear fit to the rocking curve. Where reconstructions failed to map expected values, calculations of the Takagi number permitted distinction between the violation of the geometrical optics conditions and the failure of curve fitting procedures. The need for synchronized object/detector translation stages was removed by using a large, divergent beam and imaging the object in segments. Our image acquisition and reconstruction procedure enables quantitative phase retrieval for systems with a divergent source and accounts for imperfections in the analyser.

A high-density genetic map with array-based markers facilitates structural and quantitative trait locus analyses of the common wheat genome.

PubMed

Iehisa, Julio Cesar Masaru; Ohno, Ryoko; Kimura, Tatsuro; Enoki, Hiroyuki; Nishimura, Satoru; Okamoto, Yuki; Nasuda, Shuhei; Takumi, Shigeo

2014-10-01

The large genome and allohexaploidy of common wheat have complicated construction of a high-density genetic map. Although improvements in the throughput of next-generation sequencing (NGS) technologies have made it possible to obtain a large amount of genotyping data for an entire mapping population by direct sequencing, including hexaploid wheat, a significant number of missing data points are often apparent due to the low coverage of sequencing. In the present study, a microarray-based polymorphism detection system was developed using NGS data obtained from complexity-reduced genomic DNA of two common wheat cultivars, Chinese Spring (CS) and Mironovskaya 808. After design and selection of polymorphic probes, 13,056 new markers were added to the linkage map of a recombinant inbred mapping population between CS and Mironovskaya 808. On average, 2.49 missing data points per marker were observed in the 201 recombinant inbred lines, with a maximum of 42. Around 40% of the new markers were derived from genic regions and 11% from repetitive regions. The low number of retroelements indicated that the new polymorphic markers were mainly derived from the less repetitive region of the wheat genome. Around 25% of the mapped sequences were useful for alignment with the physical map of barley. Quantitative trait locus (QTL) analyses of 14 agronomically important traits related to flowering, spikes, and seeds demonstrated that the new high-density map showed improved QTL detection, resolution, and accuracy over the original simple sequence repeat map. © The Author 2014. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Industrial ecology: Quantitative methods for exploring a lower carbon future

NASA Astrophysics Data System (ADS)

Thomas, Valerie M.

2015-03-01

Quantitative methods for environmental and cost analyses of energy, industrial, and infrastructure systems are briefly introduced and surveyed, with the aim of encouraging broader utilization and development of quantitative methods in sustainable energy research. Material and energy flow analyses can provide an overall system overview. The methods of engineering economics and cost benefit analysis, such as net present values, are the most straightforward approach for evaluating investment options, with the levelized cost of energy being a widely used metric in electricity analyses. Environmental lifecycle assessment has been extensively developed, with both detailed process-based and comprehensive input-output approaches available. Optimization methods provide an opportunity to go beyond engineering economics to develop detailed least-cost or least-impact combinations of many different choices.

Effectiveness of a systematic approach to promote intersectoral collaboration in comprehensive school health promotion-a multiple-case study using quantitative and qualitative data.

PubMed

Pucher, Katharina K; Candel, Math J J M; Krumeich, Anja; Boot, Nicole M W M; De Vries, Nanne K

2015-07-05

We report on the longitudinal quantitative and qualitative data resulting from a two-year trajectory (2008-2011) based on the DIagnosis of Sustainable Collaboration (DISC) model. This trajectory aimed to support regional coordinators of comprehensive school health promotion (CSHP) in systematically developing change management and project management to establish intersectoral collaboration. Multilevel analyses of quantitative data on the determinants of collaborations according to the DISC model were done, with 90 respondents (response 57 %) at pretest and 69 respondents (52 %) at posttest. Nvivo analyses of the qualitative data collected during the trajectory included minutes of monthly/bimonthly personal/telephone interviews (N = 65) with regional coordinators, and documents they produced about their activities. Quantitative data showed major improvements in change management and project management. There were also improvements in consensus development, commitment formation, formalization of the CSHP, and alignment of policies, although organizational problems within the collaboration increased. Content analyses of qualitative data identified five main management styles, including (1) facilitating active involvement of relevant parties; (2) informing collaborating parties; (3) controlling and (4) supporting their task accomplishment; and (5) coordinating the collaborative processes. We have contributed to the fundamental understanding of the development of intersectoral collaboration by combining qualitative and quantitative data. Our results support a systematic approach to intersectoral collaboration using the DISC model. They also suggest five main management styles to improve intersectoral collaboration in the initial stage. The outcomes are useful for health professionals involved in similar ventures.

A comparative study of quantitative microsegregation analyses performed during the solidification of the Ni-base superalloy CMSX-10

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

Seo, Seong-Moon, E-mail: castme@kims.re.kr; Jeong, Hi-Won; Ahn, Young-Keun

Quantitative microsegregation analyses were systematically carried out during the solidification of the Ni-base superalloy CMSX-10 to clarify the methodological effect on the quantification of microsegregation and to fully understand the solidification microstructure. Three experimental techniques, namely, mushy zone quenching (MZQ), planar directional solidification followed by quenching (PDSQ), and random sampling (RS), were implemented for the analysis of microsegregation tendency and the magnitude of solute elements by electron probe microanalysis. The microprobe data and the calculation results of the diffusion field ahead of the solid/liquid (S/L) interface of PDSQ samples revealed that the liquid composition at the S/L interface is significantlymore » influenced by quenching. By applying the PDSQ technique, it was also found that the partition coefficients of all solute elements do not change appreciably during the solidification of primary γ. All three techniques could reasonably predict the segregation behavior of most solute elements. Nevertheless, the RS approach has a tendency to overestimate the magnitude of segregation for most solute elements when compared to the MZQ and PDSQ techniques. Moreover, the segregation direction of Cr and Mo predicted by the RS approach was found to be opposite from the results obtained by the MZQ and PDSQ techniques. This conflicting segregation behavior of Cr and Mo was discussed intensively. It was shown that the formation of Cr-rich areas near the γ/γ′ eutectic in various Ni-base superalloys, including the CMSX-10 alloy, could be successfully explained by the results of microprobe analysis performed on a sample quenched during the planar directional solidification of γ/γ′ eutectic. - Highlights: • Methodological effect on the quantification of microsegregation was clarified. • The liquid composition at the S/L interface was influenced by quenching. • The segregation direction of Cr varied depending on

Impact of Including Higher Actinides in Fast Reactor Transmutation Analyses

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

B. Forget; M. Asgari; R. Ferrer

2007-09-01

Previous fast reactor transmutation studies generally disregarded higher mass minor actinides beyond Cm-246 due to various considerations including deficiencies in nuclear cross-section data. Although omission of these higher mass actinides does not significantly impact the neutronic calculations and fuel cycle performance parameters follow-on neutron dose calculations related to fuel recycling, transportation and handling are significantly impacted. This report shows that including the minor actinides in the equilibrium fast reactor calculations will increase the predicted neutron emission by about 30%. In addition a sensitivity study was initiated by comparing the impact of different cross-section evaluation file for representing these minor actinides.

Quantitative approaches in climate change ecology

PubMed Central

Brown, Christopher J; Schoeman, David S; Sydeman, William J; Brander, Keith; Buckley, Lauren B; Burrows, Michael; Duarte, Carlos M; Moore, Pippa J; Pandolfi, John M; Poloczanska, Elvira; Venables, William; Richardson, Anthony J

2011-01-01

Contemporary impacts of anthropogenic climate change on ecosystems are increasingly being recognized. Documenting the extent of these impacts requires quantitative tools for analyses of ecological observations to distinguish climate impacts in noisy data and to understand interactions between climate variability and other drivers of change. To assist the development of reliable statistical approaches, we review the marine climate change literature and provide suggestions for quantitative approaches in climate change ecology. We compiled 267 peer-reviewed articles that examined relationships between climate change and marine ecological variables. Of the articles with time series data (n = 186), 75% used statistics to test for a dependency of ecological variables on climate variables. We identified several common weaknesses in statistical approaches, including marginalizing other important non-climate drivers of change, ignoring temporal and spatial autocorrelation, averaging across spatial patterns and not reporting key metrics. We provide a list of issues that need to be addressed to make inferences more defensible, including the consideration of (i) data limitations and the comparability of data sets; (ii) alternative mechanisms for change; (iii) appropriate response variables; (iv) a suitable model for the process under study; (v) temporal autocorrelation; (vi) spatial autocorrelation and patterns; and (vii) the reporting of rates of change. While the focus of our review was marine studies, these suggestions are equally applicable to terrestrial studies. Consideration of these suggestions will help advance global knowledge of climate impacts and understanding of the processes driving ecological change.

Quantitative PCR measurements of Escherichia coli including shiga toxin-producing E. coli (STEC) in animal feces and environmental waters.

PubMed

Ahmed, W; Gyawali, P; Toze, S

2015-03-03

Quantitative PCR (qPCR) assays were used to determine the concentrations of E. coli including shiga toxin-producing E. coli (STEC) associated virulence genes (eaeA, stx1, stx2, and hlyA) in ten animal species (fecal sources) and environmental water samples in Southeast Queensland, Australia. The mean Log10 concentrations and standard deviations of E. coli 23S rRNA across fecal sources ranged from 1.3 ± 0.1 (horse) to 6.3 ± 0.4 (cattle wastewater) gene copies at a test concentration of 10 ng of DNA. The differences in mean concentrations of E. coli 23S rRNA gene copies among fecal source samples were significantly different from each other (P < 0.0001). Among the virulence genes, stx2 (25%, 95% CI, 17-33%) was most prevalent among fecal sources, followed by eaeA (19%, 95% CI, 12-27%), stx1 (11%, 95% CI, 5%-17%) and hlyA (8%, 95% CI, 3-13%). The Log10 concentrations of STEC virulence genes in cattle wastewater samples ranged from 3.8 to 5.0 gene copies at a test concentration of 10 ng of DNA. Of the 18 environmental water samples tested, three (17%) were positive for eaeA and two (11%) samples were also positive for the stx2 virulence genes. The data presented in this study will aid in the estimation of quantitative microbial risk assessment (QMRA) from fecal pollution of domestic and wild animals in drinking/recreational water catchments.

Environmental Sustainability - Including Land and Water Use

EPA Science Inventory

Assessments of environmental sustainability can be conducted in many ways with one of the most quantitative methods including Life Cycle Impact Assessment (LCIA). While historically LCIA has included a comprehensive list of impact categories including: ozone depletion, global c...

Quantitative 4D analyses of epithelial folding during Drosophila gastrulation.

PubMed

Khan, Zia; Wang, Yu-Chiun; Wieschaus, Eric F; Kaschube, Matthias

2014-07-01

Understanding the cellular and mechanical processes that underlie the shape changes of individual cells and their collective behaviors in a tissue during dynamic and complex morphogenetic events is currently one of the major frontiers in developmental biology. The advent of high-speed time-lapse microscopy and its use in monitoring the cellular events in fluorescently labeled developing organisms demonstrate tremendous promise in establishing detailed descriptions of these events and could potentially provide a foundation for subsequent hypothesis-driven research strategies. However, obtaining quantitative measurements of dynamic shapes and behaviors of cells and tissues in a rapidly developing metazoan embryo using time-lapse 3D microscopy remains technically challenging, with the main hurdle being the shortage of robust imaging processing and analysis tools. We have developed EDGE4D, a software tool for segmenting and tracking membrane-labeled cells using multi-photon microscopy data. Our results demonstrate that EDGE4D enables quantification of the dynamics of cell shape changes, cell interfaces and neighbor relations at single-cell resolution during a complex epithelial folding event in the early Drosophila embryo. We expect this tool to be broadly useful for the analysis of epithelial cell geometries and movements in a wide variety of developmental contexts. © 2014. Published by The Company of Biologists Ltd.

Microfluidics-based digital quantitative PCR for single-cell small RNA quantification.

PubMed

Yu, Tian; Tang, Chong; Zhang, Ying; Zhang, Ruirui; Yan, Wei

2017-09-01

Quantitative analyses of small RNAs at the single-cell level have been challenging because of limited sensitivity and specificity of conventional real-time quantitative PCR methods. A digital quantitative PCR (dqPCR) method for miRNA quantification has been developed, but it requires the use of proprietary stem-loop primers and only applies to miRNA quantification. Here, we report a microfluidics-based dqPCR (mdqPCR) method, which takes advantage of the Fluidigm BioMark HD system for both template partition and the subsequent high-throughput dqPCR. Our mdqPCR method demonstrated excellent sensitivity and reproducibility suitable for quantitative analyses of not only miRNAs but also all other small RNA species at the single-cell level. Using this method, we discovered that each sperm has a unique miRNA profile. © The Authors 2017. Published by Oxford University Press on behalf of Society for the Study of Reproduction. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Systematic Review of Health Economic Analyses of Measles and Rubella Immunization Interventions.

PubMed

Thompson, Kimberly M; Odahowski, Cassie L

2016-07-01

Economic analyses for vaccine-preventable diseases provide important insights about the value of prevention. We reviewed the literature to identify all of the peer-reviewed, published economic analyses of interventions related to measles and rubella immunization options to assess the different types of analyses performed and characterize key insights. We searched PubMed, the Science Citation Index, and references from relevant articles for studies in English and found 67 analyses that reported primary data and quantitative estimates of benefit-cost or cost-effectiveness analyses for measles and/or rubella immunization interventions. We removed studies that we characterized as cost-minimization analyses from this sample because they generally provide insights that focused on more optimal strategies to achieve the same health outcome. The 67 analyses we included demonstrate the large economic benefits associated with preventing measles and rubella infections using vaccines and the benefit of combining measles and rubella antigens into a formulation that saves the costs associated with injecting the vaccines separately. Despite the importance of population immunity and dynamic viral transmission, most of the analyses used static models to estimate cases prevented and characterize benefits, although the use of dynamic models continues to increase. Many of the analyses focused on characterizing the most significant adverse outcomes (e.g., mortality for measles, congenital rubella syndrome for rubella) and/or only direct costs, and the most complete analyses present data from high-income countries. © 2014 Society for Risk Analysis.

Advances in the Quantitative Characterization of the Shape of Ash-Sized Pyroclast Populations: Fractal Analyses Coupled to Micro- and Nano-Computed Tomography Techniques

NASA Astrophysics Data System (ADS)

Rausch, J.; Vonlanthen, P.; Grobety, B. H.

2014-12-01

The quantification of shape parameters in pyroclasts is fundamental to infer the dominant type of magma fragmentation (magmatic vs. phreatomagmatic), as well as the behavior of volcanic plumes and clouds in the atmosphere. In a case study aiming at reconstructing the fragmentation mechanisms triggering maar eruptions in two geologically and compositionally distinctive volcanic fields (West and East Eifel, Germany), the shapes of a large number of ash particle contours obtained from SEM images were analyzed by a dilation-based fractal method. Volcanic particle contours are pseudo-fractals showing mostly two distinct slopes in Richardson plots related to the fractal dimensions D1 (small-scale "textural" dimension) and D2 (large-scale "morphological" dimension). The validity of the data obtained from 2D sections was tested by analysing SEM micro-CT slices of one particle cut in different orientations and positions. Results for West Eifel maar particles yield large D1 values (> 1.023), resembling typical values of magmatic particles, which are characterized by a complex shape, especially at small scales. In contrast, the D1 values of ash particles from one East Eifel maar deposit are much smaller, coinciding with the fractal dimensions obtained from phreatomagmatic end-member particles. These quantitative morphological analyses suggest that the studied maar eruptions were triggered by two different fragmentation processes: phreatomagmatic in the East Eifel and magmatic in the West Eifel. The application of fractal analysis to quantitatively characterize the shape of pyroclasts and the linking of fractal dimensions to specific fragmentation processes has turned out to be a very promising tool for studying the fragmentation history of any volcanic eruption. The next step is to extend morphological analysis of volcanic particles to 3 dimensions. SEM micro-CT, already applied in this study, offers the required resolution, but is not suitable for the analysis of a large

Congruent climate-related genecological responses from molecular markers and quantitative traits for western white pine (Pinus monticola)

Treesearch

Bryce A. Richardson; Gerald E. Rehfeldt; Mee-Sook Kim

2009-01-01

Analyses of molecular and quantitative genetic data demonstrate the existence of congruent climate-related patterns in western white pine (Pinus monticola). Two independent studies allowed comparisons of amplified fragment length polymorphism (AFLP) markers with quantitative variation in adaptive traits. Principal component analyses...

Quantitative Susceptibility Mapping after Sports-Related Concussion.

PubMed

Koch, K M; Meier, T B; Karr, R; Nencka, A S; Muftuler, L T; McCrea, M

2018-06-07

Quantitative susceptibility mapping using MR imaging can assess changes in brain tissue structure and composition. This report presents preliminary results demonstrating changes in tissue magnetic susceptibility after sports-related concussion. Longitudinal quantitative susceptibility mapping metrics were produced from imaging data acquired from cohorts of concussed and control football athletes. One hundred thirty-six quantitative susceptibility mapping datasets were analyzed across 3 separate visits (24 hours after injury, 8 days postinjury, and 6 months postinjury). Longitudinal quantitative susceptibility mapping group analyses were performed on stability-thresholded brain tissue compartments and selected subregions. Clinical concussion metrics were also measured longitudinally in both cohorts and compared with the measured quantitative susceptibility mapping. Statistically significant increases in white matter susceptibility were identified in the concussed athlete group during the acute (24 hour) and subacute (day 8) period. These effects were most prominent at the 8-day visit but recovered and showed no significant difference from controls at the 6-month visit. The subcortical gray matter showed no statistically significant group differences. Observed susceptibility changes after concussion appeared to outlast self-reported clinical recovery metrics at a group level. At an individual subject level, susceptibility increases within the white matter showed statistically significant correlations with return-to-play durations. The results of this preliminary investigation suggest that sports-related concussion can induce physiologic changes to brain tissue that can be detected using MR imaging-based magnetic susceptibility estimates. In group analyses, the observed tissue changes appear to persist beyond those detected on clinical outcome assessments and were associated with return-to-play duration after sports-related concussion. © 2018 by American Journal of

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

DEMOGRAPHY AND VIABILITY ANALYSES OF A DIAMONDBACK TERRAPIN POPULATION

EPA Science Inventory

The diamondback terrapin Malaclemys terrapin is a long-lived species with special management requirements, but quantitative analyses to support management are lacking. I analyzed mark-recapture data and constructed an age-classified matrix population model to determine the status...

A generalised individual-based algorithm for modelling the evolution of quantitative herbicide resistance in arable weed populations.

PubMed

Liu, Chun; Bridges, Melissa E; Kaundun, Shiv S; Glasgow, Les; Owen, Micheal Dk; Neve, Paul

2017-02-01

Simulation models are useful tools for predicting and comparing the risk of herbicide resistance in weed populations under different management strategies. Most existing models assume a monogenic mechanism governing herbicide resistance evolution. However, growing evidence suggests that herbicide resistance is often inherited in a polygenic or quantitative fashion. Therefore, we constructed a generalised modelling framework to simulate the evolution of quantitative herbicide resistance in summer annual weeds. Real-field management parameters based on Amaranthus tuberculatus (Moq.) Sauer (syn. rudis) control with glyphosate and mesotrione in Midwestern US maize-soybean agroecosystems demonstrated that the model can represent evolved herbicide resistance in realistic timescales. Sensitivity analyses showed that genetic and management parameters were impactful on the rate of quantitative herbicide resistance evolution, whilst biological parameters such as emergence and seed bank mortality were less important. The simulation model provides a robust and widely applicable framework for predicting the evolution of quantitative herbicide resistance in summer annual weed populations. The sensitivity analyses identified weed characteristics that would favour herbicide resistance evolution, including high annual fecundity, large resistance phenotypic variance and pre-existing herbicide resistance. Implications for herbicide resistance management and potential use of the model are discussed. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Status and future of Quantitative Microbiological Risk Assessment in China

PubMed Central

Dong, Q.L.; Barker, G.C.; Gorris, L.G.M.; Tian, M.S.; Song, X.Y.; Malakar, P.K.

2015-01-01

Since the implementation of the Food Safety Law of the People's Republic of China in 2009 use of Quantitative Microbiological Risk Assessment (QMRA) has increased. QMRA is used to assess the risk posed to consumers by pathogenic bacteria which cause the majority of foodborne outbreaks in China. This review analyses the progress of QMRA research in China from 2000 to 2013 and discusses 3 possible improvements for the future. These improvements include planning and scoping to initiate QMRA, effectiveness of microbial risk assessment utility for risk management decision making, and application of QMRA to establish appropriate Food Safety Objectives. PMID:26089594

Focus Groups in Elderly Ophthalmologic Patients: Setting the Stage for Quantitative Preference Elicitation.

PubMed

Danner, Marion; Vennedey, Vera; Hiligsmann, Mickaël; Fauser, Sascha; Stock, Stephanie

2016-02-01

Patients suffering from age-related macular degeneration (AMD) are rarely actively involved in decision-making, despite facing preference-sensitive treatment decisions. This paper presents a qualitative study to prepare quantitative preference elicitation in AMD patients. The aims of this study were (1) to gain familiarity with and learn about the special requirements of the AMD patient population for quantitative data collection; and (2) to select/refine patient-relevant treatment attributes and levels, and gain insights into preference structures. Semi-structured focus group interviews were performed. An interview guide including preselected categories in the form of seven potentially patient-relevant treatment attributes was followed. To identify the most patient-relevant treatment attributes, a ranking exercise was performed. Deductive content analyses were done by two independent reviewers for each attribute to derive subcategories (potential levels of attributes) and depict preference trends. The focus group interviews included 21 patients. The interviews revealed that quantitative preference surveys in this population will have to be interviewer assisted to make the survey feasible for patients. The five most patient-relevant attributes were the effect on visual function [ranking score (RS): 139], injection frequency (RS: 101), approval status (RS: 83), side effects (RS: 79), and monitoring frequency (RS: 76). Attribute and level refinement was based on patients' statements. Preference trends and dependencies between attributes informed the quantitative instrument design. This study suggests that qualitative research is a very helpful step to prepare the design and administration of quantitative preference elicitation instruments. It especially facilitated familiarization with the target population and its preferences, and it supported attribute/level refinement.

A quantitative telomeric chromatin isolation protocol identifies different telomeric states

NASA Astrophysics Data System (ADS)

Grolimund, Larissa; Aeby, Eric; Hamelin, Romain; Armand, Florence; Chiappe, Diego; Moniatte, Marc; Lingner, Joachim

2013-11-01

Telomere composition changes during tumourigenesis, aging and in telomere syndromes in a poorly defined manner. Here we develop a quantitative telomeric chromatin isolation protocol (QTIP) for human cells, in which chromatin is cross-linked, immunopurified and analysed by mass spectrometry. QTIP involves stable isotope labelling by amino acids in cell culture (SILAC) to compare and identify quantitative differences in telomere protein composition of cells from various states. With QTIP, we specifically enrich telomeric DNA and all shelterin components. We validate the method characterizing changes at dysfunctional telomeres, and identify and validate known, as well as novel telomere-associated polypeptides including all THO subunits, SMCHD1 and LRIF1. We apply QTIP to long and short telomeres and detect increased density of SMCHD1 and LRIF1 and increased association of the shelterins TRF1, TIN2, TPP1 and POT1 with long telomeres. Our results validate QTIP to study telomeric states during normal development and in disease.

A thioacidolysis method tailored for higher-throughput quantitative analysis of lignin monomers

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

Harman-Ware, Anne E.; Foster, Cliff; Happs, Renee M.

Thioacidolysis is a method used to measure the relative content of lignin monomers bound by β-O-4 linkages. Current thioacidolysis methods are low-throughput as they require tedious steps for reaction product concentration prior to analysis using standard GC methods. A quantitative thioacidolysis method that is accessible with general laboratory equipment and uses a non-chlorinated organic solvent and is tailored for higher-throughput analysis is reported. The method utilizes lignin arylglycerol monomer standards for calibration, requires 1-2 mg of biomass per assay and has been quantified using fast-GC techniques including a Low Thermal Mass Modular Accelerated Column Heater (LTM MACH). Cumbersome steps, includingmore » standard purification, sample concentrating and drying have been eliminated to help aid in consecutive day-to-day analyses needed to sustain a high sample throughput for large screening experiments without the loss of quantitation accuracy. As a result, the method reported in this manuscript has been quantitatively validated against a commonly used thioacidolysis method and across two different research sites with three common biomass varieties to represent hardwoods, softwoods, and grasses.« less

A thioacidolysis method tailored for higher-throughput quantitative analysis of lignin monomers

DOE PAGES

Harman-Ware, Anne E.; Foster, Cliff; Happs, Renee M.; ...

2016-09-14

Thioacidolysis is a method used to measure the relative content of lignin monomers bound by β-O-4 linkages. Current thioacidolysis methods are low-throughput as they require tedious steps for reaction product concentration prior to analysis using standard GC methods. A quantitative thioacidolysis method that is accessible with general laboratory equipment and uses a non-chlorinated organic solvent and is tailored for higher-throughput analysis is reported. The method utilizes lignin arylglycerol monomer standards for calibration, requires 1-2 mg of biomass per assay and has been quantified using fast-GC techniques including a Low Thermal Mass Modular Accelerated Column Heater (LTM MACH). Cumbersome steps, includingmore » standard purification, sample concentrating and drying have been eliminated to help aid in consecutive day-to-day analyses needed to sustain a high sample throughput for large screening experiments without the loss of quantitation accuracy. As a result, the method reported in this manuscript has been quantitatively validated against a commonly used thioacidolysis method and across two different research sites with three common biomass varieties to represent hardwoods, softwoods, and grasses.« less

Clinicopathological characteristics including BRAF V600E mutation status and PET/CT findings in papillary thyroid carcinoma.

PubMed

Choi, Eun Kyoung; Chong, Ari; Ha, Jung-Min; Jung, Chan Kwon; O, Joo Hyun; Kim, Sung Hoon

2017-07-01

We assessed the associations between FDG uptake in primary papillary thyroid carcinomas (PTCs) and clinicopathological features, including the BRAF V600E mutation, using quantitative and qualitative analyses of preoperative PET/CT data. This was a retrospective review of 106 patients with PTC who underwent PET/CT scans between February 2009 and January 2011 before undergoing total thyroidectomy. Data collected from surgical specimens were compared with FDG uptake in the primary tumour using quantitative and qualitative analyses of preoperative PET/CT data. Clinicopathological data included the primary tumour size, subtype, capsular invasion, extrathyroid extension, multifocality, BRAF V600E mutation status, lymph node metastasis and distant metastasis. The SUVmax of the primary tumour was significantly higher in patients with a primary tumour >1 cm, extrathyroid extension or the BRAF V600E mutation than in patients without these features (P<.001, .049 and <.001). Univariate analyses showed that primary tumour size, extrathyroid extension and BRAF V600E mutation status were associated with the SUVmax of the PTC. Multivariate analysis indicated that primary tumour size and the BRAF V600E mutation were associated with the SUVmax of the PTC. In a visual assessment, the primary tumour size was larger in FDG-avid than in non-FDG-avid PTCs (P<.001). There was no significant difference in the presence of multifocality, thyroid capsular invasion, extrathyroid extension, BRAF V600E mutation, lymph node metastasis or distant metastasis between FDG-avid and non-FDG-avid PTCs. Primary tumour size and the BRAF V600E mutation are significant factors associated with the SUVmax on preoperative PET/CT in patients with PTC. © 2017 John Wiley & Sons Ltd.

Diagnostic Comparison of Meteorological Analyses during the 2002 Antarctic Winter

NASA Technical Reports Server (NTRS)

Manney, Gloria L.; Allen, Douglas R.; Kruger, Kirstin; Naujokat, Barbara; Santee, Michelle L.; Sabutis, Joseph L.; Pawson, Steven; Swinbank, Richard; Randall, Cora E.; Simmons, Adrian J.;

Correlation between quantitative and semiquantitative parameters in DCE-MRI with a blood pool agent in rectal cancer: can semiquantitative parameters be used as a surrogate for quantitative parameters?

PubMed

Dijkhoff, Rebecca A P; Maas, Monique; Martens, Milou H; Papanikolaou, Nikolaos; Lambregts, Doenja M J; Beets, Geerard L; Beets-Tan, Regina G H

2017-05-01

The aim of this study was to assess correlation between quantitative and semiquantitative parameters in dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) in rectal cancer patients, both in a primary staging and restaging setting. Nineteen patients were included with DCE-MRI before and/or after neoadjuvant therapy. DCE-MRI was performed with gadofosveset trisodium (Ablavar ® , Lantheus Medical Imaging, North Billerica, Massachusetts, USA). Regions of interest were placed in the tumor and quantitative parameters were extracted with Olea Sphere 2.2 software permeability module using the extended Tofts model. Semiquantitative parameters were calculated on a pixel-by-pixel basis. Spearman rank correlation tests were used for assessment of correlation between parameters. A p value ≤0.05 was considered statistically significant. Strong positive correlations were found between mean peak enhancement and mean K trans : 0.79 (all patients, p<0.0001), 0.83 (primary staging, p = 0.003), and 0.81 (restaging, p = 0.054). Mean wash-in correlated significantly with mean V p and K ep (0.79 and 0.58, respectively, p<0.0001 and p = 0.009) in all patients. Mean wash-in showed a significant correlation with mean K ep (0.67, p = 0.033) in the primary staging group. On the restaging MRI, mean wash-in only strongly correlated with mean V p (0.81, p = 0.054). This study shows a strong correlation between quantitative and semiquantitative parameters in DCE-MRI for rectal cancer. Peak enhancement correlates strongly with K trans and wash-in showed strong correlation with V p and K ep . These parameters have been reported to predict tumor aggressiveness and response in rectal cancer. Therefore, semiquantitative analyses might be a surrogate for quantitative analyses.

Quantitative Analysis of Repertoire-Scale Immunoglobulin Properties in Vaccine-Induced B-Cell Responses

DTIC Science & Technology

2017-05-10

repertoire-wide properties. Finally, through 75 the use of appropriate statistical analyses, the repertoire profiles can be quantitatively compared and 76...cell response to eVLP and 503 quantitatively compare GC B-cell repertoires from immunization conditions. We partitioned the 504 resulting clonotype... Quantitative analysis of repertoire-scale immunoglobulin properties in vaccine-induced B-cell responses Ilja V. Khavrutskii1, Sidhartha Chaudhury*1

Design and analysis issues in quantitative proteomics studies.

PubMed

Karp, Natasha A; Lilley, Kathryn S

2007-09-01

Quantitative proteomics is the comparison of distinct proteomes which enables the identification of protein species which exhibit changes in expression or post-translational state in response to a given stimulus. Many different quantitative techniques are being utilized and generate large datasets. Independent of the technique used, these large datasets need robust data analysis to ensure valid conclusions are drawn from such studies. Approaches to address the problems that arise with large datasets are discussed to give insight into the types of statistical analyses of data appropriate for the various experimental strategies that can be employed by quantitative proteomic studies. This review also highlights the importance of employing a robust experimental design and highlights various issues surrounding the design of experiments. The concepts and examples discussed within will show how robust design and analysis will lead to confident results that will ensure quantitative proteomics delivers.

A simple quantitative diagnostic alternative for MGMT DNA-methylation testing on RCL2 fixed paraffin embedded tumors using restriction coupled qPCR.

PubMed

Pulverer, Walter; Hofner, Manuela; Preusser, Matthias; Dirnberger, Elisabeth; Hainfellner, Johannes A; Weinhaeusel, Andreas

2014-01-01

MGMT promoter methylation is associated with favorable prognosis and chemosensitivity in glioblastoma multiforme (GBM), especially in elderly patients. We aimed to develop a simple methylation-sensitive restriction enzyme (MSRE)-based quantitative PCR (qPCR) assay, allowing the quantification of MGMT promoter methylation. DNA was extracted from non-neoplastic brain (n = 24) and GBM samples (n = 20) upon 3 different sample conservation conditions (-80 °C, formalin-fixed and paraffin-embedded (FFPE); RCL2-fixed). We evaluated the suitability of each fixation method with respect to the MSRE-coupled qPCR methylation analyses. Methylation data were validated by MALDITOF. qPCR was used for evaluation of alternative tissue conservation procedures. DNA from FFPE tissue failed reliable testing; DNA from both RCL2-fixed and fresh frozen tissues performed equally well and was further used for validation of the quantitative MGMT methylation assay (limit of detection (LOD): 19.58 pg), using individual's undigested sample DNA for calibration. MGMT methylation analysis in non-neoplastic brain identified a background methylation of 0.10 ± 11% which we used for defining a cut-off of 0.32% for patient stratification. Of GBM patients 9 were MGMT methylationpositive (range: 0.56 - 91.95%), and 11 tested negative. MALDI-TOF measurements resulted in a concordant classification of 94% of GBM samples in comparison to qPCR. The presented methodology allows quantitative MGMT promoter methylation analyses. An amount of 200 ng DNA is sufficient for triplicate analyses including control reactions and individual calibration curves, thus excluding any DNA qualityderived bias. The combination of RCL2-fixation and quantitative methylation analyses improves pathological routine examination when histological and molecular analyses on limited amounts of tumor samples are necessary for patient stratification.

Orthodontic archwire composition and phase analyses by neutron spectroscopy.

PubMed

Tian, Kun V; Festa, Giulia; Basoli, Francesco; Laganà, Giuseppina; Scherillo, Antonella; Andreani, Carla; Bollero, Patrizio; Licoccia, Silvia; Senesi, Roberto; Cozza, Paola

2017-05-31

Quantitative metallurgical and phase analyses employing neutron diffraction technique were conducted on two as-received commercial rectangular austenitic stainless steel orthodontic archwires, G&H and Azdent, 0.43×0.64 mm (0.017×0.025 inch). Results showed a bi-phase structure containing martensitic phase (45.67% for G&H and 6.62% for Azdent) in addition to the expected metastable austenite. The former may be a strain-induced phase-transformation arising during the cold working process of wire fabrication. Further neutron resonance capture analysis determinations provided atomic and isotopic compositions, including alloying elements in each sample, complementary to the results of traditional energy dispersive X-ray spectroscopy. Together, these results assist in relating commercial alloying recipes and processing histories with mechanical performance, strength and ductility in particular.

Less label, more free: approaches in label-free quantitative mass spectrometry.

PubMed

Neilson, Karlie A; Ali, Naveid A; Muralidharan, Sridevi; Mirzaei, Mehdi; Mariani, Michael; Assadourian, Gariné; Lee, Albert; van Sluyter, Steven C; Haynes, Paul A

2011-02-01

In this review we examine techniques, software, and statistical analyses used in label-free quantitative proteomics studies for area under the curve and spectral counting approaches. Recent advances in the field are discussed in an order that reflects a logical workflow design. Examples of studies that follow this design are presented to highlight the requirement for statistical assessment and further experiments to validate results from label-free quantitation. Limitations of label-free approaches are considered, label-free approaches are compared with labelling techniques, and forward-looking applications for label-free quantitative data are presented. We conclude that label-free quantitative proteomics is a reliable, versatile, and cost-effective alternative to labelled quantitation. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Methodology for Conducting Integrative Mixed Methods Research and Data Analyses

PubMed Central

Castro, Felipe González; Kellison, Joshua G.; Boyd, Stephen J.; Kopak, Albert

2011-01-01

Mixed methods research has gained visibility within the last few years, although limitations persist regarding the scientific caliber of certain mixed methods research designs and methods. The need exists for rigorous mixed methods designs that integrate various data analytic procedures for a seamless transfer of evidence across qualitative and quantitative modalities. Such designs can offer the strength of confirmatory results drawn from quantitative multivariate analyses, along with “deep structure” explanatory descriptions as drawn from qualitative analyses. This article presents evidence generated from over a decade of pilot research in developing an integrative mixed methods methodology. It presents a conceptual framework and methodological and data analytic procedures for conducting mixed methods research studies, and it also presents illustrative examples from the authors' ongoing integrative mixed methods research studies. PMID:22167325

Post-Irradiation Non-Destructive Analyses of the AFIP-7 Experiment

NASA Astrophysics Data System (ADS)

Williams, W. J.; Robinson, A. B.; Rabin, B. H.

2017-12-01

This article reports the results and interpretation of post-irradiation non-destructive examinations performed on four curved full-size fuel plates that comprise the AFIP-7 experiment. These fuel plates, having a U-10 wt.%Mo monolithic design, were irradiated under moderate operating conditions in the Advanced Test Reactor to assess fuel performance for geometries that are prototypic of research reactor fuel assemblies. Non-destructive examinations include visual examination, neutron radiography, profilometry, and precision gamma scanning. This article evaluates the qualitative and quantitative data taken for each plate, compares corresponding data sets, and presents the results of swelling analyses. These characterization results demonstrate that the fuel meets established irradiation performance requirements for mechanical integrity, geometric stability, and stable and predictable behavior.

SDAR 1.0 a New Quantitative Toolkit for Analyze Stratigraphic Data

NASA Astrophysics Data System (ADS)

Ortiz, John; Moreno, Carlos; Cardenas, Andres; Jaramillo, Carlos

2015-04-01

Since the foundation of stratigraphy geoscientists have recognized that data obtained from stratigraphic columns (SC), two dimensional schemes recording descriptions of both geological and paleontological features (e.g., thickness of rock packages, grain size, fossil and lithological components, and sedimentary structures), are key elements for establishing reliable hypotheses about the distribution in space and time of rock sequences, and ancient sedimentary environmental and paleobiological dynamics. Despite the tremendous advances on the way geoscientists store, plot, and quantitatively analyze sedimentological and paleontological data (e.g., Macrostrat [http://www.macrostrat.org/], Paleobiology Database [http://www.paleodb.org/], respectively), there is still a lack of computational methodologies designed to quantitatively examine data from a highly detailed SCs. Moreover, frequently the stratigraphic information is plotted "manually" using vector graphics editors (e.g., Corel Draw, Illustrator), however, this information although store on a digital format, cannot be used readily for any quantitative analysis. Therefore, any attempt to examine the stratigraphic data in an analytical fashion necessarily takes further steps. Given these issues, we have developed the sofware 'Stratigraphic Data Analysis in R' (SDAR), which stores in a database all sedimentological, stratigraphic, and paleontological information collected from a SC, allowing users to generate high-quality graphic plots (including one or multiple features stored in the database). SDAR also encompasses quantitative analyses helping users to quantify stratigraphic information (e.g. grain size, sorting and rounding, proportion of sand/shale). Finally, given that the SDAR analysis module, has been written in the open-source high-level computer language "R graphics/statistics language" [R Development Core Team, 2014], it is already loaded with many of the crucial features required to accomplish basic and

The Quantitative Preparation of Future Geoscience Graduate Students

NASA Astrophysics Data System (ADS)

Manduca, C. A.; Hancock, G. S.

2006-12-01

Modern geoscience is a highly quantitative science. In February, a small group of faculty and graduate students from across the country met to discuss the quantitative preparation of geoscience majors for graduate school. The group included ten faculty supervising graduate students in quantitative areas spanning the earth, atmosphere, and ocean sciences; five current graduate students in these areas; and five faculty teaching undergraduate students in the spectrum of institutions preparing students for graduate work. Discussion focused in four key ares: Are incoming graduate students adequately prepared for the quantitative aspects of graduate geoscience programs? What are the essential quantitative skills are that are required for success in graduate school? What are perceived as the important courses to prepare students for the quantitative aspects of graduate school? What programs/resources would be valuable in helping faculty/departments improve the quantitative preparation of students? The participants concluded that strengthening the quantitative preparation of undergraduate geoscience majors would increase their opportunities in graduate school. While specifics differed amongst disciplines, a special importance was placed on developing the ability to use quantitative skills to solve geoscience problems. This requires the ability to pose problems so they can be addressed quantitatively, understand the relationship between quantitative concepts and physical representations, visualize mathematics, test the reasonableness of quantitative results, creatively move forward from existing models/techniques/approaches, and move between quantitative and verbal descriptions. A list of important quantitative competencies desirable in incoming graduate students includes mechanical skills in basic mathematics, functions, multi-variate analysis, statistics and calculus, as well as skills in logical analysis and the ability to learn independently in quantitative ways

Quantitative Myocardial Perfusion Imaging Versus Visual Analysis in Diagnosing Myocardial Ischemia: A CE-MARC Substudy.

PubMed

Biglands, John D; Ibraheem, Montasir; Magee, Derek R; Radjenovic, Aleksandra; Plein, Sven; Greenwood, John P

2018-05-01

This study sought to compare the diagnostic accuracy of visual and quantitative analyses of myocardial perfusion cardiovascular magnetic resonance against a reference standard of quantitative coronary angiography. Visual analysis of perfusion cardiovascular magnetic resonance studies for assessing myocardial perfusion has been shown to have high diagnostic accuracy for coronary artery disease. However, only a few small studies have assessed the diagnostic accuracy of quantitative myocardial perfusion. This retrospective study included 128 patients randomly selected from the CE-MARC (Clinical Evaluation of Magnetic Resonance Imaging in Coronary Heart Disease) study population such that the distribution of risk factors and disease status was proportionate to the full population. Visual analysis results of cardiovascular magnetic resonance perfusion images, by consensus of 2 expert readers, were taken from the original study reports. Quantitative myocardial blood flow estimates were obtained using Fermi-constrained deconvolution. The reference standard for myocardial ischemia was a quantitative coronary x-ray angiogram stenosis severity of ≥70% diameter in any coronary artery of >2 mm diameter, or ≥50% in the left main stem. Diagnostic performance was calculated using receiver-operating characteristic curve analysis. The area under the curve for visual analysis was 0.88 (95% confidence interval: 0.81 to 0.95) with a sensitivity of 81.0% (95% confidence interval: 69.1% to 92.8%) and specificity of 86.0% (95% confidence interval: 78.7% to 93.4%). For quantitative stress myocardial blood flow the area under the curve was 0.89 (95% confidence interval: 0.83 to 0.96) with a sensitivity of 87.5% (95% confidence interval: 77.3% to 97.7%) and specificity of 84.5% (95% confidence interval: 76.8% to 92.3%). There was no statistically significant difference between the diagnostic performance of quantitative and visual analyses (p = 0.72). Incorporating rest myocardial

Mapping of quantitative trait loci controlling adaptive traits in coastal Douglas-fir

Treesearch

Nicholas C. Wheeler; Kathleen D. Jermstad; Konstantin V. Krutovsky; Sally N. Aitken; Glenn T. Howe; Jodie Krakowski; David B. Neale

2005-01-01

Quantitative trait locus (QTL) analyses are used by geneticists to characterize the genetic architecture of quantitative traits, provide a foundation for marker-aided-selection (MAS), and provide a framework for positional selection of candidate genes. The most useful QTL for breeding applications are those that have been verified in time, space, and/or genetic...

Quantitative structure-retention relationship studies for taxanes including epimers and isomeric metabolites in ultra fast liquid chromatography.

PubMed

Dong, Pei-Pei; Ge, Guang-Bo; Zhang, Yan-Yan; Ai, Chun-Zhi; Li, Guo-Hui; Zhu, Liang-Liang; Luan, Hong-Wei; Liu, Xing-Bao; Yang, Ling

2009-10-16

Seven pairs of epimers and one pair of isomeric metabolites of taxanes, each pair of which have similar structures but different retention behaviors, together with additional 13 taxanes with different substitutions were chosen to investigate the quantitative structure-retention relationship (QSRR) of taxanes in ultra fast liquid chromatography (UFLC). Monte Carlo variable selection (MCVS) method was adopted to choose descriptors. The selected four descriptors were used to build QSRR model with multi-linear regression (MLR) and artificial neural network (ANN) modeling techniques. Both linear and nonlinear models show good predictive ability, of which ANN model was better with the determination coefficient R(2) for training, validation and test set being 0.9892, 0.9747 and 0.9840, respectively. The results of 100 times' leave-12-out cross validation showed the robustness of this model. All the isomers can be correctly differentiated by this model. According to the selected descriptors, the three dimensional structural information was critical for recognition of epimers. Hydrophobic interaction was the uppermost factor for retention in UFLC. Molecules' polarizability and polarity properties were also closely correlated with retention behaviors. This QSRR model will be useful for separation and identification of taxanes including epimers and metabolites from botanical or biological samples.

An Overview of Advanced SILAC-Labeling Strategies for Quantitative Proteomics.

PubMed

Terzi, F; Cambridge, S

2017-01-01

Comparative, quantitative mass spectrometry of proteins provides great insight to protein abundance and function, but some molecular characteristics related to protein dynamics are not so easily obtained. Because the metabolic incorporation of stable amino acid isotopes allows the extraction of distinct temporal and spatial aspects of protein dynamics, the SILAC methodology is uniquely suited to be adapted for advanced labeling strategies. New SILAC strategies have emerged that allow deeper foraging into the complexity of cellular proteomes. Here, we review a few advanced SILAC-labeling strategies that have been published during last the years. Among them, different subsaturating-labeling as well as dual-labeling schemes are most prominent for a range of analyses including those of neuronal proteomes, secretion, or cell-cell-induced stimulations. These recent developments suggest that much more information can be gained from proteomic analyses if the labeling strategies are specifically tailored toward the experimental design. © 2017 Elsevier Inc. All rights reserved.

Challenge in Enhancing the Teaching and Learning of Variable Measurements in Quantitative Research

ERIC Educational Resources Information Center

Kee, Chang Peng; Osman, Kamisah; Ahmad, Fauziah

2013-01-01

Statistical analysis is one component that cannot be avoided in a quantitative research. Initial observations noted that students in higher education institution faced difficulty analysing quantitative data which were attributed to the confusions of various variable measurements. This paper aims to compare the outcomes of two approaches applied in…

Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses*

PubMed Central

Rudnick, Paul A.; Clauser, Karl R.; Kilpatrick, Lisa E.; Tchekhovskoi, Dmitrii V.; Neta, Pedatsur; Blonder, Nikša; Billheimer, Dean D.; Blackman, Ronald K.; Bunk, David M.; Cardasis, Helene L.; Ham, Amy-Joan L.; Jaffe, Jacob D.; Kinsinger, Christopher R.; Mesri, Mehdi; Neubert, Thomas A.; Schilling, Birgit; Tabb, David L.; Tegeler, Tony J.; Vega-Montoto, Lorenzo; Variyath, Asokan Mulayath; Wang, Mu; Wang, Pei; Whiteaker, Jeffrey R.; Zimmerman, Lisa J.; Carr, Steven A.; Fisher, Susan J.; Gibson, Bradford W.; Paulovich, Amanda G.; Regnier, Fred E.; Rodriguez, Henry; Spiegelman, Cliff; Tempst, Paul; Liebler, Daniel C.; Stein, Stephen E.

2010-01-01

A major unmet need in LC-MS/MS-based proteomics analyses is a set of tools for quantitative assessment of system performance and evaluation of technical variability. Here we describe 46 system performance metrics for monitoring chromatographic performance, electrospray source stability, MS1 and MS2 signals, dynamic sampling of ions for MS/MS, and peptide identification. Applied to data sets from replicate LC-MS/MS analyses, these metrics displayed consistent, reasonable responses to controlled perturbations. The metrics typically displayed variations less than 10% and thus can reveal even subtle differences in performance of system components. Analyses of data from interlaboratory studies conducted under a common standard operating procedure identified outlier data and provided clues to specific causes. Moreover, interlaboratory variation reflected by the metrics indicates which system components vary the most between laboratories. Application of these metrics enables rational, quantitative quality assessment for proteomics and other LC-MS/MS analytical applications. PMID:19837981

A quantitative test of population genetics using spatiogenetic patterns in bacterial colonies.

PubMed

Korolev, Kirill S; Xavier, João B; Nelson, David R; Foster, Kevin R

2011-10-01

It is widely accepted that population-genetics theory is the cornerstone of evolutionary analyses. Empirical tests of the theory, however, are challenging because of the complex relationships between space, dispersal, and evolution. Critically, we lack quantitative validation of the spatial models of population genetics. Here we combine analytics, on- and off-lattice simulations, and experiments with bacteria to perform quantitative tests of the theory. We study two bacterial species, the gut microbe Escherichia coli and the opportunistic pathogen Pseudomonas aeruginosa, and show that spatiogenetic patterns in colony biofilms of both species are accurately described by an extension of the one-dimensional stepping-stone model. We use one empirical measure, genetic diversity at the colony periphery, to parameterize our models and show that we can then accurately predict another key variable: the degree of short-range cell migration along an edge. Moreover, the model allows us to estimate other key parameters, including effective population size (density) at the expansion frontier. While our experimental system is a simplification of natural microbial community, we argue that it constitutes proof of principle that the spatial models of population genetics can quantitatively capture organismal evolution.

A Quantitative Assessment of the Reporting Quality of Herbal Medicine Research: The Road to Improvement.

PubMed

Naumann, Ken

2018-02-01

To quantify different aspects of the quality of reporting of herbal medicine clinical trials, to determine how that quality is affecting the conclusions of meta-analyses, and to target areas for improvement in future herbal medicine research reporting. The Electronic databases PubMed, Academic Search Premier, ScienceDirect, and Alt HealthWatch were searched for meta-analyses of herbal medicines in refereed journals and Cochrane Reviews in the years 2000-2004 and 2010-2014. The search was limited to meta-analyses of randomized controlled trials involving humans and published in English. Judgments and descriptions within the meta-analyses were used to report on risks of bias in the included clinical trials and the meta-analyses themselves. Out of 3264 citations, 9 journal-published meta-analyses were selected from 2000 to 2004, 116 from 2010 to 2014, and 44 Cochrane Reviews from 2010 to 2014. Across both time frames and categories of publication, <42% of the trials included in the meta-analyses described adequate randomization; <19% described concealment methods; <26% described double blinding; <29% described outcome assessment blinding, ≤53% discussed incomplete data, and <36% were nonselective in their reporting. Less than 54% of trials reported on adverse events and 64% of meta-analyses did not include a single trial with a low risk of bias. Taxonomic verification and chemical characterization of test products were infrequent in trials. Only 40% of meta-analyses considered publication bias and, of those that did, 90% found evidence for it. Cochrane Reviews were more likely than other sources to make negative conclusions of efficacy or to defer conclusions because of the absence of high quality trials. Meta-analyses of herbal medicines include a significant number of clinical trials that do not meet the recommended standards for clinical trial reporting. This quantitative assessment identified significant publication bias and other bias risks that may be due to

Histological and morphometric analyses for rat carotid balloon injury model.

PubMed

Tulis, David A

2007-01-01

Experiments aimed at analyzing the response of blood vessels to mechanical injury and ensuing remodeling responses often employ the highly characterized carotid artery balloon injury model in laboratory rats. This approach utilizes luminal insertion of a balloon embolectomy catheter into the common carotid artery with inflation and withdrawal resulting in an injury characterized by vascular endothelial cell (EC) denudation and medial wall distension. The adaptive response to this injury is typified by robust vascular smooth muscle cell (SMC) replication and migration, SMC apoptosis and necrosis, enhanced synthesis and deposition of extracellular matrix (ECM) components, partial vascular EC regeneration from the border zones, luminal narrowing, and establishment of a neointima in time-dependent fashion. Evaluation of these adaptive responses to blood vessel injury can include acute and longer term qualitative and quantitative measures including expression analyses, activity assays, immunostaining for a plethora of factors and signals, and morphometry of neointima formation and gross mural remodeling. This chapter presents a logical continuation of Chapter 1 that offers details for performing the rat carotid artery balloon injury model in a standard laboratory setting by providing commonly used protocols for performing histological and morphometric analyses in such studies. Moreover, procedures, caveats, and considerations included in this chapter are highly relevant for alternative animal vascular physiology/pathophysiology studies and in particular those related to mechanisms of vascular injury and repair. Included in this chapter are specifics for in situ perfusion-fixation, tissue harvesting and processing for both snap-frozen and paraffin-embedded protocols, specimen embedding and sectioning, slide preparation, several standard histological staining steps, and routine morphological assessment.

Modern quantitative schlieren techniques

NASA Astrophysics Data System (ADS)

Hargather, Michael; Settles, Gary

2010-11-01

Schlieren optical techniques have traditionally been used to qualitatively visualize refractive flowfields in transparent media. Modern schlieren optics, however, are increasingly focused on obtaining quantitative information such as temperature and density fields in a flow -- once the sole purview of interferometry -- without the need for coherent illumination. Quantitative data are obtained from schlieren images by integrating the measured refractive index gradient to obtain the refractive index field in an image. Ultimately this is converted to a density or temperature field using the Gladstone-Dale relationship, an equation of state, and geometry assumptions for the flowfield of interest. Several quantitative schlieren methods are reviewed here, including background-oriented schlieren (BOS), schlieren using a weak lens as a "standard," and "rainbow schlieren." Results are presented for the application of these techniques to measure density and temperature fields across a supersonic turbulent boundary layer and a low-speed free-convection boundary layer in air. Modern equipment, including digital cameras, LED light sources, and computer software that make this possible are also discussed.

Whale song analyses using bioinformatics sequence analysis approaches

NASA Astrophysics Data System (ADS)

Chen, Yian A.; Almeida, Jonas S.; Chou, Lien-Siang

2005-04-01

Animal songs are frequently analyzed using discrete hierarchical units, such as units, themes and songs. Because animal songs and bio-sequences may be understood as analogous, bioinformatics analysis tools DNA/protein sequence alignment and alignment-free methods are proposed to quantify the theme similarities of the songs of false killer whales recorded off northeast Taiwan. The eighteen themes with discrete units that were identified in an earlier study [Y. A. Chen, masters thesis, University of Charleston, 2001] were compared quantitatively using several distance metrics. These metrics included the scores calculated using the Smith-Waterman algorithm with the repeated procedure; the standardized Euclidian distance and the angle metrics based on word frequencies. The theme classifications based on different metrics were summarized and compared in dendrograms using cluster analyses. The results agree with earlier classifications derived by human observation qualitatively. These methods further quantify the similarities among themes. These methods could be applied to the analyses of other animal songs on a larger scale. For instance, these techniques could be used to investigate song evolution and cultural transmission quantifying the dissimilarities of humpback whale songs across different seasons, years, populations, and geographic regions. [Work supported by SC Sea Grant, and Ilan County Government, Taiwan.

A quantitative assessment of alkaptonuria: testing the reliability of two disease severity scoring systems.

PubMed

Cox, Trevor F; Ranganath, Lakshminarayan

2011-12-01

Alkaptonuria (AKU) is due to excessive homogentisic acid accumulation in body fluids due to lack of enzyme homogentisate dioxygenase leading in turn to varied clinical manifestations mainly by a process of conversion of HGA to a polymeric melanin-like pigment known as ochronosis. A potential treatment, a drug called nitisinone, to decrease formation of HGA is available. However, successful demonstration of its efficacy in modifying the natural history of AKU requires an effective quantitative assessment tool. We have described two potential tools that could be used to quantitate disease burden in AKU. One tool describes scoring the clinical features that includes clinical assessments, investigations and questionnaires in 15 patients with AKU. The second tool describes a scoring system that only includes items obtained from questionnaires used in 44 people with AKU. Statistical analyses were carried out on the two patient datasets to assess the AKU tools; these included the calculation of Chronbach's alpha, multidimensional scaling and simple linear regression analysis. The conclusion was that there was good evidence that the tools could be adopted as AKU assessment tools, but perhaps with further refinement before being used in the practical setting of a clinical trial.

Beyond Math Skills: Measuring Quantitative Reasoning in Context

ERIC Educational Resources Information Center

Grawe, Nathan D.

2011-01-01

It might be argued that quantitative and qualitative analyses are merely two alternative reflections of an overarching critical thinking. For instance, just as instructors of numeracy warn their charges to consider the construction of variables, teachers of qualitative approaches caution students to define terms. Similarly, an advocate of…

Knowledge management for efficient quantitative analyses during regulatory reviews.

PubMed

Krudys, Kevin; Li, Fang; Florian, Jeffry; Tornoe, Christoffer; Chen, Ying; Bhattaram, Atul; Jadhav, Pravin; Neal, Lauren; Wang, Yaning; Gobburu, Joga; Lee, Peter I D

2011-11-01

Knowledge management comprises the strategies and methods employed to generate and leverage knowledge within an organization. This report outlines the activities within the Division of Pharmacometrics at the US FDA to effectively manage knowledge with the ultimate goal of improving drug development and advancing public health. The infrastructure required for pharmacometric knowledge management includes provisions for data standards, queryable databases, libraries of modeling tools, archiving of analysis results and reporting templates for effective communication. Two examples of knowledge management systems developed within the Division of Pharmacometrics are used to illustrate these principles. The benefits of sound knowledge management include increased productivity, allowing reviewers to focus on research questions spanning new drug applications, such as improved trial design and biomarker development. The future of knowledge management depends on the collaboration between the FDA and industry to implement data and model standards to enhance sharing and dissemination of knowledge.

Quantitative analysis of tympanic membrane perforation: a simple and reliable method.

PubMed

Ibekwe, T S; Adeosun, A A; Nwaorgu, O G

2009-01-01

Accurate assessment of the features of tympanic membrane perforation, especially size, site, duration and aetiology, is important, as it enables optimum management. To describe a simple, cheap and effective method of quantitatively analysing tympanic membrane perforations. The system described comprises a video-otoscope (capable of generating still and video images of the tympanic membrane), adapted via a universal serial bus box to a computer screen, with images analysed using the Image J geometrical analysis software package. The reproducibility of results and their correlation with conventional otoscopic methods of estimation were tested statistically with the paired t-test and correlational tests, using the Statistical Package for the Social Sciences version 11 software. The following equation was generated: P/T x 100 per cent = percentage perforation, where P is the area (in pixels2) of the tympanic membrane perforation and T is the total area (in pixels2) for the entire tympanic membrane (including the perforation). Illustrations are shown. Comparison of blinded data on tympanic membrane perforation area obtained independently from assessments by two trained otologists, of comparative years of experience, using the video-otoscopy system described, showed similar findings, with strong correlations devoid of inter-observer error (p = 0.000, r = 1). Comparison with conventional otoscopic assessment also indicated significant correlation, comparing results for two trained otologists, but some inter-observer variation was present (p = 0.000, r = 0.896). Correlation between the two methods for each of the otologists was also highly significant (p = 0.000). A computer-adapted video-otoscope, with images analysed by Image J software, represents a cheap, reliable, technology-driven, clinical method of quantitative analysis of tympanic membrane perforations and injuries.

Re-evaluation of a novel approach for quantitative myocardial oedema detection by analysing tissue inhomogeneity in acute myocarditis using T2-mapping.

PubMed

Baeßler, Bettina; Schaarschmidt, Frank; Treutlein, Melanie; Stehning, Christian; Schnackenburg, Bernhard; Michels, Guido; Maintz, David; Bunck, Alexander C

2017-12-01

To re-evaluate a recently suggested approach of quantifying myocardial oedema and increased tissue inhomogeneity in myocarditis by T2-mapping. Cardiac magnetic resonance data of 99 patients with myocarditis were retrospectively analysed. Thirthy healthy volunteers served as controls. T2-mapping data were acquired at 1.5 T using a gradient-spin-echo T2-mapping sequence. T2-maps were segmented according to the 16-segments AHA-model. Segmental T2-values, segmental pixel-standard deviation (SD) and the derived parameters maxT2, maxSD and madSD were analysed and compared to the established Lake Louise criteria (LLC). A re-estimation of logistic regression models revealed that all models containing an SD-parameter were superior to any model containing global myocardial T2. Using a combined cut-off of 1.8 ms for madSD + 68 ms for maxT2 resulted in a diagnostic sensitivity of 75% and specificity of 80% and showed a similar diagnostic performance compared to LLC in receiver-operating-curve analyses. Combining madSD, maxT2 and late gadolinium enhancement (LGE) in a model resulted in a superior diagnostic performance compared to LLC (sensitivity 93%, specificity 83%). The results show that the novel T2-mapping-derived parameters exhibit an additional diagnostic value over LGE with the inherent potential to overcome the current limitations of T2-mapping. • A novel quantitative approach to myocardial oedema imaging in myocarditis was re-evaluated. • The T2-mapping-derived parameters maxT2 and madSD were compared to traditional Lake-Louise criteria. • Using maxT2 and madSD with dedicated cut-offs performs similarly to Lake-Louise criteria. • Adding maxT2 and madSD to LGE results in further increased diagnostic performance. • This novel approach has the potential to overcome the limitations of T2-mapping.

Review of Department of Defense Education Activity (DoDEA) Schools. Volume II: Quantitative Analysis of Educational Quality. IDA Paper.

ERIC Educational Resources Information Center

Anderson, Lowell Bruce; Bracken, Jerome; Bracken, Marilyn C.

This volume compiles, and presents in integrated form, the Institute for Defense Analyses' (IDA) quantitative analysis of educational quality provided by the Department of Defense's dependent schools. It covers the quantitative aspects of volume 1 in greater detail and presents some analyses deemed too technical for that volume. The first task in…

Global earthquake casualties due to secondary effects: A quantitative analysis for improving rapid loss analyses

USGS Publications Warehouse

Marano, K.D.; Wald, D.J.; Allen, T.I.

2010-01-01

This study presents a quantitative and geospatial description of global losses due to earthquake-induced secondary effects, including landslide, liquefaction, tsunami, and fire for events during the past 40 years. These processes are of great importance to the US Geological Survey's (USGS) Prompt Assessment of Global Earthquakes for Response (PAGER) system, which is currently being developed to deliver rapid earthquake impact and loss assessments following large/significant global earthquakes. An important question is how dominant are losses due to secondary effects (and under what conditions, and in which regions)? Thus, which of these effects should receive higher priority research efforts in order to enhance PAGER's overall assessment of earthquakes losses and alerting for the likelihood of secondary impacts? We find that while 21.5% of fatal earthquakes have deaths due to secondary (non-shaking) causes, only rarely are secondary effects the main cause of fatalities. The recent 2004 Great Sumatra-Andaman Islands earthquake is a notable exception, with extraordinary losses due to tsunami. The potential for secondary hazards varies greatly, and systematically, due to regional geologic and geomorphic conditions. Based on our findings, we have built country-specific disclaimers for PAGER that address potential for each hazard (Earle et al., Proceedings of the 14th World Conference of the Earthquake Engineering, Beijing, China, 2008). We will now focus on ways to model casualties from secondary effects based on their relative importance as well as their general predictability. ?? Springer Science+Business Media B.V. 2009.

Qualitative and Quantitative Drug residue analyses: Florfenicol in white-tailed deer (Odocoileus virginianus) and supermarket meat by liquid chromatography tandem-mass spectrometry.

PubMed

Anderson, Shanoy C; Subbiah, Seenivasan; Gentles, Angella; Austin, Galen; Stonum, Paul; Brooks, Tiffanie A; Brooks, Chance; Smith, Ernest E

2016-10-15

A method for confirmation and detection of Florfenicol amine residues in white-tailed deer tissues was developed and validated in our laboratory. Tissue samples were extracted with ethyl acetate and cleaned up on sorbent (Chem-elut) cartridges. Liguid chromatography (LC) separation was achieved on a Zorbax Eclipse plus C18 column with gradient elution using a mobile phase composed of ammonium acetate in water and methanol at a flow rate of 300μL/min. Qualitative and quantitative analyses were carried out using liquid chromatography - heated electrospray ionization(HESI) and atmospheric pressure chemical ionization (APCI)-tandem mass spectrometry in the multiple reaction monitoring (MRM) interface. The limits of detection (LODs) for HESI and APCI probe were 1.8ng/g and 1.4ng/g respectively. Limits of quantitation (LOQs) for HESI and APCI probe were 5.8ng/g and 3.4ng/g respectively. Mean recovery values ranged from 79% to 111% for APCI and 30% to 60% for HESI. The validated method was used to determine white-tailed deer florfenicol tissue residue concentration 10-days after exposure. Florfenicol tissue residues concentration ranged from 0.4 to 0.6μg/g for liver and 0.02-0.05μg/g for muscle and a trace in blood samples. The concentration found in the tested edible tissues were lower than the maximum residual limit (MRL) values established by the federal drug administration (FDA) for bovine tissues. In summary, the resulting optimization procedures using the sensitivity of HESI and APCI probes in the determination of florfenicol in white-tailed deer tissue are the most compelling conclusions in this study, to the extent that we have applied this method in the evaluation of supermarket samples drug residue levels as a proof of principle. Copyright © 2016. Published by Elsevier B.V.

Structural and quantitative expression analyses of HERV gene family in human tissues.

PubMed

Ahn, Kung; Kim, Heui-Soo

2009-08-31

Human endogenous retroviruses (HERVs) have been implicated in the pathogenesis of several human diseases as multi-copy members in the human genome. Their gene expression profiling could provide us with important insights into the pathogenic relationship between HERVs and cancer. In this study, we have evaluated the genomic structure and quantitatively determined the expression patterns in the env gene of a variety of HERV family members located on six specific loci by the RetroTector 10 program, as well as real-time RT-PCR amplification. The env gene transcripts evidenced significant differences in the human tumor/normal adjacent tissues (colon, liver, uterus, lung and testis). As compared to the adjacent normal tissues, high levels of expression were noted in testis tumor tissues for HERV-K, in liver and lung tumor tissues for HERV-R, in liver, lung, and testis tumor tissues for HERV-H, and in colon and liver tumor tissues for HERV-P. These data warrant further studies with larger groups of patients to develop biomarkers for specific human cancers.

CIU and Main Event Analyses of the Structured Discourse of Older and Younger Adults

ERIC Educational Resources Information Center

Capilouto, Gilson; Wright, Heather Harris; Wagovich, Stacy A.

2005-01-01

Correct information unit (CIU) and main event analyses are quantitative measures for analyzing discourse of individuals with aphasia. Comparative data from healthy younger (YG) and older (OD) adults and an investigation of the influence of stimuli type would considerably extend the usefulness of such analyses. The objectives were (a) to compare…

Identification among morphologically similar Argyreia (Convolvulaceae) based on leaf anatomy and phenetic analyses.

PubMed

Traiperm, Paweena; Chow, Janene; Nopun, Possathorn; Staples, G; Swangpol, Sasivimon C

2017-12-01

The genus Argyreia Lour. is one of the species-rich Asian genera in the family Convolvulaceae. Several species complexes were recognized in which taxon delimitation was imprecise, especially when examining herbarium materials without fully developed open flowers. The main goal of this study is to investigate and describe leaf anatomy for some morphologically similar Argyreia using epidermal peeling, leaf and petiole transverse sections, and scanning electron microscopy. Phenetic analyses including cluster analysis and principal component analysis were used to investigate the similarity of these morpho-types. Anatomical differences observed between the morpho-types include epidermal cell walls and the trichome types on the leaf epidermis. Additional differences in the leaf and petiole transverse sections include the epidermal cell shape of the adaxial leaf blade, the leaf margins, and the petiole transverse sectional outline. The phenogram from cluster analysis using the UPGMA method represented four groups with an R value of 0.87. Moreover, the important quantitative and qualitative leaf anatomical traits of the four groups were confirmed by the principal component analysis of the first two components. The results from phenetic analyses confirmed the anatomical differentiation between the morpho-types. Leaf anatomical features regarded as particularly informative for morpho-type differentiation can be used to supplement macro morphological identification.

Quantitative coronary plaque analysis predicts high-risk plaque morphology on coronary computed tomography angiography: results from the ROMICAT II trial.

PubMed

Liu, Ting; Maurovich-Horvat, Pál; Mayrhofer, Thomas; Puchner, Stefan B; Lu, Michael T; Ghemigian, Khristine; Kitslaar, Pieter H; Broersen, Alexander; Pursnani, Amit; Hoffmann, Udo; Ferencik, Maros

2018-02-01

Semi-automated software can provide quantitative assessment of atherosclerotic plaques on coronary CT angiography (CTA). The relationship between established qualitative high-risk plaque features and quantitative plaque measurements has not been studied. We analyzed the association between quantitative plaque measurements and qualitative high-risk plaque features on coronary CTA. We included 260 patients with plaque who underwent coronary CTA in the Rule Out Myocardial Infarction/Ischemia Using Computer Assisted Tomography (ROMICAT) II trial. Quantitative plaque assessment and qualitative plaque characterization were performed on a per coronary segment basis. Quantitative coronary plaque measurements included plaque volume, plaque burden, remodeling index, and diameter stenosis. In qualitative analysis, high-risk plaque was present if positive remodeling, low CT attenuation plaque, napkin-ring sign or spotty calcium were detected. Univariable and multivariable logistic regression analyses were performed to assess the association between quantitative and qualitative high-risk plaque assessment. Among 888 segments with coronary plaque, high-risk plaque was present in 391 (44.0%) segments by qualitative analysis. In quantitative analysis, segments with high-risk plaque had higher total plaque volume, low CT attenuation plaque volume, plaque burden and remodeling index. Quantitatively assessed low CT attenuation plaque volume (odds ratio 1.12 per 1 mm 3 , 95% CI 1.04-1.21), positive remodeling (odds ratio 1.25 per 0.1, 95% CI 1.10-1.41) and plaque burden (odds ratio 1.53 per 0.1, 95% CI 1.08-2.16) were associated with high-risk plaque. Quantitative coronary plaque characteristics (low CT attenuation plaque volume, positive remodeling and plaque burden) measured by semi-automated software correlated with qualitative assessment of high-risk plaque features.

Analysing magnetism using scanning SQUID microscopy.

PubMed

Reith, P; Renshaw Wang, X; Hilgenkamp, H

2017-12-01

Scanning superconducting quantum interference device microscopy (SSM) is a scanning probe technique that images local magnetic flux, which allows for mapping of magnetic fields with high field and spatial accuracy. Many studies involving SSM have been published in the last few decades, using SSM to make qualitative statements about magnetism. However, quantitative analysis using SSM has received less attention. In this work, we discuss several aspects of interpreting SSM images and methods to improve quantitative analysis. First, we analyse the spatial resolution and how it depends on several factors. Second, we discuss the analysis of SSM scans and the information obtained from the SSM data. Using simulations, we show how signals evolve as a function of changing scan height, SQUID loop size, magnetization strength, and orientation. We also investigated 2-dimensional autocorrelation analysis to extract information about the size, shape, and symmetry of magnetic features. Finally, we provide an outlook on possible future applications and improvements.

Analysing magnetism using scanning SQUID microscopy

NASA Astrophysics Data System (ADS)

Reith, P.; Renshaw Wang, X.; Hilgenkamp, H.

2017-12-01

Scanning superconducting quantum interference device microscopy (SSM) is a scanning probe technique that images local magnetic flux, which allows for mapping of magnetic fields with high field and spatial accuracy. Many studies involving SSM have been published in the last few decades, using SSM to make qualitative statements about magnetism. However, quantitative analysis using SSM has received less attention. In this work, we discuss several aspects of interpreting SSM images and methods to improve quantitative analysis. First, we analyse the spatial resolution and how it depends on several factors. Second, we discuss the analysis of SSM scans and the information obtained from the SSM data. Using simulations, we show how signals evolve as a function of changing scan height, SQUID loop size, magnetization strength, and orientation. We also investigated 2-dimensional autocorrelation analysis to extract information about the size, shape, and symmetry of magnetic features. Finally, we provide an outlook on possible future applications and improvements.

Value of MR histogram analyses for prediction of microvascular invasion of hepatocellular carcinoma.

PubMed

Huang, Ya-Qin; Liang, He-Yue; Yang, Zhao-Xia; Ding, Ying; Zeng, Meng-Su; Rao, Sheng-Xiang

2016-06-01

The objective is to explore the value of preoperative magnetic resonance (MR) histogram analyses in predicting microvascular invasion (MVI) of hepatocellular carcinoma (HCC).Fifty-one patients with histologically confirmed HCC who underwent diffusion-weighted and contrast-enhanced MR imaging were included. Histogram analyses were performed and mean, variance, skewness, kurtosis, 1th, 10th, 50th, 90th, and 99th percentiles were derived. Quantitative histogram parameters were compared between HCCs with and without MVI. Receiver operating characteristics (ROC) analyses were generated to compare the diagnostic performance of tumor size, histogram analyses of apparent diffusion coefficient (ADC) maps, and MR enhancement.The mean, 1th, 10th, and 50th percentiles of ADC maps, and the mean, variance. 1th, 10th, 50th, 90th, and 99th percentiles of the portal venous phase (PVP) images were significantly different between the groups with and without MVI (P <0.05), with area under the ROC curves (AUCs) of 0.66 to 0.74 for ADC and 0.76 to 0.88 for PVP. The largest AUC of PVP (1th percentile) showed significantly higher accuracy compared with that of arterial phase (AP) or tumor size (P <0.001).MR histogram analyses-in particular for 1th percentile for PVP images-held promise for prediction of MVI of HCC.

A Primer on Systematic Reviews and Meta-Analyses.

PubMed

Nguyen, Nghia H; Singh, Siddharth

2018-05-01

With the rapid growth of biomedical literature, there is increasing need to make meaningful inferences from a comprehensive and complex body of evidence. Systematic reviews with or without meta-analyses offer an objective and summative approach to synthesize knowledge and critically appraise evidence to inform clinical practice. Systematic reviews also help identify key knowledge gaps for future investigation. In this review, the authors provide a step-by-step approach to conducting a systematic review. These include: (1) formulating a focused and clinically-relevant question; (2) designing a detailed review protocol with explicit inclusion and exclusion criteria; (3) performing a systematic literature search of multiple databases and unpublished data, in consultation with a medical librarian, to identify relevant studies; (4) meticulous data abstraction by at least two sets of investigators independently; (5) assessing risk of bias in individual studies; (6) quantitative synthesis with meta-analysis; and (7) critically and transparently ascertaining quality of evidence. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

Young children's core symbolic and nonsymbolic quantitative knowledge in the prediction of later mathematics achievement.

PubMed

Geary, David C; vanMarle, Kristy

2016-12-01

At the beginning of preschool (M = 46 months of age), 197 (94 boys) children were administered tasks that assessed a suite of nonsymbolic and symbolic quantitative competencies as well as their executive functions, verbal and nonverbal intelligence, preliteracy skills, and their parents' education level. The children's mathematics achievement was assessed at the end of preschool (M = 64 months). We used a series of Bayesian and standard regression analyses to winnow this broad set of competencies down to the core subset of quantitative skills that predict later mathematics achievement, controlling other factors. This knowledge included children's fluency in reciting the counting string, their understanding of the cardinal value of number words, and recognition of Arabic numerals, as well as their sensitivity to the relative quantity of 2 collections of objects. The results inform theoretical models of the foundations of children's early quantitative development and have practical implications for the design of early interventions for children at risk for poor long-term mathematics achievement. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

[Progress in stable isotope labeled quantitative proteomics methods].

PubMed

Zhou, Yuan; Shan, Yichu; Zhang, Lihua; Zhang, Yukui

2013-06-01

Quantitative proteomics is an important research field in post-genomics era. There are two strategies for proteome quantification: label-free methods and stable isotope labeling methods which have become the most important strategy for quantitative proteomics at present. In the past few years, a number of quantitative methods have been developed, which support the fast development in biology research. In this work, we discuss the progress in the stable isotope labeling methods for quantitative proteomics including relative and absolute quantitative proteomics, and then give our opinions on the outlook of proteome quantification methods.

Quantitative thermal sensory testing -- value of testing for both cold and warm sensation detection in evaluation of small fiber neuropathy.

PubMed

Shukla, Garima; Bhatia, Manvir; Behari, Madhuri

2005-10-01

Small fiber neuropathy is a common neurological disorder, often missed or ignored by physicians, since examination and routine nerve conduction studies are usually normal in this condition. Many methods including quantitative thermal sensory testing are currently being used for early detection of this condition, so as to enable timely investigation and treatment. This study was conducted to assess the yield of quantitative thermal sensory testing in diagnosis of small fiber neuropathy. We included patients presenting with history suggestive of positive and/or negative sensory symptoms, with normal examination findings, clinically suggestive of small fiber neuropathy, with normal or minimally abnormal routine nerve conduction studies. These patients were subjected to quantitative thermal sensory testing using a Medoc TSA-II Neurosensory analyser at two sites and for two modalities. QST data were compared with those in 120 normal healthy controls. Twenty-five patients (16 males, 9 females) with mean age 46.8+/-16.6 years (range: 21-75 years) were included in the study. The mean duration of symptoms was 1.6+/-1.6 years (range: 3 months-6 years). Eighteen patients (72%) had abnormal thresholds in at least one modality. Thermal thresholds were normal in 7 out of the 25 patients. This study demonstrates that quantitative thermal sensory testing is a fairly sensitive method for detection of small fiber neuropathy especially in patients with normal routine nerve conduction studies.

Note on the chromatographic analyses of marine polyunsaturated fatty acids

USGS Publications Warehouse

Schultz, D.M.; Quinn, J.G.

1977-01-01

Gas-liquid chromatography was used to study the effects of saponification/methylation and thin-layer chromatographic isolation on the analyses of polyunsaturated fatty acids. Using selected procedures, the qualitative and quantitative distribution of these acids in marine organisms can be determined with a high degree of accuracy. ?? 1977 Springer-Verlag.

Transcriptome-wide analyses indicate mitochondrial responses to particulate air pollution exposure.

PubMed

Winckelmans, Ellen; Nawrot, Tim S; Tsamou, Maria; Den Hond, Elly; Baeyens, Willy; Kleinjans, Jos; Lefebvre, Wouter; Van Larebeke, Nicolas; Peusens, Martien; Plusquin, Michelle; Reynders, Hans; Schoeters, Greet; Vanpoucke, Charlotte; de Kok, Theo M; Vrijens, Karen

2017-08-18

Due to their lack of repair capacity mitochondria are critical targets for environmental toxicants. We studied genes and pathways reflecting mitochondrial responses to short- and medium-term PM 10 exposure. Whole genome gene expression was measured in peripheral blood of 98 adults (49% women). We performed linear regression analyses stratified by sex and adjusted for individual and temporal characteristics to investigate alterations in gene expression induced by short-term (week before blood sampling) and medium-term (month before blood sampling) PM 10 exposure. Overrepresentation analyses (ConsensusPathDB) were performed to identify enriched mitochondrial associated pathways and gene ontology sets. Thirteen Human MitoCarta genes were measured by means of quantitative real-time polymerase chain reaction (qPCR) along with mitochondrial DNA (mtDNA) content in an independent validation cohort (n = 169, 55.6% women). Overrepresentation analyses revealed significant pathways (p-value <0.05) related to mitochondrial genome maintenance and apoptosis for short-term exposure and to the electron transport chain (ETC) for medium-term exposure in women. For men, medium-term PM 10 exposure was associated with the Tri Carbonic Acid cycle. In an independent study population, we validated several ETC genes, including UQCRH and COX7C (q-value <0.05), and some genes crucial for the maintenance of the mitochondrial genome, including LONP1 (q-value: 0.07) and POLG (q-value: 0.04) in women. In this exploratory study, we identified mitochondrial genes and pathways associated with particulate air pollution indicating upregulation of energy producing pathways as a potential mechanism to compensate for PM-induced mitochondrial damage.

Object-oriented fault tree evaluation program for quantitative analyses

NASA Technical Reports Server (NTRS)

Patterson-Hine, F. A.; Koen, B. V.

1988-01-01

Object-oriented programming can be combined with fault free techniques to give a significantly improved environment for evaluating the safety and reliability of large complex systems for space missions. Deep knowledge about system components and interactions, available from reliability studies and other sources, can be described using objects that make up a knowledge base. This knowledge base can be interrogated throughout the design process, during system testing, and during operation, and can be easily modified to reflect design changes in order to maintain a consistent information source. An object-oriented environment for reliability assessment has been developed on a Texas Instrument (TI) Explorer LISP workstation. The program, which directly evaluates system fault trees, utilizes the object-oriented extension to LISP called Flavors that is available on the Explorer. The object representation of a fault tree facilitates the storage and retrieval of information associated with each event in the tree, including tree structural information and intermediate results obtained during the tree reduction process. Reliability data associated with each basic event are stored in the fault tree objects. The object-oriented environment on the Explorer also includes a graphical tree editor which was modified to display and edit the fault trees.

Quantitative and qualitative analysis of semantic verbal fluency in patients with temporal lobe epilepsy.

PubMed

Jaimes-Bautista, A G; Rodríguez-Camacho, M; Martínez-Juárez, I E; Rodríguez-Agudelo, Y

2017-08-29

Patients with temporal lobe epilepsy (TLE) perform poorly on semantic verbal fluency (SVF) tasks. Completing these tasks successfully involves multiple cognitive processes simultaneously. Therefore, quantitative analysis of SVF (number of correct words in one minute), conducted in most studies, has been found to be insufficient to identify cognitive dysfunction underlying SVF difficulties in TLE. To determine whether a sample of patients with TLE had SVF difficulties compared with a control group (CG), and to identify the cognitive components associated with SVF difficulties using quantitative and qualitative analysis. SVF was evaluated in 25 patients with TLE and 24 healthy controls; the semantic verbal fluency test included 5 semantic categories: animals, fruits, occupations, countries, and verbs. All 5 categories were analysed quantitatively (number of correct words per minute and interval of execution: 0-15, 16-30, 31-45, and 46-60seconds); the categories animals and fruits were also analysed qualitatively (clusters, cluster size, switches, perseverations, and intrusions). Patients generated fewer words for all categories and intervals and fewer clusters and switches for animals and fruits than the CG (P<.01). Differences between groups were not significant in terms of cluster size and number of intrusions and perseverations (P>.05). Our results suggest an association between SVF difficulties in TLE and difficulty activating semantic networks, impaired strategic search, and poor cognitive flexibility. Attention, inhibition, and working memory are preserved in these patients. Copyright © 2017 Sociedad Española de Neurología. Publicado por Elsevier España, S.L.U. All rights reserved.

Quantitative Analyse der Korallenbesiedlung eines Vorriffareals bei Aqaba (Rotes Meer)

NASA Astrophysics Data System (ADS)

Mergner, H.; Schuhmacher, H.

1981-09-01

Previous descriptions of the ecology and zonation of Aqaba reefs (Mergner & Schuhmacher, 1974) are supplemented by this quantitative study of a test quadrat (5×5 m in size), randomly chosen in some 10 m depth in the middle fore reef of a coastal fringing reef. Of the total surface of 25 m2 Cnidaria represent 42.31%, sponges 0.17%, calcareous algae 0.20%, dead coral rock and pebble 30.27% and sand and coral debris 26.15%. The cnidarian cover is roughly equally contributed by 50.86% Scleractinia and 48.61% Alcyonaria, mainly Xeniidae (35.81%). For each species the percentage of the total cover (measured as vertical projection), colony number, average and maximal colony size are given. A total number of 104 cnidarian species was recorded, among which the 78 scleractinian species represent 34 of the 55 coral genera known from the Red Sea. The well balanced regime of moderate light and current conditions which are tolerated both by shallow and deep water species may account for the high species number. Disturbances such as occasional sedimentation, grazing of sea urchins (Diadema setosum) and overgrowth of stony corals by xeniids result in continuous fluctuations of the coral community, in small colony size and in high colony number. Abiotic factors and biotic interactions maintain a diversity (H=3.67) which ranks among the greatest ever found in reef communities. The data obtained from the fore reef square are compared with those of a similar test square in the lagoon of the same reef and with results from transect zonations on the opposite coast of the Gulf of Aqaba. These comparisons indicate that the fore reef harbours the richest coral fauna in the reef. The inventory of coral species at the northern end of the Gulf of Aqaba, one of the northernmost outposts of the coral reef belt, is only little reduced when compared with that of the central Red Sea; this great species diversity is in contrast to the worldwide decrease of species number towards the periphery of

Adapting CALIPSO Climate Measurements for Near Real Time Analyses and Forecasting

NASA Technical Reports Server (NTRS)

Vaughan, Mark A.; Trepte, Charles R.; Winker, David M.; Avery, Melody A.; Campbell, James; Hoff, Ray; Young, Stuart; Getzewich, Brian J.; Tackett, Jason L.; Kar, Jayanta

2011-01-01

The Cloud-Aerosol Lidar and Infrared Pathfinder satellite Observations (CALIPSO) mission was originally conceived and designed as a climate measurements mission, with considerable latency between data acquisition and the release of the level 1 and level 2 data products. However, the unique nature of the CALIPSO lidar backscatter profiles quickly led to the qualitative use of CALIPSO?s near real time (i.e., ? expedited?) lidar data imagery in several different forecasting applications. To enable quantitative use of their near real time analyses, the CALIPSO project recently expanded their expedited data catalog to include all of the standard level 1 and level 2 lidar data products. Also included is a new cloud cleared level 1.5 profile product developed for use by operational forecast centers for verification of aerosol predictions. This paper describes the architecture and content of the CALIPSO expedited data products. The fidelity and accuracy of the expedited products are assessed via comparisons to the standard CALIPSO data products.

Vibrational algorithms for quantitative crystallographic analyses of hydroxyapatite-based biomaterials: I, theoretical foundations.

PubMed

Pezzotti, Giuseppe; Zhu, Wenliang; Boffelli, Marco; Adachi, Tetsuya; Ichioka, Hiroaki; Yamamoto, Toshiro; Marunaka, Yoshinori; Kanamura, Narisato

2015-05-01

The Raman spectroscopic method has quantitatively been applied to the analysis of local crystallographic orientation in both single-crystal hydroxyapatite and human teeth. Raman selection rules for all the vibrational modes of the hexagonal structure were expanded into explicit functions of Euler angles in space and six Raman tensor elements (RTE). A theoretical treatment has also been put forward according to the orientation distribution function (ODF) formalism, which allows one to resolve the statistical orientation patterns of the nm-sized hydroxyapatite crystallite comprised in the Raman microprobe. Close-form solutions could be obtained for the Euler angles and their statistical distributions resolved with respect to the direction of the average texture axis. Polarized Raman spectra from single-crystalline hydroxyapatite and textured polycrystalline (teeth enamel) samples were compared, and a validation of the proposed Raman method could be obtained through confirming the agreement between RTE values obtained from different samples.

Appraising Quantitative Research in Health Education: Guidelines for Public Health Educators

PubMed Central

Hayes, Sandra C.; Scharalda, Jeanfreau G.; Stetson, Barbara; Jones-Jack, Nkenge H.; Valliere, Matthew; Kirchain, William R.; Fagen, Michael; LeBlanc, Cris

2010-01-01

Many practicing health educators do not feel they possess the skills necessary to critically appraise quantitative research. This publication is designed to help provide practicing health educators with basic tools helpful to facilitate a better understanding of quantitative research. This article describes the major components—title, introduction, methods, analyses, results and discussion sections—of quantitative research. Readers will be introduced to information on the various types of study designs and seven key questions health educators can use to facilitate the appraisal process. Upon reading, health educators will be in a better position to determine whether research studies are well designed and executed. PMID:20400654

Feared consequences of panic attacks in panic disorder: a qualitative and quantitative analysis.

PubMed

Raffa, Susan D; White, Kamila S; Barlow, David H

2004-01-01

Cognitions are hypothesized to play a central role in panic disorder (PD). Previous studies have used questionnaires to assess cognitive content, focusing on prototypical cognitions associated with PD; however, few studies have qualitatively examined cognitions associated with the feared consequences of panic attacks. The purpose of this study was to conduct a qualitative and quantitative analysis of feared consequences of panic attacks. The initial, qualitative analysis resulted in the development of 32 categories of feared consequences. The categories were derived from participant responses to a standardized, semi-structured question (n = 207). Five expert-derived categories were then utilized to quantitatively examine the relationship between cognitions and indicators of PD severity. Cognitions did not predict PD severity; however, correlational analyses indicated some predictive validity to the expert-derived categories. The qualitative analysis identified additional areas of patient-reported concern not included in previous research that may be important in the assessment and treatment of PD.

A quantitative study of nanoparticle skin penetration with interactive segmentation.

PubMed

Lee, Onseok; Lee, See Hyun; Jeong, Sang Hoon; Kim, Jaeyoung; Ryu, Hwa Jung; Oh, Chilhwan; Son, Sang Wook

2016-10-01

In the last decade, the application of nanotechnology techniques has expanded within diverse areas such as pharmacology, medicine, and optical science. Despite such wide-ranging possibilities for implementation into practice, the mechanisms behind nanoparticle skin absorption remain unknown. Moreover, the main mode of investigation has been qualitative analysis. Using interactive segmentation, this study suggests a method of objectively and quantitatively analyzing the mechanisms underlying the skin absorption of nanoparticles. Silica nanoparticles (SNPs) were assessed using transmission electron microscopy and applied to the human skin equivalent model. Captured fluorescence images of this model were used to evaluate degrees of skin penetration. These images underwent interactive segmentation and image processing in addition to statistical quantitative analyses of calculated image parameters including the mean, integrated density, skewness, kurtosis, and area fraction. In images from both groups, the distribution area and intensity of fluorescent silica gradually increased in proportion to time. Since statistical significance was achieved after 2 days in the negative charge group and after 4 days in the positive charge group, there is a periodic difference. Furthermore, the quantity of silica per unit area showed a dramatic change after 6 days in the negative charge group. Although this quantitative result is identical to results obtained by qualitative assessment, it is meaningful in that it was proven by statistical analysis with quantitation by using image processing. The present study suggests that the surface charge of SNPs could play an important role in the percutaneous absorption of NPs. These findings can help achieve a better understanding of the percutaneous transport of NPs. In addition, these results provide important guidance for the design of NPs for biomedical applications.

Descriptive and Experimental Analyses of Potential Precursors to Problem Behavior

PubMed Central

Borrero, Carrie S.W; Borrero, John C

2008-01-01

We conducted descriptive observations of severe problem behavior for 2 individuals with autism to identify precursors to problem behavior. Several comparative probability analyses were conducted in addition to lag-sequential analyses using the descriptive data. Results of the descriptive analyses showed that the probability of the potential precursor was greater given problem behavior compared to the unconditional probability of the potential precursor. Results of the lag-sequential analyses showed a marked increase in the probability of a potential precursor in the 1-s intervals immediately preceding an instance of problem behavior, and that the probability of problem behavior was highest in the 1-s intervals immediately following an instance of the precursor. We then conducted separate functional analyses of problem behavior and the precursor to identify respective operant functions. Results of the functional analyses showed that both problem behavior and the precursor served the same operant functions. These results replicate prior experimental analyses on the relation between problem behavior and precursors and extend prior research by illustrating a quantitative method to identify precursors to more severe problem behavior. PMID:18468281

Quantitative magnetic resonance imaging in traumatic brain injury.

PubMed

Bigler, E D

2001-04-01

Quantitative neuroimaging has now become a well-established method for analyzing magnetic resonance imaging in traumatic brain injury (TBI). A general review of studies that have examined quantitative changes following TBI is presented. The consensus of quantitative neuroimaging studies is that most brain structures demonstrate changes in volume or surface area after injury. The patterns of atrophy are consistent with the generalized nature of brain injury and diffuse axonal injury. Various clinical caveats are provided including how quantitative neuroimaging findings can be used clinically and in predicting rehabilitation outcome. The future of quantitative neuroimaging also is discussed.

On normality, ethnicity, and missing values in quantitative trait locus mapping

PubMed Central

Labbe, Aurélie; Wormald, Hanna

2005-01-01

Background This paper deals with the detection of significant linkage for quantitative traits using a variance components approach. Microsatellite markers were obtained for the Genetic Analysis Workshop 14 Collaborative Study on the Genetics of Alcoholism data. Ethnic heterogeneity, highly skewed quantitative measures, and a high rate of missing values are all present in this dataset and well known to impact upon linkage analysis. This makes it a good candidate for investigation. Results As expected, we observed a number of changes in LOD scores, especially for chromosomes 1, 7, and 18, along with the three factors studied. A dramatic example of such changes can be found in chromosome 7. Highly significant linkage to one of the quantitative traits became insignificant when a proper normalizing transformation of the trait was used and when analysis was carried out on an ethnically homogeneous subset of the original pedigrees. Conclusion In agreement with existing literature, transforming a trait to ensure normality using a Box-Cox transformation is highly recommended in order to avoid false-positive linkages. Furthermore, pedigrees should be sorted by ethnic groups and analyses should be carried out separately. Finally, one should be aware that the inclusion of covariates with a high rate of missing values reduces considerably the number of subjects included in the model. In such a case, the loss in power may be large. Imputation methods are then recommended. PMID:16451664

Statistical methods for meta-analyses including information from studies without any events-add nothing to nothing and succeed nevertheless.

PubMed

Kuss, O

2015-03-30

Meta-analyses with rare events, especially those that include studies with no event in one ('single-zero') or even both ('double-zero') treatment arms, are still a statistical challenge. In the case of double-zero studies, researchers in general delete these studies or use continuity corrections to avoid them. A number of arguments against both options has been given, and statistical methods that use the information from double-zero studies without using continuity corrections have been proposed. In this paper, we collect them and compare them by simulation. This simulation study tries to mirror real-life situations as completely as possible by deriving true underlying parameters from empirical data on actually performed meta-analyses. It is shown that for each of the commonly encountered effect estimators valid statistical methods are available that use the information from double-zero studies without using continuity corrections. Interestingly, all of them are truly random effects models, and so also the current standard method for very sparse data as recommended from the Cochrane collaboration, the Yusuf-Peto odds ratio, can be improved on. For actual analysis, we recommend to use beta-binomial regression methods to arrive at summary estimates for the odds ratio, the relative risk, or the risk difference. Methods that ignore information from double-zero studies or use continuity corrections should no longer be used. We illustrate the situation with an example where the original analysis ignores 35 double-zero studies, and a superior analysis discovers a clinically relevant advantage of off-pump surgery in coronary artery bypass grafting. Copyright © 2014 John Wiley & Sons, Ltd.

Quantitative Estimation of the Electronic Effects of Substituents in Five-membered Nitrogen-containing Aromatic Heterocycles

NASA Astrophysics Data System (ADS)

Lopyrev, Valentin A.; Larina, Ludmila I.; Vakul'skaya, Tamara I.

1986-05-01

Data, characterising quantitatively the effect of substituents on the reactivity and physicochemical properties of five-membered nitrogen-containing heterocyclic compounds, which have accumulated in the literature during the last 15 years, are compiled in the review and discussed. The possibility of applying the Hammett and Jaffe equations in the determination of the direction of transmission of the electronic effects of substituents is analysed and the likely usefulness of this approach to the study of electronic influences by taking into account separately the inductive and resonance constants is demonstrated. The bibliography includes 215 references.

Highly Reproducible Label Free Quantitative Proteomic Analysis of RNA Polymerase Complexes*

PubMed Central

Mosley, Amber L.; Sardiu, Mihaela E.; Pattenden, Samantha G.; Workman, Jerry L.; Florens, Laurence; Washburn, Michael P.

2011-01-01

The use of quantitative proteomics methods to study protein complexes has the potential to provide in-depth information on the abundance of different protein components as well as their modification state in various cellular conditions. To interrogate protein complex quantitation using shotgun proteomic methods, we have focused on the analysis of protein complexes using label-free multidimensional protein identification technology and studied the reproducibility of biological replicates. For these studies, we focused on three highly related and essential multi-protein enzymes, RNA polymerase I, II, and III from Saccharomyces cerevisiae. We found that label-free quantitation using spectral counting is highly reproducible at the protein and peptide level when analyzing RNA polymerase I, II, and III. In addition, we show that peptide sampling does not follow a random sampling model, and we show the need for advanced computational models to predict peptide detection probabilities. In order to address these issues, we used the APEX protocol to model the expected peptide detectability based on whole cell lysate acquired using the same multidimensional protein identification technology analysis used for the protein complexes. Neither method was able to predict the peptide sampling levels that we observed using replicate multidimensional protein identification technology analyses. In addition to the analysis of the RNA polymerase complexes, our analysis provides quantitative information about several RNAP associated proteins including the RNAPII elongation factor complexes DSIF and TFIIF. Our data shows that DSIF and TFIIF are the most highly enriched RNAP accessory factors in Rpb3-TAP purifications and demonstrate our ability to measure low level associated protein abundance across biological replicates. In addition, our quantitative data supports a model in which DSIF and TFIIF interact with RNAPII in a dynamic fashion in agreement with previously published reports. PMID

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

Charting organellar importomes by quantitative mass spectrometry

PubMed Central

Peikert, Christian D.; Mani, Jan; Morgenstern, Marcel; Käser, Sandro; Knapp, Bettina; Wenger, Christoph; Harsman, Anke; Oeljeklaus, Silke; Schneider, André; Warscheid, Bettina

2017-01-01

Protein import into organelles is essential for all eukaryotes and facilitated by multi-protein translocation machineries. Analysing whether a protein is transported into an organelle is largely restricted to single constituents. This renders knowledge about imported proteins incomplete, limiting our understanding of organellar biogenesis and function. Here we introduce a method that enables charting an organelle's importome. The approach relies on inducible RNAi-mediated knockdown of an essential subunit of a translocase to impair import and quantitative mass spectrometry. To highlight its potential, we established the mitochondrial importome of Trypanosoma brucei, comprising 1,120 proteins including 331 new candidates. Furthermore, the method allows for the identification of proteins with dual or multiple locations and the substrates of distinct protein import pathways. We demonstrate the specificity and versatility of this ImportOmics method by targeting import factors in mitochondria and glycosomes, which demonstrates its potential for globally studying protein import and inventories of organelles. PMID:28485388

10 CFR 61.13 - Technical analyses.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 2 2010-01-01 2010-01-01 false Technical analyses. 61.13 Section 61.13 Energy NUCLEAR....13 Technical analyses. The specific technical information must also include the following analyses... air, soil, groundwater, surface water, plant uptake, and exhumation by burrowing animals. The analyses...

Continuous Measurements of Eyeball Area and Their Spectrum Analyses -- Toward the Quantification of Rest Rhythm of Horses by Image Processing

DTIC Science & Technology

2001-10-25

analyses of electroencephalogram at half- closed eye and fully closed eye. This study aimed at quantitative estimating rest rhythm of horses by the...analyses of eyeball movement. The mask attached with a miniature CCD camera was newly developed. The continuous images of the horse eye for about 24...eyeball area were calculated. As for the results, the fluctuating status of eyeball area was analyzed quantitatively, and the rest rhythm of horses was

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).

Quantitative and qualitative approaches in educational research — problems and examples of controlled understanding through interpretive methods

NASA Astrophysics Data System (ADS)

Neumann, Karl

1987-06-01

In the methodological discussion of recent years it has become apparent that many research problems, including problems relating to the theory of educational science, cannot be solved by using quantitative methods. The multifaceted aspects of human behaviour and all its environment-bound subtle nuances, especially the process of education or the development of identity, cannot fully be taken into account within a rigid neopositivist approach. In employing the paradigm of symbolic interactionism as a suitable model for the analysis of processes of education and formation, the research has generally to start out from complex reciprocal social interactions instead of unambigious connections of causes. In analysing several particular methodological problems, the article demonstrates some weaknesses of quantitative approaches and then shows the advantages in and the necessity for using qualitative research tools.

High resolution rare-earth elements analyses of natural apatite and its application in geo-sciences: Combined micro-PIXE, quantitative CL spectroscopy and electron spin resonance analyses

NASA Astrophysics Data System (ADS)

Habermann, D.; Götte, T.; Meijer, J.; Stephan, A.; Richter, D. K.; Niklas, J. R.

2000-03-01

The rare-earth element (REE) distribution in natural apatite is analysed by micro-PIXE, cathodoluminescence (CL) microscopy and spectroscopy and electron spin resonance (ESR) spectroscopy. The micro-PIXE analyses of an apatite crystal from Cerro de Mercado (Mexico) and the summary of 20 analyses of six francolite (conodonts of Triassic age) samples indicate that most of the REEs are enriched in apatite and francolite comparative to average shale standard (NASC). The analyses of fossil francolite revealing the REE-distribution not to be in balance with the REE-distribution of seawater and fish bone debris. Strong inhomogenous lateral REE-distribution in fossil conodont material is shown by CL-mapping and most probably not being a vital effect. Therefore, the resulting REE-signal from fossil francolite is the sum of vital and post-mortem incorporation. The necessary charge compensation for the substitution of divalent Ca by trivalent REE being done by different kind of electron defects and defect ions.

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.

Analyses on Regional Cultivated Land Changebased on Quantitative Method

NASA Astrophysics Data System (ADS)

Cao, Yingui; Yuan, Chun; Zhou, Wei; Wang, Jing

Three Gorges Project is the great project in the world, which accelerates economic development in the reservoir area of Three Gorges Project. In the process of development in the reservoir area of Three Gorges Project, cultivated land has become the important resources, a lot of cultivated land has been occupied and become the constructing land. In the same time, a lot of cultivated land has been flooded because of the rising of the water level. This paper uses the cultivated land areas and social economic indicators of reservoir area of Three Gorges in 1990-2004, takes the statistic analyses and example research in order to analyze the process of cultivated land, get the driving forces of cultivated land change, find the new methods to stimulate and forecast the cultivated land areas in the future, and serve for the cultivated land protection and successive development in reservoir area of Three Gorges. The results indicate as follow, firstly, in the past 15 years, the cultivated land areas has decreased 200142 hm2, the decreasing quantity per year is 13343 hm2. The whole reservoir area is divided into three different areas, they are upper reaches area, belly area and lower reaches area. The trends of cultivated land change in different reservoir areas are similar to the whole reservoir area. Secondly, the curve of cultivated land areas and per capita GDP takes on the reverse U, and the steps between the change rate of cultivated land and the change rate of GDP are different in some years, which indicates that change of cultivated land and change of GDP are decoupling, besides that, change of cultivated land is connection with the development of urbanization and the policy of returning forestry greatly. Lastly, the precision of multi-regression is lower than the BP neural network in the stimulation of cultivated land, then takes use of the BP neural network to forecast the cultivated land areas in 2005, 2010 and 2015, and the forecasting results are reasonable.

Diagnostic accuracy of semi-automatic quantitative metrics as an alternative to expert reading of CT myocardial perfusion in the CORE320 study.

PubMed

Ostovaneh, Mohammad R; Vavere, Andrea L; Mehra, Vishal C; Kofoed, Klaus F; Matheson, Matthew B; Arbab-Zadeh, Armin; Fujisawa, Yasuko; Schuijf, Joanne D; Rochitte, Carlos E; Scholte, Arthur J; Kitagawa, Kakuya; Dewey, Marc; Cox, Christopher; DiCarli, Marcelo F; George, Richard T; Lima, Joao A C

To determine the diagnostic accuracy of semi-automatic quantitative metrics compared to expert reading for interpretation of computed tomography perfusion (CTP) imaging. The CORE320 multicenter diagnostic accuracy clinical study enrolled patients between 45 and 85 years of age who were clinically referred for invasive coronary angiography (ICA). Computed tomography angiography (CTA), CTP, single photon emission computed tomography (SPECT), and ICA images were interpreted manually in blinded core laboratories by two experienced readers. Additionally, eight quantitative CTP metrics as continuous values were computed semi-automatically from myocardial and blood attenuation and were combined using logistic regression to derive a final quantitative CTP metric score. For the reference standard, hemodynamically significant coronary artery disease (CAD) was defined as a quantitative ICA stenosis of 50% or greater and a corresponding perfusion defect by SPECT. Diagnostic accuracy was determined by area under the receiver operating characteristic curve (AUC). Of the total 377 included patients, 66% were male, median age was 62 (IQR: 56, 68) years, and 27% had prior myocardial infarction. In patient based analysis, the AUC (95% CI) for combined CTA-CTP expert reading and combined CTA-CTP semi-automatic quantitative metrics was 0.87(0.84-0.91) and 0.86 (0.83-0.9), respectively. In vessel based analyses the AUC's were 0.85 (0.82-0.88) and 0.84 (0.81-0.87), respectively. No significant difference in AUC was found between combined CTA-CTP expert reading and CTA-CTP semi-automatic quantitative metrics in patient based or vessel based analyses(p > 0.05 for all). Combined CTA-CTP semi-automatic quantitative metrics is as accurate as CTA-CTP expert reading to detect hemodynamically significant CAD. Copyright © 2018 Society of Cardiovascular Computed Tomography. Published by Elsevier Inc. All rights reserved.

Quantitative expression and localization of cysteine and aspartic proteases in human abdominal aortic aneurysms

PubMed Central

Lohoefer, Fabian; Reeps, Christian; Lipp, Christina; Rudelius, Martina; Haertl, Felix; Matevossian, Edouard; Zernecke, Alma; Eckstein, Hans-Henning; Pelisek, Jaroslav

2014-01-01

Cysteine and aspartic proteases possess high elastolytic activity and might contribute to the degradation of the abdominal aortic aneurysm (AAA) wall. The aim of this study was to analyze, in detail, the proteases (cathepsins B, D, K, L and S, and inhibitor cystatin C) found in human AAA and healthy aortic tissue samples. The vessel walls from AAA patients (n=36) and nonaneurysmal aortae (n=10) were retrieved using conventional surgical repair and autopsy methods. Serum samples from the same AAA patients and 10 healthy volunteers were also collected. Quantitative expression analyses were performed at the mRNA level using real-time reverse transcriptase-PCR (RT–PCR). Furthermore, analyses at the protein level included western blot and immunoprecipitation analyses. Cellular sources of cysteine/aspartic proteases and cystatin C were identified by immunohistochemistry (IHC). All cysteine/aspartic proteases and cystatin C were detected in the AAA and control samples. Using quantitative RT–PCR, a significant increase in expression was observed for cathepsins B (P=0.021) and L (P=0.018), compared with the controls. Cathepsin B and cystatin C were also detected in the serum of AAA patients. Using IHC, smooth muscle cells (SMCs) and macrophages were positive for all of the tested cathepsins, as well as cystatin C; in addition, the lymphocytes were mainly positive for cathepsin B, followed by cathepsins D and S. All cysteine/aspartic proteases analyzed in our study were detected in the AAA and healthy aorta. The highest expression was found in macrophages and SMCs. Consequently, cysteine/aspartic proteases might play a substantial role in AAA. PMID:24833013

Spotsizer: High-throughput quantitative analysis of microbial growth.

PubMed

Bischof, Leanne; Převorovský, Martin; Rallis, Charalampos; Jeffares, Daniel C; Arzhaeva, Yulia; Bähler, Jürg

2016-10-01

Microbial colony growth can serve as a useful readout in assays for studying complex genetic interactions or the effects of chemical compounds. Although computational tools for acquiring quantitative measurements of microbial colonies have been developed, their utility can be compromised by inflexible input image requirements, non-trivial installation procedures, or complicated operation. Here, we present the Spotsizer software tool for automated colony size measurements in images of robotically arrayed microbial colonies. Spotsizer features a convenient graphical user interface (GUI), has both single-image and batch-processing capabilities, and works with multiple input image formats and different colony grid types. We demonstrate how Spotsizer can be used for high-throughput quantitative analysis of fission yeast growth. The user-friendly Spotsizer tool provides rapid, accurate, and robust quantitative analyses of microbial growth in a high-throughput format. Spotsizer is freely available at https://data.csiro.au/dap/landingpage?pid=csiro:15330 under a proprietary CSIRO license.

Challenges and perspectives in quantitative NMR.

PubMed

Giraudeau, Patrick

2017-01-01

This perspective article summarizes, from the author's point of view at the beginning of 2016, the major challenges and perspectives in the field of quantitative NMR. The key concepts in quantitative NMR are first summarized; then, the most recent evolutions in terms of resolution and sensitivity are discussed, as well as some potential future research directions in this field. A particular focus is made on methodologies capable of boosting the resolution and sensitivity of quantitative NMR, which could open application perspectives in fields where the sample complexity and the analyte concentrations are particularly challenging. These include multi-dimensional quantitative NMR and hyperpolarization techniques such as para-hydrogen-induced polarization or dynamic nuclear polarization. Because quantitative NMR cannot be dissociated from the key concepts of analytical chemistry, i.e. trueness and precision, the methodological developments are systematically described together with their level of analytical performance. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

7 CFR 94.102 - Analyses available.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 3 2010-01-01 2010-01-01 false Analyses available. 94.102 Section 94.102 Agriculture... POULTRY AND EGG PRODUCTS Voluntary Analyses of Egg Products § 94.102 Analyses available. A wide array of analyses for voluntary egg product samples is available. Voluntary egg product samples include surveillance...

Quantitative imaging methods in osteoporosis.

PubMed

Oei, Ling; Koromani, Fjorda; Rivadeneira, Fernando; Zillikens, M Carola; Oei, Edwin H G

2016-12-01

Osteoporosis is characterized by a decreased bone mass and quality resulting in an increased fracture risk. Quantitative imaging methods are critical in the diagnosis and follow-up of treatment effects in osteoporosis. Prior radiographic vertebral fractures and bone mineral density (BMD) as a quantitative parameter derived from dual-energy X-ray absorptiometry (DXA) are among the strongest known predictors of future osteoporotic fractures. Therefore, current clinical decision making relies heavily on accurate assessment of these imaging features. Further, novel quantitative techniques are being developed to appraise additional characteristics of osteoporosis including three-dimensional bone architecture with quantitative computed tomography (QCT). Dedicated high-resolution (HR) CT equipment is available to enhance image quality. At the other end of the spectrum, by utilizing post-processing techniques such as the trabecular bone score (TBS) information on three-dimensional architecture can be derived from DXA images. Further developments in magnetic resonance imaging (MRI) seem promising to not only capture bone micro-architecture but also characterize processes at the molecular level. This review provides an overview of various quantitative imaging techniques based on different radiological modalities utilized in clinical osteoporosis care and research.

Value of MR histogram analyses for prediction of microvascular invasion of hepatocellular carcinoma

PubMed Central

Huang, Ya-Qin; Liang, He-Yue; Yang, Zhao-Xia; Ding, Ying; Zeng, Meng-Su; Rao, Sheng-Xiang

2016-01-01

Abstract The objective is to explore the value of preoperative magnetic resonance (MR) histogram analyses in predicting microvascular invasion (MVI) of hepatocellular carcinoma (HCC). Fifty-one patients with histologically confirmed HCC who underwent diffusion-weighted and contrast-enhanced MR imaging were included. Histogram analyses were performed and mean, variance, skewness, kurtosis, 1th, 10th, 50th, 90th, and 99th percentiles were derived. Quantitative histogram parameters were compared between HCCs with and without MVI. Receiver operating characteristics (ROC) analyses were generated to compare the diagnostic performance of tumor size, histogram analyses of apparent diffusion coefficient (ADC) maps, and MR enhancement. The mean, 1th, 10th, and 50th percentiles of ADC maps, and the mean, variance. 1th, 10th, 50th, 90th, and 99th percentiles of the portal venous phase (PVP) images were significantly different between the groups with and without MVI (P <0.05), with area under the ROC curves (AUCs) of 0.66 to 0.74 for ADC and 0.76 to 0.88 for PVP. The largest AUC of PVP (1th percentile) showed significantly higher accuracy compared with that of arterial phase (AP) or tumor size (P <0.001). MR histogram analyses—in particular for 1th percentile for PVP images—held promise for prediction of MVI of HCC. PMID:27368028

Morphological analyses suggest a new taxonomic circumscription for Hymenaea courbaril L. (Leguminosae, Caesalpinioideae)

PubMed Central

Souza, Isys Mascarenhas; Funch, Ligia Silveira; de Queiroz, Luciano Paganucci

2014-01-01

Abstract Hymenaea is a genus of the Resin-producing Clade of the tribe Detarieae (Leguminosae: Caesalpinioideae) with 14 species. Hymenaea courbaril is the most widespread species of the genus, ranging from southern Mexico to southeastern Brazil. As currently circumscribed, Hymenaea courbaril is a polytypic species with six varieties: var. altissima, var. courbaril, var. longifolia, var. stilbocarpa, var. subsessilis, and var. villosa. These varieties are distinguishable mostly by traits related to leaflet shape and indumentation, and calyx indumentation. We carried out morphometric analyses of 14 quantitative (continuous) leaf characters in order to assess the taxonomy of Hymenaea courbaril under the Unified Species Concept framework. Cluster analysis used the Unweighted Pair Group Method with Arithmetic Mean (UPGMA) based on Bray-Curtis dissimilarity matrices. Principal Component Analyses (PCA) were carried out based on the same morphometric matrix. Two sets of Analyses of Similarity and Non Parametric Multivariate Analysis of Variance were carried out to evaluate statistical support (1) for the major groups recovered using UPGMA and PCA, and (2) for the varieties. All analyses recovered three major groups coincident with (1) var. altissima, (2) var. longifolia, and (3) all other varieties. These results, together with geographical and habitat information, were taken as evidence of three separate metapopulation lineages recognized here as three distinct species. Nomenclatural adjustments, including reclassifying formerly misapplied types, are proposed. PMID:25009440

Morphological analyses suggest a new taxonomic circumscription for Hymenaea courbaril L. (Leguminosae, Caesalpinioideae).

PubMed

Souza, Isys Mascarenhas; Funch, Ligia Silveira; de Queiroz, Luciano Paganucci

2014-01-01

Hymenaea is a genus of the Resin-producing Clade of the tribe Detarieae (Leguminosae: Caesalpinioideae) with 14 species. Hymenaea courbaril is the most widespread species of the genus, ranging from southern Mexico to southeastern Brazil. As currently circumscribed, Hymenaea courbaril is a polytypic species with six varieties: var. altissima, var. courbaril, var. longifolia, var. stilbocarpa, var. subsessilis, and var. villosa. These varieties are distinguishable mostly by traits related to leaflet shape and indumentation, and calyx indumentation. We carried out morphometric analyses of 14 quantitative (continuous) leaf characters in order to assess the taxonomy of Hymenaea courbaril under the Unified Species Concept framework. Cluster analysis used the Unweighted Pair Group Method with Arithmetic Mean (UPGMA) based on Bray-Curtis dissimilarity matrices. Principal Component Analyses (PCA) were carried out based on the same morphometric matrix. Two sets of Analyses of Similarity and Non Parametric Multivariate Analysis of Variance were carried out to evaluate statistical support (1) for the major groups recovered using UPGMA and PCA, and (2) for the varieties. All analyses recovered three major groups coincident with (1) var. altissima, (2) var. longifolia, and (3) all other varieties. These results, together with geographical and habitat information, were taken as evidence of three separate metapopulation lineages recognized here as three distinct species. Nomenclatural adjustments, including reclassifying formerly misapplied types, are proposed.

Three-dimensional modeling and quantitative analysis of gap junction distributions in cardiac tissue.

PubMed

Lackey, Daniel P; Carruth, Eric D; Lasher, Richard A; Boenisch, Jan; Sachse, Frank B; Hitchcock, Robert W

2011-11-01

Gap junctions play a fundamental role in intercellular communication in cardiac tissue. Various types of heart disease including hypertrophy and ischemia are associated with alterations of the spatial arrangement of gap junctions. Previous studies applied two-dimensional optical and electron-microscopy to visualize gap junction arrangements. In normal cardiomyocytes, gap junctions were primarily found at cell ends, but can be found also in more central regions. In this study, we extended these approaches toward three-dimensional reconstruction of gap junction distributions based on high-resolution scanning confocal microscopy and image processing. We developed methods for quantitative characterization of gap junction distributions based on analysis of intensity profiles along the principal axes of myocytes. The analyses characterized gap junction polarization at cell ends and higher-order statistical image moments of intensity profiles. The methodology was tested in rat ventricular myocardium. Our analysis yielded novel quantitative data on gap junction distributions. In particular, the analysis demonstrated that the distributions exhibit significant variability with respect to polarization, skewness, and kurtosis. We suggest that this methodology provides a quantitative alternative to current approaches based on visual inspection, with applications in particular in characterization of engineered and diseased myocardium. Furthermore, we propose that these data provide improved input for computational modeling of cardiac conduction.

Population pharmacokinetic characterization of BAY 81-8973, a full-length recombinant factor VIII: lessons learned - importance of including samples with factor VIII levels below the quantitation limit.

PubMed

Garmann, D; McLeay, S; Shah, A; Vis, P; Maas Enriquez, M; Ploeger, B A

2017-07-01

The pharmacokinetics (PK), safety and efficacy of BAY 81-8973, a full-length, unmodified, recombinant human factor VIII (FVIII), were evaluated in the LEOPOLD trials. The aim of this study was to develop a population PK model based on pooled data from the LEOPOLD trials and to investigate the importance of including samples with FVIII levels below the limit of quantitation (BLQ) to estimate half-life. The analysis included 1535 PK observations (measured by the chromogenic assay) from 183 male patients with haemophilia A aged 1-61 years from the 3 LEOPOLD trials. The limit of quantitation was 1.5 IU dL -1 for the majority of samples. Population PK models that included or excluded BLQ samples were used for FVIII half-life estimations, and simulations were performed using both estimates to explore the influence on the time below a determined FVIII threshold. In the data set used, approximately 16.5% of samples were BLQ, which is not uncommon for FVIII PK data sets. The structural model to describe the PK of BAY 81-8973 was a two-compartment model similar to that seen for other FVIII products. If BLQ samples were excluded from the model, FVIII half-life estimations were longer compared with a model that included BLQ samples. It is essential to assess the importance of BLQ samples when performing population PK estimates of half-life for any FVIII product. Exclusion of BLQ data from half-life estimations based on population PK models may result in an overestimation of half-life and underestimation of time under a predetermined FVIII threshold, resulting in potential underdosing of patients. © 2017 Bayer AG. Haemophilia Published by John Wiley & Sons Ltd.

Assessment of acute myocarditis by cardiac magnetic resonance imaging: Comparison of qualitative and quantitative analysis methods.

PubMed

Imbriaco, Massimo; Nappi, Carmela; Puglia, Marta; De Giorgi, Marco; Dell'Aversana, Serena; Cuocolo, Renato; Ponsiglione, Andrea; De Giorgi, Igino; Polito, Maria Vincenza; Klain, Michele; Piscione, Federico; Pace, Leonardo; Cuocolo, Alberto

2017-10-26

To compare cardiac magnetic resonance (CMR) qualitative and quantitative analysis methods for the noninvasive assessment of myocardial inflammation in patients with suspected acute myocarditis (AM). A total of 61 patients with suspected AM underwent coronary angiography and CMR. Qualitative analysis was performed applying Lake-Louise Criteria (LLC), followed by quantitative analysis based on the evaluation of edema ratio (ER) and global relative enhancement (RE). Diagnostic performance was assessed for each method by measuring the area under the curves (AUC) of the receiver operating characteristic analyses. The final diagnosis of AM was based on symptoms and signs suggestive of cardiac disease, evidence of myocardial injury as defined by electrocardiogram changes, elevated troponin I, exclusion of coronary artery disease by coronary angiography, and clinical and echocardiographic follow-up at 3 months after admission to the chest pain unit. In all patients, coronary angiography did not show significant coronary artery stenosis. Troponin I levels and creatine kinase were higher in patients with AM compared to those without (both P < .001). There were no significant differences among LLC, T2-weighted short inversion time inversion recovery (STIR) sequences, early (EGE), and late (LGE) gadolinium-enhancement sequences for diagnosis of AM. The AUC for qualitative (T2-weighted STIR 0.92, EGE 0.87 and LGE 0.88) and quantitative (ER 0.89 and global RE 0.80) analyses were also similar. Qualitative and quantitative CMR analysis methods show similar diagnostic accuracy for the diagnosis of AM. These findings suggest that a simplified approach using a shortened CMR protocol including only T2-weighted STIR sequences might be useful to rule out AM in patients with acute coronary syndrome and normal coronary angiography.

Quantitative radiomics studies for tissue characterization: a review of technology and methodological procedures.

PubMed

Larue, Ruben T H M; Defraene, Gilles; De Ruysscher, Dirk; Lambin, Philippe; van Elmpt, Wouter

2017-02-01

Quantitative analysis of tumour characteristics based on medical imaging is an emerging field of research. In recent years, quantitative imaging features derived from CT, positron emission tomography and MR scans were shown to be of added value in the prediction of outcome parameters in oncology, in what is called the radiomics field. However, results might be difficult to compare owing to a lack of standardized methodologies to conduct quantitative image analyses. In this review, we aim to present an overview of the current challenges, technical routines and protocols that are involved in quantitative imaging studies. The first issue that should be overcome is the dependency of several features on the scan acquisition and image reconstruction parameters. Adopting consistent methods in the subsequent target segmentation step is evenly crucial. To further establish robust quantitative image analyses, standardization or at least calibration of imaging features based on different feature extraction settings is required, especially for texture- and filter-based features. Several open-source and commercial software packages to perform feature extraction are currently available, all with slightly different functionalities, which makes benchmarking quite challenging. The number of imaging features calculated is typically larger than the number of patients studied, which emphasizes the importance of proper feature selection and prediction model-building routines to prevent overfitting. Even though many of these challenges still need to be addressed before quantitative imaging can be brought into daily clinical practice, radiomics is expected to be a critical component for the integration of image-derived information to personalize treatment in the future.

Detection of Organic Constituents Including Chloromethylpropene in the Analyses of the ROCKNEST Drift by Sample Analysis at Mars (SAM)

NASA Technical Reports Server (NTRS)

Eigenbrode, J. L.; Glavin, D.; Coll, P.; Summons, R. E.; Mahaffy, P.; Archer, D.; Brunner, A.; Conrad, P.; Freissinet, C.; Martin, M.;

Folding Properties of Two-Dimensional Deployable Membrane Using FEM Analyses

NASA Astrophysics Data System (ADS)

Satou, Yasutaka; Furuya, Hiroshi

Folding FEM analyses are presented to examine folding properties of a two-dimensional deployable membrane for a precise deployment simulation. A fold model of the membrane is proposed by dividing the wrapping fold process into two regions which are the folded state and the transient process. The cross-section of the folded state is assumed to be a repeating structure, and analytical procedures of the repeating structure are constructed. To investigate the mechanical properties of the crease in detail, the bending stiffness is considered in the FEM analyses. As the results of the FEM analyses, the configuration of the membrane and the contact force by the adjacent membrane are obtained quantitatively for an arbitrary layer pitch. Possible occurrence of the plastic deformation is estimated using the Mises stress in the crease. The FEM results are compared with one-dimensional approximation analyses to evaluate these results.

Quantitative X-ray diffraction and fluorescence analysis of paint pigment systems : final report.

DOT National Transportation Integrated Search

1978-01-01

This study attempted to correlate measured X-ray intensities with concentrations of each member of paint pigment systems, thereby establishing calibration curves for the quantitative analyses of such systems.

Histological and Morphometric Analyses for Rat Carotid Artery Balloon Injury Studies

PubMed Central

Tulis, David Anthony

2010-01-01

i. Summary Experiments aimed at analyzing the response of blood vessels to mechanical injury and ensuing remodeling responses often employ the highly characterized carotid artery balloon injury model in laboratory rats. This approach utilizes luminal insertion of a balloon embolectomy catheter into the common carotid artery with inflation and withdrawal resulting in an injury characterized by vascular endothelial cell (EC) denudation and medial wall distension. The adaptive response to this injury is typified by robust vascular smooth muscle cell (SMC) replication and migration, SMC apoptosis and necrosis, enhanced synthesis and deposition of extracellular matrix (ECM) components, partial vascular EC regeneration from the border zones, luminal narrowing and establishment of a neointima in time-dependent fashion. Evaluation of these adaptive responses to blood vessel injury can include acute and longer-term qualitative and quantitative measures including expression analyses, activity assays, immunostaining for a plethora of factors and signals, and morphometry of neointima formation and gross mural remodeling. This chapter presents a logical continuation of Chapter    in this series that offers details for performing the rat carotid artery balloon injury model in a standard laboratory setting by providing commonly used protocols for performing histological and morphometric analyses in such studies. Moreover, procedures, caveats, and considerations included in this chapter are highly relevant for alternative animal vascular physiology/pathophysiology studies and in particular those related to mechanisms of vascular injury and repair. Included in this chapter are specifics for in situ perfusion-fixation, tissue harvesting and processing for both snap-frozen and paraffin-embedded protocols, specimen embedding and sectioning, slide preparation, several standard histological staining steps, and routine morphological assessment. Included in Notes are important caveats

Utility of DWI with quantitative ADC values in ovarian tumors: a meta-analysis of diagnostic test performance.

PubMed

Pi, Shan; Cao, Rong; Qiang, Jin Wei; Guo, Yan Hui

2018-01-01

Background Diffusion-weighted imaging (DWI) and quantitative apparent diffusion coefficient (ADC) values are widely used in the differential diagnosis of ovarian tumors. Purpose To assess the diagnostic performance of quantitative ADC values in ovarian tumors. Material and Methods PubMed, Embase, the Cochrane Library, and local databases were searched for studies assessing ovarian tumors using quantitative ADC values. We quantitatively analyzed the diagnostic performances for two clinical problems: benign vs. malignant tumors and borderline vs. malignant tumors. We evaluated diagnostic performances by the pooled sensitivity and specificity values and by summary receiver operating characteristic (SROC) curves. Subgroup analyses were used to analyze study heterogeneity. Results From the 742 studies identified in the search results, 16 studies met our inclusion criteria. A total of ten studies evaluated malignant vs. benign ovarian tumors and six studies assessed malignant vs. borderline ovarian tumors. Regarding the diagnostic accuracy of quantitative ADC values for distinguishing between malignant and benign ovarian tumors, the pooled sensitivity and specificity values were 0.91 and 0.91, respectively. The area under the SROC curve (AUC) was 0.96. For differentiating borderline from malignant tumors, the pooled sensitivity and specificity values were 0.89 and 0.79, and the AUC was 0.91. The methodological quality of the included studies was moderate. Conclusion Quantitative ADC values could serve as useful preoperative markers for predicting the nature of ovarian tumors. Nevertheless, prospective trials focused on standardized imaging parameters are needed to evaluate the clinical value of quantitative ADC values in ovarian tumors.

Refining the quantitative pathway of the Pathways to Mathematics model.

PubMed

Sowinski, Carla; LeFevre, Jo-Anne; Skwarchuk, Sheri-Lynn; Kamawar, Deepthi; Bisanz, Jeffrey; Smith-Chant, Brenda

2015-03-01

In the current study, we adopted the Pathways to Mathematics model of LeFevre et al. (2010). In this model, there are three cognitive domains--labeled as the quantitative, linguistic, and working memory pathways--that make unique contributions to children's mathematical development. We attempted to refine the quantitative pathway by combining children's (N=141 in Grades 2 and 3) subitizing, counting, and symbolic magnitude comparison skills using principal components analysis. The quantitative pathway was examined in relation to dependent numerical measures (backward counting, arithmetic fluency, calculation, and number system knowledge) and a dependent reading measure, while simultaneously accounting for linguistic and working memory skills. Analyses controlled for processing speed, parental education, and gender. We hypothesized that the quantitative, linguistic, and working memory pathways would account for unique variance in the numerical outcomes; this was the case for backward counting and arithmetic fluency. However, only the quantitative and linguistic pathways (not working memory) accounted for unique variance in calculation and number system knowledge. Not surprisingly, only the linguistic pathway accounted for unique variance in the reading measure. These findings suggest that the relative contributions of quantitative, linguistic, and working memory skills vary depending on the specific cognitive task. Copyright © 2014 Elsevier Inc. All rights reserved.

RECENT ADVANCES IN QUANTITATIVE NEUROPROTEOMICS

PubMed Central

Craft, George E; Chen, Anshu; Nairn, Angus C

2014-01-01

The field of proteomics is undergoing rapid development in a number of different areas including improvements in mass spectrometric platforms, peptide identification algorithms and bioinformatics. In particular, new and/or improved approaches have established robust methods that not only allow for in-depth and accurate peptide and protein identification and modification, but also allow for sensitive measurement of relative or absolute quantitation. These methods are beginning to be applied to the area of neuroproteomics, but the central nervous system poses many specific challenges in terms of quantitative proteomics, given the large number of different neuronal cell types that are intermixed and that exhibit distinct patterns of gene and protein expression. This review highlights the recent advances that have been made in quantitative neuroproteomics, with a focus on work published over the last five years that applies emerging methods to normal brain function as well as to various neuropsychiatric disorders including schizophrenia and drug addiction as well as of neurodegenerative diseases including Parkinson’s disease and Alzheimer’s disease. While older methods such as two-dimensional polyacrylamide electrophoresis continued to be used, a variety of more in-depth MS-based approaches including both label (ICAT, iTRAQ, TMT, SILAC, SILAM), label-free (label-free, MRM, SWATH) and absolute quantification methods, are rapidly being applied to neurobiological investigations of normal and diseased brain tissue as well as of cerebrospinal fluid (CSF). While the biological implications of many of these studies remain to be clearly established, that there is a clear need for standardization of experimental design and data analysis, and that the analysis of protein changes in specific neuronal cell types in the central nervous system remains a serious challenge, it appears that the quality and depth of the more recent quantitative proteomics studies is beginning to

Recent advances in quantitative neuroproteomics.

PubMed

Craft, George E; Chen, Anshu; Nairn, Angus C

2013-06-15

The field of proteomics is undergoing rapid development in a number of different areas including improvements in mass spectrometric platforms, peptide identification algorithms and bioinformatics. In particular, new and/or improved approaches have established robust methods that not only allow for in-depth and accurate peptide and protein identification and modification, but also allow for sensitive measurement of relative or absolute quantitation. These methods are beginning to be applied to the area of neuroproteomics, but the central nervous system poses many specific challenges in terms of quantitative proteomics, given the large number of different neuronal cell types that are intermixed and that exhibit distinct patterns of gene and protein expression. This review highlights the recent advances that have been made in quantitative neuroproteomics, with a focus on work published over the last five years that applies emerging methods to normal brain function as well as to various neuropsychiatric disorders including schizophrenia and drug addiction as well as of neurodegenerative diseases including Parkinson's disease and Alzheimer's disease. While older methods such as two-dimensional polyacrylamide electrophoresis continued to be used, a variety of more in-depth MS-based approaches including both label (ICAT, iTRAQ, TMT, SILAC, SILAM), label-free (label-free, MRM, SWATH) and absolute quantification methods, are rapidly being applied to neurobiological investigations of normal and diseased brain tissue as well as of cerebrospinal fluid (CSF). While the biological implications of many of these studies remain to be clearly established, that there is a clear need for standardization of experimental design and data analysis, and that the analysis of protein changes in specific neuronal cell types in the central nervous system remains a serious challenge, it appears that the quality and depth of the more recent quantitative proteomics studies is beginning to shed

Employment-related difficulties and distressed living condition in patients with hepatitis B virus: A qualitative and quantitative study.

PubMed

Oka, Taeko; Enoki, Hiroaki; Tokimoto, Yukari; Kawanishi, Teruaki; Minami, Meguru; Okuizumi, Takahiro; Katahira, Kiyohiko

2017-06-12

In Japan, an estimated 400,000 people have the hepatitis B virus (HBV), many of whom were infected as a result of group vaccinations. People with HBV face many challenges, including disease progression, employment-related difficulties, and increased medical expenses. The relationship between HBV victims' daily life suffering and poverty associated with HBV-related employment changes has not been examined. We aimed to clarify the employment-related hardships experienced by Japanese HBV victims, and the relationships between these hardships and daily life suffering, including poverty, through qualitative and quantitative analyses. The study population comprised 11,046 people infected with HBV via group vaccination who filed lawsuits in Japan's District Courts by 2014. First, we conducted a qualitative study (2013) using the KJ method, with 107 participants (68 men, mean age 58.9 years; 39 women, mean age 55.3 years). Semi-structured interviews were conducted covering participants' current condition, treatment, medical expenses, and life difficulties (employment- and family-related problems). In 2014, we conducted a quantitative study. We mailed questionnaires to the entire study population, investigating the topics covered in the interviews (response rate 60.1%). Daily life suffering was determined by responses to the question "What do you think about your everyday life situation?" We performed binomial logistic regression analyses to verify the relationships between daily life suffering and disease, employment, and income status. Interview data were integrated into seven islands: intention to work, lack of understanding of HBV in the workplace, inability to buy life insurance, burden due to medical expenses, life failure, dissatisfaction with the system, and wishing for life balance. The quantitative analyses showed significant positive correlations between daily life suffering and liver cancer (odds ratio [OR] 1.47, 95% confidence interval [CI]: 1.00-2.17, p

Generalized PSF modeling for optimized quantitation in PET imaging.

PubMed

Ashrafinia, Saeed; Mohy-Ud-Din, Hassan; Karakatsanis, Nicolas A; Jha, Abhinav K; Casey, Michael E; Kadrmas, Dan J; Rahmim, Arman

2017-06-21

Point-spread function (PSF) modeling offers the ability to account for resolution degrading phenomena within the PET image generation framework. PSF modeling improves resolution and enhances contrast, but at the same time significantly alters image noise properties and induces edge overshoot effect. Thus, studying the effect of PSF modeling on quantitation task performance can be very important. Frameworks explored in the past involved a dichotomy of PSF versus no-PSF modeling. By contrast, the present work focuses on quantitative performance evaluation of standard uptake value (SUV) PET images, while incorporating a wide spectrum of PSF models, including those that under- and over-estimate the true PSF, for the potential of enhanced quantitation of SUVs. The developed framework first analytically models the true PSF, considering a range of resolution degradation phenomena (including photon non-collinearity, inter-crystal penetration and scattering) as present in data acquisitions with modern commercial PET systems. In the context of oncologic liver FDG PET imaging, we generated 200 noisy datasets per image-set (with clinically realistic noise levels) using an XCAT anthropomorphic phantom with liver tumours of varying sizes. These were subsequently reconstructed using the OS-EM algorithm with varying PSF modelled kernels. We focused on quantitation of both SUV mean and SUV max , including assessment of contrast recovery coefficients, as well as noise-bias characteristics (including both image roughness and coefficient of-variability), for different tumours/iterations/PSF kernels. It was observed that overestimated PSF yielded more accurate contrast recovery for a range of tumours, and typically improved quantitative performance. For a clinically reasonable number of iterations, edge enhancement due to PSF modeling (especially due to over-estimated PSF) was in fact seen to lower SUV mean bias in small tumours. Overall, the results indicate that exactly matched PSF

Genome-wide analyses implicate 33 loci in heritable dog osteosarcoma, including regulatory variants near CDKN2A/B

PubMed Central

2013-01-01

Background Canine osteosarcoma is clinically nearly identical to the human disease, but is common and highly heritable, making genetic dissection feasible. Results Through genome-wide association analyses in three breeds (greyhounds, Rottweilers, and Irish wolfhounds), we identify 33 inherited risk loci explaining 55% to 85% of phenotype variance in each breed. The greyhound locus exhibiting the strongest association, located 150 kilobases upstream of the genes CDKN2A/B, is also the most rearranged locus in canine osteosarcoma tumors. The top germline candidate variant is found at a >90% frequency in Rottweilers and Irish wolfhounds, and alters an evolutionarily constrained element that we show has strong enhancer activity in human osteosarcoma cells. In all three breeds, osteosarcoma-associated loci and regions of reduced heterozygosity are enriched for genes in pathways connected to bone differentiation and growth. Several pathways, including one of genes regulated by miR124, are also enriched for somatic copy-number changes in tumors. Conclusions Mapping a complex cancer in multiple dog breeds reveals a polygenic spectrum of germline risk factors pointing to specific pathways as drivers of disease. PMID:24330828

Partial differential equation techniques for analysing animal movement: A comparison of different methods.

PubMed

Wang, Yi-Shan; Potts, Jonathan R

2017-03-07

Recent advances in animal tracking have allowed us to uncover the drivers of movement in unprecedented detail. This has enabled modellers to construct ever more realistic models of animal movement, which aid in uncovering detailed patterns of space use in animal populations. Partial differential equations (PDEs) provide a popular tool for mathematically analysing such models. However, their construction often relies on simplifying assumptions which may greatly affect the model outcomes. Here, we analyse the effect of various PDE approximations on the analysis of some simple movement models, including a biased random walk, central-place foraging processes and movement in heterogeneous landscapes. Perhaps the most commonly-used PDE method dates back to a seminal paper of Patlak from 1953. However, our results show that this can be a very poor approximation in even quite simple models. On the other hand, more recent methods, based on transport equation formalisms, can provide more accurate results, as long as the kernel describing the animal's movement is sufficiently smooth. When the movement kernel is not smooth, we show that both the older and newer methods can lead to quantitatively misleading results. Our detailed analysis will aid future researchers in the appropriate choice of PDE approximation for analysing models of animal movement. Copyright © 2017 Elsevier Ltd. All rights reserved.

Issues to Consider When Measuring and Applying Socioeconomic Position Quantitatively in Immigrant Health Research

PubMed Central

Nielsen, Signe Smith; Hempler, Nana Folmann; Krasnik, Allan

2013-01-01

The relationship between migration and health is complex, yet, immigrant-related inequalities in health are largely influenced by socioeconomic position. Drawing upon previous findings, this paper discusses issues to consider when measuring and applying socioeconomic position in quantitative immigrant health research. When measuring socioeconomic position, it is important to be aware of four aspects: (1) there is a lack of clarity about how socioeconomic position should be measured; (2) different types of socioeconomic position may be relevant to immigrants compared with the native-born population; (3) choices of measures of socioeconomic position in quantitative analyses often rely on data availability; and (4) different measures of socioeconomic position have different effects in population groups. Therefore, caution should be used in the collection, presentation, analyses, and interpretation of data and researchers need to display their proposed conceptual models and data limitations as well as apply different approaches for analyses. PMID:24287857

Phylogenetic analyses indicate little variation among reticuloendotheliosis viruses infecting avian species, including the endangered Attwater's prairie chicken.

PubMed

Bohls, Ryan L; Linares, Jose A; Gross, Shannon L; Ferro, Pam J; Silvy, Nova J; Collisson, Ellen W

2006-08-01

Reticuloendotheliosis virus infection, which typically causes systemic lymphomas and high mortality in the endangered Attwater's prairie chicken, has been described as a major obstacle in repopulation efforts of captive breeding facilities in Texas. Although antigenic relationships among reticuloendotheliosis virus (REV) strains have been previously determined, phylogenetic relationships have not been reported. The pol and env of REV proviral DNA from prairie chickens (PC-R92 and PC-2404), from poxvirus lesions in domestic chickens, the prototype poultry derived REV-A and chick syncytial virus (CSV), and duck derived spleen necrosis virus (SNV) were PCR amplified and sequenced. The 5032bp, that included the pol and most of env genes, of the PC-R92 and REV-A were 98% identical, and nucleotide sequence identities of smaller regions within the pol and env from REV strains examined ranged from 95 to 99% and 93 to 99%, respectively. The putative amino acid sequences were 97-99% identical in the polymerase and 90-98% in the envelope. Phylogenetic analyses of the nucleotide and amino acid sequences indicated the closest relationship among the recent fowl pox-associated chicken isolates, the prairie chicken isolates and the prototype CSV while only the SNV appeared to be distinctly divergent. While the origin of the naturally occurring viruses is not known, the avian poxvirus may be a critical component of transmission of these ubiquitous oncogenic viruses.

Limited diagnostic value of Dual-Time-Point (18)F-FDG PET/CT imaging for classifying solitary pulmonary nodules in granuloma-endemic regions both at visual and quantitative analyses.

PubMed

Chen, Song; Li, Xuena; Chen, Meijie; Yin, Yafu; Li, Na; Li, Yaming

2016-10-01

This study is aimed to compare the diagnostic power of using quantitative analysis or visual analysis with single time point imaging (STPI) PET/CT and dual time point imaging (DTPI) PET/CT for the classification of solitary pulmonary nodules (SPN) lesions in granuloma-endemic regions. SPN patients who received early and delayed (18)F-FDG PET/CT at 60min and 180min post-injection were retrospectively reviewed. Diagnoses are confirmed by pathological results or follow-ups. Three quantitative metrics, early SUVmax, delayed SUVmax and retention index(the percentage changes between the early SUVmax and delayed SUVmax), were measured for each lesion. Three 5-point scale score was given by blinded interpretations performed by physicians based on STPI PET/CT images, DTPI PET/CT images and CT images, respectively. ROC analysis was performed on three quantitative metrics and three visual interpretation scores. One-hundred-forty-nine patients were retrospectively included. The areas under curve (AUC) of the ROC curves of early SUVmax, delayed SUVmax, RI, STPI PET/CT score, DTPI PET/CT score and CT score are 0.73, 0.74, 0.61, 0.77 0.75 and 0.76, respectively. There were no significant differences between the AUCs in visual interpretation of STPI PET/CT images and DTPI PET/CT images, nor in early SUVmax and delayed SUVmax. The differences of sensitivity, specificity and accuracy between STPI PET/CT and DTPI PET/CT were not significantly different in either quantitative analysis or visual interpretation. In granuloma-endemic regions, DTPI PET/CT did not offer significant improvement over STPI PET/CT in differentiating malignant SPNs in both quantitative analysis and visual interpretation. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Diagnostic accuracy of stress perfusion CMR in comparison with quantitative coronary angiography: fully quantitative, semiquantitative, and qualitative assessment.

PubMed

Mordini, Federico E; Haddad, Tariq; Hsu, Li-Yueh; Kellman, Peter; Lowrey, Tracy B; Aletras, Anthony H; Bandettini, W Patricia; Arai, Andrew E

2014-01-01

This study's primary objective was to determine the sensitivity, specificity, and accuracy of fully quantitative stress perfusion cardiac magnetic resonance (CMR) versus a reference standard of quantitative coronary angiography. We hypothesized that fully quantitative analysis of stress perfusion CMR would have high diagnostic accuracy for identifying significant coronary artery stenosis and exceed the accuracy of semiquantitative measures of perfusion and qualitative interpretation. Relatively few studies apply fully quantitative CMR perfusion measures to patients with coronary disease and comparisons to semiquantitative and qualitative methods are limited. Dual bolus dipyridamole stress perfusion CMR exams were performed in 67 patients with clinical indications for assessment of myocardial ischemia. Stress perfusion images alone were analyzed with a fully quantitative perfusion (QP) method and 3 semiquantitative methods including contrast enhancement ratio, upslope index, and upslope integral. Comprehensive exams (cine imaging, stress/rest perfusion, late gadolinium enhancement) were analyzed qualitatively with 2 methods including the Duke algorithm and standard clinical interpretation. A 70% or greater stenosis by quantitative coronary angiography was considered abnormal. The optimum diagnostic threshold for QP determined by receiver-operating characteristic curve occurred when endocardial flow decreased to <50% of mean epicardial flow, which yielded a sensitivity of 87% and specificity of 93%. The area under the curve for QP was 92%, which was superior to semiquantitative methods: contrast enhancement ratio: 78%; upslope index: 82%; and upslope integral: 75% (p = 0.011, p = 0.019, p = 0.004 vs. QP, respectively). Area under the curve for QP was also superior to qualitative methods: Duke algorithm: 70%; and clinical interpretation: 78% (p < 0.001 and p < 0.001 vs. QP, respectively). Fully quantitative stress perfusion CMR has high diagnostic accuracy for

Speleogenesis, geometry, and topology of caves: A quantitative study of 3D karst conduits

NASA Astrophysics Data System (ADS)

Jouves, Johan; Viseur, Sophie; Arfib, Bruno; Baudement, Cécile; Camus, Hubert; Collon, Pauline; Guglielmi, Yves

2017-12-01

Karst systems are hierarchically spatially organized three-dimensional (3D) networks of conduits behaving as drains for groundwater flow. Recently, geostatistical approaches proposed to generate karst networks from data and parameters stemming from analogous observed karst features. Other studies have qualitatively highlighted relationships between speleogenetic processes and cave patterns. However, few studies have been performed to quantitatively define these relationships. This paper reports a quantitative study of cave geometries and topologies that takes the underlying speleogenetic processes into account. In order to study the spatial organization of caves, a 3D numerical database was built from 26 caves, corresponding to 621 km of cumulative cave passages representative of the variety of karst network patterns. The database includes 3D speleological surveys for which the speleogenetic context is known, allowing the polygenic karst networks to be divided into 48 monogenic cave samples and classified into four cave patterns: vadose branchwork (VB), water-table cave (WTC), looping cave (LC), and angular maze (AM). Eight morphometric cave descriptors were calculated, four geometrical parameters (width-height ratio, tortuosity, curvature, and vertical index) and four topological ones (degree of node connectivity, α and γ graph indices, and ramification index) respectively. The results were validated by statistical analyses (Kruskal-Wallis test and PCA). The VB patterns are clearly distinct from AM ones and from a third group including WTC and LC. A quantitative database of cave morphology characteristics is provided, depending on their speleogenetic processes. These characteristics can be used to constrain and/or validate 3D geostatistical simulations. This study shows how important it is to relate the geometry and connectivity of cave networks to recharge and flow processes. Conversely, the approach developed here provides proxies to estimate the evolution of

A gold nanoparticle-based semi-quantitative and quantitative ultrasensitive paper sensor for the detection of twenty mycotoxins

NASA Astrophysics Data System (ADS)

Kong, Dezhao; Liu, Liqiang; Song, Shanshan; Suryoprabowo, Steven; Li, Aike; Kuang, Hua; Wang, Libing; Xu, Chuanlai

2016-02-01

A semi-quantitative and quantitative multi-immunochromatographic (ICA) strip detection assay was developed for the simultaneous detection of twenty types of mycotoxins from five classes, including zearalenones (ZEAs), deoxynivalenols (DONs), T-2 toxins (T-2s), aflatoxins (AFs), and fumonisins (FBs), in cereal food samples. Sensitive and specific monoclonal antibodies were selected for this assay. The semi-quantitative results were obtained within 20 min by the naked eye, with visual limits of detection for ZEAs, DONs, T-2s, AFs and FBs of 0.1-0.5, 2.5-250, 0.5-1, 0.25-1 and 2.5-10 μg kg-1, and cut-off values of 0.25-1, 5-500, 1-10, 0.5-2.5 and 5-25 μg kg-1, respectively. The quantitative results were obtained using a hand-held strip scan reader, with the calculated limits of detection for ZEAs, DONs, T-2s, AFs and FBs of 0.04-0.17, 0.06-49, 0.15-0.22, 0.056-0.49 and 0.53-1.05 μg kg-1, respectively. The analytical results of spiked samples were in accordance with the accurate content in the simultaneous detection analysis. This newly developed ICA strip assay is suitable for the on-site detection and rapid initial screening of mycotoxins in cereal samples, facilitating both semi-quantitative and quantitative determination.A semi-quantitative and quantitative multi-immunochromatographic (ICA) strip detection assay was developed for the simultaneous detection of twenty types of mycotoxins from five classes, including zearalenones (ZEAs), deoxynivalenols (DONs), T-2 toxins (T-2s), aflatoxins (AFs), and fumonisins (FBs), in cereal food samples. Sensitive and specific monoclonal antibodies were selected for this assay. The semi-quantitative results were obtained within 20 min by the naked eye, with visual limits of detection for ZEAs, DONs, T-2s, AFs and FBs of 0.1-0.5, 2.5-250, 0.5-1, 0.25-1 and 2.5-10 μg kg-1, and cut-off values of 0.25-1, 5-500, 1-10, 0.5-2.5 and 5-25 μg kg-1, respectively. The quantitative results were obtained using a hand-held strip scan

Toward best practices in data processing and analysis for intact biotherapeutics by MS in quantitative bioanalysis.

PubMed

Kellie, John F; Kehler, Jonathan R; Karlinsey, Molly Z; Summerfield, Scott G

2017-12-01

Typically, quantitation of biotherapeutics from biological matrices by LC-MS is based on a surrogate peptide approach to determine molecule concentration. Recent efforts have focused on quantitation of the intact protein molecules or larger mass subunits of monoclonal antibodies. To date, there has been limited guidance for large or intact protein mass quantitation for quantitative bioanalysis. Intact- and subunit-level analyses of biotherapeutics from biological matrices are performed at 12-25 kDa mass range with quantitation data presented. Linearity, bias and other metrics are presented along with recommendations made on the viability of existing quantitation approaches. This communication is intended to start a discussion around intact protein data analysis and processing, recognizing that other published contributions will be required.

Comprehensive Genomic Analyses of the OM43 Clade, Including a Novel Species from the Red Sea, Indicate Ecotype Differentiation among Marine Methylotrophs

PubMed Central

Jimenez-Infante, Francy; Ngugi, David Kamanda; Vinu, Manikandan; Alam, Intikhab; Kamau, Allan Anthony; Blom, Jochen; Bajic, Vladimir B.

2015-01-01

The OM43 clade within the family Methylophilaceae of Betaproteobacteria represents a group of methylotrophs that play important roles in the metabolism of C1 compounds in marine environments and other aquatic environments around the globe. Using dilution-to-extinction cultivation techniques, we successfully isolated a novel species of this clade (here designated MBRS-H7) from the ultraoligotrophic open ocean waters of the central Red Sea. Phylogenomic analyses indicate that MBRS-H7 is a novel species that forms a distinct cluster together with isolate KB13 from Hawaii (Hawaii-Red Sea [H-RS] cluster) that is separate from the cluster represented by strain HTCC2181 (from the Oregon coast). Phylogenetic analyses using the robust 16S-23S internal transcribed spacer revealed a potential ecotype separation of the marine OM43 clade members, which was further confirmed by metagenomic fragment recruitment analyses that showed trends of higher abundance in low-chlorophyll and/or high-temperature provinces for the H-RS cluster but a preference for colder, highly productive waters for the HTCC2181 cluster. This potential environmentally driven niche differentiation is also reflected in the metabolic gene inventories, which in the case of the H-RS cluster include those conferring resistance to high levels of UV irradiation, temperature, and salinity. Interestingly, we also found different energy conservation modules between these OM43 subclades, namely, the existence of the NADH:quinone oxidoreductase complex I (NUO) system in the H-RS cluster and the nonhomologous NADH:quinone oxidoreductase (NQR) system in the HTCC2181 cluster, which might have implications for their overall energetic yields. PMID:26655752

Quantitative glycomics.

PubMed

Orlando, Ron

2010-01-01

The ability to quantitatively determine changes is an essential component of comparative glycomics. Multiple strategies are available by which this can be accomplished. These include label-free approaches and strategies where an isotopic label is incorporated into the glycans prior to analysis. The focus of this chapter is to describe each of these approaches while providing insight into their strengths and weaknesses, so that glycomic investigators can make an educated choice of the strategy that is best suited for their particular application.

An Improved Method for Measuring Quantitative Resistance to the Wheat Pathogen Zymoseptoria tritici Using High-Throughput Automated Image Analysis.

PubMed

Stewart, Ethan L; Hagerty, Christina H; Mikaberidze, Alexey; Mundt, Christopher C; Zhong, Ziming; McDonald, Bruce A

2016-07-01

Zymoseptoria tritici causes Septoria tritici blotch (STB) on wheat. An improved method of quantifying STB symptoms was developed based on automated analysis of diseased leaf images made using a flatbed scanner. Naturally infected leaves (n = 949) sampled from fungicide-treated field plots comprising 39 wheat cultivars grown in Switzerland and 9 recombinant inbred lines (RIL) grown in Oregon were included in these analyses. Measures of quantitative resistance were percent leaf area covered by lesions, pycnidia size and gray value, and pycnidia density per leaf and lesion. These measures were obtained automatically with a batch-processing macro utilizing the image-processing software ImageJ. All phenotypes in both locations showed a continuous distribution, as expected for a quantitative trait. The trait distributions at both sites were largely overlapping even though the field and host environments were quite different. Cultivars and RILs could be assigned to two or more statistically different groups for each measured phenotype. Traditional visual assessments of field resistance were highly correlated with quantitative resistance measures based on image analysis for the Oregon RILs. These results show that automated image analysis provides a promising tool for assessing quantitative resistance to Z. tritici under field conditions.

Spectral analyses, climatology, and interannual variability of Nimbus-7 TOMS version 6 total column ozone

NASA Technical Reports Server (NTRS)

Stanford, J. L.; Ziemke, J. R.; Mcpeters, R. D.; Krueger, A. J.; Bhartia, P. K.

1995-01-01

This reference publication presents selected results from space-time spectral analyses of 13 years of version 6 daily global ozone fields from the Total Ozone Mapping Spectrometer (TOMS). One purpose is to illustrate more quantitatively the well-known richness of structure and variation in total ozone. A second purpose is to provide, for use by modelers and for comparison with other analysts' work, quantitative measures of zonal waves 1, 2, 3, and medium-scale waves 4-7 in total ozone. Their variations throughout the year and at a variety of latitudes are presented, from equatorial to polar regions. The 13-year averages are given, along with selected individual years which illustrate year-to-year variability. The largest long wave amplitudes occur in the polar winters and early springs of each hemisphere, and are related to strong wave amplification during major warning events. In low attitudes total ozone wave amplitudes are an order of magnitude smaller than at high latitudes. However, TOMS fields contain a number of equatorial dynamical features, including Rossby-gravity and Kelvin waves.

Age determination by teeth examination: a comparison between different morphologic and quantitative analyses.

PubMed

Amariti, M L; Restori, M; De Ferrari, F; Paganelli, C; Faglia, R; Legnani, G

1999-06-01

Age determination by teeth examination is one of the main means of determining personal identification. Current studies have suggested different techniques for determining the age of a subject by means of the analysis of microscopic and macroscopic structural modifications of the tooth with ageing. The histological approach is useful among the various methodologies utilized for this purpose. It is still unclear as to what is the best technique, as almost all the authors suggest the use of the approach they themselves have tested. In the present study, age determination by means of microscopic techniques has been based on the quantitative analysis of three parameters, all well recognized in specialized literature: 1. dentinal tubules density/sclerosis 2. tooth translucency 3. analysis of the cementum thickness. After a description of the three methodologies (with automatic image processing of the dentinal sclerosis utilizing an appropriate computer program developed by the authors) the results obtained on cases using the three different approaches are presented, and the merits and failings of each technique are identified with the intention of identifying the one offering the least degree of error in age determination.

Missing heritability in the tails of quantitative traits? A simulation study on the impact of slightly altered true genetic models.

PubMed

Pütter, Carolin; Pechlivanis, Sonali; Nöthen, Markus M; Jöckel, Karl-Heinz; Wichmann, Heinz-Erich; Scherag, André

2011-01-01

Genome-wide association studies have identified robust associations between single nucleotide polymorphisms and complex traits. As the proportion of phenotypic variance explained is still limited for most of the traits, larger and larger meta-analyses are being conducted to detect additional associations. Here we investigate the impact of the study design and the underlying assumption about the true genetic effect in a bimodal mixture situation on the power to detect associations. We performed simulations of quantitative phenotypes analysed by standard linear regression and dichotomized case-control data sets from the extremes of the quantitative trait analysed by standard logistic regression. Using linear regression, markers with an effect in the extremes of the traits were almost undetectable, whereas analysing extremes by case-control design had superior power even for much smaller sample sizes. Two real data examples are provided to support our theoretical findings and to explore our mixture and parameter assumption. Our findings support the idea to re-analyse the available meta-analysis data sets to detect new loci in the extremes. Moreover, our investigation offers an explanation for discrepant findings when analysing quantitative traits in the general population and in the extremes. Copyright © 2011 S. Karger AG, Basel.

Signal-Detection Analyses of Conditional Discrimination and Delayed Matching-to-Sample Performance

ERIC Educational Resources Information Center

Alsop, Brent

2004-01-01

Quantitative analyses of stimulus control and reinforcer control in conditional discriminations and delayed matching-to-sample procedures often encounter a problem; it is not clear how to analyze data when subjects have not made errors. The present article examines two common methods for overcoming this problem. Monte Carlo simulations of…

Identification and Quantitation of Anthocyanins in Purple-Fleshed Sweet Potatoes Cultivated in China by UPLC-PDA and UPLC-QTOF-MS/MS.

PubMed

He, Wei; Zeng, Maomao; Chen, Jie; Jiao, Yuzhi; Niu, Fuxiang; Tao, Guanjun; Zhang, Shuang; Qin, Fang; He, Zhiyong

2016-01-13

The identification and quantitation of the anthocyanins in 12 purple-fleshed sweet potato (PFSP) cultivars ('Jihei 1', 'Xuzi 3', 'Xuzi 6', 'Zhezi 4', 'Ningzi 1', 'Ningzi 2', 'Ningzi 3', 'Ning 2-2', 'Ning 6-8', 'Guangzi 1', 'Ziluolan', and 'Qinzi 1') in China were carried out using a combination of ultraperformance liquid chromatography-photodiode array (UPLC-PDA), quadrupole-time-of-flight mass spectrometry (QTOF-MS), and tandem mass spectrometry (MS/MS) analyses. Thirteen acylated anthocyanins were tentatively characterized, including two new PFSP anthocyanins, cyanidin 3-caffeoyl-vanilloyl sophoroside-5-glucoside and peonidin 3-caffeoyl-vanilloyl sophoroside-5-glucoside. The quantitative analyses of these anthocyanins were conducted using cyanidin 3-O-glucoside as a standard. The total anthocyanin content of the PFSPs depended on the cultivar. The five PFSP cultivars with the highest content of anthocyanins were 'Jihei 1', 'Xuzi 3', 'Zhezi 4', 'Ziluolan', and 'Qinzi 1'. This is the first report of the 'Ningzi 2', 'Ningzi 3', and 'Ning 2-2' PFSP cultivars containing only diacylated anthocyanins and of the 'Xuzi 6' cultivar containing single anthocyanidin-based anthocyanins.

Quantitative optical metrology with CMOS cameras

NASA Astrophysics Data System (ADS)

Furlong, Cosme; Kolenovic, Ervin; Ferguson, Curtis F.

2004-08-01

Recent advances in laser technology, optical sensing, and computer processing of data, have lead to the development of advanced quantitative optical metrology techniques for high accuracy measurements of absolute shapes and deformations of objects. These techniques provide noninvasive, remote, and full field of view information about the objects of interest. The information obtained relates to changes in shape and/or size of the objects, characterizes anomalies, and provides tools to enhance fabrication processes. Factors that influence selection and applicability of an optical technique include the required sensitivity, accuracy, and precision that are necessary for a particular application. In this paper, sensitivity, accuracy, and precision characteristics in quantitative optical metrology techniques, and specifically in optoelectronic holography (OEH) based on CMOS cameras, are discussed. Sensitivity, accuracy, and precision are investigated with the aid of National Institute of Standards and Technology (NIST) traceable gauges, demonstrating the applicability of CMOS cameras in quantitative optical metrology techniques. It is shown that the advanced nature of CMOS technology can be applied to challenging engineering applications, including the study of rapidly evolving phenomena occurring in MEMS and micromechatronics.

Acousto-Optic Tunable Filter Spectroscopic Instrumentation for Quantitative Near-Ir Analysis of Organic Materials.

NASA Astrophysics Data System (ADS)

Eilert, Arnold James

1995-01-01

The utility of near-IR spectroscopy for routine quantitative analyses of a wide variety of compositional, chemical, or physical parameters of organic materials is well understood. It can be used for relatively fast and inexpensive non-destructive bulk material analysis before, during, and after processing. It has been demonstrated as being a particularly useful technique for numerous analytical applications in cereal (food and feed) science and industry. Further fulfillment of the potential of near-IR spectroscopic analysis, both in the process and laboratory environment, is reliant upon the development of instrumentation that is capable of meeting the challenges of increasingly difficult applications. One approach to the development of near-IR spectroscopic instrumentation that holds a great deal of promise is acousto-optic tunable filter (AOTF) technology. A combination of attributes offered by AOTF spectrometry, including speed, optical throughput, wavelength reproducibility, ruggedness (no -moving-parts operation) and flexibility, make it particularly desirable for numerous applications. A series of prototype (research model) acousto -optic tunable filter instruments were developed and tested in order to investigate the feasibility of the technology for quantitative near-IR spectrometry. Development included design, component procurement, assembly and/or configuration of the optical and electronic subsystems of which each functional spectrometer arrangement was comprised, as well as computer interfacing and acquisition/control software development. Investigation of this technology involved an evolution of several operational spectrometer systems, each of which offered improvements over its predecessor. Appropriate testing was conducted at various stages of development. Demonstrations of the potential applicability of our AOTF spectrometer to quantitative process monitoring or laboratory analysis of numerous organic substances, including food materials, were

Qualitative and quantitative analyses of Epimedium wushanense by high-performance liquid chromatography coupled with diode array detection and electrospray ionization tandem mass spectrometry.

PubMed

Li, Hui-fang; Guan, Xiang-yu; Ye, Min; Xiang, Cheng; Lin, Chang-hu; Sun, Chao; Guo, De-an

2011-06-01

A new HPLC-DAD-ESI-MS(n) method was developed for rapid separation, characterization and quantitation of flavonoids in Epimedium wushanense, a popular Chinese herbal medicine. For qualitative identification, a total of 37 compounds were characterized from the underground and aerial parts of E. wushanense. Among them, 28 compounds were prenylated flavonoids, and 23 were confirmed by comparing with reference standards. For quantitative analysis, 12 major flavonoids including kaempferol glycosides, desmethylicaritin glycosides, and icaritin glycosides were simultaneously determined by HPLC/UV. Samples were separated on a Waters Symmetry C(18) column at 35 °C eluted with a gradient three-component mobile phase of acetonitrile, methanol, and water containing 0.03% v/v formic acid. All the flavonoids showed good linearity (r(2) ≥0.9997). The recoveries varied from 92.6 to 106.1% at three concentration levels. This method was applied to the determination of 20 samples of different geographical sources, harvesting time, and plant parts. Contents of the predominant flavonoid, epimedin C, ranged from 1.4 to 5.1% in aerial parts and 1.0 to 2.8% in underground parts. The methods established in this paper were simple and reliable and could be used for the quality control of E. wushanense. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Optofluidic time-stretch quantitative phase microscopy.

PubMed

Guo, Baoshan; Lei, Cheng; Wu, Yi; Kobayashi, Hirofumi; Ito, Takuro; Yalikun, Yaxiaer; Lee, Sangwook; Isozaki, Akihiro; Li, Ming; Jiang, Yiyue; Yasumoto, Atsushi; Di Carlo, Dino; Tanaka, Yo; Yatomi, Yutaka; Ozeki, Yasuyuki; Goda, Keisuke

2018-03-01

Innovations in optical microscopy have opened new windows onto scientific research, industrial quality control, and medical practice over the last few decades. One of such innovations is optofluidic time-stretch quantitative phase microscopy - an emerging method for high-throughput quantitative phase imaging that builds on the interference between temporally stretched signal and reference pulses by using dispersive properties of light in both spatial and temporal domains in an interferometric configuration on a microfluidic platform. It achieves the continuous acquisition of both intensity and phase images with a high throughput of more than 10,000 particles or cells per second by overcoming speed limitations that exist in conventional quantitative phase imaging methods. Applications enabled by such capabilities are versatile and include characterization of cancer cells and microalgal cultures. In this paper, we review the principles and applications of optofluidic time-stretch quantitative phase microscopy and discuss its future perspective. Copyright © 2017 Elsevier Inc. All rights reserved.

Quantitative trait loci analyses and RNA-seq identify genes affecting stress response in rainbow trout

USDA-ARS?s Scientific Manuscript database

Genomic analyses have the potential to impact aquaculture production traits by identifying markers as proxies for traits which are expensive or difficult to measure and characterizing genetic variation and biochemical mechanisms underlying phenotypic variation. One such trait is the response of rai...

Energy Dispersive Spectrometry and Quantitative Analysis Short Course. Introduction to X-ray Energy Dispersive Spectrometry and Quantitative Analysis

NASA Technical Reports Server (NTRS)

Carpenter, Paul; Curreri, Peter A. (Technical Monitor)

2002-01-01

This course will cover practical applications of the energy-dispersive spectrometer (EDS) to x-ray microanalysis. Topics covered will include detector technology, advances in pulse processing, resolution and performance monitoring, detector modeling, peak deconvolution and fitting, qualitative and quantitative analysis, compositional mapping, and standards. An emphasis will be placed on use of the EDS for quantitative analysis, with discussion of typical problems encountered in the analysis of a wide range of materials and sample geometries.

A quantitative reconstruction software suite for SPECT imaging

NASA Astrophysics Data System (ADS)

Namías, Mauro; Jeraj, Robert

2017-11-01

Quantitative Single Photon Emission Tomography (SPECT) imaging allows for measurement of activity concentrations of a given radiotracer in vivo. Although SPECT has usually been perceived as non-quantitative by the medical community, the introduction of accurate CT based attenuation correction and scatter correction from hybrid SPECT/CT scanners has enabled SPECT systems to be as quantitative as Positron Emission Tomography (PET) systems. We implemented a software suite to reconstruct quantitative SPECT images from hybrid or dedicated SPECT systems with a separate CT scanner. Attenuation, scatter and collimator response corrections were included in an Ordered Subset Expectation Maximization (OSEM) algorithm. A novel scatter fraction estimation technique was introduced. The SPECT/CT system was calibrated with a cylindrical phantom and quantitative accuracy was assessed with an anthropomorphic phantom and a NEMA/IEC image quality phantom. Accurate activity measurements were achieved at an organ level. This software suite helps increasing quantitative accuracy of SPECT scanners.

Quantitative and fingerprint analyses of Chinese sweet tea plant (Rubus Suavissimus S. Lee)

PubMed Central

Chou, Guixin; Xu, Shun-Jun; Liu, Dong; Koh, Gar Yee; Zhang, Jian; Liu, Zhijun

2009-01-01

Quality of botanical food is increasingly assessed by the content of multiple bioactive compounds. In this study we report, for the first time, an HPLC fingerprinting method for the quality evaluation of Rubus suavissimus leaves possessing multiple bioactivities. Five constituents, gallic acid, rutin, ellagic acid, rubusoside, and steviol monoside were quantified and used in developing qualitative chromatographic fingerprints. The limits of detection and quantification ranged from 0.29 μg/mL to 37.86 μg/mL. The relative standard deviations (RSDs) of intra- and inter-day precisions were no more than 3.14% and 3.01%, respectively. The average recoveries were between 93.1% and 97.5%. The developed method was validated in analyzing fourteen leaf samples with satisfactory results. The contents of the five marker compounds accounted for an average of about 6% w/w with a variability of 16% among the fourteen samples collected from a single site and year. Gallic acid was the least whereas steviol monoside the most variable compounds among the fourteen leaf samples. The characteristic compound rubusoside that is responsible for the sweet taste accounted for 5% of leaf weight. The validated method can now be used to quantitatively and qualitatively assess the quality of Rubus suavissimus leaves as traditional beverage or potential medicines. PMID:19138116

Functional analyses of the digestive ß-Glucosidase of Formosan Subterranean Termites (Coptotermes formosanus)

USDA-ARS?s Scientific Manuscript database

The research was to elucidate the function of the ß-glucosidase of Formosan subterranean termites in vitro and in vivo. Quantitative RT-PCR analyses indicated that the gene transcript was relatively more abundant in the foraging worker caste than in other castes and salivary glands were the major ex...

Nonindependence and sensitivity analyses in ecological and evolutionary meta-analyses.

PubMed

Noble, Daniel W A; Lagisz, Malgorzata; O'dea, Rose E; Nakagawa, Shinichi

2017-05-01

Meta-analysis is an important tool for synthesizing research on a variety of topics in ecology and evolution, including molecular ecology, but can be susceptible to nonindependence. Nonindependence can affect two major interrelated components of a meta-analysis: (i) the calculation of effect size statistics and (ii) the estimation of overall meta-analytic estimates and their uncertainty. While some solutions to nonindependence exist at the statistical analysis stages, there is little advice on what to do when complex analyses are not possible, or when studies with nonindependent experimental designs exist in the data. Here we argue that exploring the effects of procedural decisions in a meta-analysis (e.g. inclusion of different quality data, choice of effect size) and statistical assumptions (e.g. assuming no phylogenetic covariance) using sensitivity analyses are extremely important in assessing the impact of nonindependence. Sensitivity analyses can provide greater confidence in results and highlight important limitations of empirical work (e.g. impact of study design on overall effects). Despite their importance, sensitivity analyses are seldom applied to problems of nonindependence. To encourage better practice for dealing with nonindependence in meta-analytic studies, we present accessible examples demonstrating the impact that ignoring nonindependence can have on meta-analytic estimates. We also provide pragmatic solutions for dealing with nonindependent study designs, and for analysing dependent effect sizes. Additionally, we offer reporting guidelines that will facilitate disclosure of the sources of nonindependence in meta-analyses, leading to greater transparency and more robust conclusions. © 2017 John Wiley & Sons Ltd.

Combining qualitative and quantitative research within mixed method research designs: a methodological review.

PubMed

Östlund, Ulrika; Kidd, Lisa; Wengström, Yvonne; Rowa-Dewar, Neneh

2011-03-01

It has been argued that mixed methods research can be useful in nursing and health science because of the complexity of the phenomena studied. However, the integration of qualitative and quantitative approaches continues to be one of much debate and there is a need for a rigorous framework for designing and interpreting mixed methods research. This paper explores the analytical approaches (i.e. parallel, concurrent or sequential) used in mixed methods studies within healthcare and exemplifies the use of triangulation as a methodological metaphor for drawing inferences from qualitative and quantitative findings originating from such analyses. This review of the literature used systematic principles in searching CINAHL, Medline and PsycINFO for healthcare research studies which employed a mixed methods approach and were published in the English language between January 1999 and September 2009. In total, 168 studies were included in the results. Most studies originated in the United States of America (USA), the United Kingdom (UK) and Canada. The analytic approach most widely used was parallel data analysis. A number of studies used sequential data analysis; far fewer studies employed concurrent data analysis. Very few of these studies clearly articulated the purpose for using a mixed methods design. The use of the methodological metaphor of triangulation on convergent, complementary, and divergent results from mixed methods studies is exemplified and an example of developing theory from such data is provided. A trend for conducting parallel data analysis on quantitative and qualitative data in mixed methods healthcare research has been identified in the studies included in this review. Using triangulation as a methodological metaphor can facilitate the integration of qualitative and quantitative findings, help researchers to clarify their theoretical propositions and the basis of their results. This can offer a better understanding of the links between theory and

The Eudaimonic and Hedonic Components of Happiness: Qualitative and Quantitative Findings

ERIC Educational Resources Information Center

Fave, Antonella Delle; Brdar, Ingrid; Freire, Teresa; Vella-Brodrick, Dianne; Wissing, Marie P.

2011-01-01

This paper illustrates a new project developed by a cross-country team of researchers, with the aim of studying the hedonic and eudaimonic components of happiness through a mixed method approach combining both qualitative and quantitative analyses. Data were collected from 666 participants in Australia, Croatia, Germany, Italy, Portugal, Spain,…

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 Thermochemical Measurements in High-Pressure Gaseous Combustion

NASA Technical Reports Server (NTRS)

Kojima, Jun J.; Fischer, David G.

2012-01-01

We present our strategic experiment and thermochemical analyses on combustion flow using a subframe burst gating (SBG) Raman spectroscopy. This unconventional laser diagnostic technique has promising ability to enhance accuracy of the quantitative scalar measurements in a point-wise single-shot fashion. In the presentation, we briefly describe an experimental methodology that generates transferable calibration standard for the routine implementation of the diagnostics in hydrocarbon flames. The diagnostic technology was applied to simultaneous measurements of temperature and chemical species in a swirl-stabilized turbulent flame with gaseous methane fuel at elevated pressure (17 atm). Statistical analyses of the space-/time-resolved thermochemical data provide insights into the nature of the mixing process and it impact on the subsequent combustion process in the model combustor.

Nondestructive application of laser-induced fluorescence spectroscopy for quantitative analyses of phenolic compounds in strawberry fruits (Fragaria x ananassa).

PubMed

Wulf, J S; Rühmann, S; Rego, I; Puhl, I; Treutter, D; Zude, M

2008-05-14

Laser-induced fluorescence spectroscopy (LIFS) was nondestructively applied on strawberries (EX = 337 nm, EM = 400-820 nm) to test the feasibility of quantitatively determining native phenolic compounds in strawberries. Eighteen phenolic compounds were identified in fruit skin by UV and MS spectroscopy and quantitatively determined by use of rp-HPLC for separation and diode-array or chemical reaction detection. Partial least-squares calibration models were built for single phenolic compounds by means of nondestructively recorded fluorescence spectra in the blue-green wavelength range using different data preprocessing methods. The direct orthogonal signal correction resulted in r (2) = 0.99 and rmsep < 8% for p-coumaroyl-glucose, and r (2) = 0.99 and rmsep < 24% for cinnamoyl-glucose. In comparison, the correction of the fluorescence spectral data with simultaneously recorded reflectance spectra did not further improve the calibration models. Results show the potential of LIFS for a rapid and nondestructive assessment of contents of p-coumaroyl-glucose and cinnamoyl-glucose in strawberry fruits.

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

From themes to hypotheses: following up with quantitative methods.

PubMed

Morgan, David L

2015-06-01

One important category of mixed-methods research designs consists of quantitative studies that follow up on qualitative research. In this case, the themes that serve as the results from the qualitative methods generate hypotheses for testing through the quantitative methods. That process requires operationalization to translate the concepts from the qualitative themes into quantitative variables. This article illustrates these procedures with examples that range from simple operationalization to the evaluation of complex models. It concludes with an argument for not only following up qualitative work with quantitative studies but also the reverse, and doing so by going beyond integrating methods within single projects to include broader mutual attention from qualitative and quantitative researchers who work in the same field. © The Author(s) 2015.

LC–MS/MS Quantitation of Esophagus Disease Blood Serum Glycoproteins by Enrichment with Hydrazide Chemistry and Lectin Affinity Chromatography

PubMed Central

2015-01-01

Changes in glycosylation have been shown to have a profound correlation with development/malignancy in many cancer types. Currently, two major enrichment techniques have been widely applied in glycoproteomics, namely, lectin affinity chromatography (LAC)-based and hydrazide chemistry (HC)-based enrichments. Here we report the LC–MS/MS quantitative analyses of human blood serum glycoproteins and glycopeptides associated with esophageal diseases by LAC- and HC-based enrichment. The separate and complementary qualitative and quantitative data analyses of protein glycosylation were performed using both enrichment techniques. Chemometric and statistical evaluations, PCA plots, or ANOVA test, respectively, were employed to determine and confirm candidate cancer-associated glycoprotein/glycopeptide biomarkers. Out of 139, 59 common glycoproteins (42% overlap) were observed in both enrichment techniques. This overlap is very similar to previously published studies. The quantitation and evaluation of significantly changed glycoproteins/glycopeptides are complementary between LAC and HC enrichments. LC–ESI–MS/MS analyses indicated that 7 glycoproteins enriched by LAC and 11 glycoproteins enriched by HC showed significantly different abundances between disease-free and disease cohorts. Multiple reaction monitoring quantitation resulted in 13 glycopeptides by LAC enrichment and 10 glycosylation sites by HC enrichment to be statistically different among disease cohorts. PMID:25134008

Quantitative Effects of P Elements on Hybrid Dysgenesis in Drosophila Melanogaster

PubMed Central

Rasmusson, K. E.; Simmons, M. J.; Raymond, J. D.; McLarnon, C. F.

1990-01-01

Genetic analyses involving chromosomes from seven inbred lines derived from a single M' strain were used to study the quantitative relationships between the incidence and severity of P-M hybrid dysgenesis and the number of genomic P elements. In four separate analyses, the mutability of sn(w), a P element-insertion mutation of the X-linked singed locus, was found to be inversely related to the number of autosomal P elements. Since sn(w) mutability is caused by the action of the P transposase, this finding supports the hypothesis that genomic P elements titrate the transposase present within a cell. Other analyses demonstrated that autosomal transmission ratios were distorted by P element action. In these analyses, the amount of distortion against an autosome increased more or less linearly with the number of P elements carried by the autosome. Additional analyses showed that the magnitude of this distortion was reduced when a second P element-containing autosome was present in the genome. This reduction could adequately be explained by transposase titration; there was no evidence that it was due to repressor molecules binding to P elements and inhibiting their movement. The influence of genomic P elements on the incidence of gonadal dysgenesis was also investigated. Although no simple relationship between the number of P elements and the incidence of the trait could be discerned, it was clear that even a small number of elements could increase the incidence markedly. The failure to find a quantitative relationship between P element number and the incidence of gonadal dysgenesis probably reflects the complex etiology of this trait. PMID:2155853

Size-exclusive Nanosensor for Quantitative Analysis of Fullerene C60: A Concept Paper

EPA Science Inventory

This paper presents the first development of a mass-sensitive nanosensor for the isolation and quantitative analyses of engineered fullerene (C₆₀) nanoparticles, while excluding mixtures of structurally similar fullerenes. Amino-modified beta cyclodextrin (β-CD-NH

Recombinant plasmid-based quantitative Real-Time PCR analysis of Salmonella enterica serotypes and its application to milk samples.

PubMed

Gokduman, Kurtulus; Avsaroglu, M Dilek; Cakiris, Aris; Ustek, Duran; Gurakan, G Candan

2016-03-01

The aim of the current study was to develop, a new, rapid, sensitive and quantitative Salmonella detection method using a Real-Time PCR technique based on an inexpensive, easy to produce, convenient and standardized recombinant plasmid positive control. To achieve this, two recombinant plasmids were constructed as reference molecules by cloning the two most commonly used Salmonella-specific target gene regions, invA and ttrRSBC. The more rapid detection enabled by the developed method (21 h) compared to the traditional culture method (90 h) allows the quantitative evaluation of Salmonella (quantification limits of 10(1)CFU/ml and 10(0)CFU/ml for the invA target and the ttrRSBC target, respectively), as illustrated using milk samples. Three advantages illustrated by the current study demonstrate the potential of the newly developed method to be used in routine analyses in the medical, veterinary, food and water/environmental sectors: I--The method provides fast analyses including the simultaneous detection and determination of correct pathogen counts; II--The method is applicable to challenging samples, such as milk; III--The method's positive controls (recombinant plasmids) are reproducible in large quantities without the need to construct new calibration curves. Copyright © 2016 Elsevier B.V. All rights reserved.

Combating substance abuse with ibogaine: pre- and posttreatment recommendations and an example of successive model fitting analyses.

PubMed

Hittner, James B; Quello, Susan B

2004-06-01

Ibogaine is an indole alkaloid derived from the root bark of the African shrub Tabernan the iboga and it has been used for many years as a medicinal and ceremonial agent in West Central Africa. Furthermore, both anecdotal observations and recent studies suggest that ibogaine alleviates withdrawal symptoms and reduces drug cravings. Although ibogaine articles typically include information bearing on the duration of drug abstinence following treatment, little if any attention is given to the psychological and environmental factors that might facilitate a positive treatment outcome. Hence, a major purpose of the present review is to suggest a number of theory-driven, pretreatment and posttreatment recommendations that have good potential for enhancing ibogaine's effectiveness. The second major purpose of this review is to demonstrate, through a reanalysis of previously published results, the utility of conducting successive model fitting analyses on ibogaine treatment data. Such analyses are useful for determining both the strength and form of the association between pre-ibogaine treatment variables and post-ibogaine treatment outcomes. Finally, in order to facilitate future quantitative reviews, the authors recommend that a minimum set of patient- and treatment-related variables be included in all ibogaine publications involving human participants.

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.

High-throughput SISCAPA quantitation of peptides from human plasma digests by ultrafast, liquid chromatography-free mass spectrometry.

PubMed

Razavi, Morteza; Frick, Lauren E; LaMarr, William A; Pope, Matthew E; Miller, Christine A; Anderson, N Leigh; Pearson, Terry W

2012-12-07

We investigated the utility of an SPE-MS/MS platform in combination with a modified SISCAPA workflow for chromatography-free MRM analysis of proteotypic peptides in digested human plasma. This combination of SISCAPA and SPE-MS/MS technology allows sensitive, MRM-based quantification of peptides from plasma digests with a sample cycle time of ∼7 s, a 300-fold improvement over typical MRM analyses with analysis times of 30-40 min that use liquid chromatography upstream of MS. The optimized system includes capture and enrichment to near purity of target proteotypic peptides using rigorously selected, high affinity, antipeptide monoclonal antibodies and reduction of background peptides using a novel treatment of magnetic bead immunoadsorbents. Using this method, we have successfully quantitated LPS-binding protein and mesothelin (concentrations of ∼5000 ng/mL and ∼10 ng/mL, respectively) in human plasma. The method eliminates the need for upstream liquid-chromatography and can be multiplexed, thus facilitating quantitative analysis of proteins, including biomarkers, in large sample sets. The method is ideal for high-throughput biomarker validation after affinity enrichment and has the potential for applications in clinical laboratories.

Project analysis and integration economic analyses summary

NASA Technical Reports Server (NTRS)

Macomber, H. L.

1986-01-01

An economic-analysis summary was presented for the manufacture of crystalline-silicon modules involving silicon ingot/sheet, growth, slicing, cell manufacture, and module assembly. Economic analyses provided: useful quantitative aspects for complex decision-making to the Flat-plate Solar Array (FSA) Project; yardsticks for design and performance to industry; and demonstration of how to evaluate and understand the worth of research and development both to JPL and other government agencies and programs. It was concluded that future research and development funds for photovoltaics must be provided by the Federal Government because the solar industry today does not reap enough profits from its present-day sales of photovoltaic equipment.

Pooled exposure-response analyses and risk assessment for lung cancer in 10 cohorts of silica-exposed workers: an IARC multicentre study.

PubMed

Steenland, K; Mannetje, A; Boffetta, P; Stayner, L; Attfield, M; Chen, J; Dosemeci, M; DeKlerk, N; Hnizdo, E; Koskela, R; Checkoway, H

2001-11-01

Silica is one of the most common occupational exposures worldwide. In 1997 the International Agency for Research on Cancer (IARC) classified inhaled crystalline silica as a human carcinogen (group 1), but acknowledged limitations in the epidemiologic data, including inconsistencies across studies and the lack of extensive exposure-response data. We have conducted a pooled exposure-response analysis of 10 silica-exposed cohorts to investigate lung cancer. The pooled cohort included 65,980 workers (44,160 miners, 21,820 nominees), and 1,072 lung cancer deaths (663 miners, 409 nonminers). Follow-up has been extended for five of these cohorts beyond published data. Quantitative exposure estimates by job and calendar time were adopted, modified, or developed to permit common analyses by respirable silica (mg/m3) across cohorts. The log of cumulative exposure, with a 15-year lag, was a strong predictor of lung cancer (p = 0.0001), with consistency across studies (test for heterogeneity, p = 0.34). Results for the log of cumulative exposure were consistent between underground mines and other facilities. Categorical analyses by quintile of cumulative exposure resulted in a monotonic trend with odds ratios of 1.0. 1.0, 1.3, 1.5, 1.6. Analyses using a spline curve also showed a monotonic increase in risk with increasing exposure. The estimated excess lifetime risk (through age 75) of lung cancer for a worker exposed from age 20 to 65 at 0.1 mg/m3 respirable crystalline silica (the permissible level in many countries) was 1.1-1.7%, above background risks of 3-6%. Our results support the decision by the IARC to classify inhaled silica in occupational settings as a carcinogen, and suggest that the current exposure limits in many countries may be inadequate. These data represent the first quantitative exposure-response analysis and risk assessment for silica using data from multiple studies.

Semi-quantitative spectrographic analysis and rank correlation in geochemistry

USGS Publications Warehouse

Flanagan, F.J.

1957-01-01

The rank correlation coefficient, rs, which involves less computation than the product-moment correlation coefficient, r, can be used to indicate the degree of relationship between two elements. The method is applicable in situations where the assumptions underlying normal distribution correlation theory may not be satisfied. Semi-quantitative spectrographic analyses which are reported as grouped or partly ranked data can be used to calculate rank correlations between elements. ?? 1957.

Quantitative Approaches to Group Research: Suggestions for Best Practices

ERIC Educational Resources Information Center

McCarthy, Christopher J.; Whittaker, Tiffany A.; Boyle, Lauren H.; Eyal, Maytal

2017-01-01

Rigorous scholarship is essential to the continued growth of group work, yet the unique nature of this counseling specialty poses challenges for quantitative researchers. The purpose of this proposal is to overview unique challenges to quantitative research with groups in the counseling field, including difficulty in obtaining large sample sizes…

Assessing signal-to-noise in quantitative proteomics: multivariate statistical analysis in DIGE experiments.

PubMed

Friedman, David B

2012-01-01

All quantitative proteomics experiments measure variation between samples. When performing large-scale experiments that involve multiple conditions or treatments, the experimental design should include the appropriate number of individual biological replicates from each condition to enable the distinction between a relevant biological signal from technical noise. Multivariate statistical analyses, such as principal component analysis (PCA), provide a global perspective on experimental variation, thereby enabling the assessment of whether the variation describes the expected biological signal or the unanticipated technical/biological noise inherent in the system. Examples will be shown from high-resolution multivariable DIGE experiments where PCA was instrumental in demonstrating biologically significant variation as well as sample outliers, fouled samples, and overriding technical variation that would not be readily observed using standard univariate tests.

Whole-brain ex-vivo quantitative MRI of the cuprizone mouse model

PubMed Central

Hurley, Samuel A.; Vernon, Anthony C.; Torres, Joel; Dell’Acqua, Flavio; Williams, Steve C.R.; Cash, Diana

2016-01-01

Myelin is a critical component of the nervous system and a major contributor to contrast in Magnetic Resonance (MR) images. However, the precise contribution of myelination to multiple MR modalities is still under debate. The cuprizone mouse is a well-established model of demyelination that has been used in several MR studies, but these have often imaged only a single slice and analysed a small region of interest in the corpus callosum. We imaged and analyzed the whole brain of the cuprizone mouse ex-vivo using high-resolution quantitative MR methods (multi-component relaxometry, Diffusion Tensor Imaging (DTI) and morphometry) and found changes in multiple regions, including the corpus callosum, cerebellum, thalamus and hippocampus. The presence of inflammation, confirmed with histology, presents difficulties in isolating the sensitivity and specificity of these MR methods to demyelination using this model. PMID:27833805

Quantitative evolutionary design

PubMed Central

Diamond, Jared

2002-01-01

The field of quantitative evolutionary design uses evolutionary reasoning (in terms of natural selection and ultimate causation) to understand the magnitudes of biological reserve capacities, i.e. excesses of capacities over natural loads. Ratios of capacities to loads, defined as safety factors, fall in the range 1.2-10 for most engineered and biological components, even though engineered safety factors are specified intentionally by humans while biological safety factors arise through natural selection. Familiar examples of engineered safety factors include those of buildings, bridges and elevators (lifts), while biological examples include factors of bones and other structural elements, of enzymes and transporters, and of organ metabolic performances. Safety factors serve to minimize the overlap zone (resulting in performance failure) between the low tail of capacity distributions and the high tail of load distributions. Safety factors increase with coefficients of variation of load and capacity, with capacity deterioration with time, and with cost of failure, and decrease with costs of initial construction, maintenance, operation, and opportunity. Adaptive regulation of many biological systems involves capacity increases with increasing load; several quantitative examples suggest sublinear increases, such that safety factors decrease towards 1.0. Unsolved questions include safety factors of series systems, parallel or branched pathways, elements with multiple functions, enzyme reaction chains, and equilibrium enzymes. The modest sizes of safety factors imply the existence of costs that penalize excess capacities. Those costs are likely to involve wasted energy or space for large or expensive components, but opportunity costs of wasted space at the molecular level for minor components. PMID:12122135

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

Doing Quantitative Research in Education with SPSS Second edition Daniel Muijs Doing Quantitative Research in Education with SPSS Second edition £24.99 264pp 9781849203241 1849203245 [Formula: see text].

PubMed

2012-07-19

THIS TEXT is a straightforward, no nonsense guide for novice researchers venturing into research involving quantitative methodologies. It is also an excellent resource to refresh more experienced researchers. It is well written in plain English and encourages researchers to carry out their own analyses.

EvolQG - An R package for evolutionary quantitative genetics

PubMed Central

Melo, Diogo; Garcia, Guilherme; Hubbe, Alex; Assis, Ana Paula; Marroig, Gabriel

2016-01-01

We present an open source package for performing evolutionary quantitative genetics analyses in the R environment for statistical computing. Evolutionary theory shows that evolution depends critically on the available variation in a given population. When dealing with many quantitative traits this variation is expressed in the form of a covariance matrix, particularly the additive genetic covariance matrix or sometimes the phenotypic matrix, when the genetic matrix is unavailable and there is evidence the phenotypic matrix is sufficiently similar to the genetic matrix. Given this mathematical representation of available variation, the \\textbf{EvolQG} package provides functions for calculation of relevant evolutionary statistics; estimation of sampling error; corrections for this error; matrix comparison via correlations, distances and matrix decomposition; analysis of modularity patterns; and functions for testing evolutionary hypotheses on taxa diversification. PMID:27785352

Quantitative High-Resolution Genomic Analysis of Single Cancer Cells

PubMed Central

Hannemann, Juliane; Meyer-Staeckling, Sönke; Kemming, Dirk; Alpers, Iris; Joosse, Simon A.; Pospisil, Heike; Kurtz, Stefan; Görndt, Jennifer; Püschel, Klaus; Riethdorf, Sabine; Pantel, Klaus; Brandt, Burkhard

2011-01-01

During cancer progression, specific genomic aberrations arise that can determine the scope of the disease and can be used as predictive or prognostic markers. The detection of specific gene amplifications or deletions in single blood-borne or disseminated tumour cells that may give rise to the development of metastases is of great clinical interest but technically challenging. In this study, we present a method for quantitative high-resolution genomic analysis of single cells. Cells were isolated under permanent microscopic control followed by high-fidelity whole genome amplification and subsequent analyses by fine tiling array-CGH and qPCR. The assay was applied to single breast cancer cells to analyze the chromosomal region centred by the therapeutical relevant EGFR gene. This method allows precise quantitative analysis of copy number variations in single cell diagnostics. PMID:22140428

Quantitative high-resolution genomic analysis of single cancer cells.

PubMed

Hannemann, Juliane; Meyer-Staeckling, Sönke; Kemming, Dirk; Alpers, Iris; Joosse, Simon A; Pospisil, Heike; Kurtz, Stefan; Görndt, Jennifer; Püschel, Klaus; Riethdorf, Sabine; Pantel, Klaus; Brandt, Burkhard

2011-01-01

During cancer progression, specific genomic aberrations arise that can determine the scope of the disease and can be used as predictive or prognostic markers. The detection of specific gene amplifications or deletions in single blood-borne or disseminated tumour cells that may give rise to the development of metastases is of great clinical interest but technically challenging. In this study, we present a method for quantitative high-resolution genomic analysis of single cells. Cells were isolated under permanent microscopic control followed by high-fidelity whole genome amplification and subsequent analyses by fine tiling array-CGH and qPCR. The assay was applied to single breast cancer cells to analyze the chromosomal region centred by the therapeutical relevant EGFR gene. This method allows precise quantitative analysis of copy number variations in single cell diagnostics.

DRIFTSEL: an R package for detecting signals of natural selection in quantitative traits.

PubMed

Karhunen, M; Merilä, J; Leinonen, T; Cano, J M; Ovaskainen, O

2013-07-01

Approaches and tools to differentiate between natural selection and genetic drift as causes of population differentiation are of frequent demand in evolutionary biology. Based on the approach of Ovaskainen et al. (2011), we have developed an R package (DRIFTSEL) that can be used to differentiate between stabilizing selection, diversifying selection and random genetic drift as causes of population differentiation in quantitative traits when neutral marker and quantitative genetic data are available. Apart from illustrating the use of this method and the interpretation of results using simulated data, we apply the package on data from three-spined sticklebacks (Gasterosteus aculeatus) to highlight its virtues. DRIFTSEL can also be used to perform usual quantitative genetic analyses in common-garden study designs. © 2013 John Wiley & Sons Ltd.

Are Quantitative Measures of Academic Productivity Correlated with Academic Rank in Plastic Surgery? A National Study.

PubMed

Susarla, Srinivas M; Lopez, Joseph; Swanson, Edward W; Miller, Devin; O'Brien-Coon, Devin; Zins, James E; Serletti, Joseph M; Yaremchuk, Michael J; Manson, Paul N; Gordon, Chad R

2015-09-01

The purpose of this study was to investigate the correlation between quantitative measures of academic productivity and academic rank among full-time academic plastic surgeons. Bibliometric indices were computed for all full-time academic plastic surgeons in the United States. The primary study variable was academic rank. Bibliometric predictors included the Hirsch index, I-10 index, number of publications, number of citations, and highest number of citations for a single publication. Descriptive, bivariate, and correlation analyses were computed. Multiple comparisons testing was used to calculate adjusted associations for subgroups. For all analyses, a value of p < 0.05 was considered significant. The cohort consisted of 607 plastic surgeons across 91 Accreditation Council for Graduate Medical Education-approved programs. Of them, 4.1 percent were instructors/lecturers, 43.7 percent were assistant professors, 22.1 percent were associate professors, 25.7 percent were professors, and 4.4 percent were endowed professors. Mean values were as follows: Hirsch index, 10.2 ± 9.0; I-10 index, 17.2 ± 10.2; total number of publications, 45.5 ± 69.4; total number of citations, 725.0 ± 1448.8; and highest number of citations for a single work, 117.8 ± 262.4. Correlation analyses revealed strong associations of the Hirsch index, I-10 index, number of publications, and number of citations with academic rank (rs = 0.62 to 0.64; p < 0.001). Academic rank in plastic surgery is strongly correlated with several quantitative metrics of research productivity. Although academic promotion is the result of success in multiple different areas, bibliometric measures may be useful adjuncts for assessment of research productivity.

Quantitative trait loci controlling leaf venation in Arabidopsis.

PubMed

Rishmawi, Louai; Bühler, Jonas; Jaegle, Benjamin; Hülskamp, Martin; Koornneef, Maarten

2017-08-01

Leaf veins provide the mechanical support and are responsible for the transport of nutrients and water to the plant. High vein density is a prerequisite for plants to have C4 photosynthesis. We investigated the genetic variation and genetic architecture of leaf venation traits within the species Arabidopsis thaliana using natural variation. Leaf venation traits, including leaf vein density (LVD) were analysed in 66 worldwide accessions and 399 lines of the multi-parent advanced generation intercross population. It was shown that there is no correlation between LVD and photosynthesis parameters within A. thaliana. Association mapping was performed for LVD and identified 16 and 17 putative quantitative trait loci (QTLs) in the multi-parent advanced generation intercross and worldwide sets, respectively. There was no overlap between the identified QTLs suggesting that many genes can affect the traits. In addition, linkage mapping was performed using two biparental recombinant inbred line populations. Combining linkage and association mapping revealed seven candidate genes. For one of the candidate genes, RCI2c, we demonstrated its function in leaf venation patterning. © 2017 John Wiley & Sons Ltd.

Comprehensive and quantitative proteomic analyses of zebrafish plasma reveals conserved protein profiles between genders and between zebrafish and human.

PubMed

Li, Caixia; Tan, Xing Fei; Lim, Teck Kwang; Lin, Qingsong; Gong, Zhiyuan

2016-04-13

Omic approaches have been increasingly used in the zebrafish model for holistic understanding of molecular events and mechanisms of tissue functions. However, plasma is rarely used for omic profiling because of the technical challenges in collecting sufficient blood. In this study, we employed two mass spectrometric (MS) approaches for a comprehensive characterization of zebrafish plasma proteome, i.e. conventional shotgun liquid chromatography-tandem mass spectrometry (LC-MS/MS) for an overview study and quantitative SWATH (Sequential Window Acquisition of all THeoretical fragment-ion spectra) for comparison between genders. 959 proteins were identified in the shotgun profiling with estimated concentrations spanning almost five orders of magnitudes. Other than the presence of a few highly abundant female egg yolk precursor proteins (vitellogenins), the proteomic profiles of male and female plasmas were very similar in both number and abundance and there were basically no other highly gender-biased proteins. The types of plasma proteins based on IPA (Ingenuity Pathway Analysis) classification and tissue sources of production were also very similar. Furthermore, the zebrafish plasma proteome shares significant similarities with human plasma proteome, in particular in top abundant proteins including apolipoproteins and complements. Thus, the current study provided a valuable dataset for future evaluation of plasma proteins in zebrafish.

Comprehensive and quantitative proteomic analyses of zebrafish plasma reveals conserved protein profiles between genders and between zebrafish and human

PubMed Central

Li, Caixia; Tan, Xing Fei; Lim, Teck Kwang; Lin, Qingsong; Gong, Zhiyuan

2016-01-01

Omic approaches have been increasingly used in the zebrafish model for holistic understanding of molecular events and mechanisms of tissue functions. However, plasma is rarely used for omic profiling because of the technical challenges in collecting sufficient blood. In this study, we employed two mass spectrometric (MS) approaches for a comprehensive characterization of zebrafish plasma proteome, i.e. conventional shotgun liquid chromatography-tandem mass spectrometry (LC-MS/MS) for an overview study and quantitative SWATH (Sequential Window Acquisition of all THeoretical fragment-ion spectra) for comparison between genders. 959 proteins were identified in the shotgun profiling with estimated concentrations spanning almost five orders of magnitudes. Other than the presence of a few highly abundant female egg yolk precursor proteins (vitellogenins), the proteomic profiles of male and female plasmas were very similar in both number and abundance and there were basically no other highly gender-biased proteins. The types of plasma proteins based on IPA (Ingenuity Pathway Analysis) classification and tissue sources of production were also very similar. Furthermore, the zebrafish plasma proteome shares significant similarities with human plasma proteome, in particular in top abundant proteins including apolipoproteins and complements. Thus, the current study provided a valuable dataset for future evaluation of plasma proteins in zebrafish. PMID:27071722

Religion and body weight: a review of quantitative studies.

PubMed

Yeary, Karen Hye-Cheon Kim; Sobal, Jeffery; Wethington, Elaine

2017-10-01

Increasing interest in relationships between religion and health has encouraged research about religion and body weight, which has produced mixed findings. We systematically searched 11 bibliographic databases for quantitative studies of religion and weight, locating and coding 85 studies. We conducted a systematic review, analysing descriptive characteristics of the studies as well as relevant religion-body weight associations related to study characteristics. We summarized findings for two categories of religion variables: religious affiliation and religiosity. For religious affiliation, we found evidence for significant associations with body weight in both cross-sectional and longitudinal studies. In particular, Seventh-Day Adventists had lower body weight than other denominations in cross-sectional analyses. For religiosity, significant associations occurred between greater religiosity and higher body weight in both cross-sectional and longitudinal studies. In particular, greater religiosity was significantly associated with higher body weight in bivariate analyses but less so in multivariate analyses. A greater proportion of studies that used a representative sample, longitudinal analyses, and samples with only men reported significant associations between religiosity and weight. Evidence in seven studies suggested that health behaviours and psychosocial factors mediate religion-weight relationships. More longitudinal studies and analyses of mediators are needed to provide stronger evidence and further elucidate religion-weight relationships. © 2017 World Obesity Federation.

Determinants of accepting non-invasive ventilation treatment in motor neurone disease: a quantitative analysis at point of need.

PubMed

Cousins, Rosanna; Ando, Hikari; Thornton, Everard; Chakrabarti, Biswajit; Angus, Robert; Young, Carolyn

2013-01-01

Objectives : Motor neurone disease (MND) progressively damages the nervous system causing wasting to muscles, including those used for breathing. There is robust evidence that non-invasive ventilation (NIV) relieves respiratory symptoms and improves quality of life in MND. Nevertheless, about a third of those who would benefit from NIV decline the treatment. The purpose of the study was to understand this phenomenon. Design : A cross-sectional quantitative analysis. Methods : Data including age, sex, MND symptomatology, general physical and mental health and psychological measures were collected from 27 patients and their family caregivers at the point of being offered ventilatory support based on physiological markers. Results : Quantitative analyses indicated no difference in patient characteristics or symptomatology between those who tolerated ( n  = 17) and those who declined ( n  = 10) NIV treatment. A comparison of family caregivers found no differences in physical or mental health or in caregiving distress, emphasising that this was high in both groups; however, family caregivers supporting NIV treatment were significantly more resilient, less neurotic and less anxious than family caregivers who did not. Regression analyses, forcing MND symptoms to enter the equation first, found caregiver resilience:commitment the strongest predictor of uptake of NIV treatment adding 22% to the 56% explained variance. Conclusion : Patients who tolerated NIV treatment had family caregivers who cope through finding meaning and purpose in their situation. Psychological support and proactive involvement for family caregivers in the management of the illness situation is indicated if acceptance of NIV treatment is to be maximised in MND.

Determinants of accepting non-invasive ventilation treatment in motor neurone disease: a quantitative analysis at point of need

PubMed Central

Cousins, Rosanna; Ando, Hikari; Thornton, Everard; Chakrabarti, Biswajit; Angus, Robert; Young, Carolyn

2013-01-01

Objectives: Motor neurone disease (MND) progressively damages the nervous system causing wasting to muscles, including those used for breathing. There is robust evidence that non-invasive ventilation (NIV) relieves respiratory symptoms and improves quality of life in MND. Nevertheless, about a third of those who would benefit from NIV decline the treatment. The purpose of the study was to understand this phenomenon. Design: A cross-sectional quantitative analysis. Methods: Data including age, sex, MND symptomatology, general physical and mental health and psychological measures were collected from 27 patients and their family caregivers at the point of being offered ventilatory support based on physiological markers. Results: Quantitative analyses indicated no difference in patient characteristics or symptomatology between those who tolerated (n = 17) and those who declined (n = 10) NIV treatment. A comparison of family caregivers found no differences in physical or mental health or in caregiving distress, emphasising that this was high in both groups; however, family caregivers supporting NIV treatment were significantly more resilient, less neurotic and less anxious than family caregivers who did not. Regression analyses, forcing MND symptoms to enter the equation first, found caregiver resilience:commitment the strongest predictor of uptake of NIV treatment adding 22% to the 56% explained variance. Conclusion: Patients who tolerated NIV treatment had family caregivers who cope through finding meaning and purpose in their situation. Psychological support and proactive involvement for family caregivers in the management of the illness situation is indicated if acceptance of NIV treatment is to be maximised in MND. PMID:25264500

Are we hammering square pegs into round holes? An investigation of the meta-analyses of reading research with students who are d/Deaf or hard of hearing and students who are hearing.

PubMed

Wang, Ye; Williams, Cheri

2014-01-01

In a qualitative meta-analysis, the researchers systematically reviewed qualitative and quantitative meta-analyses on reading research with PK-12 students published after the 2000 National Reading Panel (NRP) report. Eleven qualitative and 39 quantitative meta-analyses were reviewed examining reading research with typically developing hearing students, special education hearing students (including English Language Learners), and d/Deaf or hard of hearing (d/Dhh) students. Generally, the meta-analysis yielded findings similar to and corroborative of the NRP's. Contradictory results (e.g., regarding the role of rhyme awareness in reading outcomes) most often resulted from differing definitions of interventions and their measurements. The analysis provided evidence of several instructional approaches that support reading development. On the basis of the qualitative similarity hypothesis (Paul, 2010, 2012; Paul & Lee, 2010; Paul & Wang, 2012; Paul, Wang, & Williams, 2013), the researchers argue that these instructional strategies also should effectively support d/Dhh children's reading development.

When Should Zero Be Included on a Scale Showing Magnitude?

ERIC Educational Resources Information Center

Kozak, Marcin

2011-01-01

This article addresses an important problem of graphing quantitative data: should one include zero on the scale showing magnitude? Based on a real time series example, the problem is discussed and some recommendations are proposed.

Correlation between quantitative traits and correlation between corresponding LOD scores: detection of pleiotropic effects.

PubMed

Ulgen, Ayse; Han, Zhihua; Li, Wentian

2003-12-31

We address the question of whether statistical correlations among quantitative traits lead to correlation of linkage results of these traits. Five measured quantitative traits (total cholesterol, fasting glucose, HDL cholesterol, blood pressure, and triglycerides), and one derived quantitative trait (total cholesterol divided by the HDL cholesterol) are used for phenotype correlation studies. Four of them are used for linkage analysis. We show that although correlation among phenotypes partially reflects the correlation among linkage analysis results, the LOD-score correlations are on average low. The most significant peaks found by using different traits do not often overlap. Studying covariances at specific locations in LOD scores may provide clues for further bivariate linkage analyses.

Single-case synthesis tools II: Comparing quantitative outcome measures.

PubMed

Zimmerman, Kathleen N; Pustejovsky, James E; Ledford, Jennifer R; Barton, Erin E; Severini, Katherine E; Lloyd, Blair P

2018-03-07

Varying methods for evaluating the outcomes of single case research designs (SCD) are currently used in reviews and meta-analyses of interventions. Quantitative effect size measures are often presented alongside visual analysis conclusions. Six measures across two classes-overlap measures (percentage non-overlapping data, improvement rate difference, and Tau) and parametric within-case effect sizes (standardized mean difference and log response ratio [increasing and decreasing])-were compared to determine if choice of synthesis method within and across classes impacts conclusions regarding effectiveness. The effectiveness of sensory-based interventions (SBI), a commonly used class of treatments for young children, was evaluated. Separately from evaluations of rigor and quality, authors evaluated behavior change between baseline and SBI conditions. SBI were unlikely to result in positive behavior change across all measures except IRD. However, subgroup analyses resulted in variable conclusions, indicating that the choice of measures for SCD meta-analyses can impact conclusions. Suggestions for using the log response ratio in SCD meta-analyses and considerations for understanding variability in SCD meta-analysis conclusions are discussed. Copyright © 2018 Elsevier Ltd. All rights reserved.

Quantitative ptychographic reconstruction by applying a probe constraint

NASA Astrophysics Data System (ADS)

Reinhardt, J.; Schroer, C. G.

2018-04-01

The coherent scanning technique X-ray ptychography has become a routine tool for high-resolution imaging and nanoanalysis in various fields of research such as chemistry, biology or materials science. Often the ptychographic reconstruction results are analysed in order to yield absolute quantitative values for the object transmission and illuminating probe function. In this work, we address a common ambiguity encountered in scaling the object transmission and probe intensity via the application of an additional constraint to the reconstruction algorithm. A ptychographic measurement of a model sample containing nanoparticles is used as a test data set against which to benchmark in the reconstruction results depending on the type of constraint used. Achieving quantitative absolute values for the reconstructed object transmission is essential for advanced investigation of samples that are changing over time, e.g., during in-situ experiments or in general when different data sets are compared.

A Quantitative Gas Chromatographic Ethanol Determination.

ERIC Educational Resources Information Center

Leary, James J.

1983-01-01

Describes a gas chromatographic experiment for the quantitative determination of volume percent ethanol in water ethanol solutions. Background information, procedures, and typical results are included. Accuracy and precision of results are both on the order of two percent. (JN)

Quantitative proteomics in the field of microbiology.

PubMed

Otto, Andreas; Becher, Dörte; Schmidt, Frank

2014-03-01

Quantitative proteomics has become an indispensable analytical tool for microbial research. Modern microbial proteomics covers a wide range of topics in basic and applied research from in vitro characterization of single organisms to unravel the physiological implications of stress/starvation to description of the proteome content of a cell at a given time. With the techniques available, ranging from classical gel-based procedures to modern MS-based quantitative techniques, including metabolic and chemical labeling, as well as label-free techniques, quantitative proteomics is today highly successful in sophisticated settings of high complexity such as host-pathogen interactions, mixed microbial communities, and microbial metaproteomics. In this review, we will focus on the vast range of techniques practically applied in current research with an introduction of the workflows used for quantitative comparisons, a description of the advantages/disadvantages of the various methods, reference to hallmark publications and presentation of applications in current microbial research. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantitative analysis of single-molecule superresolution images

PubMed Central

Coltharp, Carla; Yang, Xinxing; Xiao, Jie

2014-01-01

This review highlights the quantitative capabilities of single-molecule localization-based superresolution imaging methods. In addition to revealing fine structural details, the molecule coordinate lists generated by these methods provide the critical ability to quantify the number, clustering, and colocalization of molecules with 10 – 50 nm resolution. Here we describe typical workflows and precautions for quantitative analysis of single-molecule superresolution images. These guidelines include potential pitfalls and essential control experiments, allowing critical assessment and interpretation of superresolution images. PMID:25179006

How often do sensitivity analyses for economic parameters change cost-utility analysis conclusions?

PubMed

Schackman, Bruce R; Gold, Heather Taffet; Stone, Patricia W; Neumann, Peter J

2004-01-01

There is limited evidence about the extent to which sensitivity analysis has been used in the cost-effectiveness literature. Sensitivity analyses for health-related QOL (HR-QOL), cost and discount rate economic parameters are of particular interest because they measure the effects of methodological and estimation uncertainties. To investigate the use of sensitivity analyses in the pharmaceutical cost-utility literature in order to test whether a change in economic parameters could result in a different conclusion regarding the cost effectiveness of the intervention analysed. Cost-utility analyses of pharmaceuticals identified in a prior comprehensive audit (70 articles) were reviewed and further audited. For each base case for which sensitivity analyses were reported (n = 122), up to two sensitivity analyses for HR-QOL (n = 133), cost (n = 99), and discount rate (n = 128) were examined. Article mentions of thresholds for acceptable cost-utility ratios were recorded (total 36). Cost-utility ratios were denominated in US dollars for the year reported in each of the original articles in order to determine whether a different conclusion would have been indicated at the time the article was published. Quality ratings from the original audit for articles where sensitivity analysis results crossed the cost-utility ratio threshold above the base-case result were compared with those that did not. The most frequently mentioned cost-utility thresholds were $US20,000/QALY, $US50,000/QALY, and $US100,000/QALY. The proportions of sensitivity analyses reporting quantitative results that crossed the threshold above the base-case results (or where the sensitivity analysis result was dominated) were 31% for HR-QOL sensitivity analyses, 20% for cost-sensitivity analyses, and 15% for discount-rate sensitivity analyses. Almost half of the discount-rate sensitivity analyses did not report quantitative results. Articles that reported sensitivity analyses where results crossed the cost

How to Make Nothing Out of Something: Analyses of the Impact of Study Sampling and Statistical Interpretation in Misleading Meta-Analytic Conclusions

PubMed Central

Cunningham, Michael R.; Baumeister, Roy F.

2016-01-01

The limited resource model states that self-control is governed by a relatively finite set of inner resources on which people draw when exerting willpower. Once self-control resources have been used up or depleted, they are less available for other self-control tasks, leading to a decrement in subsequent self-control success. The depletion effect has been studied for over 20 years, tested or extended in more than 600 studies, and supported in an independent meta-analysis (Hagger et al., 2010). Meta-analyses are supposed to reduce bias in literature reviews. Carter et al.’s (2015) meta-analysis, by contrast, included a series of questionable decisions involving sampling, methods, and data analysis. We provide quantitative analyses of key sampling issues: exclusion of many of the best depletion studies based on idiosyncratic criteria and the emphasis on mini meta-analyses with low statistical power as opposed to the overall depletion effect. We discuss two key methodological issues: failure to code for research quality, and the quantitative impact of weak studies by novice researchers. We discuss two key data analysis issues: questionable interpretation of the results of trim and fill and Funnel Plot Asymmetry test procedures, and the use and misinterpretation of the untested Precision Effect Test and Precision Effect Estimate with Standard Error (PEESE) procedures. Despite these serious problems, the Carter et al. (2015) meta-analysis results actually indicate that there is a real depletion effect – contrary to their title. PMID:27826272

Landslide inventories: The essential part of seismic landslide hazard analyses

USGS Publications Warehouse

Harp, E.L.; Keefer, D.K.; Sato, H.P.; Yagi, H.

2011-01-01

A detailed and accurate landslide inventory is an essential part of seismic landslide hazard analysis. An ideal inventory would cover the entire area affected by an earthquake and include all of the landslides that are possible to detect down to sizes of 1-5. m in length. The landslides must also be located accurately and mapped as polygons depicting their true shapes. Such mapped landslide distributions can then be used to perform seismic landslide hazard analysis and other quantitative analyses. Detailed inventory maps of landslide triggered by earthquakes began in the early 1960s with the use of aerial photography. In recent years, advances in technology have resulted in the accessibility of satellite imagery with sufficiently high resolution to identify and map all but the smallest of landslides triggered by a seismic event. With this ability to view any area of the globe, we can acquire imagery for any earthquake that triggers significant numbers of landslides. However, a common problem of incomplete coverage of the full distributions of landslides has emerged along with the advent of high resolution satellite imagery. ?? 2010.

Development of a Biological Science Quantitative Reasoning Exam (BioSQuaRE)

PubMed Central

Stanhope, Liz; Ziegler, Laura; Haque, Tabassum; Le, Laura; Vinces, Marcelo; Davis, Gregory K.; Zieffler, Andrew; Brodfuehrer, Peter; Preest, Marion; M. Belitsky, Jason; Umbanhowar, Charles; Overvoorde, Paul J.

2017-01-01

Multiple reports highlight the increasingly quantitative nature of biological research and the need to innovate means to ensure that students acquire quantitative skills. We present a tool to support such innovation. The Biological Science Quantitative Reasoning Exam (BioSQuaRE) is an assessment instrument designed to measure the quantitative skills of undergraduate students within a biological context. The instrument was developed by an interdisciplinary team of educators and aligns with skills included in national reports such as BIO2010, Scientific Foundations for Future Physicians, and Vision and Change. Undergraduate biology educators also confirmed the importance of items included in the instrument. The current version of the BioSQuaRE was developed through an iterative process using data from students at 12 postsecondary institutions. A psychometric analysis of these data provides multiple lines of evidence for the validity of inferences made using the instrument. Our results suggest that the BioSQuaRE will prove useful to faculty and departments interested in helping students acquire the quantitative competencies they need to successfully pursue biology, and useful to biology students by communicating the importance of quantitative skills. We invite educators to use the BioSQuaRE at their own institutions. PMID:29196427

Quantitative nephelometry

MedlinePlus

... this page: //medlineplus.gov/ency/article/003545.htm Quantitative nephelometry test To use the sharing features on this page, please enable JavaScript. Quantitative nephelometry is a lab test to quickly and ...

Towards quantitative assessment of calciphylaxis

NASA Astrophysics Data System (ADS)

Deserno, Thomas M.; Sárándi, István.; Jose, Abin; Haak, Daniel; Jonas, Stephan; Specht, Paula; Brandenburg, Vincent

2014-03-01

Calciphylaxis is a rare disease that has devastating conditions associated with high morbidity and mortality. Calciphylaxis is characterized by systemic medial calcification of the arteries yielding necrotic skin ulcerations. In this paper, we aim at supporting the installation of multi-center registries for calciphylaxis, which includes a photographic documentation of skin necrosis. However, photographs acquired in different centers under different conditions using different equipment and photographers cannot be compared quantitatively. For normalization, we use a simple color pad that is placed into the field of view, segmented from the image, and its color fields are analyzed. In total, 24 colors are printed on that scale. A least-squares approach is used to determine the affine color transform. Furthermore, the card allows scale normalization. We provide a case study for qualitative assessment. In addition, the method is evaluated quantitatively using 10 images of two sets of different captures of the same necrosis. The variability of quantitative measurements based on free hand photography is assessed regarding geometric and color distortions before and after our simple calibration procedure. Using automated image processing, the standard deviation of measurements is significantly reduced. The coefficients of variations yield 5-20% and 2-10% for geometry and color, respectively. Hence, quantitative assessment of calciphylaxis becomes practicable and will impact a better understanding of this rare but fatal disease.

Quantitation of N,N-dimethyltryptamine and harmala alkaloids in human plasma after oral dosing with ayahuasca.

PubMed

Callaway, J C; Raymon, L P; Hearn, W L; McKenna, D J; Grob, C S; Brito, G S; Mash, D C

1996-10-01

Harmine, harmaline, tetrahydroharmine (THH), and N,N-dimethyltryptamine (DMT) were quantitated in plasma from 15 healthy male volunteers after the ingestion of ayahuasca, a beverage that has been used for religious purposes in Brazil since pre-Columbian times. A growing awareness of the interest in this ancient shamanistic practice in modern urban cultures and the widespread popular dissemination of the inebriant effects and type and sources of the plant admixtures used to prepare the beverage have provided additional impetus for this study. The three harmala alkaloids were quantitated from protein-precipitated plasma by high-performance liquid chromatography using fluorescence detection. Recovery from blank human plasma was quantitative, and the limit of quantitation (LOQ) was below 2 ng/mL of plasma for each of the harmala alkaloids. Standard concentrations ranged from 10 to 250 ng/mL for harmine and THH and from 1.0 to 25.0 ng/mL for harmaline, respectively. Linearity was observed for harmine, harmaline, and THH within these respective ranges. The highest concentrations of harmala alkaloids in human plasma were found to be 222.3 ng/mL for harmine, 134.5 ng/mL for THH, and 9.4 ng/mL for harmaline. DMT was quantitated by gas chromatography using nitrogen-phosphorus detection after liquid-liquid extraction with diphenhydramine as an internal standard. DMT recovery was quantitative, and the limit of detection and LOQ were 0.5 and 5 ng/mL, respectively. Linearity for DMT was observed from 5 to 1000 ng/mL. The one-step extraction method for DMT and the protein precipitation method for the three harmala alkaloids afford rapid, sensitive, and quantitative analyses of these alkaloids with minimal analyte loss. The analytical methods also may be applicable to other matrices, including whole blood and urine samples and homogenized tissue specimens. These are the first reported observations of DMT and harmala alkaloids in plasma after ritual ingestion of ayahuasca.

Sender–receiver systems and applying information theory for quantitative synthetic biology

PubMed Central

Barcena Menendez, Diego; Senthivel, Vivek Raj; Isalan, Mark

2015-01-01

Sender–receiver (S–R) systems abound in biology, with communication systems sending information in various forms. Information theory provides a quantitative basis for analysing these processes and is being applied to study natural genetic, enzymatic and neural networks. Recent advances in synthetic biology are providing us with a wealth of artificial S–R systems, giving us quantitative control over networks with a finite number of well-characterised components. Combining the two approaches can help to predict how to maximise signalling robustness, and will allow us to make increasingly complex biological computers. Ultimately, pushing the boundaries of synthetic biology will require moving beyond engineering the flow of information and towards building more sophisticated circuits that interpret biological meaning. PMID:25282688

Model-Based Linkage Analysis of a Quantitative Trait.

PubMed

Song, Yeunjoo E; Song, Sunah; Schnell, Audrey H

2017-01-01

Linkage Analysis is a family-based method of analysis to examine whether any typed genetic markers cosegregate with a given trait, in this case a quantitative trait. If linkage exists, this is taken as evidence in support of a genetic basis for the trait. Historically, linkage analysis was performed using a binary disease trait, but has been extended to include quantitative disease measures. Quantitative traits are desirable as they provide more information than binary traits. Linkage analysis can be performed using single-marker methods (one marker at a time) or multipoint (using multiple markers simultaneously). In model-based linkage analysis the genetic model for the trait of interest is specified. There are many software options for performing linkage analysis. Here, we use the program package Statistical Analysis for Genetic Epidemiology (S.A.G.E.). S.A.G.E. was chosen because it also includes programs to perform data cleaning procedures and to generate and test genetic models for a quantitative trait, in addition to performing linkage analysis. We demonstrate in detail the process of running the program LODLINK to perform single-marker analysis, and MLOD to perform multipoint analysis using output from SEGREG, where SEGREG was used to determine the best fitting statistical model for the trait.

Candidate gene association analyses for ketosis resistance in Holsteins.

PubMed

Kroezen, V; Schenkel, F S; Miglior, F; Baes, C F; Squires, E J

2018-06-01

High-yielding dairy cattle are susceptible to ketosis, a metabolic disease that negatively affects the health, fertility, and milk production of the cow. Interest in breeding for more robust dairy cattle with improved resistance to disease is global; however, genetic evaluations for ketosis would benefit from the additional information provided by genetic markers. Candidate genes that are proposed to have a biological role in the pathogenesis of ketosis were investigated in silico and a custom panel of 998 putative single nucleotide polymorphism (SNP) markers was developed. The objective of this study was to test the associations of these new markers with deregressed estimated breeding values (EBV) for ketosis. A sample of 653 Canadian Holstein cows that had been previously genotyped with a medium-density SNP chip were regenotyped with the custom panel. The EBV for ketosis in first and later lactations were obtained for each animal and deregressed for use as pseudo-phenotypes for association analyses. Results of the mixed inheritance model for single SNP association analyses suggested 15 markers in 6 unique candidate genes were associated with the studied trait. Genes encoding proteins involved in metabolic processes, including the synthesis and degradation of fatty acids and ketone bodies, gluconeogenesis, lipid mobilization, and the citric acid cycle, were identified to contain SNP associated with ketosis resistance. This work confirmed the presence of previously described quantitative trait loci for dairy cattle, suggested novel markers for ketosis-resistance, and provided insight into the underlying biology of this disease. Copyright © 2018 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Prepotent response inhibition and interference control in autism spectrum disorders: two meta-analyses.

PubMed

Geurts, Hilde M; van den Bergh, Sanne F W M; Ruzzano, Laura

2014-08-01

There is a substantial amount of data providing evidence for, but also against the hypothesis that individuals with autism spectrum disorders (ASD) encounter inhibitory control deficits. ASD is often associated with interference control deficits rather than prepotent response inhibition. Moreover, the developmental trajectory for these inhibitory control processes is hypothesized to differ in ASD as compared to typical development. In efforts to gain a more comprehensive perspective of inhibition in ASD, separate quantitative analysis for prepotent response inhibition studies and interference control studies were conducted. Together, these two meta-analyses included 41 studies with a combined sample size of 1,091 people with ASD (M age 14.8 years), and 1,306 typically developing (TD) controls (M age 13.8 years).The meta-analyses indicated that individuals with ASD show increased difficulties in prepotent response inhibition (effect size 0.55) and in interference control (effect size 0.31). In addition, age was a relevant moderator for prepotent response inhibition but not for interference control. Exploratory analyses revealed that when IQ was taken into account, heterogeneity considerably decreased among interference control studies but not among prepotent response inhibition. In contrast to the general belief, both prepotent response inhibition and interference control problems were observed in individuals with ASD. However, a large variation between studies was also found. Therefore, there remain factors beyond inhibition type, age, or IQ that significantly influence inhibitory control performance among individuals with ASD. © 2014 International Society for Autism Research, Wiley Periodicals, Inc.

Quantitative analysis of amygdalin and prunasin in Prunus serotina Ehrh. using (1) H-NMR spectroscopy.

PubMed

Santos Pimenta, Lúcia P; Schilthuizen, Menno; Verpoorte, Robert; Choi, Young Hae

2014-01-01

Prunus serotina is native to North America but has been invasively introduced in Europe since the seventeenth century. This plant contains cyanogenic glycosides that are believed to be related to its success as an invasive plant. For these compounds, chromatographic- or spectrometric-based (targeting on HCN hydrolysis) methods of analysis have been employed so far. However, the conventional methods require tedious preparation steps and a long measuring time. To develop a fast and simple method to quantify the cyanogenic glycosides, amygdalin and prunasin in dried Prunus serotina leaves without any pre-purification steps using (1) H-NMR spectroscopy. Extracts of Prunus serotina leaves using CH3 OH-d4 and KH2 PO4 buffer in D2 O (1:1) were quantitatively analysed for amygdalin and prunasin using (1) H-NMR spectroscopy. Different internal standards were evaluated for accuracy and stability. The purity of quantitated (1) H-NMR signals was evaluated using several two-dimensional NMR experiments. Trimethylsilylpropionic acid sodium salt-d4 proved most suitable as the internal standard for quantitative (1) H-NMR analysis. Two-dimensional J-resolved NMR was shown to be a useful tool to confirm the structures and to check for possible signal overlapping with the target signals for the quantitation. Twenty-two samples of P. serotina were subsequently quantitatively analysed for the cyanogenic glycosides prunasin and amygdalin. The NMR method offers a fast, high-throughput analysis of cyanogenic glycosides in dried leaves permitting simultaneous quantification and identification of prunasin and amygdalin in Prunus serotina. Copyright © 2013 John Wiley & Sons, Ltd.

The Relationship between Quantitative and Qualitative Measures of Writing Skills.

ERIC Educational Resources Information Center

Howerton, Mary Lou P.; And Others

The relationships of quantitative measures of writing skills to overall writing quality as measured by the E.T.S. Composition Evaluation Scale (CES) were examined. Quantitative measures included indices of language productivity, vocabulary diversity, spelling, and syntactic maturity. Power of specific indices to account for variation in overall…

Quantitative single-molecule imaging by confocal laser scanning microscopy.

PubMed

Vukojevic, Vladana; Heidkamp, Marcus; Ming, Yu; Johansson, Björn; Terenius, Lars; Rigler, Rudolf

2008-11-25

A new approach to quantitative single-molecule imaging by confocal laser scanning microscopy (CLSM) is presented. It relies on fluorescence intensity distribution to analyze the molecular occurrence statistics captured by digital imaging and enables direct determination of the number of fluorescent molecules and their diffusion rates without resorting to temporal or spatial autocorrelation analyses. Digital images of fluorescent molecules were recorded by using fast scanning and avalanche photodiode detectors. In this way the signal-to-background ratio was significantly improved, enabling direct quantitative imaging by CLSM. The potential of the proposed approach is demonstrated by using standard solutions of fluorescent dyes, fluorescently labeled DNA molecules, quantum dots, and the Enhanced Green Fluorescent Protein in solution and in live cells. The method was verified by using fluorescence correlation spectroscopy. The relevance for biological applications, in particular, for live cell imaging, is discussed.

Attomole quantitation of protein separations with accelerator mass spectrometry

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

Vogel, J S; Grant, P G; Buccholz, B A

2000-12-15

Quantification of specific proteins depends on separation by chromatography or electrophoresis followed by chemical detection schemes such as staining and fluorophore adhesion. Chemical exchange of short-lived isotopes, particularly sulfur, is also prevalent despite the inconveniences of counting radioactivity. Physical methods based on isotopic and elemental analyses offer highly sensitive protein quantitation that has linear response over wide dynamic ranges and is independent of protein conformation. Accelerator mass spectrometry quantifies long-lived isotopes such as 14C to sub-attomole sensitivity. We quantified protein interactions with small molecules such as toxins, vitamins, and natural biochemicals at precisions of 1-5% . Micro-proton-induced-xray-emission quantifies elemental abundancesmore » in separated metalloprotein samples to nanogram amounts and is capable of quantifying phosphorylated loci in gels. Accelerator-based quantitation is a possible tool for quantifying the genome translation into proteome.« less

Analyses of volatile organic compounds from human skin

PubMed Central

Gallagher, M.; Wysocki, C.J.; Leyden, J.J.; Spielman, A.I.; Sun, X.; Preti, G.

2008-01-01

Summary Background Human skin emits a variety of volatile metabolites, many of them odorous. Much previous work has focused upon chemical structure and biogenesis of metabolites produced in the axillae (underarms), which are a primary source of human body odour. Nonaxillary skin also harbours volatile metabolites, possibly with different biological origins than axillary odorants. Objectives To take inventory of the volatile organic compounds (VOCs) from the upper back and forearm skin, and assess their relative quantitative variation across 25 healthy subjects. Methods Two complementary sampling techniques were used to obtain comprehensive VOC profiles, viz., solid-phase micro extraction and solvent extraction. Analyses were performed using both gas chromatography/mass spectrometry and gas chromatography with flame photometric detection. Results Nearly 100 compounds were identified, some of which varied with age. The VOC profiles of the upper back and forearm within a subject were, for the most part, similar, although there were notable differences. Conclusions The natural variation in nonaxillary skin odorants described in this study provides a baseline of compounds we have identified from both endogenous and exogenous sources. Although complex, the profiles of volatile constituents suggest that the two body locations share a considerable number of compounds, but both quantitative and qualitative differences are present. In addition, quantitative changes due to ageing are also present. These data may provide future investigators of skin VOCs with a baseline against which any abnormalities can be viewed in searching for biomarkers of skin diseases. PMID:18637798

Linkage analyses of chromosome 6 loci, including HLA, in familial aggregations of Crohn disease

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

Hugot, J.P.; Laurent-Puig, P.; Gower-Rousseau, C.

1994-08-15

Segregation analyses of familial aggregations of Crohn disease have provided consistent results pointing to the involvement of a predisposing gene with a recessive mode of inheritance. Although extensively investigated, the role played by human leucocyte antigen (HLA) genes in this inflammatory bowel disease remains elusive and the major histocompatibility complex is a candidate region for the mapping of the Crohn disease susceptibility gene. A total of 25 families with multiple cases of Crohn disease was genotyped for HLA DRB1 and for 16 highly polymorphic loci evenly distributed on chromosome 6. The data were subjected to linkage analysis using the lodmore » score method. Neither individual nor combined lod scores for any family and for any locus tested reached values suggesting linkage or genetic heterogeneity. The Crohn disease predisposing locus was excluded from the whole chromosome 6 with lod scores less than -2. It was excluded from the major histocompatibility complex and from 91% of the chromosome 6 genetic map with lod scores less than -4. The major recessive gene involved in genetic predisposition to Crohn disease does not reside on the major histocompatibility complex nor on any locus mapping to chromosome 6. 37 refs., 2 figs., 2 tabs.« less

Quantitative DNA methylation analyses reveal stage dependent DNA methylation and association to clinico-pathological factors in breast tumors.

PubMed

Klajic, Jovana; Fleischer, Thomas; Dejeux, Emelyne; Edvardsen, Hege; Warnberg, Fredrik; Bukholm, Ida; Lønning, Per Eystein; Solvang, Hiroko; Børresen-Dale, Anne-Lise; Tost, Jörg; Kristensen, Vessela N

2013-10-05

Aberrant DNA methylation of regulatory genes has frequently been found in human breast cancers and correlated to clinical outcome. In the present study we investigate stage specific changes in the DNA methylation patterns in order to identify valuable markers to understand how these changes affect breast cancer progression. Quantitative DNA methylation analyses of 12 candidate genes ABCB1, BRCCA1, CDKN2A, ESR1, GSTP1, IGF2, MGMT, HMLH1, PPP2R2B, PTEN, RASSF1A and FOXC1 was performed by pyrosequencing a series of 238 breast cancer tissue samples from DCIS to invasive tumors stage I to IV. Significant differences in methylation levels between the DCIS and invasive stage II tumors were observed for six genes RASSF1A, CDKN2A, MGMT, ABCB1, GSTP1 and FOXC1. RASSF1A, ABCB1 and GSTP1 showed significantly higher methylation levels in late stage compared to the early stage breast carcinoma. Z-score analysis revealed significantly lower methylation levels in DCIS and stage I tumors compared with stage II, III and IV tumors. Methylation levels of PTEN, PPP2R2B, FOXC1, ABCB1 and BRCA1 were lower in tumors harboring TP53 mutations then in tumors with wild type TP53. Z-score analysis showed that TP53 mutated tumors had significantly lower overall methylation levels compared to tumors with wild type TP53. Methylation levels of RASSF1A, PPP2R2B, GSTP1 and FOXC1 were higher in ER positive vs. ER negative tumors and methylation levels of PTEN and CDKN2A were higher in HER2 positive vs. HER2 negative tumors. Z-score analysis also showed that HER2 positive tumors had significantly higher z-scores of methylation compared to the HER2 negative tumors. Univariate survival analysis identifies methylation status of PPP2R2B as significant predictor of overall survival and breast cancer specific survival. In the present study we report that the level of aberrant DNA methylation is higher in late stage compared with early stage of invasive breast cancers and DCIS for genes mentioned above.

Quantitative psychomotor dysfunction in schizophrenia: a loss of drive, impaired movement execution or both?

PubMed

Docx, Lise; Sabbe, Bernard; Provinciael, Pieter; Merckx, Niel; Morrens, Manuel

2013-01-01

The aim of the present study was to investigate the predictive value of qualitative psychomotor performance levels and subaspects of the negative syndrome for quantitative motor activity levels in patients with schizophrenia. Twenty-seven stabilized patients with schizophrenia and 22 age- and sex-matched healthy controls were included in the study. An extensive battery of psychomotor performance tests (Finger Tapping Test, Purdue Pegboard Test, Line Copying Test, Neurological Evaluation Scale, Salpêtrière Retardation Rating Scale), clinical rating scales (Positive and Negative Syndrome Scale) and 24-hour actigraphy were administered to all participants. Correlational analyses showed that motor activity levels were associated with avolition as well as clinically assessed psychomotor slowing. However, in a regression model, only avolition was found to be a significant predictor for motor activity levels in patients with schizophrenia; none of the psychomotor performance tests nor the severity of emotional expressivity deficits contributed to the model. Qualitative and quantitative psychomotor deficits seem to be independent phenomena in stabilized patients with schizophrenia. The diminishing in motor activity in patients with schizophrenia is related to a loss of drive and not to problems in the quality of movement execution. © 2013 S. Karger AG, Basel.

Quantitative analysis of the protein corona on FePt nanoparticles formed by transferrin binding

PubMed Central

Jiang, Xiue; Weise, Stefan; Hafner, Margit; Röcker, Carlheinz; Zhang, Feng; Parak, Wolfgang J.; Nienhaus, G. Ulrich

2010-01-01

Nanoparticles are finding a rapidly expanding range of applications in research and technology, finally entering our daily life in medical, cosmetic or food products. Their ability to invade all regions of an organism including cells and cellular organelles offers new strategies for medical diagnosis and therapy (nanomedicine), but their safe use requires a deep knowledge about their interactions with biological systems at the molecular level. Upon incorporation, nanoparticles are exposed to biological fluids from which they adsorb proteins and other biomolecules to form a ‘protein corona’. These nanoparticle–protein interactions are still poorly understood and quantitative studies to characterize them remain scarce. Here we have quantitatively analysed the adsorption of human transferrin onto small (radius approx. 5 nm) polymer-coated FePt nanoparticles by using fluorescence correlation spectroscopy. Transferrin binds to the negatively charged nanoparticles with an affinity of approximately 26 µM in a cooperative fashion and forms a monolayer with a thickness of 7 nm. By using confocal fluorescence microscopy, we have observed that the uptake of FePt nanoparticles by HeLa cells is suppressed by the protein corona compared with the bare nanoparticles. PMID:19776149

3D quantitative comparative analysis of long bone diaphysis variations in microanatomy and cross-sectional geometry.

PubMed

Houssaye, Alexandra; Taverne, Maxime; Cornette, Raphaël

2018-05-01

Long bone inner structure and cross-sectional geometry display a strong functional signal, leading to convergences, and are widely analyzed in comparative anatomy at small and large taxonomic scales. Long bone microanatomical studies have essentially been conducted on transverse sections but also on a few longitudinal ones. Recent studies highlighted the interest in analyzing variations of the inner structure along the diaphysis using a qualitative as well as a quantitative approach. With the development of microtomography, it has become possible to study three-dimensional (3D) bone microanatomy and, in more detail, the form-function relationships of these features. This study focused on the selection of quantitative parameters to describe in detail the cross-sectional shape changes and distribution of the osseous tissue along the diaphysis. Two-dimensional (2D) virtual transverse sections were also performed in the two usual reference planes and results were compared with those obtained based on the whole diaphysis analysis. The sample consisted in 14 humeri and 14 femora of various mammalian taxa that are essentially terrestrial. Comparative quantitative analyses between different datasets made it possible to highlight the parameters that are strongly impacted by size and phylogeny and the redundant ones, and thus to estimate their relevance for use in form-function analyses. The analysis illustrated that results based on 2D transverse sections are similar for both sectional planes; thus if a strong bias exists when mixing sections from the two reference planes in the same analysis, it would not problematic to use either one plane or the other in comparative studies. However, this may no longer hold for taxa showing a much stronger variation in bone microstructure along the diaphysis. Finally, the analysis demonstrated the significant contribution of the parameters describing variations along the diaphysis, and thus the interest in performing 3D analyses; this

Quantitative Resistance: More Than Just Perception of a Pathogen.

PubMed

Corwin, Jason A; Kliebenstein, Daniel J

2017-04-01

Molecular plant pathology has focused on studying large-effect qualitative resistance loci that predominantly function in detecting pathogens and/or transmitting signals resulting from pathogen detection. By contrast, less is known about quantitative resistance loci, particularly the molecular mechanisms controlling variation in quantitative resistance. Recent studies have provided insight into these mechanisms, showing that genetic variation at hundreds of causal genes may underpin quantitative resistance. Loci controlling quantitative resistance contain some of the same causal genes that mediate qualitative resistance, but the predominant mechanisms of quantitative resistance extend beyond pathogen recognition. Indeed, most causal genes for quantitative resistance encode specific defense-related outputs such as strengthening of the cell wall or defense compound biosynthesis. Extending previous work on qualitative resistance to focus on the mechanisms of quantitative resistance, such as the link between perception of microbe-associated molecular patterns and growth, has shown that the mechanisms underlying these defense outputs are also highly polygenic. Studies that include genetic variation in the pathogen have begun to highlight a potential need to rethink how the field considers broad-spectrum resistance and how it is affected by genetic variation within pathogen species and between pathogen species. These studies are broadening our understanding of quantitative resistance and highlighting the potentially vast scale of the genetic basis of quantitative resistance. © 2017 American Society of Plant Biologists. All rights reserved.

Quantitative Resistance: More Than Just Perception of a Pathogen

PubMed Central

2017-01-01

Molecular plant pathology has focused on studying large-effect qualitative resistance loci that predominantly function in detecting pathogens and/or transmitting signals resulting from pathogen detection. By contrast, less is known about quantitative resistance loci, particularly the molecular mechanisms controlling variation in quantitative resistance. Recent studies have provided insight into these mechanisms, showing that genetic variation at hundreds of causal genes may underpin quantitative resistance. Loci controlling quantitative resistance contain some of the same causal genes that mediate qualitative resistance, but the predominant mechanisms of quantitative resistance extend beyond pathogen recognition. Indeed, most causal genes for quantitative resistance encode specific defense-related outputs such as strengthening of the cell wall or defense compound biosynthesis. Extending previous work on qualitative resistance to focus on the mechanisms of quantitative resistance, such as the link between perception of microbe-associated molecular patterns and growth, has shown that the mechanisms underlying these defense outputs are also highly polygenic. Studies that include genetic variation in the pathogen have begun to highlight a potential need to rethink how the field considers broad-spectrum resistance and how it is affected by genetic variation within pathogen species and between pathogen species. These studies are broadening our understanding of quantitative resistance and highlighting the potentially vast scale of the genetic basis of quantitative resistance. PMID:28302676

Quantitative genetic tools for insecticide resistance risk assessment: estimating the heritability of resistance

Treesearch

Michael J. Firko; Jane Leslie Hayes

1990-01-01

Quantitative genetic studies of resistance can provide estimates of genetic parameters not available with other types of genetic analyses. Three methods are discussed for estimating the amount of additive genetic variation in resistance to individual insecticides and subsequent estimation of heritability (h2) of resistance. Sibling analysis and...

Validation of the Mass-Extraction-Window for Quantitative Methods Using Liquid Chromatography High Resolution Mass Spectrometry.

PubMed

Glauser, Gaétan; Grund, Baptiste; Gassner, Anne-Laure; Menin, Laure; Henry, Hugues; Bromirski, Maciej; Schütz, Frédéric; McMullen, Justin; Rochat, Bertrand

2016-03-15

A paradigm shift is underway in the field of quantitative liquid chromatography-mass spectrometry (LC-MS) analysis thanks to the arrival of recent high-resolution mass spectrometers (HRMS). The capability of HRMS to perform sensitive and reliable quantifications of a large variety of analytes in HR-full scan mode is showing that it is now realistic to perform quantitative and qualitative analysis with the same instrument. Moreover, HR-full scan acquisition offers a global view of sample extracts and allows retrospective investigations as virtually all ionized compounds are detected with a high sensitivity. In time, the versatility of HRMS together with the increasing need for relative quantification of hundreds of endogenous metabolites should promote a shift from triple-quadrupole MS to HRMS. However, a current "pitfall" in quantitative LC-HRMS analysis is the lack of HRMS-specific guidance for validated quantitative analyses. Indeed, false positive and false negative HRMS detections are rare, albeit possible, if inadequate parameters are used. Here, we investigated two key parameters for the validation of LC-HRMS quantitative analyses: the mass accuracy (MA) and the mass-extraction-window (MEW) that is used to construct the extracted-ion-chromatograms. We propose MA-parameters, graphs, and equations to calculate rational MEW width for the validation of quantitative LC-HRMS methods. MA measurements were performed on four different LC-HRMS platforms. Experimentally determined MEW values ranged between 5.6 and 16.5 ppm and depended on the HRMS platform, its working environment, the calibration procedure, and the analyte considered. The proposed procedure provides a fit-for-purpose MEW determination and prevents false detections.

PRIORITIZING FUTURE RESEACH ON OFF-LABEL PRESCRIBING: RESULTS OF A QUANTITATIVE EVALUATION

PubMed Central

Walton, Surrey M.; Schumock, Glen T.; Lee, Ky-Van; Alexander, G. Caleb; Meltzer, David; Stafford, Randall S.

2015-01-01

Background Drug use for indications not approved by the Food and Drug Administration exceeds 20% of prescribing. Available compendia indicate that a minority of off-label uses are well supported by evidence. Policy makers, however, lack information to identify where systematic reviews of the evidence or other research would be most valuable. Methods We developed a quantitative model for prioritizing individual drugs for future research on off-label uses. The base model incorporated three key factors, 1) the volume of off-label use with inadequate evidence, 2) safety, and 3) cost and market considerations. Nationally representative prescribing data were used to estimate the number of off-label drug uses by indication from 1/2005 through 6/2007 in the United States, and these indications were then categorized according to the adequacy of scientific support. Black box warnings and safety alerts were used to quantify drug safety. Drug cost, date of market entry, and marketing expenditures were used to quantify cost and market considerations. Each drug was assigned a relative value for each factor, and the factors were then weighted in the final model to produce a priority score. Sensitivity analyses were conducted by varying the weightings and model parameters. Results Drugs that were consistently ranked highly in both our base model and sensitivity analyses included quetiapine, warfarin, escitalopram, risperidone, montelukast, bupropion, sertraline, venlafaxine, celecoxib, lisinopril, duloxetine, trazodone, olanzapine, and epoetin alfa. Conclusion Future research into off-label drug use should focus on drugs used frequently with inadequate supporting evidence, particularly if further concerns are raised by known safety issues, high drug cost, recent market entry, and extensive marketing. Based on quantitative measures of these factors, we have prioritized drugs where targeted research and policy activities have high potential value. PMID:19025425

Trace-Level Volatile Quantitation by Direct Analysis in Real Time Mass Spectrometry following Headspace Extraction: Optimization and Validation in Grapes.

PubMed

Jastrzembski, Jillian A; Bee, Madeleine Y; Sacks, Gavin L

2017-10-25

Ambient ionization mass spectrometric (AI-MS) techniques like direct analysis in real time (DART) offer the potential for rapid quantitative analyses of trace volatiles in food matrices, but performance is generally limited by the lack of preconcentration and extraction steps. The sensitivity and selectivity of AI-MS approaches can be improved through solid-phase microextraction (SPME) with appropriate thin-film geometries, for example, solid-phase mesh-enhanced sorption from headspace (SPMESH). This work improves the SPMESH-DART-MS approach for use in food analyses and validates the approach for trace volatile analysis for two compounds in real samples (grape macerates). SPMESH units prepared with different sorbent coatings were evaluated for their ability to extract a range of odor-active volatiles, with poly(dimethylsiloxane)/divinylbenzene giving the most satisfactory results. In combination with high-resolution mass spectrometry (HRMS), detection limits for SPMESH-DART-MS under 4 ng/L in less than 30 s acquisition times could be achieved for some volatiles [3-isobutyl-2-methoxypyrazine (IBMP) and β-damascenone]. A comparison of SPMESH-DART-MS and SPME-GC-MS quantitation of linalool and IBMP demonstrates excellent agreement between the two methods for real grape samples (r 2 ≥ 0.90), although linalool measurements appeared to also include isobaric interference.

Temporal lobe epilepsy: quantitative MR volumetry in detection of hippocampal atrophy.

PubMed

Farid, Nikdokht; Girard, Holly M; Kemmotsu, Nobuko; Smith, Michael E; Magda, Sebastian W; Lim, Wei Y; Lee, Roland R; McDonald, Carrie R

2012-08-01

To determine the ability of fully automated volumetric magnetic resonance (MR) imaging to depict hippocampal atrophy (HA) and to help correctly lateralize the seizure focus in patients with temporal lobe epilepsy (TLE). This study was conducted with institutional review board approval and in compliance with HIPAA regulations. Volumetric MR imaging data were analyzed for 34 patients with TLE and 116 control subjects. Structural volumes were calculated by using U.S. Food and Drug Administration-cleared software for automated quantitative MR imaging analysis (NeuroQuant). Results of quantitative MR imaging were compared with visual detection of atrophy, and, when available, with histologic specimens. Receiver operating characteristic analyses were performed to determine the optimal sensitivity and specificity of quantitative MR imaging for detecting HA and asymmetry. A linear classifier with cross validation was used to estimate the ability of quantitative MR imaging to help lateralize the seizure focus. Quantitative MR imaging-derived hippocampal asymmetries discriminated patients with TLE from control subjects with high sensitivity (86.7%-89.5%) and specificity (92.2%-94.1%). When a linear classifier was used to discriminate left versus right TLE, hippocampal asymmetry achieved 94% classification accuracy. Volumetric asymmetries of other subcortical structures did not improve classification. Compared with invasive video electroencephalographic recordings, lateralization accuracy was 88% with quantitative MR imaging and 85% with visual inspection of volumetric MR imaging studies but only 76% with visual inspection of clinical MR imaging studies. Quantitative MR imaging can depict the presence and laterality of HA in TLE with accuracy rates that may exceed those achieved with visual inspection of clinical MR imaging studies. Thus, quantitative MR imaging may enhance standard visual analysis, providing a useful and viable means for translating volumetric analysis into

Quantitative Modeling of Earth Surface Processes

NASA Astrophysics Data System (ADS)

Pelletier, Jon D.

This textbook describes some of the most effective and straightforward quantitative techniques for modeling Earth surface processes. By emphasizing a core set of equations and solution techniques, the book presents state-of-the-art models currently employed in Earth surface process research, as well as a set of simple but practical research tools. Detailed case studies demonstrate application of the methods to a wide variety of processes including hillslope, fluvial, aeolian, glacial, tectonic, and climatic systems. Exercises at the end of each chapter begin with simple calculations and then progress to more sophisticated problems that require computer programming. All the necessary computer codes are available online at www.cambridge.org/9780521855976. Assuming some knowledge of calculus and basic programming experience, this quantitative textbook is designed for advanced geomorphology courses and as a reference book for professional researchers in Earth and planetary science looking for a quantitative approach to Earth surface processes.

Increasing Literacy in Quantitative Methods: The Key to the Future of Canadian Psychology

PubMed Central

Counsell, Alyssa; Cribbie, Robert A.; Harlow, Lisa. L.

2016-01-01

Quantitative methods (QM) dominate empirical research in psychology. Unfortunately most researchers in psychology receive inadequate training in QM. This creates a challenge for researchers who require advanced statistical methods to appropriately analyze their data. Many of the recent concerns about research quality, replicability, and reporting practices are directly tied to the problematic use of QM. As such, improving quantitative literacy in psychology is an important step towards eliminating these concerns. The current paper will include two main sections that discuss quantitative challenges and opportunities. The first section discusses training and resources for students and presents descriptive results on the number of quantitative courses required and available to graduate students in Canadian psychology departments. In the second section, we discuss ways of improving quantitative literacy for faculty, researchers, and clinicians. This includes a strong focus on the importance of collaboration. The paper concludes with practical recommendations for improving quantitative skills and literacy for students and researchers in Canada. PMID:28042199

Increasing Literacy in Quantitative Methods: The Key to the Future of Canadian Psychology.

PubMed

Counsell, Alyssa; Cribbie, Robert A; Harlow, Lisa L

2016-08-01

Quantitative methods (QM) dominate empirical research in psychology. Unfortunately most researchers in psychology receive inadequate training in QM. This creates a challenge for researchers who require advanced statistical methods to appropriately analyze their data. Many of the recent concerns about research quality, replicability, and reporting practices are directly tied to the problematic use of QM. As such, improving quantitative literacy in psychology is an important step towards eliminating these concerns. The current paper will include two main sections that discuss quantitative challenges and opportunities. The first section discusses training and resources for students and presents descriptive results on the number of quantitative courses required and available to graduate students in Canadian psychology departments. In the second section, we discuss ways of improving quantitative literacy for faculty, researchers, and clinicians. This includes a strong focus on the importance of collaboration. The paper concludes with practical recommendations for improving quantitative skills and literacy for students and researchers in Canada.

Determining quantitative immunophenotypes and evaluating their implications

NASA Astrophysics Data System (ADS)

Redelman, Douglas; Hudig, Dorothy; Berner, Dave; Castell, Linda M.; Roberts, Don; Ensign, Wayne

2002-05-01

Quantitative immunophenotypes varied widely among > 100 healthy young males but were maintained at characteristic levels within individuals. The initial results (SPIE Proceedings 4260:226) that examined cell numbers and the quantitative expression of adhesion and lineage-specific molecules, e.g., CD2 and CD14, have now been confirmed and extended to include the quantitative expression of inducible molecules such as HLA-DR and perforin (Pf). Some properties, such as the ratio of T helper (Th) to T cytotoxic/suppressor (Tc/s) cells, are known to be genetically determined. Other properties, e.g., the T:B cell ratio, the amount of CD19 per B cell, etc., behaved similarly and may also be inherited traits. Since some patterns observed in these healthy individuals resembled those found in pathological situations we tested whether the patterns could be associated with the occurrence of disease. The current studies shows that there were associations between quantitative immunophenotypes and the subsequent incidence and severity of disease. For example, individuals with characteristically low levels of HLA-DR or B cells or reduced numbers of Pf+ Tc/s cells had more frequent and/or more severe upper respiratory infections. Quantitative immunophenotypes will be more widely measured if the necessary standards are available and if appropriate procedures are made more accessible.

Cost-inclusive evaluation: a banquet of approaches for including costs, benefits, and cost-effectiveness and cost-benefit analyses in your next evaluation.

PubMed

Yates, Brian T

2009-02-01

An introduction to the special issue on cost-inclusive evaluation, providing a brief history of the use of costs, benefits, cost-effectiveness, and cost-benefit analyses in the evaluation of human services. Two tables present brief glossaries of terms and analyses common in cost-inclusive program evaluation.

Quantitative Real-Time PCR Analysis of Total Propidium Monazide -Resistant Fecal Indicator Bacteria in Wastewater

EPA Science Inventory

A real-time quantitative PCR (qPCR) method and a modification of this method incorporating pretreatment of samples with propidium monoazide (PMA) were evaluated for respective analyses of total and presumptively viable Enterococcus and Bacteroidales fecal indicator bacteria. Thes...

Diagnosing Conceptions about the Epistemology of Science: Contributions of a Quantitative Assessment Methodology

ERIC Educational Resources Information Center

Vázquez-Alonso, Ángel; Manassero-Mas, María-Antonia; García-Carmona, Antonio; Montesano de Talavera, Marisa

2016-01-01

This study applies a new quantitative methodological approach to diagnose epistemology conceptions in a large sample. The analyses use seven multiple-rating items on the epistemology of science drawn from the item pool Views on Science-Technology-Society (VOSTS). The bases of the new methodological diagnostic approach are the empirical…

Critically appraising qualitative research: a guide for clinicians more familiar with quantitative techniques.

PubMed

Kisely, Stephen; Kendall, Elizabeth

2011-08-01

Papers using qualitative methods are increasingly common in psychiatric journals. This overview is an introduction to critically appraising a qualitative paper for clinicians who are more familiar with quantitative methods. Qualitative research uses data from interviews (semi-structured or unstructured), focus groups, observations or written materials. Data analysis is inductive, allowing meaning to emerge from the data, rather than the more deductive, hypothesis centred approach of quantitative research. This overview compares and contrasts quantitative and qualitative research methods. Quantitative concepts such as reliability, validity, statistical power, bias and generalisability have qualitative equivalents. These include triangulation, trustworthiness, saturation, reflexivity and applicability. Reflexivity also shares features of transference. Qualitative approaches include: ethnography, action-assessment, grounded theory, case studies and mixed methods. Qualitative research can complement quantitative approaches. An understanding of both is useful in critically appraising the psychiatric literature.

Quantitative Decision Support Requires Quantitative User Guidance

NASA Astrophysics Data System (ADS)

Smith, L. A.

2009-12-01

Is it conceivable that models run on 2007 computer hardware could provide robust and credible probabilistic information for decision support and user guidance at the ZIP code level for sub-daily meteorological events in 2060? In 2090? Retrospectively, how informative would output from today’s models have proven in 2003? or the 1930’s? Consultancies in the United Kingdom, including the Met Office, are offering services to “future-proof” their customers from climate change. How is a US or European based user or policy maker to determine the extent to which exciting new Bayesian methods are relevant here? or when a commercial supplier is vastly overselling the insights of today’s climate science? How are policy makers and academic economists to make the closely related decisions facing them? How can we communicate deep uncertainty in the future at small length-scales without undermining the firm foundation established by climate science regarding global trends? Three distinct aspects of the communication of the uses of climate model output targeting users and policy makers, as well as other specialist adaptation scientists, are discussed. First, a brief scientific evaluation of the length and time scales at which climate model output is likely to become uninformative is provided, including a note on the applicability the latest Bayesian methodology to current state-of-the-art general circulation models output. Second, a critical evaluation of the language often employed in communication of climate model output, a language which accurately states that models are “better”, have “improved” and now “include” and “simulate” relevant meteorological processed, without clearly identifying where the current information is thought to be uninformative and misleads, both for the current climate and as a function of the state of the (each) climate simulation. And thirdly, a general approach for evaluating the relevance of quantitative climate model output

Tannin structural elucidation and quantitative ³¹P NMR analysis. 2. Hydrolyzable tannins and proanthocyanidins.

PubMed

Melone, Federica; Saladino, Raffaele; Lange, Heiko; Crestini, Claudia

2013-10-02

An unprecedented analytical method that allows simultaneous structural and quantitative characterization of all functional groups present in tannins is reported. In situ labeling of all labile H groups (aliphatic and phenolic hydroxyls and carboxylic acids) with a phosphorus-containing reagent (Cl-TMDP) followed by quantitative ³¹P NMR acquisition constitutes a novel fast and reliable analytical tool for the analysis of tannins and proanthocyanidins with significant implications for the fields of food and feed analyses, tannery, and the development of natural polyphenolics containing products.

An Overview of Quantitative Risk Assessment of Space Shuttle Propulsion Elements

NASA Technical Reports Server (NTRS)

Safie, Fayssal M.

1998-01-01

Since the Space Shuttle Challenger accident in 1986, NASA has been working to incorporate quantitative risk assessment (QRA) in decisions concerning the Space Shuttle and other NASA projects. One current major NASA QRA study is the creation of a risk model for the overall Space Shuttle system. The model is intended to provide a tool to estimate Space Shuttle risk and to perform sensitivity analyses/trade studies, including the evaluation of upgrades. Marshall Space Flight Center (MSFC) is a part of the NASA team conducting the QRA study; MSFC responsibility involves modeling the propulsion elements of the Space Shuttle, namely: the External Tank (ET), the Solid Rocket Booster (SRB), the Reusable Solid Rocket Motor (RSRM), and the Space Shuttle Main Engine (SSME). This paper discusses the approach that MSFC has used to model its Space Shuttle elements, including insights obtained from this experience in modeling large scale, highly complex systems with a varying availability of success/failure data. Insights, which are applicable to any QRA study, pertain to organizing the modeling effort, obtaining customer buy-in, preparing documentation, and using varied modeling methods and data sources. Also provided is an overall evaluation of the study results, including the strengths and the limitations of the MSFC QRA approach and of qRA technology in general.

Quantitative Imaging Biomarkers of NAFLD

PubMed Central

Kinner, Sonja; Reeder, Scott B.

2016-01-01

Conventional imaging modalities, including ultrasonography (US), computed tomography (CT), and magnetic resonance (MR), play an important role in the diagnosis and management of patients with nonalcoholic fatty liver disease (NAFLD) by allowing noninvasive diagnosis of hepatic steatosis. However, conventional imaging modalities are limited as biomarkers of NAFLD for various reasons. Multi-parametric quantitative MRI techniques overcome many of the shortcomings of conventional imaging and allow comprehensive and objective evaluation of NAFLD. MRI can provide unconfounded biomarkers of hepatic fat, iron, and fibrosis in a single examination—a virtual biopsy has become a clinical reality. In this article, we will review the utility and limitation of conventional US, CT, and MR imaging for the diagnosis NAFLD. Recent advances in imaging biomarkers of NAFLD are also discussed with an emphasis in multi-parametric quantitative MRI. PMID:26848588

China's Only Children and Psychopathology: A Quantitative Synthesis

PubMed Central

Falbo, Toni; Hooper, Sophia Y.

2015-01-01

The goal of this study is to synthesize quantitatively the results of studies of psychopathology among Chinese only children. Since 1979, China's one-child policy has generated large numbers of only children, especially in large urban centers, where the one-child family has become a social norm. Motivated by concern for mental health, 22 studies, based on the SCL-90, have been published that compare the scores of only children to their peers with siblings. The raw effect sizes generated by each study underwent adjustments in order to enhance the reliability of the findings, including the identification and replacement of outliers, and weighting by inverse-sample size. In addition, analyses were conducted to evaluate the degree of publication bias exhibited by this collection of studies and the results from the SCL-90 studies were compared to studies using alternative measures of anxiety and depression. Overall, the synthesis found small, but significant advantages for only children compared to their peers with siblings, regardless of subscale. However, moderators of this only-child effect were also found: only children as college students reported significantly fewer symptoms, regardless of subscale; while only children as military recruits reported more symptoms, although the findings about military recruits received less support from the analyses. Furthermore, the size of the only-child advantage was found to be greater for only children born after the policy. Conclusions based on this synthesis are limited by the fact that this body of studies is based on convenience samples of relatively successful youth. PMID:25894306

Quantitative body fluid proteomics in medicine - A focus on minimal invasiveness.

PubMed

Csősz, Éva; Kalló, Gergő; Márkus, Bernadett; Deák, Eszter; Csutak, Adrienne; Tőzsér, József

2017-02-05

Identification of new biomarkers specific for various pathological conditions is an important field in medical sciences. Body fluids have emerging potential in biomarker studies especially those which are continuously available and can be collected by non-invasive means. Changes in the protein composition of body fluids such as tears, saliva, sweat, etc. may provide information on both local and systemic conditions of medical relevance. In this review, our aim is to discuss the quantitative proteomics techniques used in biomarker studies, and to present advances in quantitative body fluid proteomics of non-invasively collectable body fluids with relevance to biomarker identification. The advantages and limitations of the widely used quantitative proteomics techniques are also presented. Based on the reviewed literature, we suggest an ideal pipeline for body fluid analyses aiming at biomarkers discoveries: starting from identification of biomarker candidates by shotgun quantitative proteomics or protein arrays, through verification of potential biomarkers by targeted mass spectrometry, to the antibody-based validation of biomarkers. The importance of body fluids as a rich source of biomarkers is discussed. Quantitative proteomics is a challenging part of proteomics applications. The body fluids collected by non-invasive means have high relevance in medicine; they are good sources for biomarkers used in establishing the diagnosis, follow up of disease progression and predicting high risk groups. The review presents the most widely used quantitative proteomics techniques in body fluid analysis and lists the potential biomarkers identified in tears, saliva, sweat, nasal mucus and urine for local and systemic diseases. Copyright © 2016 Elsevier B.V. All rights reserved.

Quantitative analysis of periodontal pathogens by ELISA and real-time polymerase chain reaction.

PubMed

Hamlet, Stephen M

2010-01-01

The development of analytical methods enabling the accurate identification and enumeration of bacterial species colonizing the oral cavity has led to the identification of a small number of bacterial pathogens that are major factors in the etiology of periodontal disease. Further, these methods also underpin more recent epidemiological analyses of the impact of periodontal disease on general health. Given the complex milieu of over 700 species of microorganisms known to exist within the complex biofilms found in the oral cavity, the identification and enumeration of oral periodontopathogens has not been an easy task. In recent years however, some of the intrinsic limitations of the more traditional microbiological analyses previously used have been overcome with the advent of immunological and molecular analytical methods. Of the plethora of methodologies reported in the literature, the enzyme-linked immunosorbent assay (ELISA), which combines the specificity of antibody with the sensitivity of simple enzyme assays and the polymerase chain reaction (PCR), has been widely utilized in both laboratory and clinical applications. Although conventional PCR does not allow quantitation of the target organism, real-time PCR (rtPCR) has the ability to detect amplicons as they accumulate in "real time" allowing subsequent quantitation. These methods enable the accurate quantitation of as few as 10(2) (using rtPCR) to 10(4) (using ELISA) periodontopathogens in dental plaque samples.

Qualitative and quantitative aspects of information processing in first psychosis: latent class analyses in patients, at-risk subjects, and controls.

PubMed

van Tricht, Mirjam J; Bour, Lo J; Koelman, Johannes H T M; Derks, Eske M; Braff, David L; de Wilde, Odette M; Boerée, Thijs; Linszen, Don H; de Haan, Lieuwe; Nieman, Dorien H

2015-04-01

We aimed to determine profiles of information processing deficits in the pathway to first psychosis. Sixty-one subjects at ultrahigh risk (UHR) for psychosis were assessed, of whom 18 converted to a first episode of psychosis (FEP) within the follow-up period. Additionally, 47 FEP and 30 control subjects were included. Using 10 neurophysiological parameters associated with information processing, latent class analyses yielded three classes at baseline. Class membership was related to group status. Within the UHR sample, two classes were found. Transition to psychosis was nominally associated with class membership. Neurophysiological profiles were unstable over time, but associations between specific neurophysiological components at baseline and follow-up were found. We conclude that certain constellations of neurophysiological variables aid in the differentiation between controls and patients in the prodrome and after first psychosis. Copyright © 2014 Society for Psychophysiological Research.

Some Epistemological Considerations Concerning Quantitative Analysis

ERIC Educational Resources Information Center

Dobrescu, Emilian

2008-01-01

This article presents the author's address at the 2007 "Journal of Applied Quantitative Methods" ("JAQM") prize awarding festivity. The festivity was included in the opening of the 4th International Conference on Applied Statistics, November 22, 2008, Bucharest, Romania. In the address, the author reflects on three theses that…

Impact of implementation choices on quantitative predictions of cell-based computational models

NASA Astrophysics Data System (ADS)

Kursawe, Jochen; Baker, Ruth E.; Fletcher, Alexander G.

2017-09-01

'Cell-based' models provide a powerful computational tool for studying the mechanisms underlying the growth and dynamics of biological tissues in health and disease. An increasing amount of quantitative data with cellular resolution has paved the way for the quantitative parameterisation and validation of such models. However, the numerical implementation of cell-based models remains challenging, and little work has been done to understand to what extent implementation choices may influence model predictions. Here, we consider the numerical implementation of a popular class of cell-based models called vertex models, which are often used to study epithelial tissues. In two-dimensional vertex models, a tissue is approximated as a tessellation of polygons and the vertices of these polygons move due to mechanical forces originating from the cells. Such models have been used extensively to study the mechanical regulation of tissue topology in the literature. Here, we analyse how the model predictions may be affected by numerical parameters, such as the size of the time step, and non-physical model parameters, such as length thresholds for cell rearrangement. We find that vertex positions and summary statistics are sensitive to several of these implementation parameters. For example, the predicted tissue size decreases with decreasing cell cycle durations, and cell rearrangement may be suppressed by large time steps. These findings are counter-intuitive and illustrate that model predictions need to be thoroughly analysed and implementation details carefully considered when applying cell-based computational models in a quantitative setting.

Atmospheric tether mission analyses

NASA Technical Reports Server (NTRS)

1996-01-01

NASA is considering the use of tethered satellites to explore regions of the atmosphere inaccessible to spacecraft or high altitude research balloons. This report summarizes the Lockheed Martin Astronautics (LMA) effort for the engineering study team assessment of an Orbiter-based atmospheric tether mission. Lockheed Martin responsibilities included design recommendations for the deployer and tether, as well as tether dynamic analyses for the mission. Three tether configurations were studied including single line, multistrand (Hoytether) and tape designs.

Chemoenzymatic method for glycomics: isolation, identification, and quantitation

PubMed Central

Yang, Shuang; Rubin, Abigail; Eshghi, Shadi Toghi; Zhang, Hui

2015-01-01

Over the past decade, considerable progress has been made with respect to the analytical methods for analysis of glycans from biological sources. Regardless of the specific methods that are used, glycan analysis includes isolation, identification, and quantitation. Derivatization is indispensable to increase their identification. Derivatization of glycans can be performed by permethylation or carbodiimide coupling / esterification. By introducing a fluorophore or chromophore at their reducing end, glycans can be separated by electrophoresis or chromatography. The fluorogenically labeled glycans can be quantitated using fluorescent detection. The recently developed approaches using solid-phase such as glycoprotein immobilization for glycan extraction and on-tissue glycan mass spectrometry imaging demonstrate advantages over methods performed in solution. Derivatization of sialic acids is favorably implemented on the solid support using carbodiimide coupling, and the released glycans can be further modified at the reducing end or permethylated for quantitative analysis. In this review, methods for glycan isolation, identification, and quantitation are discussed. PMID:26390280

Quantitative structure-activity relationship (QSAR) for insecticides: development of predictive in vivo insecticide activity models.

PubMed

Naik, P K; Singh, T; Singh, H

2009-07-01

Quantitative structure-activity relationship (QSAR) analyses were performed independently on data sets belonging to two groups of insecticides, namely the organophosphates and carbamates. Several types of descriptors including topological, spatial, thermodynamic, information content, lead likeness and E-state indices were used to derive quantitative relationships between insecticide activities and structural properties of chemicals. A systematic search approach based on missing value, zero value, simple correlation and multi-collinearity tests as well as the use of a genetic algorithm allowed the optimal selection of the descriptors used to generate the models. The QSAR models developed for both organophosphate and carbamate groups revealed good predictability with r(2) values of 0.949 and 0.838 as well as [image omitted] values of 0.890 and 0.765, respectively. In addition, a linear correlation was observed between the predicted and experimental LD(50) values for the test set data with r(2) of 0.871 and 0.788 for both the organophosphate and carbamate groups, indicating that the prediction accuracy of the QSAR models was acceptable. The models were also tested successfully from external validation criteria. QSAR models developed in this study should help further design of novel potent insecticides.

A Critical Appraisal of Techniques, Software Packages, and Standards for Quantitative Proteomic Analysis

PubMed Central

Lawless, Craig; Hubbard, Simon J.; Fan, Jun; Bessant, Conrad; Hermjakob, Henning; Jones, Andrew R.

2012-01-01

Abstract New methods for performing quantitative proteome analyses based on differential labeling protocols or label-free techniques are reported in the literature on an almost monthly basis. In parallel, a correspondingly vast number of software tools for the analysis of quantitative proteomics data has also been described in the literature and produced by private companies. In this article we focus on the review of some of the most popular techniques in the field and present a critical appraisal of several software packages available to process and analyze the data produced. We also describe the importance of community standards to support the wide range of software, which may assist researchers in the analysis of data using different platforms and protocols. It is intended that this review will serve bench scientists both as a useful reference and a guide to the selection and use of different pipelines to perform quantitative proteomics data analysis. We have produced a web-based tool (http://www.proteosuite.org/?q=other_resources) to help researchers find appropriate software for their local instrumentation, available file formats, and quantitative methodology. PMID:22804616

Improvement of Quantitative Measurements in Multiplex Proteomics Using High-Field Asymmetric Waveform Spectrometry.

PubMed

Pfammatter, Sibylle; Bonneil, Eric; Thibault, Pierre

2016-12-02

Quantitative proteomics using isobaric reagent tandem mass tags (TMT) or isobaric tags for relative and absolute quantitation (iTRAQ) provides a convenient approach to compare changes in protein abundance across multiple samples. However, the analysis of complex protein digests by isobaric labeling can be undermined by the relative large proportion of co-selected peptide ions that lead to distorted reporter ion ratios and affect the accuracy and precision of quantitative measurements. Here, we investigated the use of high-field asymmetric waveform ion mobility spectrometry (FAIMS) in proteomic experiments to reduce sample complexity and improve protein quantification using TMT isobaric labeling. LC-FAIMS-MS/MS analyses of human and yeast protein digests led to significant reductions in interfering ions, which increased the number of quantifiable peptides by up to 68% while significantly improving the accuracy of abundance measurements compared to that with conventional LC-MS/MS. The improvement in quantitative measurements using FAIMS is further demonstrated for the temporal profiling of protein abundance of HEK293 cells following heat shock treatment.

Calibration of Wide-Field Deconvolution Microscopy for Quantitative Fluorescence Imaging

PubMed Central

Lee, Ji-Sook; Wee, Tse-Luen (Erika); Brown, Claire M.

2014-01-01

Deconvolution enhances contrast in fluorescence microscopy images, especially in low-contrast, high-background wide-field microscope images, improving characterization of features within the sample. Deconvolution can also be combined with other imaging modalities, such as confocal microscopy, and most software programs seek to improve resolution as well as contrast. Quantitative image analyses require instrument calibration and with deconvolution, necessitate that this process itself preserves the relative quantitative relationships between fluorescence intensities. To ensure that the quantitative nature of the data remains unaltered, deconvolution algorithms need to be tested thoroughly. This study investigated whether the deconvolution algorithms in AutoQuant X3 preserve relative quantitative intensity data. InSpeck Green calibration microspheres were prepared for imaging, z-stacks were collected using a wide-field microscope, and the images were deconvolved using the iterative deconvolution algorithms with default settings. Afterwards, the mean intensities and volumes of microspheres in the original and the deconvolved images were measured. Deconvolved data sets showed higher average microsphere intensities and smaller volumes than the original wide-field data sets. In original and deconvolved data sets, intensity means showed linear relationships with the relative microsphere intensities given by the manufacturer. Importantly, upon normalization, the trend lines were found to have similar slopes. In original and deconvolved images, the volumes of the microspheres were quite uniform for all relative microsphere intensities. We were able to show that AutoQuant X3 deconvolution software data are quantitative. In general, the protocol presented can be used to calibrate any fluorescence microscope or image processing and analysis procedure. PMID:24688321

The calibration of video cameras for quantitative measurements

NASA Technical Reports Server (NTRS)

Snow, Walter L.; Childers, Brooks A.; Shortis, Mark R.

1993-01-01

Several different recent applications of velocimetry at Langley Research Center are described in order to show the need for video camera calibration for quantitative measurements. Problems peculiar to video sensing are discussed, including synchronization and timing, targeting, and lighting. The extension of the measurements to include radiometric estimates is addressed.

Connecting qualitative observation and quantitative measurement for enhancing quantitative literacy in plant anatomy course

NASA Astrophysics Data System (ADS)

Nuraeni, E.; Rahmat, A.

2018-05-01

Forming of cognitive schemes of plant anatomy concepts is performed by processing of qualitative and quantitative data obtained from microscopic observations. To enhancing student’s quantitative literacy, strategy of plant anatomy course was modified by adding the task to analyze quantitative data produced by quantitative measurement of plant anatomy guided by material course. Participant in this study was 24 biology students and 35 biology education students. Quantitative Literacy test, complex thinking in plant anatomy test and questioner used to evaluate the course. Quantitative literacy capability data was collected by quantitative literacy test with the rubric from the Association of American Colleges and Universities, Complex thinking in plant anatomy by test according to Marzano and questioner. Quantitative literacy data are categorized according to modified Rhodes and Finley categories. The results showed that quantitative literacy of biology education students is better than biology students.

Quantitative analysis of urine vapor and breath by gas-liquid partition chromatography.

PubMed

Pauling, L; Robinson, A B; Teranishi, R; Cary, P

1971-10-01

When a human being is placed for several days on a completely defined diet, consisting almost entirely of small molecules that are absorbed from the stomach into the blood, intestinal flora disappear because of lack of nutrition. By this technique, the composition of body fluids can be made constant (standard deviation about 10%) after a few days, permitting significant quantitative analyses to be performed. A method of temperature-programmed gas-liquid partition chromatography has been developed for this purpose. It permits the quantitative determination of about 250 substances in a sample of breath, and of about 280 substances in a sample of urine vapor. The technique should be useful in the application of the principles of orthomolecular medicine.

Quantitative imaging of mammalian transcriptional dynamics: from single cells to whole embryos.

PubMed

Zhao, Ziqing W; White, Melanie D; Bissiere, Stephanie; Levi, Valeria; Plachta, Nicolas

2016-12-23

Probing dynamic processes occurring within the cell nucleus at the quantitative level has long been a challenge in mammalian biology. Advances in bio-imaging techniques over the past decade have enabled us to directly visualize nuclear processes in situ with unprecedented spatial and temporal resolution and single-molecule sensitivity. Here, using transcription as our primary focus, we survey recent imaging studies that specifically emphasize the quantitative understanding of nuclear dynamics in both time and space. These analyses not only inform on previously hidden physical parameters and mechanistic details, but also reveal a hierarchical organizational landscape for coordinating a wide range of transcriptional processes shared by mammalian systems of varying complexity, from single cells to whole embryos.

Supramolecular assembly affording a ratiometric two-photon fluorescent nanoprobe for quantitative detection and bioimaging.

PubMed

Wang, Peng; Zhang, Cheng; Liu, Hong-Wen; Xiong, Mengyi; Yin, Sheng-Yan; Yang, Yue; Hu, Xiao-Xiao; Yin, Xia; Zhang, Xiao-Bing; Tan, Weihong

2017-12-01

Fluorescence quantitative analyses for vital biomolecules are in great demand in biomedical science owing to their unique detection advantages with rapid, sensitive, non-damaging and specific identification. However, available fluorescence strategies for quantitative detection are usually hard to design and achieve. Inspired by supramolecular chemistry, a two-photon-excited fluorescent supramolecular nanoplatform ( TPSNP ) was designed for quantitative analysis with three parts: host molecules (β-CD polymers), a guest fluorophore of sensing probes (Np-Ad) and a guest internal reference (NpRh-Ad). In this strategy, the TPSNP possesses the merits of (i) improved water-solubility and biocompatibility; (ii) increased tissue penetration depth for bioimaging by two-photon excitation; (iii) quantitative and tunable assembly of functional guest molecules to obtain optimized detection conditions; (iv) a common approach to avoid the limitation of complicated design by adjustment of sensing probes; and (v) accurate quantitative analysis by virtue of reference molecules. As a proof-of-concept, we utilized the two-photon fluorescent probe NHS-Ad-based TPSNP-1 to realize accurate quantitative analysis of hydrogen sulfide (H 2 S), with high sensitivity and good selectivity in live cells, deep tissues and ex vivo -dissected organs, suggesting that the TPSNP is an ideal quantitative indicator for clinical samples. What's more, TPSNP will pave the way for designing and preparing advanced supramolecular sensors for biosensing and biomedicine.

How can my research paper be useful for future meta-analyses on forest restoration practices?

Treesearch

Enrique Andivia; Pedro Villar‑Salvador; Juan A. Oliet; Jaime Puertolas; R. Kasten Dumroese

2018-01-01

Statistical meta-analysis is a powerful and useful tool to quantitatively synthesize the information conveyed in published studies on a particular topic. It allows identifying and quantifying overall patterns and exploring causes of variation. The inclusion of published works in meta-analyses requires, however, a minimum quality standard of the reported data and...

Quantitative fractography by digital image processing: NIH Image macro tools for stereo pair analysis and 3-D reconstruction.

PubMed

Hein, L R

2001-10-01

A set of NIH Image macro programs was developed to make qualitative and quantitative analyses from digital stereo pictures produced by scanning electron microscopes. These tools were designed for image alignment, anaglyph representation, animation, reconstruction of true elevation surfaces, reconstruction of elevation profiles, true-scale elevation mapping and, for the quantitative approach, surface area and roughness calculations. Limitations on time processing, scanning techniques and programming concepts are also discussed.

Systematic prevention of overweight and obesity in adults: a qualitative and quantitative literature analysis.

PubMed

Kremers, S; Reubsaet, A; Martens, M; Gerards, S; Jonkers, R; Candel, M; de Weerdt, I; de Vries, N

2010-05-01

To date, most interventions aimed at preventing obesity have underemphasized the application of systematic intervention development, implementation and evaluation. The present review provides a thorough insight in factors promoting implementation and/or effectiveness in interventions aimed at preventing overweight/obesity among adults. A total of 46 studies evaluating interventions aimed at preventing obesity were reviewed, followed by both qualitative and quantitative analyses. The Intervention Mapping protocol and the Environmental Research framework for weight Gain prevention (EnRG) were applied to analyse and classify the included studies. The interventions were categorized by setting (workplace, community, health care) and target group (ethnic minorities, pregnant women, [pre]menopausal women, smokers, people with intellectual disabilities). Generally, interventions were found to have potential in changing energy balance-related behaviours and anthropometric outcomes. Effect sizes for changes in body mass index ranged between -0.09 and 0.45. When the programme goal specifically aimed at weight management, the intervention was found to be more successful than interventions with programme goals that were aimed at preventing cardiovascular disease or improving general health status. Although a considerable part of studies included motivational interventions, only some actually assessed the effects on potential cognitive mediators. A general lack of reporting underlying theoretical models for behaviour change was observed as well as the inclusion of linkage groups and strategies to promote empowerment.

Improved micromethod for mezlocillin quantitation in serum and urine by high-pressure liquid chromatography.

PubMed Central

Fiore, D; Auger, F A; Drusano, G L; Dandu, V R; Lesko, L J

1984-01-01

A rapid, sensitive, and specific method of analysis for mezlocillin in serum and urine by high-pressure liquid chromatography is described. A solid-phase extraction column was used to remove interfering substances from samples before chromatography. Quantitation included the use of an internal standard, nafcillin. Mezlocillin was chromatographed with a phosphate buffer-acetonitrile (73:27) mobile phase and a C-18 reverse-phase column and detected at a wavelength of 220 nm. The assay had a sensitivity of 1.6 micrograms/ml and a linearity of up to 600 micrograms/ml and 16 mg/ml in serum and urine, respectively, with only 0.1 ml of sample. The interday and intraday coefficients of variation for replicate analyses of spiked serum and urine specimens were less than 6.5%. PMID:6517560

Quantitative morphology in canine cutaneous soft tissue sarcomas.

PubMed

Simeonov, R; Ananiev, J; Gulubova, M

2015-12-01

Stained cytological specimens from 24 dogs with spontaneous soft tissue sarcomas [fibrosarcoma (n = 8), liposarcoma (n = 8) and haemangiopericytoma (n = 8)], and 24 dogs with reactive connective tissue lesions [granulation tissue (n = 12) and dermal fibrosis (n = 12)] were analysed by computer-assisted nuclear morphometry. The studied morphometric parameters were: mean nuclear area (MNA; µm(2)), mean nuclear perimeter (MNP; µm), mean nuclear diameter (MND mean; µm), minimum nuclear diameter (Dmin; µm) and maximum nuclear diameter (Dmax; µm). The study aimed to evaluate (1) possibility for quantitative differentiation of soft tissue sarcomas from reactive connective tissue lesions and (2) by using cytomorphometry, to differentiate the various histopathological soft tissue sarcomas subtypes in dogs. The mean values of all nuclear cytomorphometric parameters (except for Dmax) were statistically significantly higher in reactive connective tissue processes than in soft tissue sarcomas. At the same time, however, there were no considerable differences among the different sarcoma subtypes. The results demonstrated that the quantitative differentiation of reactive connective tissue processes from soft tissue sarcomas in dogs is possible, but the same was not true for the different canine soft tissue sarcoma subtypes. Further investigations on this topic are necessary for thorough explication of the role of quantitative morphology in the diagnostics of mesenchymal neoplasms and tumour-like fibrous lesions in dogs. © 2014 John Wiley & Sons Ltd.

Evaluation of a rapid quantitative determination method of PSA concentration with gold immunochromatographic strips.

PubMed

Wu, Cheng-Ching; Lin, Hung-Yu; Wang, Chao-Ping; Lu, Li-Fen; Yu, Teng-Hung; Hung, Wei-Chin; Houng, Jer-Yiing; Chung, Fu-Mei; Lee, Yau-Jiunn; Hu, Jin-Jia

2015-11-03

Prostate cancer remains the most common cancer in men. Qualitative or semi-quantitative immunochromatographic measurements of prostate specific antigen (PSA) have been shown to be simple, noninvasive and feasible. The aim of this study was to evaluate an optimized gold immunochromatographic strip device for the detection of PSA, in which the results can be analysed using a Chromogenic Rapid Test Reader to quantitatively assess the test results. This reader measures the reflectance of the signal line via a charge-coupled device camera. For quantitative analysis, PSA concentration was computed via a calibration equation. Capillary blood samples from 305 men were evaluated, and two independent observers interpreted the test results after 12 min. Blood samples were also collected and tested with a conventional quantitative assay. Sensitivity, specificity, positive and negative predictive values, and accuracy of the PSA rapid quantitative test system were 100, 96.6, 89.5, 100, and 97.4 %, respectively. Reproducibility of the test was 99.2, and interobserver variation was 8 % with a false positive rate of 3.4 %. The correlation coefficient between the ordinary quantitative assay and the rapid quantitative test was 0.960. The PSA rapid quantitative test system provided results quickly and was easy to use, so that tests using this system can be easily performed at outpatient clinics or elsewhere. This system may also be useful for initial cancer screening and for point-of-care testing, because results can be obtained within 12 min and at a cost lower than that of conventional quantitative assays.

Rock Slide Risk Assessment: A Semi-Quantitative Approach

NASA Astrophysics Data System (ADS)

Duzgun, H. S. B.

2009-04-01

Rock slides can be better managed by systematic risk assessments. Any risk assessment methodology for rock slides involves identification of rock slide risk components, which are hazard, elements at risk and vulnerability. For a quantitative/semi-quantitative risk assessment for rock slides, a mathematical value the risk has to be computed and evaluated. The quantitative evaluation of risk for rock slides enables comparison of the computed risk with the risk of other natural and/or human-made hazards and providing better decision support and easier communication for the decision makers. A quantitative/semi-quantitative risk assessment procedure involves: Danger Identification, Hazard Assessment, Elements at Risk Identification, Vulnerability Assessment, Risk computation, Risk Evaluation. On the other hand, the steps of this procedure require adaptation of existing or development of new implementation methods depending on the type of landslide, data availability, investigation scale and nature of consequences. In study, a generic semi-quantitative risk assessment (SQRA) procedure for rock slides is proposed. The procedure has five consecutive stages: Data collection and analyses, hazard assessment, analyses of elements at risk and vulnerability and risk assessment. The implementation of the procedure for a single rock slide case is illustrated for a rock slope in Norway. Rock slides from mountain Ramnefjell to lake Loen are considered to be one of the major geohazards in Norway. Lake Loen is located in the inner part of Nordfjord in Western Norway. Ramnefjell Mountain is heavily jointed leading to formation of vertical rock slices with height between 400-450 m and width between 7-10 m. These slices threaten the settlements around Loen Valley and tourists visiting the fjord during summer season, as the released slides have potential of creating tsunami. In the past, several rock slides had been recorded from the Mountain Ramnefjell between 1905 and 1950. Among them

Journals Not Included in BIOSIS Previews Have a Notable Impact in Biology

ERIC Educational Resources Information Center

Lascar, Claudia; Barnett, Philip

2009-01-01

The purpose of this study was to reveal influential journals used by life scientists; journals not currently included in "BIOSIS Previews," but included in either "PubMed" or "Science Citation Index Expanded". These 252 journals were revealed by the Eigenfactor, an iterative ranking scheme which quantitatively measures the scientific influence of…

Transcontinental communication and quantitative digital histopathology via the Internet; with special reference to prostate neoplasia

PubMed Central

Montironi, R; Thompson, D; Scarpelli, M; Bartels, H G; Hamilton, P W; Da Silva, V D; Sakr, W A; Weyn, B; Van Daele, A; Bartels, P H

2002-01-01

Objective: To describe practical experiences in the sharing of very large digital data bases of histopathological imagery via the Internet, by investigators working in Europe, North America, and South America. Materials: Experiences derived from medium power (sampling density 2.4 pixels/μm) and high power (6 pixels/μm) imagery of prostatic tissues, skin shave biopsies, breast lesions, endometrial sections, and colonic lesions. Most of the data included in this paper were from prostate. In particular, 1168 histological images of normal prostate, high grade prostatic intraepithelial neoplasia (PIN), and prostate cancer (PCa) were recorded, archived in an image format developed at the Optical Sciences Center (OSC), University of Arizona, and transmitted to Ancona, Italy, as JPEG (joint photographic experts group) files. Images were downloaded for review using the Internet application FTP (file transfer protocol). The images were then sent from Ancona to other laboratories for additional histopathological review and quantitative analyses. They were viewed using Adobe Photoshop, Paint Shop Pro, and Imaging for Windows. For karyometric analysis full resolution imagery was used, whereas histometric analyses were carried out on JPEG imagery also. Results: The three applications of the telecommunication system were remote histopathological assessment, remote data acquisition, and selection of material. Typical data volumes for each project ranged from 120 megabytes to one gigabyte, and transmission times were usually less than one hour. There were only negligible transmission errors, and no problem in efficient communication, although real time communication was an exception, because of the time zone differences. As far as the remote histopathological assessment of the prostate was concerned, agreement between the pathologist's electronic diagnosis and the diagnostic label applied to the images by the recording scientist was present in 96.6% of instances. When these

Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices.

PubMed

He, Ji-Zheng; Shen, Ju-Pei; Zhang, Li-Mei; Zhu, Yong-Guan; Zheng, Yuan-Ming; Xu, Ming-Gang; Di, Hongjie

2007-09-01

The abundance and composition of soil ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were investigated by using quantitative real-time polymerase chain reaction, cloning and sequencing approaches based on amoA genes. The soil, classified as agri-udic ferrosols with pH (H(2)O) ranging from 3.7 to 6.0, was sampled in summer and winter from long-term field experimental plots which had received 16 years continuous fertilization treatments, including fallow (CK0), control without fertilizers (CK) and those with combinations of fertilizer nitrogen (N), phosphorus (P) and potassium (K): N, NP, NK, PK, NPK and NPK plus organic manure (OM). Population sizes of AOB and AOA changed greatly in response to the different fertilization treatments. The NPK + OM treatment had the highest copy numbers of AOB and AOA amoA genes among the treatments that received mineral fertilizers, whereas the lowest copy numbers were recorded in the N treatment. Ammonia-oxidizing archaea were more abundant than AOB in all the corresponding treatments, with AOA to AOB ratios ranging from 1.02 to 12.36. Significant positive correlations were observed among the population sizes of AOB and AOA, soil pH and potential nitrification rates, indicating that both AOB and AOA played an important role in ammonia oxidation in the soil. Phylogenetic analyses of the amoA gene fragments showed that all AOB sequences from different treatments were affiliated with Nitrosospira or Nitrosospira-like species and grouped into cluster 3, and little difference in AOB community composition was recorded among different treatments. All AOA sequences fell within cluster S (soil origin) and cluster M (marine and sediment origin). Cluster M dominated exclusively in the N, NP, NK and PK treatments, indicating a pronounced difference in the community composition of AOA in response to the long-term fertilization treatments. These findings could be fundamental to improve our understanding of the importance of

Pathway models for analysing and managing the introduction of alien plant pests—an overview and categorization

Treesearch

J.C. Douma; M. Pautasso; R.C. Venette; C. Robinet; L. Hemerik; M.C.M. Mourits; J. Schans; W. van der Werf

2016-01-01

Alien plant pests are introduced into new areas at unprecedented rates through global trade, transport, tourism and travel, threatening biodiversity and agriculture. Increasingly, the movement and introduction of pests is analysed with pathway models to provide risk managers with quantitative estimates of introduction risks and effectiveness of management options....

Toward Monitoring Parkinson's Through Analysis of Static Handwriting Samples: A Quantitative Analytical Framework.

PubMed

Zhi, Naiqian; Jaeger, Beverly Kris; Gouldstone, Andrew; Sipahi, Rifat; Frank, Samuel

2017-03-01

Detection of changes in micrographia as a manifestation of symptomatic progression or therapeutic response in Parkinson's disease (PD) is challenging as such changes can be subtle. A computerized toolkit based on quantitative analysis of handwriting samples would be valuable as it could supplement and support clinical assessments, help monitor micrographia, and link it to PD. Such a toolkit would be especially useful if it could detect subtle yet relevant changes in handwriting morphology, thus enhancing resolution of the detection procedure. This would be made possible by developing a set of metrics sensitive enough to detect and discern micrographia with specificity. Several metrics that are sensitive to the characteristics of micrographia were developed, with minimal sensitivity to confounding handwriting artifacts. These metrics capture character size-reduction, ink utilization, and pixel density within a writing sample from left to right. They are used here to "score" handwritten signatures of 12 different individuals corresponding to healthy and symptomatic PD conditions, and sample control signatures that had been artificially reduced in size for comparison purposes. Moreover, metric analyses of samples from ten of the 12 individuals for which clinical diagnosis time is known show considerable informative variations when applied to static signature samples obtained before and after diagnosis. In particular, a measure called pixel density variation showed statistically significant differences ( ) between two comparison groups of remote signature recordings: earlier versus recent, based on independent and paired t-test analyses on a total of 40 signature samples. The quantitative framework developed here has the potential to be used in future controlled experiments to study micrographia and links to PD from various aspects, including monitoring and assessment of applied interventions and treatments. The inherent value in this methodology is further enhanced by

Meta-Analyses and Orthodontic Evidence-Based Clinical Practice in the 21st Century

PubMed Central

Papadopoulos, Moschos A.

2010-01-01

Introduction: Aim of this systematic review was to assess the orthodontic related issues which currently provide the best evidence as documented by meta-analyses, by critically evaluating and discussing the methodology used in these studies. Material and Methods: Several electronic databases were searched and handsearching was also performed in order to identify the corresponding meta-analyses investigating orthodontic related subjects. In total, 197 studies were retrieved initially. After applying specific inclusion and exclusion criteria, 27 articles were identified as meta-analyses treating orthodontic-related subjects. Results: Many of these 27 papers presented sufficient quality and followed appropriate meta-analytic approaches to quantitatively synthesize data and presented adequately supported evidence. However, the methodology used in some of them presented weaknesses, limitations or deficiencies. Consequently, the topics in orthodontics which currently provide the best evidence, include some issues related to Class II or Class III treatment, treatment of transverse problems, external apical root resorption, dental anomalies, such as congenital missing teeth and tooth transposition, frequency of severe occlusal problems, nickel hypersensitivity, obstructive sleep apnea syndrome, and computer-assisted learning in orthodontic education. Conclusions: Only a few orthodontic related issues have been so far investigated by means of MAs. In addition, for some of these issues investigated in the corresponding MAs no definite conclusions could be drawn, due to significant methodological deficiencies of these studies. According to this investigation, it can be concluded that at the begin of the 21st century there is evidence for only a few orthodontic related issues as documented by meta-analyses, and more well-conducted high quality research studies are needed to produce strong evidence in order to support evidence-based clinical practice in orthodontics. PMID

On the Reproducibility of Label-Free Quantitative Cross-Linking/Mass Spectrometry

NASA Astrophysics Data System (ADS)

Müller, Fränze; Fischer, Lutz; Chen, Zhuo Angel; Auchynnikava, Tania; Rappsilber, Juri

2018-02-01

Quantitative cross-linking/mass spectrometry (QCLMS) is an emerging approach to study conformational changes of proteins and multi-subunit complexes. Distinguishing protein conformations requires reproducibly identifying and quantifying cross-linked peptides. Here we analyzed the variation between multiple cross-linking reactions using bis[sulfosuccinimidyl] suberate (BS3)-cross-linked human serum albumin (HSA) and evaluated how reproducible cross-linked peptides can be identified and quantified by LC-MS analysis. To make QCLMS accessible to a broader research community, we developed a workflow that integrates the established software tools MaxQuant for spectra preprocessing, Xi for cross-linked peptide identification, and finally Skyline for quantification (MS1 filtering). Out of the 221 unique residue pairs identified in our sample, 124 were subsequently quantified across 10 analyses with coefficient of variation (CV) values of 14% (injection replica) and 32% (reaction replica). Thus our results demonstrate that the reproducibility of QCLMS is in line with the reproducibility of general quantitative proteomics and we establish a robust workflow for MS1-based quantitation of cross-linked peptides.

The application of quantitative risk assessment to microbial food safety risks.

PubMed

Jaykus, L A

1996-01-01

Regulatory programs and guidelines for the control of foodborne microbial agents have existed in the U.S. for nearly 100 years. However, increased awareness of the scope and magnitude of foodborne disease, as well as the emergence of previously unrecognized human pathogens transmitted via the foodborne route, have prompted regulatory officials to consider new and improved strategies to reduce the health risks associated with pathogenic microorganisms in foods. Implementation of these proposed strategies will involve definitive costs for a finite level of risk reduction. While regulatory decisions regarding the management of foodborne disease risk have traditionally been done with the aid of the scientific community, a formal conceptual framework for the evaluation of health risks from pathogenic microorganisms in foods is warranted. Quantitative risk assessment (QRA), which is formally defined as the technical assessment of the nature and magnitude of a risk caused by a hazard, provides such a framework. Reproducing microorganisms in foods present a particular challenge to QRA because both their introduction and numbers may be affected by numerous factors within the food chain, with all of these factors representing significant stages in food production, handling, and consumption, in a farm-to-table type of approach. The process of QRA entails four designated phases: (1) hazard identification, (2) exposure assessment, (3) dose-response assessment, and (4) risk characterization. Specific analytical tools are available to accomplish the analyses required for each phase of the QRA. The purpose of this paper is to provide a description of the conceptual framework for quantitative microbial risk assessment within the standard description provided by the National Academy of Sciences (NAS) paradigm. Each of the sequential steps in QRA are discussed in detail, providing information on current applications, tools for conducting the analyses, and methodological and/or data

Examining social competence, self-perception, quality of life, and internalizing and externalizing symptoms in adolescent females with and without autism spectrum disorder: a quantitative design including between-groups and correlational analyses.

PubMed

Jamison, T Rene; Schuttler, Jessica Oeth

2015-01-01

Adolescent females with an autism spectrum disorder (ASD) are an understudied population, yet are also quite vulnerable, due to the increased complexities of social interaction and increased risk for internalizing symptoms in adolescence. Most research literature currently focuses on males with ASD, limiting our understanding of social experiences for females with ASD, and thus the potential to better inform supports and intervention to promote social-emotional functioning. This study examined similarities and differences in selected indicators of social-emotional health (social competence, self-perception, quality of life) and problematic behaviors such as externalizing and internalizing symptoms for adolescent females with and without ASD. This study employed a quantitative design utilizing correlational analysis as well as t test comparisons to examine selected indicators of social-emotional health and problematic symptoms using the Social Skills Improvement System (SSIS), Youth Quality of Life Instrument (YQOL), and the Self-Perceptions Profile for Adolescents (SPPA) for adolescent females with ASD in relation to their typically developing peers. Significant differences were found between females with and without ASD in terms of their self-ratings of social-emotional health and problematic behaviors. The no-ASD group rated themselves higher across all areas of social-emotional health. Findings also suggest strong relationships between these constructs, especially for females without ASD. Parent reports of autism symptoms and social-emotional health indicated that as symptoms of autism are more severe, so too was the impact on individuals' social competence. Adolescent females with ASD perceive themselves as having lower social competence, self-worth, and quality of life and higher levels of internalizing and externalizing symptoms as compared to their typically developing peers. Parent ratings indicate that higher levels of autism symptoms relate to lower

FDTD-based quantitative analysis of terahertz wave detection for multilayered structures.

PubMed

Tu, Wanli; Zhong, Shuncong; Shen, Yaochun; Zhou, Qing; Yao, Ligang

2014-10-01

Experimental investigations have shown that terahertz pulsed imaging (TPI) is able to quantitatively characterize a range of multilayered media (e.g., biological issues, pharmaceutical tablet coatings, layered polymer composites, etc.). Advanced modeling of the interaction of terahertz radiation with a multilayered medium is required to enable the wide application of terahertz technology in a number of emerging fields, including nondestructive testing. Indeed, there have already been many theoretical analyses performed on the propagation of terahertz radiation in various multilayered media. However, to date, most of these studies used 1D or 2D models, and the dispersive nature of the dielectric layers was not considered or was simplified. In the present work, the theoretical framework of using terahertz waves for the quantitative characterization of multilayered media was established. A 3D model based on the finite difference time domain (FDTD) method is proposed. A batch of pharmaceutical tablets with a single coating layer of different coating thicknesses and different refractive indices was modeled. The reflected terahertz wave from such a sample was computed using the FDTD method, assuming that the incident terahertz wave is broadband, covering a frequency range up to 3.5 THz. The simulated results for all of the pharmaceutical-coated tablets considered were found to be in good agreement with the experimental results obtained using a commercial TPI system. In addition, we studied a three-layered medium to mimic the occurrence of defects in the sample.

Gene Level Meta-Analysis of Quantitative Traits by Functional Linear Models.

PubMed

Fan, Ruzong; Wang, Yifan; Boehnke, Michael; Chen, Wei; Li, Yun; Ren, Haobo; Lobach, Iryna; Xiong, Momiao

2015-08-01

Meta-analysis of genetic data must account for differences among studies including study designs, markers genotyped, and covariates. The effects of genetic variants may differ from population to population, i.e., heterogeneity. Thus, meta-analysis of combining data of multiple studies is difficult. Novel statistical methods for meta-analysis are needed. In this article, functional linear models are developed for meta-analyses that connect genetic data to quantitative traits, adjusting for covariates. The models can be used to analyze rare variants, common variants, or a combination of the two. Both likelihood-ratio test (LRT) and F-distributed statistics are introduced to test association between quantitative traits and multiple variants in one genetic region. Extensive simulations are performed to evaluate empirical type I error rates and power performance of the proposed tests. The proposed LRT and F-distributed statistics control the type I error very well and have higher power than the existing methods of the meta-analysis sequence kernel association test (MetaSKAT). We analyze four blood lipid levels in data from a meta-analysis of eight European studies. The proposed methods detect more significant associations than MetaSKAT and the P-values of the proposed LRT and F-distributed statistics are usually much smaller than those of MetaSKAT. The functional linear models and related test statistics can be useful in whole-genome and whole-exome association studies. Copyright © 2015 by the Genetics Society of America.

NEW TARGET AND CONTROL ASSAYS FOR QUANTITATIVE POLYMERASE CHAIN REACTION (QPCR) ANALYSIS OF ENTEROCOCCI IN WATER

EPA Science Inventory

Enterococci are frequently monitored in water samples as indicators of fecal pollution. Attention is now shifting from culture based methods for enumerating these organisms to more rapid molecular methods such as QPCR. Accurate quantitative analyses by this method requires highly...

The Reliability and Validity of Discrete and Continuous Measures of Psychopathology: A Quantitative Review

ERIC Educational Resources Information Center

Markon, Kristian E.; Chmielewski, Michael; Miller, Christopher J.

2011-01-01

In 2 meta-analyses involving 58 studies and 59,575 participants, we quantitatively summarized the relative reliability and validity of continuous (i.e., dimensional) and discrete (i.e., categorical) measures of psychopathology. Overall, results suggest an expected 15% increase in reliability and 37% increase in validity through adoption of a…

Furthering the investigation of eruption styles through quantitative shape analyses of volcanic ash particles

NASA Astrophysics Data System (ADS)

Nurfiani, D.; Bouvet de Maisonneuve, C.

2018-04-01

Volcanic ash morphology has been quantitatively investigated for various aims such as studying the settling velocity of ash for modelling purposes and understanding the fragmentation processes at the origin of explosive eruptions. In an attempt to investigate the usefulness of ash morphometry for monitoring purposes, we analyzed the shape of volcanic ash particles through a combination of (1) traditional shape descriptors such as solidity, convexity, axial ratio and form factor and (2) fractal analysis using the Euclidean Distance transform (EDT) method. We compare ash samples from the hydrothermal eruptions of Iwodake (Japan) in 2013, Tangkuban Perahu (Indonesia) in 2013 and Marapi (Sumatra, Indonesia) in 2015, the dome explosions of Merapi (Java, Indonesia) in 2013, the Vulcanian eruptions of Merapi in 2010 and Tavurvur (Rabaul, Papaua New Guinea) in 2014, and the Plinian eruption of Kelud (Indonesia) in 2014. Particle size and shape measurements were acquired from a Particle Size Analyzer with a microscope camera attached to the instrument. Clear differences between dense/blocky particles from hydrothermal or dome explosions and vesicular particles produced by the fragmentation of gas-bearing molten magma are well highlighted by conventional shape descriptors and the fractal method. In addition, subtle differences between dense/blocky particles produced by hydrothermal explosions, dome explosions, or quench granulation during phreatomagmatic eruptions can be evidenced with the fractal method. The combination of shape descriptors and fractal analysis is therefore potentially able to distinguish between juvenile and non-juvenile magma, which is of importance for eruption monitoring.

Reference charts for young stands — a quantitative methodology for assessing tree performance

Treesearch

Lance A. Vickers; David R. Larsen; Benjamin O. Knapp; John M. Kabrick; Daniel C. Dey

2017-01-01

Reference charts have long been used in the medical field for quantitative clinical assessment of juvenile development by plotting distribution quantiles for a selected attribute (e.g., height) against age for specified peer populations.We propose that early stand dynamics is an area of study that could benefit from the descriptions and analyses offered by similar...

Temporal Lobe Epilepsy: Quantitative MR Volumetry in Detection of Hippocampal Atrophy

PubMed Central

Farid, Nikdokht; Girard, Holly M.; Kemmotsu, Nobuko; Smith, Michael E.; Magda, Sebastian W.; Lim, Wei Y.; Lee, Roland R.

2012-01-01

Purpose: To determine the ability of fully automated volumetric magnetic resonance (MR) imaging to depict hippocampal atrophy (HA) and to help correctly lateralize the seizure focus in patients with temporal lobe epilepsy (TLE). Materials and Methods: This study was conducted with institutional review board approval and in compliance with HIPAA regulations. Volumetric MR imaging data were analyzed for 34 patients with TLE and 116 control subjects. Structural volumes were calculated by using U.S. Food and Drug Administration–cleared software for automated quantitative MR imaging analysis (NeuroQuant). Results of quantitative MR imaging were compared with visual detection of atrophy, and, when available, with histologic specimens. Receiver operating characteristic analyses were performed to determine the optimal sensitivity and specificity of quantitative MR imaging for detecting HA and asymmetry. A linear classifier with cross validation was used to estimate the ability of quantitative MR imaging to help lateralize the seizure focus. Results: Quantitative MR imaging–derived hippocampal asymmetries discriminated patients with TLE from control subjects with high sensitivity (86.7%–89.5%) and specificity (92.2%–94.1%). When a linear classifier was used to discriminate left versus right TLE, hippocampal asymmetry achieved 94% classification accuracy. Volumetric asymmetries of other subcortical structures did not improve classification. Compared with invasive video electroencephalographic recordings, lateralization accuracy was 88% with quantitative MR imaging and 85% with visual inspection of volumetric MR imaging studies but only 76% with visual inspection of clinical MR imaging studies. Conclusion: Quantitative MR imaging can depict the presence and laterality of HA in TLE with accuracy rates that may exceed those achieved with visual inspection of clinical MR imaging studies. Thus, quantitative MR imaging may enhance standard visual analysis, providing a

Porous Silicon Antibody Microarrays for Quantitative Analysis: Measurement of Free and Total PSA in Clinical Plasma Samples

PubMed Central

Tojo, Axel; Malm, Johan; Marko-Varga, György; Lilja, Hans; Laurell, Thomas

2014-01-01

The antibody microarrays have become widespread, but their use for quantitative analyses in clinical samples has not yet been established. We investigated an immunoassay based on nanoporous silicon antibody microarrays for quantification of total prostate-specific-antigen (PSA) in 80 clinical plasma samples, and provide quantitative data from a duplex microarray assay that simultaneously quantifies free and total PSA in plasma. To further develop the assay the porous silicon chips was placed into a standard 96-well microtiter plate for higher throughput analysis. The samples analyzed by this quantitative microarray were 80 plasma samples obtained from men undergoing clinical PSA testing (dynamic range: 0.14-44ng/ml, LOD: 0.14ng/ml). The second dataset, measuring free PSA (dynamic range: 0.40-74.9ng/ml, LOD: 0.47ng/ml) and total PSA (dynamic range: 0.87-295ng/ml, LOD: 0.76ng/ml), was also obtained from the clinical routine. The reference for the quantification was a commercially available assay, the ProStatus PSA Free/Total DELFIA. In an analysis of 80 plasma samples the microarray platform performs well across the range of total PSA levels. This assay might have the potential to substitute for the large-scale microtiter plate format in diagnostic applications. The duplex assay paves the way for a future quantitative multiplex assay, which analyses several prostate cancer biomarkers simultaneously. PMID:22921878

Quantitation of fixative-induced morphologic and antigenic variation in mouse and human breast cancers

PubMed Central

Cardiff, Robert D; Hubbard, Neil E; Engelberg, Jesse A; Munn, Robert J; Miller, Claramae H; Walls, Judith E; Chen, Jane Q; Velásquez-García, Héctor A; Galvez, Jose J; Bell, Katie J; Beckett, Laurel A; Li, Yue-Ju; Borowsky, Alexander D

2013-01-01

Quantitative Image Analysis (QIA) of digitized whole slide images for morphometric parameters and immunohistochemistry of breast cancer antigens was used to evaluate the technical reproducibility, biological variability, and intratumoral heterogeneity in three transplantable mouse mammary tumor models of human breast cancer. The relative preservation of structure and immunogenicity of the three mouse models and three human breast cancers was also compared when fixed with representatives of four distinct classes of fixatives. The three mouse mammary tumor cell models were an ER + /PR + model (SSM2), a Her2 + model (NDL), and a triple negative model (MET1). The four breast cancer antigens were ER, PR, Her2, and Ki67. The fixatives included examples of (1) strong cross-linkers, (2) weak cross-linkers, (3) coagulants, and (4) combination fixatives. Each parameter was quantitatively analyzed using modified Aperio Technologies ImageScope algorithms. Careful pre-analytical adjustments to the algorithms were required to provide accurate results. The QIA permitted rigorous statistical analysis of results and grading by rank order. The analyses suggested excellent technical reproducibility and confirmed biological heterogeneity within each tumor. The strong cross-linker fixatives, such as formalin, consistently ranked higher than weak cross-linker, coagulant and combination fixatives in both the morphometric and immunohistochemical parameters. PMID:23399853

Quantitative nanoparticle tracking: applications to nanomedicine.

PubMed

Huang, Feiran; Dempsey, Christopher; Chona, Daniela; Suh, Junghae

2011-06-01

Particle tracking is an invaluable technique to extract quantitative and qualitative information regarding the transport of nanomaterials through complex biological environments. This technique can be used to probe the dynamic behavior of nanoparticles as they interact with and navigate through intra- and extra-cellular barriers. In this article, we focus on the recent developments in the application of particle-tracking technology to nanomedicine, including the study of synthetic and virus-based materials designed for gene and drug delivery. Specifically, we cover research where mean square displacements of nanomaterial transport were explicitly determined in order to quantitatively assess the transport of nanoparticles through biological environments. Particle-tracking experiments can provide important insights that may help guide the design of more intelligent and effective diagnostic and therapeutic nanoparticles.

Kinetic analyses of vasculogenesis inform mechanistic studies

PubMed Central

Winfree, Seth; Chu, Chenghao; Tu, Wanzhu; Blue, Emily K.; Gohn, Cassandra R.; Dunn, Kenneth W.

2017-01-01

Vasculogenesis is a complex process by which endothelial stem and progenitor cells undergo de novo vessel formation. Quantitative assessment of vasculogenesis is a central readout of endothelial progenitor cell functionality. However, current assays lack kinetic measurements. To address this issue, new approaches were developed to quantitatively assess in vitro endothelial colony-forming cell (ECFC) network formation in real time. Eight parameters of network structure were quantified using novel Kinetic Analysis of Vasculogenesis (KAV) software. KAV assessment of structure complexity identified two phases of network formation. This observation guided the development of additional vasculogenic readouts. A tissue cytometry approach was established to quantify the frequency and localization of dividing ECFCs. Additionally, Fiji TrackMate was used to quantify ECFC displacement and speed at the single-cell level during network formation. These novel approaches were then implemented to identify how intrauterine exposure to maternal diabetes mellitus (DM) impairs fetal ECFC vasculogenesis. Fetal ECFCs exposed to maternal DM form fewer initial network structures, which are not stable over time. Correlation analyses demonstrated that ECFC samples with greater division in branches form fewer closed network structures. Additionally, reductions in average ECFC movement over time decrease structural connectivity. Identification of these novel phenotypes utilizing the newly established methodologies provides evidence for the cellular mechanisms contributing to aberrant ECFC vasculogenesis. PMID:28100488

Criteria for the assessment of analyser practicability

PubMed Central

Biosca, C.; Galimany, R.

1993-01-01

This article lists the theoretical criteria that need to be considered to assess the practicability of an automatic analyser. Two essential sets of criteria should be taken into account when selecting an automatic analyser: ‘reliability’ and ‘practicability’. Practibility covers the features that provide information about the suitability of an analyser for specific working conditions. These practibility criteria are classsified in this article and include the environment; work organization; versatility and flexibility; safely controls; staff training; maintenance and operational costs. PMID:18924972

Chemical analyses of fossil bone.

PubMed

Zheng, Wenxia; Schweitzer, Mary Higby

2012-01-01

The preservation of microstructures consistent with soft tissues, cells, and other biological components in demineralized fragments of dinosaur bone tens of millions of years old was unexpected, and counter to current hypotheses of tissue, cellular, and molecular degradation. Although the morphological similarity of these tissues to extant counterparts was unmistakable, after at least 80 million years exposed to geochemical influences, morphological similarity is insufficient to support an endogenous source. To test this hypothesis, and to characterize these materials at a molecular level, we applied multiple independent chemical, molecular, and microscopic analyses to identify the presence of original components produced by the extinct organisms. Microscopic techniques included field emission scanning electron microscopy, analytical transmission electron microscopy, transmitted light microscopy (LM), and fluorescence microscopy (FM). The chemical and molecular techniques include enzyme-linked immunosorbant assay, sodium dodecyl sulfate polyacrylamide gel electrophoresis, western blot (immunoblot), and attenuated total reflectance infrared spectroscopy. In situ analyses performed directly on tissues included immunohistochemistry and time-of-flight secondary ion mass spectrometry. The details of sample preparation and methodology are described in detail herein.

Growth and maturity: A quantitative systematic review and network analysis in anthropometric history.

PubMed

Galofré-Vilà, Gregori

2018-02-01

This paper reviews the current wealth of anthropometric history since the early efforts of Robert Fogel in the 1970s. The survey is based on a quantitative systematic review of the literature and counts a total of 447 peer-reviewed articles being published in the main leading journals in economic history, economics and biology. Data are analysed using network analysis by journal and author and the main contributions of anthropometric history are highlighted, pointing to future areas of inquiry. The contributions of books and book chapters are also quantified and analysed. Copyright © 2017 Elsevier B.V. All rights reserved.

Generating Linear Equations Based on Quantitative Reasoning

ERIC Educational Resources Information Center

Lee, Mi Yeon

2017-01-01

The Common Core's Standards for Mathematical Practice encourage teachers to develop their students' ability to reason abstractly and quantitatively by helping students make sense of quantities and their relationships within problem situations. The seventh-grade content standards include objectives pertaining to developing linear equations in…

LOD score exclusion analyses for candidate QTLs using random population samples.

PubMed

Deng, Hong-Wen

2003-11-01

While extensive analyses have been conducted to test for, no formal analyses have been conducted to test against, the importance of candidate genes as putative QTLs using random population samples. Previously, we developed an LOD score exclusion mapping approach for candidate genes for complex diseases. Here, we extend this LOD score approach for exclusion analyses of candidate genes for quantitative traits. Under this approach, specific genetic effects (as reflected by heritability) and inheritance models at candidate QTLs can be analyzed and if an LOD score is < or = -2.0, the locus can be excluded from having a heritability larger than that specified. Simulations show that this approach has high power to exclude a candidate gene from having moderate genetic effects if it is not a QTL and is robust to population admixture. Our exclusion analysis complements association analysis for candidate genes as putative QTLs in random population samples. The approach is applied to test the importance of Vitamin D receptor (VDR) gene as a potential QTL underlying the variation of bone mass, an important determinant of osteoporosis.

Automated thin-film analyses of anhydrous interplanetary dust particles in the analytical electron microscope

NASA Technical Reports Server (NTRS)

Bradley, J. P.; Germani, M. S.; Brownlee, D. E.

1989-01-01

An AEM apparatus equipped with digital beam control has obtained quantitative point-count analyses of thin sections taken from eight anhydrous chondritic interplanetary dust particles (IDPs); between 200 and 500 X-ray analyses were collected from each thin section and analyzed for Mg, Al, Si, S, Ca, Cr, Mn, Fe, and Ni. Two types of anhydrous chondritic aggregates were observed in the eight IDPs: one highly porous, the other less so. The eight anhydrous IDPs are characterizable as mixtures of fine- and coarse-grained aggregates, large mineral grains, glass, and carbonaceous materials. Their elemental concentrations follow those of solar abundances, suggesting that they are unperturbed by aqueous alteration.

Current trends in quantitative proteomics - an update.

PubMed

Li, H; Han, J; Pan, J; Liu, T; Parker, C E; Borchers, C H

2017-05-01

Proteins can provide insights into biological processes at the functional level, so they are very promising biomarker candidates. The quantification of proteins in biological samples has been routinely used for the diagnosis of diseases and monitoring the treatment. Although large-scale protein quantification in complex samples is still a challenging task, a great amount of effort has been made to advance the technologies that enable quantitative proteomics. Seven years ago, in 2009, we wrote an article about the current trends in quantitative proteomics. In writing this current paper, we realized that, today, we have an even wider selection of potential tools for quantitative proteomics. These tools include new derivatization reagents, novel sampling formats, new types of analyzers and scanning techniques, and recently developed software to assist in assay development and data analysis. In this review article, we will discuss these innovative methods, and their current and potential applications in proteomics. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Applications of Micro-CT scanning in medicine and dentistry: Microstructural analyses of a Wistar Rat mandible and a urinary tract stone

NASA Astrophysics Data System (ADS)

Latief, F. D. E.; Sari, D. S.; Fitri, L. A.

2017-08-01

High-resolution tomographic imaging by means of x-ray micro-computed tomography (μCT) has been widely utilized for morphological evaluations in dentistry and medicine. The use of μCT follows a standard procedure: image acquisition, reconstruction, processing, evaluation using image analysis, and reporting of results. This paper discusses methods of μCT using a specific scanning device, the Bruker SkyScan 1173 High Energy Micro-CT. We present a description of the general workflow, information on terminology for the measured parameters and corresponding units, and further analyses that can potentially be conducted with this technology. Brief qualitative and quantitative analyses, including basic image processing (VOI selection and thresholding) and measurement of several morphometrical variables (total VOI volume, object volume, percentage of total volume, total VOI surface, object surface, object surface/volume ratio, object surface density, structure thickness, structure separation, total porosity) were conducted on two samples, the mandible of a wistar rat and a urinary tract stone, to illustrate the abilities of this device and its accompanying software package. The results of these analyses for both samples are reported, along with a discussion of the types of analyses that are possible using digital images obtained with a μCT scanning device, paying particular attention to non-diagnostic ex vivo research applications.

Quantitative Analysis of Urine Vapor and Breath by Gas-Liquid Partition Chromatography

PubMed Central

Pauling, Linus; Robinson, Arthur B.; Teranishi, Roy; Cary, Paul

1971-01-01

When a human being is placed for several days on a completely defined diet, consisting almost entirely of small molecules that are absorbed from the stomach into the blood, intestinal flora disappear because of lack of nutrition. By this technique, the composition of body fluids can be made constant (standard deviation about 10%) after a few days, permitting significant quantitative analyses to be performed. A method of temperature-programmed gas-liquid partition chromatography has been developed for this purpose. It permits the quantitative determination of about 250 substances in a sample of breath, and of about 280 substances in a sample of urine vapor. The technique should be useful in the application of the principles of orthomolecular medicine. PMID:5289873

clubber: removing the bioinformatics bottleneck in big data analyses.

PubMed

Miller, Maximilian; Zhu, Chengsheng; Bromberg, Yana

2017-06-13

With the advent of modern day high-throughput technologies, the bottleneck in biological discovery has shifted from the cost of doing experiments to that of analyzing results. clubber is our automated cluster-load balancing system developed for optimizing these "big data" analyses. Its plug-and-play framework encourages re-use of existing solutions for bioinformatics problems. clubber's goals are to reduce computation times and to facilitate use of cluster computing. The first goal is achieved by automating the balance of parallel submissions across available high performance computing (HPC) resources. Notably, the latter can be added on demand, including cloud-based resources, and/or featuring heterogeneous environments. The second goal of making HPCs user-friendly is facilitated by an interactive web interface and a RESTful API, allowing for job monitoring and result retrieval. We used clubber to speed up our pipeline for annotating molecular functionality of metagenomes. Here, we analyzed the Deepwater Horizon oil-spill study data to quantitatively show that the beach sands have not yet entirely recovered. Further, our analysis of the CAMI-challenge data revealed that microbiome taxonomic shifts do not necessarily correlate with functional shifts. These examples (21 metagenomes processed in 172 min) clearly illustrate the importance of clubber in the everyday computational biology environment.

clubber: removing the bioinformatics bottleneck in big data analyses

PubMed Central

Miller, Maximilian; Zhu, Chengsheng; Bromberg, Yana

2018-01-01

With the advent of modern day high-throughput technologies, the bottleneck in biological discovery has shifted from the cost of doing experiments to that of analyzing results. clubber is our automated cluster-load balancing system developed for optimizing these “big data” analyses. Its plug-and-play framework encourages re-use of existing solutions for bioinformatics problems. clubber’s goals are to reduce computation times and to facilitate use of cluster computing. The first goal is achieved by automating the balance of parallel submissions across available high performance computing (HPC) resources. Notably, the latter can be added on demand, including cloud-based resources, and/or featuring heterogeneous environments. The second goal of making HPCs user-friendly is facilitated by an interactive web interface and a RESTful API, allowing for job monitoring and result retrieval. We used clubber to speed up our pipeline for annotating molecular functionality of metagenomes. Here, we analyzed the Deepwater Horizon oil-spill study data to quantitatively show that the beach sands have not yet entirely recovered. Further, our analysis of the CAMI-challenge data revealed that microbiome taxonomic shifts do not necessarily correlate with functional shifts. These examples (21 metagenomes processed in 172 min) clearly illustrate the importance of clubber in the everyday computational biology environment. PMID:28609295

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

Quantitative Analyse von Korallengemeinschaften des Sanganeb-Atolls (mittleres Rotes Meer). I. Die Besiedlungsstruktur hydrodynamisch unterschiedlich exponierter Außen- und Innenriffe

NASA Astrophysics Data System (ADS)

Mergner, H.; Schuhmacher, H.

1985-12-01

The Sanganeb-Atoll off Port Sudan is an elongate annular reef which rests on a probably raised block in the fracture zone along the Red Sea-graben. Its gross morphology was most likely formed by subaerial erosion during low sealevel conditions. Features of its topography and hydrography are described. The prevailing wind waves are from NE, Hence, the outer and inner reef slopes are exposed to different hydrodynamic conditions. The sessile benthos was analysed using the quadrat method. Four test quadrats (5×5 m each) were selected on the outer and inner slopes at a depth of 10 m along a SSW-NNE transect across the atoll. Cnidaria were by far the most dominating group; coralline algae, Porifera, Bryozoa and Ascidia, however, counted for just under 3 % living cover. Light and temperature intensities did not differ significantly at the sites studied; water movement, however, decreased in the following order: TQ IV (outer NE side of the reef ring) was exposed to strong swell and surf; TQ II (inner side of the SW-ring) was met by a strong longreef current; TQ I was situated on the outer lee of the SW-atoll ring and TQ III in the inner lee of the NE-side. This hydrodynamic gradient correlates with the composition of the coral communities from predominantly branching Scleractinia (staghorn-like and other Acropora species and Pocillopora) in TQ IV, through a Lobophyllia, Porites and Xenia-dominated community in TQ II, and a mixed community with an increasing percentage of xeniid and alcyoniid soft corals in TQ I, to a community in TQ III which is dominated by the soft corals Sinularia and Dendronephthya. The cnidarian cover ranged between 42.4 and 56.6 % whereby the two exposed test quadrats had a higher living coverage than the protected ones. In total, 2649 colonies comprising 124 species of stony, soft and hydrocorals were recorded by an elaborate method of accurate in-situ mapping. The 90 scleractinian species found include 3 species new to the Red Sea and 11 hitherto

Quantitative force measurements using frequency modulation atomic force microscopy—theoretical foundations

NASA Astrophysics Data System (ADS)

Sader, John E.; Uchihashi, Takayuki; Higgins, Michael J.; Farrell, Alan; Nakayama, Yoshikazu; Jarvis, Suzanne P.

2005-03-01

Use of the atomic force microscope (AFM) in quantitative force measurements inherently requires a theoretical framework enabling conversion of the observed deflection properties of the cantilever to an interaction force. In this paper, the theoretical foundations of using frequency modulation atomic force microscopy (FM-AFM) in quantitative force measurements are examined and rigorously elucidated, with consideration being given to both 'conservative' and 'dissipative' interactions. This includes a detailed discussion of the underlying assumptions involved in such quantitative force measurements, the presentation of globally valid explicit formulae for evaluation of so-called 'conservative' and 'dissipative' forces, discussion of the origin of these forces, and analysis of the applicability of FM-AFM to quantitative force measurements in liquid.

Public and patient involvement in quantitative health research: A statistical perspective.

PubMed

Hannigan, Ailish

2018-06-19

The majority of studies included in recent reviews of impact for public and patient involvement (PPI) in health research had a qualitative design. PPI in solely quantitative designs is underexplored, particularly its impact on statistical analysis. Statisticians in practice have a long history of working in both consultative (indirect) and collaborative (direct) roles in health research, yet their perspective on PPI in quantitative health research has never been explicitly examined. To explore the potential and challenges of PPI from a statistical perspective at distinct stages of quantitative research, that is sampling, measurement and statistical analysis, distinguishing between indirect and direct PPI. Statistical analysis is underpinned by having a representative sample, and a collaborative or direct approach to PPI may help achieve that by supporting access to and increasing participation of under-represented groups in the population. Acknowledging and valuing the role of lay knowledge of the context in statistical analysis and in deciding what variables to measure may support collective learning and advance scientific understanding, as evidenced by the use of participatory modelling in other disciplines. A recurring issue for quantitative researchers, which reflects quantitative sampling methods, is the selection and required number of PPI contributors, and this requires further methodological development. Direct approaches to PPI in quantitative health research may potentially increase its impact, but the facilitation and partnership skills required may require further training for all stakeholders, including statisticians. © 2018 The Authors Health Expectations published by John Wiley & Sons Ltd.

Use of MRI in Differentiation of Papillary Renal Cell Carcinoma Subtypes: Qualitative and Quantitative Analysis.

PubMed

Doshi, Ankur M; Ream, Justin M; Kierans, Andrea S; Bilbily, Matthew; Rusinek, Henry; Huang, William C; Chandarana, Hersh

2016-03-01

The purpose of this study was to determine whether qualitative and quantitative MRI feature analysis is useful for differentiating type 1 from type 2 papillary renal cell carcinoma (PRCC). This retrospective study included 21 type 1 and 17 type 2 PRCCs evaluated with preoperative MRI. Two radiologists independently evaluated various qualitative features, including signal intensity, heterogeneity, and margin. For the quantitative analysis, a radiology fellow and a medical student independently drew 3D volumes of interest over the entire tumor on T2-weighted HASTE images, apparent diffusion coefficient parametric maps, and nephrographic phase contrast-enhanced MR images to derive first-order texture metrics. Qualitative and quantitative features were compared between the groups. For both readers, qualitative features with greater frequency in type 2 PRCC included heterogeneous enhancement, indistinct margin, and T2 heterogeneity (all, p < 0.035). Indistinct margins and heterogeneous enhancement were independent predictors (AUC, 0.822). Quantitative analysis revealed that apparent diffusion coefficient, HASTE, and contrast-enhanced entropy were greater in type 2 PRCC (p < 0.05; AUC, 0.682-0.716). A combined quantitative and qualitative model had an AUC of 0.859. Qualitative features within the model had interreader concordance of 84-95%, and the quantitative data had intraclass coefficients of 0.873-0.961. Qualitative and quantitative features can help discriminate between type 1 and type 2 PRCC. Quantitative analysis may capture useful information that complements the qualitative appearance while benefiting from high interobserver agreement.

MaGelLAn 1.0: a software to facilitate quantitative and population genetic analysis of maternal inheritance by combination of molecular and pedigree information.

PubMed

Ristov, Strahil; Brajkovic, Vladimir; Cubric-Curik, Vlatka; Michieli, Ivan; Curik, Ino

2016-09-10

Identification of genes or even nucleotides that are responsible for quantitative and adaptive trait variation is a difficult task due to the complex interdependence between a large number of genetic and environmental factors. The polymorphism of the mitogenome is one of the factors that can contribute to quantitative trait variation. However, the effects of the mitogenome have not been comprehensively studied, since large numbers of mitogenome sequences and recorded phenotypes are required to reach the adequate power of analysis. Current research in our group focuses on acquiring the necessary mitochondria sequence information and analysing its influence on the phenotype of a quantitative trait. To facilitate these tasks we have produced software for processing pedigrees that is optimised for maternal lineage analysis. We present MaGelLAn 1.0 (maternal genealogy lineage analyser), a suite of four Python scripts (modules) that is designed to facilitate the analysis of the impact of mitogenome polymorphism on quantitative trait variation by combining molecular and pedigree information. MaGelLAn 1.0 is primarily used to: (1) optimise the sampling strategy for molecular analyses; (2) identify and correct pedigree inconsistencies; and (3) identify maternal lineages and assign the corresponding mitogenome sequences to all individuals in the pedigree, this information being used as input to any of the standard software for quantitative genetic (association) analysis. In addition, MaGelLAn 1.0 allows computing the mitogenome (maternal) effective population sizes and probability of mitogenome (maternal) identity that are useful for conservation management of small populations. MaGelLAn is the first tool for pedigree analysis that focuses on quantitative genetic analyses of mitogenome data. It is conceived with the purpose to significantly reduce the effort in handling and preparing large pedigrees for processing the information linked to maternal lines. The software source

Quantitative Silylation Speciations of Primary Phenylalkyl Amines, Including Amphetamine and 3,4-Methylenedioxyamphetamine Prior to Their Analysis by GC/MS.

PubMed

Molnár, Borbála; Fodor, Blanka; Boldizsár, Imre; Molnár-Perl, Ibolya

2015-10-20

A novel, quantitative trimethylsilylation approach derivatizing 11 primary phenylalkyl amines (PPAAs), including amphetamine (A) and 3,4-methylenedioxyamphetamine (MDA), was noted. Triggering the fully derivatized ditrimethylsilyl (diTMS) species with the N-methyl-N-(trimethylsilyl)-trifluoroacetamide (MSTFA) reagent, a new principle was recognized followed by GC/MS. In the course of method optimization, the complementary impact of solvents (acetonitrile, ACN; ethyl acetate, ETAC; pyridine, PYR) and catalysts (trimethylchlorosilane, TMCS; trimethyliodosilane, TMIS) was studied: the role of solvent and catalyst proved to be equally crucial. Optimum, proportional, huge responses were obtained with the MSTFA/PYR = 2/1-9/1 (v/v) reagent applying catalysts; A and MDA needed the TMIS, while the rest of PPAAs provided the diTMS products also with TMCS. Similar to derivatives generated with hexamethyldisilazane and perfluorocarboxylic acid (HMDS and PFCA) ( Molnár et al. Anal. Chem. 2015 , 87 , 848 - 852 ), the fully silylated PPAAs offer several advantages. Both of our methods save time and cost by allowing for direct injection of analytes into the column; this is in stark contrast with the requirement to evaporate acid anhydrides by nitrogen prior to their injection. Efficiences of the novel catalyzed trimethylsilylation (MSTFA) and our recently introduced (now, for A and MDA extended) acylation principle were contrasted. Catalyzed trimethylsilylation led to diTMS derivatives resulting in on average a 1.7 times larger response compared to the corresponding acylated species. Catalyzed trimethylsilylation of PPAAs, A, and MDA were characterized with retention, mass fragmentation, and analytical performance properties (R(2), LOQ values). The practical utility of ditrimethylsilyation was shown by analyzing A in urine and mescaline (MSC) in cactus samples.

Comparative Genomics Analyses Reveal Extensive Chromosome Colinearity and Novel Quantitative Trait Loci in Eucalyptus.

PubMed

Li, Fagen; Zhou, Changpin; Weng, Qijie; Li, Mei; Yu, Xiaoli; Guo, Yong; Wang, Yu; Zhang, Xiaohong; Gan, Siming

2015-01-01

Dense genetic maps, along with quantitative trait loci (QTLs) detected on such maps, are powerful tools for genomics and molecular breeding studies. In the important woody genus Eucalyptus, the recent release of E. grandis genome sequence allows for sequence-based genomic comparison and searching for positional candidate genes within QTL regions. Here, dense genetic maps were constructed for E. urophylla and E. tereticornis using genomic simple sequence repeats (SSR), expressed sequence tag (EST) derived SSR, EST-derived cleaved amplified polymorphic sequence (EST-CAPS), and diversity arrays technology (DArT) markers. The E. urophylla and E. tereticornis maps comprised 700 and 585 markers across 11 linkage groups, totaling at 1,208.2 and 1,241.4 cM in length, respectively. Extensive synteny and colinearity were observed as compared to three earlier DArT-based eucalypt maps (two maps with E. grandis × E. urophylla and one map of E. globulus) and with the E. grandis genome sequence. Fifty-three QTLs for growth (10-56 months of age) and wood density (56 months) were identified in 22 discrete regions on both maps, in which only one colocalizaiton was found between growth and wood density. Novel QTLs were revealed as compared with those previously detected on DArT-based maps for similar ages in Eucalyptus. Eleven to 585 positional candidate genes were obained for a 56-month-old QTL through aligning QTL confidence interval with the E. grandis genome. These results will assist in comparative genomics studies, targeted gene characterization, and marker-assisted selection in Eucalyptus and the related taxa.

Comparative Genomics Analyses Reveal Extensive Chromosome Colinearity and Novel Quantitative Trait Loci in Eucalyptus

PubMed Central

Weng, Qijie; Li, Mei; Yu, Xiaoli; Guo, Yong; Wang, Yu; Zhang, Xiaohong; Gan, Siming

2015-01-01

Dense genetic maps, along with quantitative trait loci (QTLs) detected on such maps, are powerful tools for genomics and molecular breeding studies. In the important woody genus Eucalyptus, the recent release of E. grandis genome sequence allows for sequence-based genomic comparison and searching for positional candidate genes within QTL regions. Here, dense genetic maps were constructed for E. urophylla and E. tereticornis using genomic simple sequence repeats (SSR), expressed sequence tag (EST) derived SSR, EST-derived cleaved amplified polymorphic sequence (EST-CAPS), and diversity arrays technology (DArT) markers. The E. urophylla and E. tereticornis maps comprised 700 and 585 markers across 11 linkage groups, totaling at 1,208.2 and 1,241.4 cM in length, respectively. Extensive synteny and colinearity were observed as compared to three earlier DArT-based eucalypt maps (two maps with E. grandis × E. urophylla and one map of E. globulus) and with the E. grandis genome sequence. Fifty-three QTLs for growth (10–56 months of age) and wood density (56 months) were identified in 22 discrete regions on both maps, in which only one colocalizaiton was found between growth and wood density. Novel QTLs were revealed as compared with those previously detected on DArT-based maps for similar ages in Eucalyptus. Eleven to 585 positional candidate genes were obained for a 56-month-old QTL through aligning QTL confidence interval with the E. grandis genome. These results will assist in comparative genomics studies, targeted gene characterization, and marker-assisted selection in Eucalyptus and the related taxa. PMID:26695430

On-Going Laboratory Efforts to Quantitatively Address Clay Abundance on Mars

NASA Technical Reports Server (NTRS)

Roush, Ted L.; Bishop, Janice L.; Brown, Adrian J.; Blake, David F.; Bristow, Thomas F.

2012-01-01

Data obtained at visible and near-infrared wavelengths by OMEGA on MarsExpress and CRISM on MRO provide definitive evidence for the presence of phyllosilicates and other hydrated phases on Mars. A diverse range of both Fe/Mg-OH and Al-OH-bearing phyllosilicates were identified including the smectites, nontronite, saponite, and montmorillonite. In order to constrain the abundances of these phyllosilicates spectral analyses of mixtures are needed. We report on our on-going effort to enable the quantitative evaluation of the abundance of hydrated-hydroxylated silicates when they are contained in mixtures. We include two component mixtures of hydrated/hydroxylated silicates with each other and with two analogs for other martian materials; pyroxene (enstatite) and palagonitic soil (an alteration product of basaltic glass). For the hydrated-hydroxylated silicates we include saponite and montmorillonite (Mg- and Al- rich smectites). We prepared three size separates of each end-member for study: 20-45, 63-90, and 125-150 µm. As the second phase of our effort we used scanning electron microscopy imaging and x-ray diffraction to characterize the grain size distribution, and structural nature, respectively, of the mixtures. Visible and near-infrared reflectance spectra of the 63-90 micrometers grain size of the mixture samples are shown in Figure 1. We discuss the results of our measurements of these mixtures.

Reproducibility and quantitation of amplicon sequencing-based detection

PubMed Central

Zhou, Jizhong; Wu, Liyou; Deng, Ye; Zhi, Xiaoyang; Jiang, Yi-Huei; Tu, Qichao; Xie, Jianping; Van Nostrand, Joy D; He, Zhili; Yang, Yunfeng

2011-01-01

To determine the reproducibility and quantitation of the amplicon sequencing-based detection approach for analyzing microbial community structure, a total of 24 microbial communities from a long-term global change experimental site were examined. Genomic DNA obtained from each community was used to amplify 16S rRNA genes with two or three barcode tags as technical replicates in the presence of a small quantity (0.1% wt/wt) of genomic DNA from Shewanella oneidensis MR-1 as the control. The technical reproducibility of the amplicon sequencing-based detection approach is quite low, with an average operational taxonomic unit (OTU) overlap of 17.2%±2.3% between two technical replicates, and 8.2%±2.3% among three technical replicates, which is most likely due to problems associated with random sampling processes. Such variations in technical replicates could have substantial effects on estimating β-diversity but less on α-diversity. A high variation was also observed in the control across different samples (for example, 66.7-fold for the forward primer), suggesting that the amplicon sequencing-based detection approach could not be quantitative. In addition, various strategies were examined to improve the comparability of amplicon sequencing data, such as increasing biological replicates, and removing singleton sequences and less-representative OTUs across biological replicates. Finally, as expected, various statistical analyses with preprocessed experimental data revealed clear differences in the composition and structure of microbial communities between warming and non-warming, or between clipping and non-clipping. Taken together, these results suggest that amplicon sequencing-based detection is useful in analyzing microbial community structure even though it is not reproducible and quantitative. However, great caution should be taken in experimental design and data interpretation when the amplicon sequencing-based detection approach is used for quantitative

Reduced short term memory in congenital adrenal hyperplasia (CAH) and its relationship to spatial and quantitative performance.

PubMed

Collaer, Marcia L; Hindmarsh, Peter C; Pasterski, Vickie; Fane, Briony A; Hines, Melissa

2016-02-01

Girls and women with classical congenital adrenal hyperplasia (CAH) experience elevated androgens prenatally and show increased male-typical development for certain behaviors. Further, individuals with CAH receive glucocorticoid (GC) treatment postnatally, and this GC treatment could have negative cognitive consequences. We investigated two alternative hypotheses, that: (a) early androgen exposure in females with CAH masculinizes (improves) spatial perception and quantitative abilities at which males typically outperform females, or (b) CAH is associated with performance decrements in these domains, perhaps due to reduced short-term-memory (STM). Adolescent and adult individuals with CAH (40 female and 29 male) were compared with relative controls (29 female and 30 male) on spatial perception and quantitative abilities as well as on Digit Span (DS) to assess STM and on Vocabulary to assess general intelligence. Females with CAH did not perform better (more male-typical) on spatial perception or quantitative abilities than control females, failing to support the hypothesis of cognitive masculinization. Rather, in the sample as a whole individuals with CAH scored lower on spatial perception (p ≤ .009), a quantitative composite (p ≤ .036), and DS (p ≤ .001), despite no differences in general intelligence. Separate analyses of adolescent and adult participants suggested the spatial and quantitative effects might be present only in adult patients with CAH; however, reduced DS performance was found in patients with CAH regardless of age group. Separate regression analyses showed that DS predicted both spatial perception and quantitative performance (both p ≤ .001), when age, sex, and diagnosis status were controlled. Thus, reduced STM in CAH patients versus controls may have more general cognitive consequences, potentially reducing spatial perception and quantitative skills. Although hyponatremia or other aspects of salt-wasting crises or additional hormone

Qualitative, semi-quantitative, and quantitative simulation of the osmoregulation system in yeast

PubMed Central

Pang, Wei; Coghill, George M.

2015-01-01

In this paper we demonstrate how Morven, a computational framework which can perform qualitative, semi-quantitative, and quantitative simulation of dynamical systems using the same model formalism, is applied to study the osmotic stress response pathway in yeast. First the Morven framework itself is briefly introduced in terms of the model formalism employed and output format. We then built a qualitative model for the biophysical process of the osmoregulation in yeast, and a global qualitative-level picture was obtained through qualitative simulation of this model. Furthermore, we constructed a Morven model based on existing quantitative model of the osmoregulation system. This model was then simulated qualitatively, semi-quantitatively, and quantitatively. The obtained simulation results are presented with an analysis. Finally the future development of the Morven framework for modelling the dynamic biological systems is discussed. PMID:25864377

Rigour in quantitative research.

PubMed

Claydon, Leica Sarah

2015-07-22

This article which forms part of the research series addresses scientific rigour in quantitative research. It explores the basis and use of quantitative research and the nature of scientific rigour. It examines how the reader may determine whether quantitative research results are accurate, the questions that should be asked to determine accuracy and the checklists that may be used in this process. Quantitative research has advantages in nursing, since it can provide numerical data to help answer questions encountered in everyday practice.

Quantitative Analyses about Market- and Prevalence-Based Needs for Adapted Physical Education Teachers in the Public Schools in the United States

ERIC Educational Resources Information Center

Zhang, Jiabei

2011-01-01

The purpose of this study was to analyze quantitative needs for more adapted physical education (APE) teachers based on both market- and prevalence-based models. The market-based need for more APE teachers was examined based on APE teacher positions funded, while the prevalence-based need for additional APE teachers was analyzed based on students…

DNA DAMAGE QUANTITATION BY ALKALINE GEL ELECTROPHORESIS.

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

SUTHERLAND,B.M.; BENNETT,P.V.; SUTHERLAND, J.C.

2004-03-24

Physical and chemical agents in the environment, those used in clinical applications, or encountered during recreational exposures to sunlight, induce damages in DNA. Understanding the biological impact of these agents requires quantitation of the levels of such damages in laboratory test systems as well as in field or clinical samples. Alkaline gel electrophoresis provides a sensitive (down to {approx} a few lesions/5Mb), rapid method of direct quantitation of a wide variety of DNA damages in nanogram quantities of non-radioactive DNAs from laboratory, field, or clinical specimens, including higher plants and animals. This method stems from velocity sedimentation studies of DNAmore » populations, and from the simple methods of agarose gel electrophoresis. Our laboratories have developed quantitative agarose gel methods, analytical descriptions of DNA migration during electrophoresis on agarose gels (1-6), and electronic imaging for accurate determinations of DNA mass (7-9). Although all these components improve sensitivity and throughput of large numbers of samples (7,8,10), a simple version using only standard molecular biology equipment allows routine analysis of DNA damages at moderate frequencies. We present here a description of the methods, as well as a brief description of the underlying principles, required for a simplified approach to quantitation of DNA damages by alkaline gel electrophoresis.« less

The Effects of Intravenous Immunoglobulins in Women with Recurrent Miscarriages: A Systematic Review of Randomised Trials with Meta-Analyses and Trial Sequential Analyses Including Individual Patient Data.

PubMed

Egerup, Pia; Lindschou, Jane; Gluud, Christian; Christiansen, Ole Bjarne

2015-01-01

Immunological disturbances are hypothesised to play a role in recurrent miscarriage (RM) and therefore intravenous immunoglubulins (IVIg) have been tested in RM patients. The objectives were to investigate the benefits and harms of IVIg versus placebo, no intervention, or treatment as usual in women with RM. We searched the published literature in all relevant databases. Randomised trials investigating IVIg versus placebo, no intervention, or treatment as usual in women with RM. We undertook meta-analyses of aggregated data and individual patient data using a two-step approach, and we conducted bias domain assessments and trial sequential analyses to assess the risks of systematic and random errors. We identified 11 randomised clinical trials. No significant difference in the frequency of no live birth was found when IVIg was compared with placebo or treatment as usual (RR 0.92, 95% CI 0.75-1.12, p = 0.42). Trial sequential analysis showed that the required information size of 1,008 participants was not obtained. IVIg compared with placebo seems to increase the risk of adverse events. Subgroup analysis suggests that women with RM after a birth (secondary RM) seemed most likely to obtain a potential beneficial effect of IVIg (RR for no live birth 0.77, 95%CI 0.58-1.02, p = 0.06), however, trial sequential analysis showed that insufficient information is presently accrued. We cannot recommend or refute IVIg in women with RM. IVIg should therefore be assessed in further randomised clinical trials with positive outcomes before any clinical use is considered.

Revisiting the Quantitative-Qualitative Debate: Implications for Mixed-Methods Research

PubMed Central

SALE, JOANNA E. M.; LOHFELD, LYNNE H.; BRAZIL, KEVIN

2015-01-01

Health care research includes many studies that combine quantitative and qualitative methods. In this paper, we revisit the quantitative-qualitative debate and review the arguments for and against using mixed-methods. In addition, we discuss the implications stemming from our view, that the paradigms upon which the methods are based have a different view of reality and therefore a different view of the phenomenon under study. Because the two paradigms do not study the same phenomena, quantitative and qualitative methods cannot be combined for cross-validation or triangulation purposes. However, they can be combined for complementary purposes. Future standards for mixed-methods research should clearly reflect this recommendation. PMID:26523073

Overlapping meta-analyses on the same topic: survey of published studies.

PubMed

Siontis, Konstantinos C; Hernandez-Boussard, Tina; Ioannidis, John P A

2013-07-19

To assess how common it is to have multiple overlapping meta-analyses of randomized trials published on the same topic. Survey of published meta-analyses. PubMed. Meta-analyses published in 2010 were identified, and 5% of them were randomly selected. We further selected those that included randomized trials and examined effectiveness of any medical intervention. For eligible meta-analyses, we searched for other meta-analyses on the same topic (covering the same comparisons, indications/settings, and outcomes or overlapping subsets of them) published until February 2013. Of 73 eligible meta-analyses published in 2010, 49 (67%) had at least one other overlapping meta-analysis (median two meta-analyses per topic, interquartile range 1-4, maximum 13). In 17 topics at least one author was involved in at least two of the overlapping meta-analyses. No characteristics of the index meta-analyses were associated with the potential for overlapping meta-analyses. Among pairs of overlapping meta-analyses in 20 randomly selected topics, 13 of the more recent meta-analyses did not include any additional outcomes. In three of the four topics with eight or more published meta-analyses, many meta-analyses examined only a subset of the eligible interventions or indications/settings covered by the index meta-analysis. Conversely, for statins in the prevention of atrial fibrillation after cardiac surgery, 11 meta-analyses were published with similar eligibility criteria for interventions and setting: there was still variability on which studies were included, but the results were always similar or even identical across meta-analyses. While some independent replication of meta-analyses by different teams is possibly useful, the overall picture suggests that there is a waste of efforts with many topics covered by multiple overlapping meta-analyses.

Quantitative Measures of Immersion in Cloud and the Biogeography of Cloud Forests

NASA Technical Reports Server (NTRS)

Lawton, R. O.; Nair, U. S.; Ray, D.; Regmi, A.; Pounds, J. A.; Welch, R. M.

2010-01-01

Sites described as tropical montane cloud forests differ greatly, in part because observers tend to differ in their opinion as to what constitutes frequent and prolonged immersion in cloud. This definitional difficulty interferes with hydrologic analyses, assessments of environmental impacts on ecosystems, and biogeographical analyses of cloud forest communities and species. Quantitative measurements of cloud immersion can be obtained on site, but the observations are necessarily spatially limited, although well-placed observers can examine 10 50 km of a mountain range under rainless conditions. Regional analyses, however, require observations at a broader scale. This chapter discusses remote sensing and modeling approaches that can provide quantitative measures of the spatiotemporal patterns of cloud cover and cloud immersion in tropical mountain ranges. These approaches integrate remote sensing tools of various spatial resolutions and frequencies of observation, digital elevation models, regional atmospheric models, and ground-based observations to provide measures of cloud cover, cloud base height, and the intersection of cloud and terrain. This combined approach was applied to the Monteverde region of northern Costa Rica to illustrate how the proportion of time the forest is immersed in cloud may vary spatially and temporally. The observed spatial variation was largely due to patterns of airflow over the mountains. The temporal variation reflected the diurnal rise and fall of the orographic cloud base, which was influenced in turn by synoptic weather conditions, the seasonal movement of the Intertropical Convergence Zone and the north-easterly trade winds. Knowledge of the proportion of the time that sites are immersed in clouds should facilitate ecological comparisons and biogeographical analyses, as well as land use planning and hydrologic assessments in areas where intensive on-site work is not feasible.

Diagnostic accuracy of semi-quantitative and quantitative culture techniques for the diagnosis of catheter-related infections in newborns and molecular typing of isolated microorganisms.

PubMed

Riboli, Danilo Flávio Moraes; Lyra, João César; Silva, Eliane Pessoa; Valadão, Luisa Leite; Bentlin, Maria Regina; Corrente, José Eduardo; Rugolo, Ligia Maria Suppo de Souza; da Cunha, Maria de Lourdes Ribeiro de Souza

2014-05-22

Catheter-related bloodstream infections (CR-BSIs) have become the most common cause of healthcare-associated bloodstream infections in neonatal intensive care units (ICUs). Microbiological evidence implicating catheters as the source of bloodstream infection is necessary to establish the diagnosis of CR-BSIs. Semi-quantitative culture is used to determine the presence of microorganisms on the external catheter surface, whereas quantitative culture also isolates microorganisms present inside the catheter. The main objective of this study was to determine the sensitivity and specificity of these two techniques for the diagnosis of CR-BSIs in newborns from a neonatal ICU. In addition, PFGE was used for similarity analysis of the microorganisms isolated from catheters and blood cultures. Semi-quantitative and quantitative methods were used for the culture of catheter tips obtained from newborns. Strains isolated from catheter tips and blood cultures which exhibited the same antimicrobial susceptibility profile were included in the study as positive cases of CR-BSI. PFGE of the microorganisms isolated from catheters and blood cultures was performed for similarity analysis and detection of clones in the ICU. A total of 584 catheter tips from 399 patients seen between November 2005 and June 2012 were analyzed. Twenty-nine cases of CR-BSI were confirmed. Coagulase-negative staphylococci (CoNS) were the most frequently isolated microorganisms, including S. epidermidis as the most prevalent species (65.5%), followed by S. haemolyticus (10.3%), yeasts (10.3%), K. pneumoniae (6.9%), S. aureus (3.4%), and E. coli (3.4%). The sensitivity of the semi-quantitative and quantitative techniques was 72.7% and 59.3%, respectively, and specificity was 95.7% and 94.4%. The diagnosis of CR-BSIs based on PFGE analysis of similarity between strains isolated from catheter tips and blood cultures showed 82.6% sensitivity and 100% specificity. The semi-quantitative culture method showed higher

Critical Quantitative Inquiry in Context

ERIC Educational Resources Information Center

Stage, Frances K.; Wells, Ryan S.

2014-01-01

This chapter briefly traces the development of the concept of critical quantitative inquiry, provides an expanded conceptualization of the tasks of critical quantitative research, offers theoretical explanation and justification for critical research using quantitative methods, and previews the work of quantitative criticalists presented in this…

Identification of Mediator Kinase Substrates in Human Cells using Cortistatin A and Quantitative Phosphoproteomics.

PubMed

Poss, Zachary C; Ebmeier, Christopher C; Odell, Aaron T; Tangpeerachaikul, Anupong; Lee, Thomas; Pelish, Henry E; Shair, Matthew D; Dowell, Robin D; Old, William M; Taatjes, Dylan J

2016-04-12

Cortistatin A (CA) is a highly selective inhibitor of the Mediator kinases CDK8 and CDK19. Using CA, we now report a large-scale identification of Mediator kinase substrates in human cells (HCT116). We identified over 16,000 quantified phosphosites including 78 high-confidence Mediator kinase targets within 64 proteins, including DNA-binding transcription factors and proteins associated with chromatin, DNA repair, and RNA polymerase II. Although RNA-seq data correlated with Mediator kinase targets, the effects of CA on gene expression were limited and distinct from CDK8 or CDK19 knockdown. Quantitative proteome analyses, tracking around 7,000 proteins across six time points (0-24 hr), revealed that CA selectively affected pathways implicated in inflammation, growth, and metabolic regulation. Contrary to expectations, increased turnover of Mediator kinase targets was not generally observed. Collectively, these data support Mediator kinases as regulators of chromatin and RNA polymerase II activity and suggest their roles extend beyond transcription to metabolism and DNA repair. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Vibrational algorithms for quantitative crystallographic analyses of hydroxyapatite-based biomaterials: II, application to decayed human teeth.

PubMed

Adachi, Tetsuya; Pezzotti, Giuseppe; Yamamoto, Toshiro; Ichioka, Hiroaki; Boffelli, Marco; Zhu, Wenliang; Kanamura, Narisato

2015-05-01

A systematic investigation, based on highly spectrally resolved Raman spectroscopy, was undertaken to research the efficacy of vibrational assessments in locating chemical and crystallographic fingerprints for the characterization of dental caries and the early detection of non-cavitated carious lesions. Raman results published by other authors have indicated possible approaches for this method. However, they conspicuously lacked physical insight at the molecular scale and, thus, the rigor necessary to prove the efficacy of this spectroscopy method. After solving basic physical challenges in a companion paper, we apply them here in the form of newly developed Raman algorithms for practical dental research. Relevant differences in mineral crystallite (average) orientation and texture distribution were revealed for diseased enamel at different stages compared with healthy mineralized enamel. Clear spectroscopy features could be directly translated in terms of a rigorous and quantitative classification of crystallography and chemical characteristics of diseased enamel structures. The Raman procedure enabled us to trace back otherwise invisible characteristics in early caries, in the translucent zone (i.e., the advancing front of the disease) and in the body of lesion of cavitated caries.

Non-manipulation quantitative designs.

PubMed

Rumrill, Phillip D

2004-01-01

The article describes non-manipulation quantitative designs of two types, correlational and causal comparative studies. Both of these designs are characterized by the absence of random assignment of research participants to conditions or groups and non-manipulation of the independent variable. Without random selection or manipulation of the independent variable, no attempt is made to draw causal inferences regarding relationships between independent and dependent variables. Nonetheless, non-manipulation studies play an important role in rehabilitation research, as described in this article. Examples from the contemporary rehabilitation literature are included. Copyright 2004 IOS Press

Qualitative, semi-quantitative, and quantitative simulation of the osmoregulation system in yeast.

PubMed

Pang, Wei; Coghill, George M

2015-05-01

In this paper we demonstrate how Morven, a computational framework which can perform qualitative, semi-quantitative, and quantitative simulation of dynamical systems using the same model formalism, is applied to study the osmotic stress response pathway in yeast. First the Morven framework itself is briefly introduced in terms of the model formalism employed and output format. We then built a qualitative model for the biophysical process of the osmoregulation in yeast, and a global qualitative-level picture was obtained through qualitative simulation of this model. Furthermore, we constructed a Morven model based on existing quantitative model of the osmoregulation system. This model was then simulated qualitatively, semi-quantitatively, and quantitatively. The obtained simulation results are presented with an analysis. Finally the future development of the Morven framework for modelling the dynamic biological systems is discussed. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Quantitative Ultrasound for Nondestructive Characterization of Engineered Tissues and Biomaterials

PubMed Central

Dalecki, Diane; Mercado, Karla P.; Hocking, Denise C.

2015-01-01

Non-invasive, non-destructive technologies for imaging and quantitatively monitoring the development of artificial tissues are critical for the advancement of tissue engineering. Current standard techniques for evaluating engineered tissues, including histology, biochemical assays and mechanical testing, are destructive approaches. Ultrasound is emerging as a valuable tool for imaging and quantitatively monitoring the properties of engineered tissues and biomaterials longitudinally during fabrication and post-implantation. Ultrasound techniques are rapid, non-invasive, non-destructive and can be easily integrated into sterile environments necessary for tissue engineering. Furthermore, high-frequency quantitative ultrasound techniques can enable volumetric characterization of the structural, biological, and mechanical properties of engineered tissues during fabrication and post-implantation. This review provides an overview of ultrasound imaging, quantitative ultrasound techniques, and elastography, with representative examples of applications of these ultrasound-based techniques to the field of tissue engineering. PMID:26581347

Quantitative dispersion microscopy

PubMed Central

Fu, Dan; Choi, Wonshik; Sung, Yongjin; Yaqoob, Zahid; Dasari, Ramachandra R.; Feld, Michael

2010-01-01

Refractive index dispersion is an intrinsic optical property and a useful source of contrast in biological imaging studies. In this report, we present the first dispersion phase imaging of living eukaryotic cells. We have developed quantitative dispersion microscopy based on the principle of quantitative phase microscopy. The dual-wavelength quantitative phase microscope makes phase measurements at 310 nm and 400 nm wavelengths to quantify dispersion (refractive index increment ratio) of live cells. The measured dispersion of living HeLa cells is found to be around 1.088, which agrees well with that measured directly for protein solutions using total internal reflection. This technique, together with the dry mass and morphology measurements provided by quantitative phase microscopy, could prove to be a useful tool for distinguishing different types of biomaterials and studying spatial inhomogeneities of biological samples. PMID:21113234

Structural Brain Anomalies and Chronic Pain: A Quantitative Meta-Analysis of Gray Matter Volume

PubMed Central

Smallwood, Rachel F.; Laird, Angela R.; Ramage, Amy E.; Parkinson, Amy L.; Lewis, Jeffrey; Clauw, Daniel J.; Williams, David A.; Schmidt-Wilcke, Tobias; Farrell, Michael J.; Eickhoff, Simon B.; Robin, Donald A.

2016-01-01

The diversity of chronic pain syndromes and the methods employed to study them make integrating experimental findings challenging. This study performed coordinate-based meta-analyses using voxel-based morphometry imaging results to examine gray matter volume (GMV) differences between chronic pain patients and healthy controls. There were 12 clusters where GMV was decreased in patients compared with controls, including many regions thought to be part of the “pain matrix” of regions involved in pain perception, but also including many other regions that are not commonly regarded as pain-processing areas. The right hippocampus and parahippocampal gyrus were the only regions noted to have increased GMV in patients. Functional characterizations were implemented using the BrainMap database to determine which behavioral domains were significantly represented in these regions. The most common behavioral domains associated with these regions were cognitive, affective, and perceptual domains. Because many of these regions are not classically connected with pain and because there was such significance in functionality outside of perception, it is proposed that many of these regions are related to the constellation of comorbidities of chronic pain, such as fatigue and cognitive and emotional impairments. Further research into the mechanisms of GMV changes could provide a perspective on these findings. Perspective Quantitative meta-analyses revealed structural differences between brains of individuals with chronic pain and healthy controls. These differences may be related to comorbidities of chronic pain. PMID:23685185

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

PubMed

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

2014-01-01

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

IWGT report on quantitative approaches to genotoxicity risk ...

EPA Pesticide Factsheets

This is the second of two reports from the International Workshops on Genotoxicity Testing (IWGT) Working Group on Quantitative Approaches to Genetic Toxicology Risk Assessment (the QWG). The first report summarized the discussions and recommendations of the QWG related to the need for quantitative dose–response analysis of genetic toxicology data, the existence and appropriate evaluation of threshold responses, and methods to analyze exposure-response relationships and derive points of departure (PoDs) from which acceptable exposure levels could be determined. This report summarizes the QWG discussions and recommendations regarding appropriate approaches to evaluate exposure-related risks of genotoxic damage, including extrapolation below identified PoDs and across test systems and species. Recommendations include the selection of appropriate genetic endpoints and target tissues, uncertainty factors and extrapolation methods to be considered, the importance and use of information on mode of action, toxicokinetics, metabolism, and exposure biomarkers when using quantitative exposure-response data to determine acceptable exposure levels in human populations or to assess the risk associated with known or anticipated exposures. The empirical relationship between genetic damage (mutation and chromosomal aberration) and cancer in animal models was also examined. It was concluded that there is a general correlation between cancer induction and mutagenic and/or clast

Implementing online quantitative support modules in an intermediate-level course

NASA Astrophysics Data System (ADS)

Daly, J.

2011-12-01

While instructors typically anticipate that students in introductory geology courses enter a class with a wide range of quantitative ability, we often overlook the fact that this may also be true in upper-level courses. Some students are drawn to the subject and experience success in early courses with an emphasis on descriptive geology, then experience frustration and disappointment in mid- and upper-level courses that are more quantitative. To bolster student confidence in quantitative skills and enhance their performance in an upper-level course, I implemented several modules from The Math You Need (TMYN) online resource with a 200-level geomorphology class. Student facility with basic quantitative skills (rearranging equations, manipulating units, and graphing) was assessed with an online pre- and post-test. During the semester, modules were assigned to complement existing course activities (for example, the module on manipulating units was assigned prior to a lab on measurement of channel area and water velocity, then calculation of discharge). The implementation was designed to be a concise review of relevant skills for students with higher confidence in their quantitative abilities, and to provide a self-paced opportunity for students with less quantitative facility to build skills. This course already includes a strong emphasis on quantitative data collection, analysis, and presentation; in the past, student performance in the course has been strongly influenced by their individual quantitative ability. I anticipate that giving students the opportunity to improve mastery of fundamental quantitative skills will improve their performance on higher-stakes assignments and exams, and will enhance their sense of accomplishment in the course.

Quantitative relation between intermolecular and intramolecular binding of pro-rich peptides to SH3 domains.

PubMed

Zhou, Huan-Xiang

2006-11-01

Flexible linkers are often found to tether binding sequence motifs or connect protein domains. Here we analyze three usages of flexible linkers: 1), intramolecular binding of proline-rich peptides (PRPs) to SH3 domains for kinase regulation; 2), intramolecular binding of PRP for increasing the folding stability of SH3 domains; and 3), covalent linking of PRPs and other ligands for high-affinity bivalent binding. The basis of these analyses is a quantitative relation between intermolecular and intramolecular binding constants. This relation has the form K(i) = K(e0)p for intramolecular binding and K(e) = K(e01)K(e02)p for bivalent binding. The effective concentration p depends on the length of the linker and the distance between the linker attachment points in the bound state. Several applications illustrate the usefulness of the quantitative relation. These include intramolecular binding to the Itk SH3 domain by an internal PRP and to a circular permutant of the alpha-spectrin SH3 domain by a designed PRP, and bivalent binding to the two SH3 domains of Grb2 by two linked PRPs. These and other examples suggest that flexible linkers and sequence motifs tethered to them, like folded protein domains, are also subject to tight control during evolution.

Quantitative Investigation of Protein-Nucleic Acid Interactions by Biosensor Surface Plasmon Resonance.

PubMed

Wang, Shuo; Poon, Gregory M K; Wilson, W David

2015-01-01

Biosensor-surface plasmon resonance (SPR) technology has emerged as a powerful label-free approach for the study of nucleic acid interactions in real time. The method provides simultaneous equilibrium and kinetic characterization for biomolecular interactions with low sample requirements and without the need for external probes. A detailed and practical guide for protein-DNA interaction analyses using biosensor-SPR methods is presented. Details of SPR technology and basic fundamentals are described with recommendations on the preparation of the SPR instrument, sensor chips and samples, experimental design, quantitative and qualitative data analyses and presentation. A specific example of the interaction of a transcription factor with DNA is provided with results evaluated by both kinetic and steady-state SPR methods.

Quantitative risk assessment system (QRAS)

NASA Technical Reports Server (NTRS)

Tan, Zhibin (Inventor); Mosleh, Ali (Inventor); Weinstock, Robert M (Inventor); Smidts, Carol S (Inventor); Chang, Yung-Hsien (Inventor); Groen, Francisco J (Inventor); Swaminathan, Sankaran (Inventor)

2001-01-01

A quantitative risk assessment system (QRAS) builds a risk model of a system for which risk of failure is being assessed, then analyzes the risk of the system corresponding to the risk model. The QRAS performs sensitivity analysis of the risk model by altering fundamental components and quantifications built into the risk model, then re-analyzes the risk of the system using the modifications. More particularly, the risk model is built by building a hierarchy, creating a mission timeline, quantifying failure modes, and building/editing event sequence diagrams. Multiplicities, dependencies, and redundancies of the system are included in the risk model. For analysis runs, a fixed baseline is first constructed and stored. This baseline contains the lowest level scenarios, preserved in event tree structure. The analysis runs, at any level of the hierarchy and below, access this baseline for risk quantitative computation as well as ranking of particular risks. A standalone Tool Box capability exists, allowing the user to store application programs within QRAS.

Spent lead-acid battery recycling in China - A review and sustainable analyses on mass flow of lead.

PubMed

Sun, Zhi; Cao, Hongbin; Zhang, Xihua; Lin, Xiao; Zheng, Wenwen; Cao, Guoqing; Sun, Yong; Zhang, Yi

2017-06-01

Lead is classified to be one of the top heavy metal pollutants in China. The corresponding environmental issues especially during the management of spent lead-acid battery have already caused significant public awareness and concern. This research gives a brief overview on the recycling situation based on an investigation of the lead industry in China and also the development of technologies for spent lead-acid batteries. The main principles and research focuses of different technologies including pyrometallurgy, hydrometallurgy and greener technologies are summarized and compared. Subsequently, the circulability of lead based on the entire life cycle analyses of lead-acid battery is calculated. By considering different recycling schemes, the recycling situation of spent lead-acid battery in China can be understood semi-quantitatively. According to this research, 30% of the primary lead production can be shut down that the lead production can still ensure consecutive life cycle operation of lead-acid battery, if proper management of the spent lead-acid battery is implemented according to current lead industry situation in China. This research provides a methodology on the view of lead circulability in the whole life cycle of a specific product and is aiming to contribute more quantitative guidelines for efficient organization of lead industry in China. Copyright © 2017 Elsevier Ltd. All rights reserved.

Seniors' Online Communities: A Quantitative Content Analysis

ERIC Educational Resources Information Center

Nimrod, Galit

2010-01-01

Purpose: To examine the contents and characteristics of seniors' online communities and to explore their potential benefits to older adults. Design and Methods: Quantitative content analysis of a full year's data from 14 leading online communities using a novel computerized system. The overall database included 686,283 messages. Results: There was…

QUEST‐RA: quantitative clinical assessment of patients with rheumatoid arthritis seen in standard rheumatology care in 15 countries

PubMed Central

Sokka, Tuulikki; Kautiainen, Hannu; Toloza, Sergio; Mäkinen, Heidi; Verstappen, Suzan M M; Hetland, Merete Lund; Naranjo, Antonio; Baecklund, Eva; Herborn, Gertraud; Rau, Rolf; Cazzato, Massimiliano; Gossec, Laure; Skakic, Vlado; Gogus, Feride; Sierakowski, Stanislaw; Bresnihan, Barry; Taylor, Peter; McClinton, Catherine; Pincus, Theodore

2007-01-01

Objective To conduct a cross‐sectional review of non‐selected consecutive outpatients with rheumatoid arthritis (RA) as part of standard clinical care in 15 countries for an overview of the characteristics of patients with RA. Methods The review included current disease activity using data from clinical assessment and a patient self‐report questionnaire, which was translated into each language. Data on demographic, disease and treatment‐related variables were collected and analysed using descriptive statistics. Variation in disease activity on DAS28 (disease activity score on 28‐joint count) within and between countries was graphically analysed. A median regression model was applied to analyse differences in disease activity between countries. Results Between January 2005 and October 2006, the QUEST‐RA (Quantitative Patient Questionnaires in Standard Monitoring of Patients with Rheumatoid Arthritis) project included 4363 patients from 48 sites in 15 countries; 78% were female, >90% Caucasian, mean age was 57 years and mean disease duration was 11.5 years. More than 80% of patients had been treated with methotrexate in all but three countries. Overall, patients had an active disease with a median DAS28 of 4.0, with a significant variation between countries (p<0.001). Among 42 sites with >50 patients included, low disease activity of DAS28 ⩽3.2 was found in the majority of patients in seven sites in five countries; in eight sites in five other countries, >50% of patients had high disease activity of DAS28 >5.1. Conclusions This international multicentre cross‐sectional database provides an overview of clinical status and treatments of patients with RA in standard clinical care in 2005–6 including countries that are infrequently involved in clinical research projects. PMID:17412740

Journal article reporting standards for quantitative research in psychology: The APA Publications and Communications Board task force report.

PubMed

Appelbaum, Mark; Cooper, Harris; Kline, Rex B; Mayo-Wilson, Evan; Nezu, Arthur M; Rao, Stephen M

2018-01-01

Following a review of extant reporting standards for scientific publication, and reviewing 10 years of experience since publication of the first set of reporting standards by the American Psychological Association (APA; APA Publications and Communications Board Working Group on Journal Article Reporting Standards, 2008), the APA Working Group on Quantitative Research Reporting Standards recommended some modifications to the original standards. Examples of modifications include division of hypotheses, analyses, and conclusions into 3 groupings (primary, secondary, and exploratory) and some changes to the section on meta-analysis. Several new modules are included that report standards for observational studies, clinical trials, longitudinal studies, replication studies, and N-of-1 studies. In addition, standards for analytic methods with unique characteristics and output (structural equation modeling and Bayesian analysis) are included. These proposals were accepted by the Publications and Communications Board of APA and supersede the standards included in the 6th edition of the Publication Manual of the American Psychological Association (APA, 2010). (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Multicenter Evaluation of a Commercial Cytomegalovirus Quantitative Standard: Effects of Commutability on Interlaboratory Concordance

PubMed Central

Shahbazian, M. D.; Valsamakis, A.; Boonyaratanakornkit, J.; Cook, L.; Pang, X. L.; Preiksaitis, J. K.; Schönbrunner, E. R.; Caliendo, A. M.

2013-01-01

Commutability of quantitative reference materials has proven important for reliable and accurate results in clinical chemistry. As international reference standards and commercially produced calibration material have become available to address the variability of viral load assays, the degree to which such materials are commutable and the effect of commutability on assay concordance have been questioned. To investigate this, 60 archived clinical plasma samples, which previously tested positive for cytomegalovirus (CMV), were retested by five different laboratories, each using a different quantitative CMV PCR assay. Results from each laboratory were calibrated both with lab-specific quantitative CMV standards (“lab standards”) and with common, commercially available standards (“CMV panel”). Pairwise analyses among laboratories were performed using mean results from each clinical sample, calibrated first with lab standards and then with the CMV panel. Commutability of the CMV panel was determined based on difference plots for each laboratory pair showing plotted values of standards that were within the 95% prediction intervals for the clinical specimens. Commutability was demonstrated for 6 of 10 laboratory pairs using the CMV panel. In half of these pairs, use of the CMV panel improved quantitative agreement compared to use of lab standards. Two of four laboratory pairs for which the CMV panel was noncommutable showed reduced quantitative agreement when that panel was used as a common calibrator. Commutability of calibration material varies across different quantitative PCR methods. Use of a common, commutable quantitative standard can improve agreement across different assays; use of a noncommutable calibrator can reduce agreement among laboratories. PMID:24025907

The Effects of Intravenous Immunoglobulins in Women with Recurrent Miscarriages: A Systematic Review of Randomised Trials with Meta-Analyses and Trial Sequential Analyses Including Individual Patient Data

PubMed Central

Egerup, Pia; Lindschou, Jane; Gluud, Christian; Christiansen, Ole Bjarne

2015-01-01

Background Immunological disturbances are hypothesised to play a role in recurrent miscarriage (RM) and therefore intravenous immunoglubulins (IVIg) have been tested in RM patients. Objectives The objectives were to investigate the benefits and harms of IVIg versus placebo, no intervention, or treatment as usual in women with RM. Search Strategy We searched the published literature in all relevant databases. Selection Criteria Randomised trials investigating IVIg versus placebo, no intervention, or treatment as usual in women with RM. Data Collection and Analysis We undertook meta-analyses of aggregated data and individual patient data using a two-step approach, and we conducted bias domain assessments and trial sequential analyses to assess the risks of systematic and random errors. Main Results We identified 11 randomised clinical trials. No significant difference in the frequency of no live birth was found when IVIg was compared with placebo or treatment as usual (RR 0.92, 95% CI 0.75–1.12, p = 0.42). Trial sequential analysis showed that the required information size of 1,008 participants was not obtained. IVIg compared with placebo seems to increase the risk of adverse events. Subgroup analysis suggests that women with RM after a birth (secondary RM) seemed most likely to obtain a potential beneficial effect of IVIg (RR for no live birth 0.77, 95%CI 0.58–1.02, p = 0.06), however, trial sequential analysis showed that insufficient information is presently accrued. Conclusion We cannot recommend or refute IVIg in women with RM. IVIg should therefore be assessed in further randomised clinical trials with positive outcomes before any clinical use is considered. PMID:26517123

Descriptive Analyses of Pediatric Food Refusal and Acceptance

ERIC Educational Resources Information Center

Borrero, Carrie S. W.; Woods, Julia N.; Borrero, John C.; Masler, Elizabeth A.; Lesser, Aaron D.

2010-01-01

Functional analyses of inappropriate mealtime behavior typically include conditions to determine if the contingent delivery of attention, tangible items, or escape reinforce food refusal. In the current investigation, descriptive analyses were conducted for 25 children who had been admitted to a program for the assessment and treatment of food…

Evaluation of a real-time quantitative PCR method with propidium monazide treatment for analyses of viable fecal indicator bacteria in wastewater samples

EPA Science Inventory

The U.S. EPA is currently evaluating rapid, real-time quantitative PCR (qPCR) methods for determining recreational water quality based on measurements of fecal indicator bacteria DNA sequences. In order to potentially use qPCR for other Clean Water Act needs, such as updating cri...

Methodological Quality Assessment of Meta-analyses in Endodontics.

PubMed

Kattan, Sereen; Lee, Su-Min; Kohli, Meetu R; Setzer, Frank C; Karabucak, Bekir

2018-01-01

The objectives of this review were to assess the methodological quality of published meta-analyses related to endodontics using the assessment of multiple systematic reviews (AMSTAR) tool and to provide a follow-up to previously published reviews. Three electronic databases were searched for eligible studies according to the inclusion and exclusion criteria: Embase via Ovid, The Cochrane Library, and Scopus. The electronic search was amended by a hand search of 6 dental journals (International Endodontic Journal; Journal of Endodontics; Australian Endodontic Journal; Oral Surgery, Oral Medicine, Oral Pathology, Oral Radiology; Endodontics and Dental Traumatology; and Journal of Dental Research). The searches were conducted to include articles published after July 2009, and the deadline for inclusion of the meta-analyses was November 30, 2016. The AMSTAR assessment tool was used to evaluate the methodological quality of all included studies. A total of 36 reports of meta-analyses were included. The overall quality of the meta-analyses reports was found to be medium, with an estimated mean overall AMSTAR score of 7.25 (95% confidence interval, 6.59-7.90). The most poorly assessed areas were providing an a priori design, the assessment of the status of publication, and publication bias. In recent publications in the field of endodontics, the overall quality of the reported meta-analyses is medium according to AMSTAR. Copyright © 2017 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

Potential of MR histogram analyses for prediction of response to chemotherapy in patients with colorectal hepatic metastases.

PubMed

Liang, He-Yue; Huang, Ya-Qin; Yang, Zhao-Xia; Ying-Ding; Zeng, Meng-Su; Rao, Sheng-Xiang

2016-07-01

To determine if magnetic resonance imaging (MRI) histogram analyses can help predict response to chemotherapy in patients with colorectal hepatic metastases by using response evaluation criteria in solid tumours (RECIST1.1) as the reference standard. Standard MRI including diffusion-weighted imaging (b=0, 500 s/mm(2)) was performed before chemotherapy in 53 patients with colorectal hepatic metastases. Histograms were performed for apparent diffusion coefficient (ADC) maps, arterial, and portal venous phase images; thereafter, mean, percentiles (1st, 10th, 50th, 90th, 99th), skewness, kurtosis, and variance were generated. Quantitative histogram parameters were compared between responders (partial and complete response, n=15) and non-responders (progressive and stable disease, n=38). Receiver operator characteristics (ROC) analyses were further analyzed for the significant parameters. The mean, 1st percentile, 10th percentile, 50th percentile, 90th percentile, 99th percentile of the ADC maps were significantly lower in responding group than that in non-responding group (p=0.000-0.002) with area under the ROC curve (AUCs) of 0.76-0.82. The histogram parameters of arterial and portal venous phase showed no significant difference (p>0.05) between the two groups. Histogram-derived parameters for ADC maps seem to be a promising tool for predicting response to chemotherapy in patients with colorectal hepatic metastases. • ADC histogram analyses can potentially predict chemotherapy response in colorectal liver metastases. • Lower histogram-derived parameters (mean, percentiles) for ADC tend to have good response. • MR enhancement histogram analyses are not reliable to predict response.

Quantitative trait nucleotide analysis using Bayesian model selection.

PubMed

Blangero, John; Goring, Harald H H; Kent, Jack W; Williams, Jeff T; Peterson, Charles P; Almasy, Laura; Dyer, Thomas D

2005-10-01

Although much attention has been given to statistical genetic methods for the initial localization and fine mapping of quantitative trait loci (QTLs), little methodological work has been done to date on the problem of statistically identifying the most likely functional polymorphisms using sequence data. In this paper we provide a general statistical genetic framework, called Bayesian quantitative trait nucleotide (BQTN) analysis, for assessing the likely functional status of genetic variants. The approach requires the initial enumeration of all genetic variants in a set of resequenced individuals. These polymorphisms are then typed in a large number of individuals (potentially in families), and marker variation is related to quantitative phenotypic variation using Bayesian model selection and averaging. For each sequence variant a posterior probability of effect is obtained and can be used to prioritize additional molecular functional experiments. An example of this quantitative nucleotide analysis is provided using the GAW12 simulated data. The results show that the BQTN method may be useful for choosing the most likely functional variants within a gene (or set of genes). We also include instructions on how to use our computer program, SOLAR, for association analysis and BQTN analysis.

Testicular Dysgenesis Syndrome and the Estrogen Hypothesis: A Quantitative Meta-Analysis

PubMed Central

Martin, Olwenn V.; Shialis, Tassos; Lester, John N.; Scrimshaw, Mark D.; Boobis, Alan R.; Voulvoulis, Nikolaos

2008-01-01

Background Male reproductive tract abnormalities such as hypospadias and cryptorchidism, and testicular cancer have been proposed to comprise a common syndrome together with impaired spermatogenesis with a common etiology resulting from the disruption of gonadal development during fetal life, the testicular dysgenesis syndrome (TDS). The hypothesis that in utero exposure to estrogenic agents could induce these disorders was first proposed in 1993. The only quantitative summary estimate of the association between prenatal exposure to estrogenic agents and testicular cancer was published over 10 years ago, and other systematic reviews of the association between estrogenic compounds, other than the potent pharmaceutical estrogen diethylstilbestrol (DES), and TDS end points have remained inconclusive. Objectives We conducted a quantitative meta-analysis of the association between the end points related to TDS and prenatal exposure to estrogenic agents. Inclusion in this analysis was based on mechanistic criteria, and the plausibility of an estrogen receptor (ER)-α–mediated mode of action was specifically explored. Results We included in this meta-analysis eight studies investigating the etiology of hypospadias and/or cryptorchidism that had not been identified in previous systematic reviews. Four additional studies of pharmaceutical estrogens yielded a statistically significant updated summary estimate for testicular cancer. Conclusions The doubling of the risk ratios for all three end points investigated after DES exposure is consistent with a shared etiology and the TDS hypothesis but does not constitute evidence of an estrogenic mode of action. Results of the subset analyses point to the existence of unidentified sources of heterogeneity between studies or within the study population. PMID:18288311

Improving the Linkages between Air Pollution Epidemiology and Quantitative Risk Assessment

PubMed Central

Bell, Michelle L.; Walker, Katy; Hubbell, Bryan

2011-01-01

Background: Air pollution epidemiology plays an integral role in both identifying the hazards of air pollution as well as supplying the risk coefficients that are used in quantitative risk assessments. Evidence from both epidemiology and risk assessments has historically supported critical environmental policy decisions. The extent to which risk assessors can properly specify a quantitative risk assessment and characterize key sources of uncertainty depends in part on the availability, and clarity, of data and assumptions in the epidemiological studies. Objectives: We discuss the interests shared by air pollution epidemiology and risk assessment communities in ensuring that the findings of epidemiological studies are appropriately characterized and applied correctly in risk assessments. We highlight the key input parameters for risk assessments and consider how modest changes in the characterization of these data might enable more accurate risk assessments that better represent the findings of epidemiological studies. Discussion: We argue that more complete information regarding the methodological choices and input data used in epidemiological studies would support more accurate risk assessments—to the benefit of both disciplines. In particular, we suggest including additional details regarding air quality, demographic, and health data, as well as certain types of data-rich graphics. Conclusions: Relatively modest changes to the data reported in epidemiological studies will improve the quality of risk assessments and help prevent the misinterpretation and mischaracterization of the results of epidemiological studies. Such changes may also benefit epidemiologists undertaking meta-analyses. We suggest workshops as a way to improve the dialogue between the two communities. PMID:21816702

Testicular dysgenesis syndrome and the estrogen hypothesis: a quantitative meta-analysis.

PubMed

Martin, Olwenn V; Shialis, Tassos; Lester, John N; Scrimshaw, Mark D; Boobis, Alan R; Voulvoulis, Nikolaos

2008-02-01

Male reproductive tract abnormalities such as hypospadias and cryptorchidism, and testicular cancer have been proposed to comprise a common syndrome together with impaired spermatogenesis with a common etiology resulting from the disruption of gonadal development during fetal life, the testicular dysgenesis syndrome (TDS). The hypothesis that in utero exposure to estrogenic agents could induce these disorders was first proposed in 1993. The only quantitative summary estimate of the association between prenatal exposure to estrogenic agents and testicular cancer was published over 10 years ago, and other systematic reviews of the association between estrogenic compounds, other than the potent pharmaceutical estrogen diethylstilbestrol (DES), and TDS end points have remained inconclusive. We conducted a quantitative meta-analysis of the association between the end points related to TDS and prenatal exposure to estrogenic agents. Inclusion in this analysis was based on mechanistic criteria, and the plausibility of an estrogen receptor (ER)-alpha-mediated mode of action was specifically explored. We included in this meta-analysis eight studies investigating the etiology of hypospadias and/or cryptorchidism that had not been identified in previous systematic reviews. Four additional studies of pharmaceutical estrogens yielded a statistically significant updated summary estimate for testicular cancer. The doubling of the risk ratios for all three end points investigated after DES exposure is consistent with a shared etiology and the TDS hypothesis but does not constitute evidence of an estrogenic mode of action. Results of the subset analyses point to the existence of unidentified sources of heterogeneity between studies or within the study population.

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

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

Formation and representation: Critical analyses of identity, supply, and demand in science, technology, engineering, and mathematics

NASA Astrophysics Data System (ADS)

Mandayam Doddamane, Prabha

2011-12-01

Considerable research, policy, and programmatic efforts have been dedicated to addressing the participation of particular populations in STEM for decades. Each of these efforts claims equity-related goals; yet, they heavily frame the problem, through pervasive STEM pipeline model discourse, in terms of national needs, workforce supply, and competitiveness. This particular framing of the problem may, indeed, be counter to equity goals, especially when paired with policy that largely relies on statistical significance and broad aggregation of data over exploring the identities and experiences of the populations targeted for equitable outcomes in that policy. In this study, I used the mixed-methods approach of critical discourse and critical quantitative analyses to understand how the pipeline model ideology has become embedded within academic discourse, research, and data surrounding STEM education and work and to provide alternatives for quantitative analysis. Using critical theory as a lens, I first conducted a critical discourse analysis of contemporary STEM workforce studies with a particular eye to pipeline ideology. Next, I used that analysis to inform logistic regression analyses of the 2006 SESTAT data. This quantitative analysis compared and contrasted different ways of thinking about identity and retention. Overall, the findings of this study show that many subjective choices are made in the construction of the large-scale datasets used to inform much national science and engineering policy and that these choices greatly influence likelihood of retention outcomes.

Quantitative and Qualitative Analysis of Nutrition and Food Safety Information in School Science Textbooks of India

ERIC Educational Resources Information Center

Subba Rao, G. M.; Vijayapushapm, T.; Venkaiah, K.; Pavarala, V.

2012-01-01

Objective: To assess quantity and quality of nutrition and food safety information in science textbooks prescribed by the Central Board of Secondary Education (CBSE), India for grades I through X. Design: Content analysis. Methods: A coding scheme was developed for quantitative and qualitative analyses. Two investigators independently coded the…

Quantitative Assays for RAS Pathway Proteins and Phosphorylation States

Cancer.gov

The NCI CPTAC program is applying its expertise in quantitative proteomics to develop assays for RAS pathway proteins. Targets include key phosphopeptides that should increase our understanding of how the RAS pathway is regulated.

Quantitative evaluation of orbital hybridization in carbon nanotubes under radial deformation using π-orbital axis vector

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

Ohnishi, Masato, E-mail: masato.ohnishi@rift.mech.tohoku.ac.jp; Suzuki, Ken; Miura, Hideo, E-mail: hmiura@rift.mech.tohoku.ac.jp

2015-04-15

When a radial strain is applied to a carbon nanotube (CNT), the increase in local curvature induces orbital hybridization. The effect of the curvature-induced orbital hybridization on the electronic properties of CNTs, however, has not been evaluated quantitatively. In this study, the strength of orbital hybridization in CNTs under homogeneous radial strain was evaluated quantitatively. Our analyses revealed the detailed procedure of the change in electronic structure of CNTs. In addition, the dihedral angle, the angle between π-orbital axis vectors of adjacent atoms, was found to effectively predict the strength of local orbital hybridization in deformed CNTs.

Detailed Chemical Composition of Condensed Tannins via Quantitative (31)P NMR and HSQC Analyses: Acacia catechu, Schinopsis balansae, and Acacia mearnsii.

PubMed

Crestini, Claudia; Lange, Heiko; Bianchetti, Giulia

2016-09-23

The chemical composition of Acacia catechu, Schinopsis balansae, and Acacia mearnsii proanthocyanidins has been determined using a novel analytical approach that rests on the concerted use of quantitative (31)P NMR and two-dimensional heteronuclear NMR spectroscopy. This approach has offered significant detailed information regarding the structure and purity of these complex and often elusive proanthocyanidins. More specifically, rings A, B, and C of their flavan-3-ol units show well-defined and resolved absorbance regions in both the quantitative (31)P NMR and HSQC spectra. By integrating each of these regions in the (31)P NMR spectra, it is possible to identify the oxygenation patterns of the flavan-3-ol units. At the same time it is possible to acquire a fingerprint of the proanthocyanidin sample and evaluate its purity via the HSQC information. This analytical approach is suitable for both the purified natural product proanthocyanidins and their commercial analogues. Overall, this effort demonstrates the power of the concerted use of these two NMR techniques for the structural elucidation of natural products containing labile hydroxy protons and a carbon framework that can be traced out via HSQC.

Effective Immunological Guidance of Genetic Analyses Including Exome Sequencing in Patients Evaluated for Hemophagocytic Lymphohistiocytosis.

PubMed

Ammann, Sandra; Lehmberg, Kai; Zur Stadt, Udo; Klemann, Christian; Bode, Sebastian F N; Speckmann, Carsten; Janka, Gritta; Wustrau, Katharina; Rakhmanov, Mirzokhid; Fuchs, Ilka; Hennies, Hans C; Ehl, Stephan

2017-11-01

We report our experience in using flow cytometry-based immunological screening prospectively as a decision tool for the use of genetic studies in the diagnostic approach to patients with hemophagocytic lymphohistiocytosis (HLH). We restricted genetic analysis largely to patients with abnormal immunological screening, but included whole exome sequencing (WES) for those with normal findings upon Sanger sequencing. Among 290 children with suspected HLH analyzed between 2010 and 2014 (including 17 affected, but asymptomatic siblings), 87/162 patients with "full" HLH and 79/111 patients with "incomplete/atypical" HLH had normal immunological screening results. In 10 patients, degranulation could not be tested. Among the 166 patients with normal screening, genetic analysis was not performed in 107 (all with uneventful follow-up), while 154 single gene tests by Sanger sequencing in the remaining 59 patients only identified a single atypical CHS patient. Flow cytometry correctly predicted all 29 patients with FHL-2, XLP1 or 2. Among 85 patients with defective NK degranulation (including 13 asymptomatic siblings), 70 were Sanger sequenced resulting in a genetic diagnosis in 55 (79%). Eight patients underwent WES, revealing mutations in two known and one unknown cytotoxicity genes and one metabolic disease. FHL3 was the most frequent genetic diagnosis. Immunological screening provided an excellent decision tool for the need and depth of genetic analysis of HLH patients and provided functionally relevant information for rapid patient classification, contributing to a significant reduction in the time from diagnosis to transplantation in recent years.

An analytical approach based on ESI-MS, LC-MS and PCA for the quali-quantitative analysis of cycloartane derivatives in Astragalus spp.

PubMed

Napolitano, Assunta; Akay, Seref; Mari, Angela; Bedir, Erdal; Pizza, Cosimo; Piacente, Sonia

2013-11-01

Astragalus species are widely used as health foods and dietary supplements, as well as drugs in traditional medicine. To rapidly evaluate metabolite similarities and differences among the EtOH extracts of the roots of eight commercial Astragalus spp., an approach based on direct analyses by ESI-MS followed by PCA of ESI-MS data, was carried out. Successively, quali-quantitative analyses of cycloartane derivatives in the eight Astragalus spp. by LC-ESI-MS(n) and PCA of LC-ESI-MS data were performed. This approach allowed to promptly highlighting metabolite similarities and differences among the various Astragalus spp. PCA results from LC-ESI-MS data of Astragalus samples were in reasonable agreement with both PCA results of ESI-MS data and quantitative results. This study affords an analytical method for the quali-quantitative determination of cycloartane derivatives in herbal preparations used as health and food supplements. Copyright © 2013 Elsevier B.V. All rights reserved.

Detection of Legionella by cultivation and quantitative real-time polymerase chain reaction in biological waste water treatment plants in Norway.

PubMed

Lund, Vidar; Fonahn, Wenche; Pettersen, Jens Erik; Caugant, Dominique A; Ask, Eirik; Nysaeter, Ase

2014-09-01

Cases of Legionnaires' disease associated with biological treatment plants (BTPs) have been reported in six countries between 1997 and 2010. However, knowledge about the occurrence of Legionella in BTPs is scarce. Hence, we undertook a qualitative and quantitative screening for Legionella in BTPs treating waste water from municipalities and industries in Norway, to assess the transmission potential of Legionella from these installations. Thirty-three plants from different industries were sampled four times within 1 year. By cultivation, 21 (16%) of 130 analyses were positive for Legionella species and 12 (9%) of 130 analyses were positive for Legionella pneumophila. By quantitative real-time polymerase chain reaction (PCR), 433 (99%) of 437 analyses were positive for Legionella species and 218 (46%) of 470 analyses were positive for L. pneumophila. This survey indicates that PCR could be the preferable method for detection of Legionella in samples from BTPs. Sequence types of L. pneumophila associated with outbreaks in Norway were not identified from the BTPs. We showed that a waste water treatment plant with an aeration basin can produce high concentrations of Legionella. Therefore, these plants should be considered as a possible source of community-acquired Legionella infections.

Quantitative trait locus for reading disability on chromosome 6

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

Cardon, L.R.; Smith, S.D.; Kimberling, W.J.

1994-10-14

Interval mapping of data from two independent samples of sib pairs, at least one member of whom was reading disabled, revealed evidence for a quantitative trait locus (QTL) on chromosome 6. Results obtained from analyses of reading performance from 114 sib pairs genotyped for DNA markers localized the QTL to 6p21.3. Analyses of corresponding data from an independent sample of 50 dizygotic twin pairs provided evidence for linkage to the same region. In combination, the replicate samples yielded a x{sup 2} value of 16.73 (P = 0.0002). Examination of twin and kindred siblings with more extreme deficits in reading performancemore » yielded even stronger evidence for a QTL (x{sup 2} = 27.35, P < 0.00001). The position of the QTL was narrowly defined with a 100:1 confidence interval to a 2-centimorgan region within the human leukocyte antigen complex. 23 refs., 4 figs.« less

Proof of the quantitative potential of immunofluorescence by mass spectrometry.

PubMed

Toki, Maria I; Cecchi, Fabiola; Hembrough, Todd; Syrigos, Konstantinos N; Rimm, David L

2017-03-01

Protein expression in formalin-fixed, paraffin-embedded patient tissue is routinely measured by Immunohistochemistry (IHC). However, IHC has been shown to be subject to variability in sensitivity, specificity and reproducibility, and is generally, at best, considered semi-quantitative. Mass spectrometry (MS) is considered by many to be the criterion standard for protein measurement, offering high sensitivity, specificity, and objective molecular quantification. Here, we seek to show that quantitative immunofluorescence (QIF) with standardization can achieve quantitative results comparable to MS. Epidermal growth factor receptor (EGFR) was measured by quantitative immunofluorescence in 15 cell lines with a wide range of EGFR expression, using different primary antibody concentrations, including the optimal signal-to-noise concentration after quantitative titration. QIF target measurement was then compared to the absolute EGFR concentration measured by Liquid Tissue-selected reaction monitoring mass spectrometry. The best agreement between the two assays was found when the EGFR primary antibody was used at the optimal signal-to-noise concentration, revealing a strong linear regression (R 2 =0.88). This demonstrates that quantitative optimization of titration by calculation of signal-to-noise ratio allows QIF to be standardized to MS and can therefore be used to assess absolute protein concentration in a linear and reproducible manner.

R as a Lingua Franca: Advantages of Using R for Quantitative Research in Applied Linguistics

ERIC Educational Resources Information Center

Mizumoto, Atsushi; Plonsky, Luke

2016-01-01

In this article, we suggest that using R, a statistical software environment, is advantageous for quantitative researchers in applied linguistics. We first provide a brief overview of the reasons why R is popular among researchers in other fields and why we recommend its use for analyses in applied linguistics. In order to illustrate these…

43 CFR 46.130 - Mitigation measures in analyses.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 43 Public Lands: Interior 1 2011-10-01 2011-10-01 false Mitigation measures in analyses. 46.130... Mitigation measures in analyses. (a) Bureau proposed action. The analysis of the proposed action and any alternatives must include an analysis of the effects of the proposed action or alternative as well as analysis...

The role of quantitative mass spectrometry in the discovery of pancreatic cancer biomarkers for translational science

PubMed Central

2014-01-01

In the post-genomic era, it has become evident that genetic changes alone are not sufficient to understand most disease processes including pancreatic cancer. Genome sequencing has revealed a complex set of genetic alterations in pancreatic cancer such as point mutations, chromosomal losses, gene amplifications and telomere shortening that drive cancerous growth through specific signaling pathways. Proteome-based approaches are important complements to genomic data and provide crucial information of the target driver molecules and their post-translational modifications. By applying quantitative mass spectrometry, this is an alternative way to identify biomarkers for early diagnosis and personalized medicine. We review the current quantitative mass spectrometric technologies and analyses that have been developed and applied in the last decade in the context of pancreatic cancer. Examples of candidate biomarkers that have been identified from these pancreas studies include among others, asporin, CD9, CXC chemokine ligand 7, fibronectin 1, galectin-1, gelsolin, intercellular adhesion molecule 1, insulin-like growth factor binding protein 2, metalloproteinase inhibitor 1, stromal cell derived factor 4, and transforming growth factor beta-induced protein. Many of these proteins are involved in various steps in pancreatic tumor progression including cell proliferation, adhesion, migration, invasion, metastasis, immune response and angiogenesis. These new protein candidates may provide essential information for the development of protein diagnostics and targeted therapies. We further argue that new strategies must be advanced and established for the integration of proteomic, transcriptomic and genomic data, in order to enhance biomarker translation. Large scale studies with meta data processing will pave the way for novel and unexpected correlations within pancreatic cancer, that will benefit the patient, with targeted treatment. PMID:24708694

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

COTS-Based Fault Tolerance in Deep Space: Qualitative and Quantitative Analyses of a Bus Network Architecture

NASA Technical Reports Server (NTRS)

Tai, Ann T.; Chau, Savio N.; Alkalai, Leon

2000-01-01

Using COTS products, standards and intellectual properties (IPs) for all the system and component interfaces is a crucial step toward significant reduction of both system cost and development cost as the COTS interfaces enable other COTS products and IPs to be readily accommodated by the target system architecture. With respect to the long-term survivable systems for deep-space missions, the major challenge for us is, under stringent power and mass constraints, to achieve ultra-high reliability of the system comprising COTS products and standards that are not developed for mission-critical applications. The spirit of our solution is to exploit the pertinent standard features of a COTS product to circumvent its shortcomings, though these standard features may not be originally designed for highly reliable systems. In this paper, we discuss our experiences and findings on the design of an IEEE 1394 compliant fault-tolerant COTS-based bus architecture. We first derive and qualitatively analyze a -'stacktree topology" that not only complies with IEEE 1394 but also enables the implementation of a fault-tolerant bus architecture without node redundancy. We then present a quantitative evaluation that demonstrates significant reliability improvement from the COTS-based fault tolerance.

Improving validation methods for molecular diagnostics: application of Bland-Altman, Deming and simple linear regression analyses in assay comparison and evaluation for next-generation sequencing