The relationship between significant wave height and Indian Ocean Dipole in the equatorial North Indian Ocean

NASA Astrophysics Data System (ADS)

Fu, Chen; Wang, Dongxiao; Yang, Lei; Luo, Yao; Zhou, Fenghua; Priyadarshana, Tilak; Yao, Jinglong

2018-05-01

Based on reanalysis data, we find that the Indian Ocean Dipole (IOD) plays an important role in the variability of wave climate in the equatorial Northern Indian Ocean (NIO). Significant wave height (SWH) in the equatorial NIO, especially over the waters southeast to Sri Lanka, exhibits strong interannual variations. SWH anomalies in the waters southeast to Sri Lanka correlate well with dipole mode index (DMI) during both summer and autumn. Negative SWH anomalies occur over the oceanic area southeast to Sri Lanka during positive IOD events and vary with different types of IOD. During positive prolonged (unseasonable) IOD, the SWH anomalies are the strongest in autumn (summer); while during positive normal IOD, the SWH anomalies are weak in both summer and autumn. Strong easterly wind anomalies over the southeast oceanic area of Sri Lanka during positive IOD events weaken the original equatorial westerly wind stress, which leads to the decrease in wind-sea waves. The longer wave period during positive IOD events further confirms less wind-sea waves. The SWH anomaly pattern during negative IOD events is nearly opposite to that during positive IOD events.

The relationship between significant wave height and Indian Ocean Dipole in the equatorial North Indian Ocean

NASA Astrophysics Data System (ADS)

Fu, Chen; Wang, Dongxiao; Yang, Lei; Luo, Yao; Zhou, Fenghua; Priyadarshana, Tilak; Yao, Jinglong

2018-06-01

Based on reanalysis data, we find that the Indian Ocean Dipole (IOD) plays an important role in the variability of wave climate in the equatorial Northern Indian Ocean (NIO). Significant wave height (SWH) in the equatorial NIO, especially over the waters southeast to Sri Lanka, exhibits strong interannual variations. SWH anomalies in the waters southeast to Sri Lanka correlate well with dipole mode index (DMI) during both summer and autumn. Negative SWH anomalies occur over the oceanic area southeast to Sri Lanka during positive IOD events and vary with different types of IOD. During positive prolonged (unseasonable) IOD, the SWH anomalies are the strongest in autumn (summer); while during positive normal IOD, the SWH anomalies are weak in both summer and autumn. Strong easterly wind anomalies over the southeast oceanic area of Sri Lanka during positive IOD events weaken the original equatorial westerly wind stress, which leads to the decrease in wind-sea waves. The longer wave period during positive IOD events further confirms less wind-sea waves. The SWH anomaly pattern during negative IOD events is nearly opposite to that during positive IOD events.

Dynamics of changing impacts of tropical Indo-Pacific variability on Indian and Australian rainfall.

PubMed

Li, Ziguang; Cai, Wenju; Lin, Xiaopei

2016-08-22

A positive Indian Ocean Dipole (IOD) and a warm phase of the El Niño-Southern Oscillation (ENSO) reduce rainfall over the Indian subcontinent and southern Australia. However, since the 1980s, El Niño's influence has been decreasing, accompanied by a strengthening in the IOD's influence on southern Australia but a reversal in the IOD's influence on the Indian subcontinent. The dynamics are not fully understood. Here we show that a post-1980 weakening in the ENSO-IOD coherence plays a key role. During the pre-1980 high coherence, ENSO drives both the IOD and regional rainfall, and the IOD's influence cannot manifest itself. During the post-1980 weak coherence, a positive IOD leads to increased Indian rainfall, offsetting the impact from El Niño. Likewise, the post-1980 weak ENSO-IOD coherence means that El Niño's pathway for influencing southern Australia cannot fully operate, and as positive IOD becomes more independent and more frequent during this period, its influence on southern Australia rainfall strengthens. There is no evidence to support that greenhouse warming plays a part in these decadal fluctuations.

On the relationship between Indian Ocean Dipole events and the precipitation of Pakistan

NASA Astrophysics Data System (ADS)

Hussain, Mian Sabir; Kim, Sunyoung; Lee, Seungho

2017-10-01

This study investigated the relationship between the Indian Ocean Dipole (IOD) and the precipitation of Pakistan using data for the period of 1958-2010. The long-term evolution of the IOD index did not show interannual patterns similar to those of the annual precipitation of Pakistan. No linkage between the co-occurring trends of the IOD and the precipitation was traced during the period of investigation. The correlation between the IOD and the precipitation of Pakistan indicated a noteworthy impact over the monsoonal regions, especially the coastal area and the western region of Pakistan, which showed a significant positive correlation between the IOD index and annual and summer precipitation. A significant positive relationship was also revealed between the precipitation of the Balochistan Plateau and the IOD index for the summer monsoon season. No connection was observed between the IOD and the precipitation of the northern regions and the upper Indus Plain of Pakistan. Positive phases of the IOD have been noted to occur along with surplus precipitation during active monsoon conditions. The southeasterly wind moves from the Arabian Sea and transports additional moisture from the Arabian Sea to the coastal and southwestern parts of Pakistan during positive phases of the IOD.

Influence of implant number on the movement of mandibular implant overdentures.

PubMed

Oda, Ken; Kanazawa, Manabu; Takeshita, Shin; Minakuchi, Shunsuke

2017-03-01

The rotational movement of an implant overdenture (IOD) has a negative effect on the perceived masticatory ability of the denture wearer. However, the influence of implant number on the movement of IODs has not been investigated. The purpose of this in vitro study was to evaluate the denture movement of mandibular IODs anchored by different numbers of implants. An edentulous mandibular test model with artificial mucosa and 5 experimental overdentures (N=5) was fabricated. The locator attachment system with blue nylon inserts was chosen for this study. Three implant positions were prepared: anterior midline (1-IOD), bilateral lateral incisor regions (2-IOD), and anterior midline and bilateral canine regions (3-IOD). Vertical loads of 50 N were applied to the mid-anterior region, the left canine region, the left premolar region, and the left first molar region. The vertical and horizontal displacements at the right distal edge and the vertical displacements at the loading point were measured. The displacement values were statistically analyzed using a 1-way analysis of variance and the post hoc Tukey honest significant difference test with the implant number as a factor. In addition, the values of the vertical and horizontal displacements at the distal edge of the overdenture were statistically compared using a paired t test, and the values of the vertical displacement at the distal edge of the overdenture were statistically analyzed by a repeated measures analysis of variance and the post hoc Tukey honest significance difference test with the loading point as a factor (a=.05). Upon anterior loading, the 2-IOD showed significantly larger vertical displacements at the right distal edge than the 1-IOD or 3-IOD (P<.01). The horizontal displacements at the right distal edge were small compared with the vertical displacements at the same point, although the displacement of the 2-IOD was significantly larger than that of the 1-IOD upon anterior loading (P=.03). The

Acute kidney damage induced by low- and iso-osmolar contrast media in rats: Comparison study with physiologic MRI and histologic-gene examination.

PubMed

Wu, Chen-Jiang; Bao, Mei-Ling; Wang, Qing; Wang, Xiao-Ning; Liu, Xi-Sheng; Shi, Hai-Bin; Zhang, Yu-Dong

2017-01-01

To investigate the physiopathological effects of low- and iso-osmolar contrast media (CM) on renal function with physiologic MRI and histologic-gene examination. Forty-eight rats underwent time-course DWI and DCE-MRI at 3.0 Tesla (T) before and 5-15 min after exposure of CM or saline (Iop.370: 370 mgI/mL iopromide; Iod.320: 320 mgI/mL iodixanol; Iod.270: 270 mgI/mL iodixanol; 4 gI/kg body weight). Intrarenal viscosity was reflected by apparent diffusion coefficient (ADC). Renal physiologies were evaluated by DCE-derived glomerular filtration rate (GFR), renal blood flow (RBF), and renal blood volume (RBV). Potential acute kidney injury (AKI) was determined by histology and the expression of kidney injury molecule 1 (Kim-1). Iop.370 mainly increased ADC in inner-medulla (△ADC IM : 12.3 ± 11.1%; P < 0.001). Iod.320 and Iod.270 mainly decreased ADC in outer-medulla (△ADC IM ; Iod.320: 16.8 ± 7.5%; Iod.270: 18.1 ± 9.5%; P < 0.001) and inner-medulla (△ADC IM ; Iod.320: 28.4 ± 9.3%; Iod.270: 30.3 ± 6.3%; P < 0.001). GFR, RBF and RBV were significantly decreased by Iod.320 (△GFR: 45.5 ± 24.1%; △RBF: 44.6 ± 19.0%; △RBV: 35.2 ± 10.1%; P < 0.001) and Iod.270 (33.2 ± 19.0%; 38.1 ± 15.6%; 30.1 ± 10.1%; P < 0.001), while rarely changed by Iop.370 and saline. Formation of vacuoles and increase in Kim-1 expression was prominently detected in group of Iod.320, while rarely in Iod.270 and Iop.370. Iso-osmolar iodixanol, given at high-dose, produced prominent AKI in nonhydrated rats. This renal dysfunction could be assessed noninvasively by physiologic MRI. 1 J. Magn. Reson. Imaging 2017;45:291-302. © 2016 International Society for Magnetic Resonance in Medicine.

Impact of Indian ocean dipole on the coastal upwelling features off the southwest coast of India

NASA Astrophysics Data System (ADS)

Nigam, Tanuja; Pant, Vimlesh; Prakash, Kumar Ravi

2018-05-01

A three-dimensional regional ocean model is used to examine the impact of positive Indian ocean dipole (pIOD) events on the coastal upwelling features at the southwest coast of India (SWCI). Two model experiments are carried out with different surface boundary conditions that prevailed in the normal and pIOD years from 1982 to 2010. Model experiments demonstrate the weakening of coastal upwelling at the SWCI in the pIOD years. The reduced southward meridional wind stress off the SWCI leads to comparatively lower offshore Ekman transport during August-October in the pIOD years to that in normal years. The suppressed coastal upwelling results in warmer sea surface temperature and deeper thermocline in the pIOD years during June-September. The offshore spatial extent of upwelled colder (< 22 °C) water was up to 75.5° E in August-September in normal years that was limited up to 76.2° E in pIOD years. The heat budget analysis reveals the decreased contribution of vertical entrainment process to the mixed layer cooling in pIOD years which is almost half of that of normal years in October. The net heat flux term shows warming tendency during May-November with a higher magnitude (+ 0.4 °C day-1) in normal years than pIOD years (+ 0.28 °C day-1). The biological productivity is found to reduce during the pIOD years as the concentration of phytoplankton and zooplankton decreases over the region of coastal upwelling at SWCI. Nitrate concentration in the pIOD years dropped by half during August-September and dropped by an order of magnitude in October as compared to its ambient concentration of 13 μmol L-1 in normal years.

Impact of Indian ocean dipole on the coastal upwelling features off the southwest coast of India

NASA Astrophysics Data System (ADS)

Nigam, Tanuja; Pant, Vimlesh; Prakash, Kumar Ravi

2018-06-01

A three-dimensional regional ocean model is used to examine the impact of positive Indian ocean dipole (pIOD) events on the coastal upwelling features at the southwest coast of India (SWCI). Two model experiments are carried out with different surface boundary conditions that prevailed in the normal and pIOD years from 1982 to 2010. Model experiments demonstrate the weakening of coastal upwelling at the SWCI in the pIOD years. The reduced southward meridional wind stress off the SWCI leads to comparatively lower offshore Ekman transport during August-October in the pIOD years to that in normal years. The suppressed coastal upwelling results in warmer sea surface temperature and deeper thermocline in the pIOD years during June-September. The offshore spatial extent of upwelled colder (< 22 °C) water was up to 75.5° E in August-September in normal years that was limited up to 76.2° E in pIOD years. The heat budget analysis reveals the decreased contribution of vertical entrainment process to the mixed layer cooling in pIOD years which is almost half of that of normal years in October. The net heat flux term shows warming tendency during May-November with a higher magnitude (+ 0.4 °C day-1) in normal years than pIOD years (+ 0.28 °C day-1). The biological productivity is found to reduce during the pIOD years as the concentration of phytoplankton and zooplankton decreases over the region of coastal upwelling at SWCI. Nitrate concentration in the pIOD years dropped by half during August-September and dropped by an order of magnitude in October as compared to its ambient concentration of 13 μmol L-1 in normal years.

Statistical image quantification toward optimal scan fusion and change quantification

NASA Astrophysics Data System (ADS)

Potesil, Vaclav; Zhou, Xiang Sean

2007-03-01

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

Impacts of El Niño Southern Oscillation and Indian Ocean Dipole on dengue incidence in Bangladesh

PubMed Central

Banu, Shahera; Guo, Yuming; Hu, Wenbiao; Dale, Pat; Mackenzie, John S.; Mengersen, Kerrie; Tong, Shilu

2015-01-01

Dengue dynamics are driven by complex interactions between hosts, vectors and viruses that are influenced by environmental and climatic factors. Several studies examined the role of El Niño Southern Oscillation (ENSO) in dengue incidence. However, the role of Indian Ocean Dipole (IOD), a coupled ocean atmosphere phenomenon in the Indian Ocean, which controls the summer monsoon rainfall in the Indian region, remains unexplored. Here, we examined the effects of ENSO and IOD on dengue incidence in Bangladesh. According to the wavelet coherence analysis, there was a very weak association between ENSO, IOD and dengue incidence, but a highly significant coherence between dengue incidence and local climate variables (temperature and rainfall). However, a distributed lag nonlinear model (DLNM) revealed that the association between dengue incidence and ENSO or IOD were comparatively stronger after adjustment for local climate variables, seasonality and trend. The estimated effects were nonlinear for both ENSO and IOD with higher relative risks at higher ENSO and IOD. The weak association between ENSO, IOD and dengue incidence might be driven by the stronger effects of local climate variables such as temperature and rainfall. Further research is required to disentangle these effects. PMID:26537857

Impacts of El Niño Southern Oscillation and Indian Ocean Dipole on dengue incidence in Bangladesh.

PubMed

Banu, Shahera; Guo, Yuming; Hu, Wenbiao; Dale, Pat; Mackenzie, John S; Mengersen, Kerrie; Tong, Shilu

2015-11-05

Dengue dynamics are driven by complex interactions between hosts, vectors and viruses that are influenced by environmental and climatic factors. Several studies examined the role of El Niño Southern Oscillation (ENSO) in dengue incidence. However, the role of Indian Ocean Dipole (IOD), a coupled ocean atmosphere phenomenon in the Indian Ocean, which controls the summer monsoon rainfall in the Indian region, remains unexplored. Here, we examined the effects of ENSO and IOD on dengue incidence in Bangladesh. According to the wavelet coherence analysis, there was a very weak association between ENSO, IOD and dengue incidence, but a highly significant coherence between dengue incidence and local climate variables (temperature and rainfall). However, a distributed lag nonlinear model (DLNM) revealed that the association between dengue incidence and ENSO or IOD were comparatively stronger after adjustment for local climate variables, seasonality and trend. The estimated effects were nonlinear for both ENSO and IOD with higher relative risks at higher ENSO and IOD. The weak association between ENSO, IOD and dengue incidence might be driven by the stronger effects of local climate variables such as temperature and rainfall. Further research is required to disentangle these effects.

Fluorescent quantification of melanin.

PubMed

Fernandes, Bruno; Matamá, Teresa; Guimarães, Diana; Gomes, Andreia; Cavaco-Paulo, Artur

2016-11-01

Melanin quantification is reportedly performed by absorption spectroscopy, commonly at 405 nm. Here, we propose the implementation of fluorescence spectroscopy for melanin assessment. In a typical in vitro assay to assess melanin production in response to an external stimulus, absorption spectroscopy clearly overvalues melanin content. This method is also incapable of distinguishing non-melanotic/amelanotic control cells from those that are actually capable of performing melanogenesis. Therefore, fluorescence spectroscopy is the best method for melanin quantification as it proved to be highly specific and accurate, detecting even small variations in the synthesis of melanin. This method can also be applied to the quantification of melanin in more complex biological matrices like zebrafish embryos and human hair. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

How strong is the impact of the Indo-ocean dipole on the surface air temperature/sea level pressure anomalies in the Mediterranean region?

NASA Astrophysics Data System (ADS)

Polonsky, Alexander B.; Basharin, Dmitry V.

2017-04-01

The aim of this paper is to study the interannual climate variability over the Mediterranean region related to the Indo-ocean dipole (IOD) using the data of re-analyses, archival data and specialized numerical experiments. It is shown that the IOD does not impact essentially the anomalies of surface air temperature (SAT) and sea level pressure (SLP) in the Mediterranean region. On average, the IOD-induced share of the SAT/SLP variance in the total variance of these fields in the Mediterranean region is smaller than 10% even in summer when it is at a maximum. However, the statistically significant IOD-induced SAT/SLP anomalies in the Mediterranean region are detectable. For definite IOD events the associated Mediterranean SAT anomalies can reach about 1 °C.

Reference ranges for foetal nasal bone length, prenasal thickness, and interocular distance at 18 to 24 weeks' gestation in low-risk pregnancies.

PubMed

Altunkeser, Ayşegül; Körez, M Kazım

2017-12-12

The aim of the present study was to establish the normal ranges for foetal nasal bone length (NBL), prenasal skin thickness (PNT), interocular distance (IOD), and ratio of prenasal thickness to- nasal bone length (PNT/ NBL) at 18-24 weeks using two-dimensional (2D) ultrasound. This study was a retrospective study of prenatal ultrasonographic records from 407 foetuses between 18 and 24 weeks gestational age (GA). The NBL, PNT, IOD, PNT/ NBL ratio, biparietal diameter (BPD), and femur length (FL) were investigated. The relationships among NBL, PNT, IOD, PNT/ NBL, and GA were evaluated. Additionally, descriptive statistics for NBL, PNT, and IOD values for each gestational week were obtained. There was a significant association between GA and NBL, PNT, and IOD between 18 and 24 weeks. NBL increased from a mean of 5.5 mm to 8.3 mm, PNT increased from a mean of 3.5 mm to 5.1 mm, and IOD increased from a mean of 11.1 mm to 14.5 mm. PNT/NBL ratio did not change with gestational age. This study showed normal ranges for NBL, PNT, IOD, and PNT/ NBL ratios for foetuses between 18 and 24 weeks in low-risk pregnancies. There was a positive linear relationship between GA and NBL, PNT, and IOD. The PNT/NBL ratio might be a more useful measurement than NBL or PNT alone.

Processing and domain selection: Quantificational variability effects

PubMed Central

Harris, Jesse A.; Clifton, Charles; Frazier, Lyn

2014-01-01

Three studies investigated how readers interpret sentences with variable quantificational domains, e.g., The army was mostly in the capital, where mostly may quantify over individuals or parts (Most of the army was in the capital) or over times (The army was in the capital most of the time). It is proposed that a general conceptual economy principle, No Extra Times (Majewski 2006, in preparation), discourages the postulation of potentially unnecessary times, and thus favors the interpretation quantifying over parts. Disambiguating an ambiguously quantified sentence to a quantification over times interpretation was rated as less natural than disambiguating it to a quantification over parts interpretation (Experiment 1). In an interpretation questionnaire, sentences with similar quantificational variability were constructed so that both interpretations of the sentence would require postulating multiple times; this resulted in the elimination of the preference for a quantification over parts interpretation, suggesting the parts preference observed in Experiment 1 is not reducible to a lexical bias of the adverb mostly (Experiment 2). An eye movement recording study showed that, in the absence of prior evidence for multiple times, readers exhibit greater difficulty when reading material that forces a quantification over times interpretation than when reading material that allows a quantification over parts interpretation (Experiment 3). These experiments contribute to understanding readers’ default assumptions about the temporal properties of sentences, which is essential for understanding the selection of a domain for adverbial quantifiers and, more generally, for understanding how situational constraints influence sentence processing. PMID:25328262

Dynamics of changing impacts of tropical Indo-Pacific variability on Indian and Australian rainfall

NASA Astrophysics Data System (ADS)

Li, Ziguang; Cai, Wenju; Lin, Xiaopei

2016-08-01

A positive Indian Ocean Dipole (IOD) and a warm phase of the El Niño-Southern Oscillation (ENSO) reduce rainfall over the Indian subcontinent and southern Australia. However, since the 1980s, El Niño’s influence has been decreasing, accompanied by a strengthening in the IOD’s influence on southern Australia but a reversal in the IOD’s influence on the Indian subcontinent. The dynamics are not fully understood. Here we show that a post-1980 weakening in the ENSO-IOD coherence plays a key role. During the pre-1980 high coherence, ENSO drives both the IOD and regional rainfall, and the IOD’s influence cannot manifest itself. During the post-1980 weak coherence, a positive IOD leads to increased Indian rainfall, offsetting the impact from El Niño. Likewise, the post-1980 weak ENSO-IOD coherence means that El Niño’s pathway for influencing southern Australia cannot fully operate, and as positive IOD becomes more independent and more frequent during this period, its influence on southern Australia rainfall strengthens. There is no evidence to support that greenhouse warming plays a part in these decadal fluctuations.

HPC Analytics Support. Requirements for Uncertainty Quantification Benchmarks

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

Paulson, Patrick R.; Purohit, Sumit; Rodriguez, Luke R.

2015-05-01

This report outlines techniques for extending benchmark generation products so they support uncertainty quantification by benchmarked systems. We describe how uncertainty quantification requirements can be presented to candidate analytical tools supporting SPARQL. We describe benchmark data sets for evaluating uncertainty quantification, as well as an approach for using our benchmark generator to produce data sets for generating benchmark data sets.

Do implant-supported dentures facilitate efficacy of eating more healthily?

PubMed

Moynihan, P J; Elfeky, A; Ellis, J S; Seal, C J; Hyland, R M; Thomason, J M

2012-10-01

Edentulous persons have poor diet quality demonstrating a need for dietary intervention. Implant-supported mandibular overdentures (IODs) have functional advantages over conventional dentures (CD), but whether they enhance the ability to eat more healthily following dietary advice is unknown. This study aimed to compare the effectiveness of dietary intervention between IODs and CD patients. Edentulous adults (28 IOD and 26 CD) received customised dietary advice. The percentage contribution of dietary fats, carbohydrate and protein to energy (kcal) intake, dietary intakes of fibre, fruits, vegetables and antioxidants, and plasma antioxidants were assessed pre- and at 3 and 6 months post-dietary intervention. Both groups increased fruit and vegetable intake at 3 and 6 months following dietary intervention but intakes between groups did not differ. The IOD group had reduced % energy from total fat at 3 and 6 months and from saturated fat at 3 months. The CD group had reduced % energy from saturated by 6 months. The IOD group had a significantly lower % energy intake from saturated fat at 3 months and higher intake of non-starch polysaccharide (NSP) compared with the CD group. Both groups showed improvements in serum antioxidant status but the IOD group had significantly higher plasma antioxidant capacity post intervention compared with the CD group. Dietary intervention benefits denture patients. IOD patients showed moderately greater dietary improvements compared with conventional denture patients. Crown Copyright © 2012. Published by Elsevier Ltd. All rights reserved.

[Recognition of international ethics codes by physicians and biomedical investigators. Are we prepared for the 21st century challenges?].

PubMed

Ponce-de-León, Sergio

2004-01-01

International oaths and declarations (IOD) represent the essence of proposals or promises on a relevant global issue for which a social group stands for. Their appropriate spread is essential in order for them to have a significant impact. The purpose of this study was to determine the frequency of recognition of several medical practice and clinical research related IOD, among medical personnel differentiated by level of clinical experience and closeness to biomedical research. Five groups were surveyed: 35 undergraduate interns, 50 internal medicine residents, 19 graduate (masters and doctoral degrees) students at the outset of courses, 18 veteran graduate students and 70 biomedical investigators. Performance in the recognition of the 6 probed IOD was uniformly poor. Barely just an average of about one declaration per subject was adequately identified. The Declaration of Helsinki was recognized by more than 50% of those belonging to the groups in which theory and practice of medical research joined together. No other IOD was recognized beyond a 40% level in any group. Comparison of university of origin showed no substantial differences. The lack of knowledge of IOD as a framework in the analysis of ethical conflicts arising along medical practice or clinical research is a worrisome issue. Medical schools seem to neglect their role in divulging them. Institutional review boards should also contribute to divulge IOD. The optimal incorporation of the IOD message comes from its acquisition through a process that links theory and practice.

43 CFR 11.71 - Quantification phase-service reduction quantification.

Code of Federal Regulations, 2011 CFR

2011-10-01

...-discharge-or-release condition. (c) Contents of the quantification. The following factors should be included...; and (6) Factors identified in the specific guidance in paragraphs (h), (i), (j), (k), and (l) of this section dealing with the different kinds of natural resources. (d) Selection of resources, services, and...

43 CFR 11.71 - Quantification phase-service reduction quantification.

Code of Federal Regulations, 2010 CFR

2010-10-01

...-discharge-or-release condition. (c) Contents of the quantification. The following factors should be included...; and (6) Factors identified in the specific guidance in paragraphs (h), (i), (j), (k), and (l) of this section dealing with the different kinds of natural resources. (d) Selection of resources, services, and...

An accurate proteomic quantification method: fluorescence labeling absolute quantification (FLAQ) using multidimensional liquid chromatography and tandem mass spectrometry.

PubMed

Liu, Junyan; Liu, Yang; Gao, Mingxia; Zhang, Xiangmin

2012-08-01

A facile proteomic quantification method, fluorescent labeling absolute quantification (FLAQ), was developed. Instead of using MS for quantification, the FLAQ method is a chromatography-based quantification in combination with MS for identification. Multidimensional liquid chromatography (MDLC) with laser-induced fluorescence (LIF) detection with high accuracy and tandem MS system were employed for FLAQ. Several requirements should be met for fluorescent labeling in MS identification: Labeling completeness, minimum side-reactions, simple MS spectra, and no extra tandem MS fragmentations for structure elucidations. A fluorescence dye, 5-iodoacetamidofluorescein, was finally chosen to label proteins on all cysteine residues. The fluorescent dye was compatible with the process of the trypsin digestion and MALDI MS identification. Quantitative labeling was achieved with optimization of reacting conditions. A synthesized peptide and model proteins, BSA (35 cysteines), OVA (five cysteines), were used for verifying the completeness of labeling. Proteins were separated through MDLC and quantified based on fluorescent intensities, followed by MS identification. High accuracy (RSD% < 1.58) and wide linearity of quantification (1-10(5) ) were achieved by LIF detection. The limit of quantitation for the model protein was as low as 0.34 amol. Parts of proteins in human liver proteome were quantified and demonstrated using FLAQ. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Realism of modelled Indian summer monsoon correlation with the tropical Indo-Pacific affects projected monsoon changes.

PubMed

Li, Ziguang; Lin, Xiaopei; Cai, Wenju

2017-07-10

El Niño-Southern Oscillation (ENSO) and the Indian Ocean Dipole (IOD) tend to exert an offsetting impact on Indian summer monsoon rainfall (ISMR), with an El Niño event tending to lower, whereas a positive IOD tending to increase ISMR. Simulation of these relationships in Phase Five of the Coupled Model Intercomparison Project has not been fully assessed, nor is their impact on the response of ISMR to greenhouse warming. Here we show that the majority of models simulate an unrealistic present-day IOD-ISMR correlation due to an overly strong control by ENSO. As such, a positive IOD is associated with an ISMR reduction in the simulated present-day climate. This unrealistic present-day correlation is relevant to future ISMR projection, inducing an underestimation in the projected ISMR increase. Thus uncertainties in ISMR projection can be in part induced by present-day simulation of ENSO, the IOD, their relationship and their rainfall correlations.

Impact of Temperature Anomalies Associated with El Niño-Southern Oscillation and Indian Ocean Dipole Events on Wine Grape Maturity in Australia

NASA Astrophysics Data System (ADS)

Jarvis, C.; Barlow, E.; Darbyshire, R.; Eckard, R.; Goodwin, I.

2016-12-01

Annual grapevine growth and development are intimately linked with growing season weather conditions. Shifts in circulation patterns resulting from atmospheric teleconnections to changes in sea surface temperature (SST) anomalies associated with El Niño-Southern Oscillation (ENSO) and Indian Ocean Dipole (IOD) events can alter seasonal weather across Australia. Both ENSO and IOD events tend to peak in austral spring, when vine and berry development is especially critical and susceptible to damage. To investigate the impacts of ENSO and IOD events on the Australian wine grape growing sector, historical gridded climate data and annual vineyard grape maturity data from a variety of wine growing regions was collected and analysed. The greatest impacts on grape maturity were found when La Niña and IOD positive events occurred in tandem. During these events, significantly dry and hot conditions persist throughout the wine grape growing season, suggesting that the IOD overrides the ENSO signal. These conditions lead to a rapid, compressed growing season, which can cause logistical complications during harvest and impact grape and wine quality. Warming of equatorial SSTs in the Indian Ocean are likely to enhance the amplitude of IOD positive events, which has serious implications for wine grape production in Australia, highlighting the importance of this research.

Assessment of the simulation of Indian Ocean Dipole in the CESM—Impacts of atmospheric physics and model resolution

NASA Astrophysics Data System (ADS)

Yao, Zhixiong; Tang, Youmin; Chen, Dake; Zhou, Lei; Li, Xiaojing; Lian, Tao; Ul Islam, Siraj

2016-12-01

This study examines the possible impacts of coupling processes on simulations of the Indian Ocean Dipole (IOD). Emphasis is placed on the atmospheric model resolution and physics. Five experiments were conducted for this purpose, including one control run of the ocean-only model, four coupled experiments using two different versions of the Community Atmosphere Model (CAM4 and CAM5) and two different resolutions. The results show that the control run could effectively simulate various features of the IOD. The coupled experiments run at the higher resolution yielded more realistic IOD period and intensity than their counterparts at the low resolution. The coupled experiments using CAM5 generally showed a better simulation skill in the tropical Indian SST climatology and phase-locking than those using CAM4, but the wind anomalies were stronger and the IOD period were longer in the former experiments than in the latter. In all coupled experiments, the IOD intensity was much stronger than the observed intensity, which is attributable to wind-thermocline depth feedback and thermocline depth-subsurface temperature feedback. The CAM5 physics seems beneficial for the simulation of summer rainfall over the eastern equatorial Indian Ocean and the CAM4 physics tends to produce less biases over the western equatorial Indian Ocean, whereas the higher resolution tends to generate unrealistically strong meridional winds. The IOD-ENSO relationship was captured reasonably well in coupled experiments, with improvements in CAM5 relative to CAM4. However, the teleconnection of the IOD-Indian summer monsoon and ENSO-Indian summer monsoon was not realistically simulated in all experiments.

Sensitivity of MJO propagation to a robust positive Indian Ocean dipole event in the superparameterized CAM

DOE PAGES

Benedict, James J.; Pritchard, Michael S.; Collins, William D.

2015-11-23

The superparameterized Community Atmosphere Model (SPCAM) is used to investigate the impact and geographic sensitivity of positive Indian Ocean Dipole (+IOD) sea-surface temperatures (SSTs) on Madden-Julian oscillation (MJO) propagation. The goal is to clarify potentially appreciable +IOD effects on MJO dynamics detected in prior studies by using a global model with explicit convection representation. Prescribed climatological October SSTs and variants of the SST distribution from October 2006, a +IOD event, force the model. Modest MJO convection weakening over the Maritime Continent occurs when either climatological SSTs, or +IOD SST anomalies restricted to the Indian Ocean, are applied. However, severe MJOmore » weakening occurs when either +IOD SST anomalies are applied globally or restricted to the equatorial Pacific. MJO disruption is associated with time-mean changes in the zonal wind profile and lower moist static energy (MSE) in subsiding air masses imported from the Subtropics by Rossby-like gyres. On intraseasonal scales, MJO disruption arises from significantly smaller MSE accumulation, weaker meridional advective moistening, and overactive submonthly eddies that mix drier subtropical air into the path of MJO convection. These results (1) demonstrate that SPCAM reproduces observed time-mean and intraseasonal changes during +IOD episodes, (2) reaffirm the role that submonthly eddies play in MJO propagation and show that such multiscale interactions are sensitive to interannual SST states, and (3) suggest that boreal fall +IOD SSTs local to the Indian Ocean have a significantly smaller impact on Maritime Continent MJO propagation compared to contemporaneous Pacific SST anomalies which, for October 2006, resemble El Ninõ-like conditions.« less

Sensitivity of MJO propagation to a robust positive Indian Ocean dipole event in the superparameterized CAM

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

Benedict, James J.; Pritchard, Michael S.; Collins, William D.

The superparameterized Community Atmosphere Model (SPCAM) is used to investigate the impact and geographic sensitivity of positive Indian Ocean Dipole (+IOD) sea-surface temperatures (SSTs) on Madden-Julian oscillation (MJO) propagation. The goal is to clarify potentially appreciable +IOD effects on MJO dynamics detected in prior studies by using a global model with explicit convection representation. Prescribed climatological October SSTs and variants of the SST distribution from October 2006, a +IOD event, force the model. Modest MJO convection weakening over the Maritime Continent occurs when either climatological SSTs, or +IOD SST anomalies restricted to the Indian Ocean, are applied. However, severe MJOmore » weakening occurs when either +IOD SST anomalies are applied globally or restricted to the equatorial Pacific. MJO disruption is associated with time-mean changes in the zonal wind profile and lower moist static energy (MSE) in subsiding air masses imported from the Subtropics by Rossby-like gyres. On intraseasonal scales, MJO disruption arises from significantly smaller MSE accumulation, weaker meridional advective moistening, and overactive submonthly eddies that mix drier subtropical air into the path of MJO convection. These results (1) demonstrate that SPCAM reproduces observed time-mean and intraseasonal changes during +IOD episodes, (2) reaffirm the role that submonthly eddies play in MJO propagation and show that such multiscale interactions are sensitive to interannual SST states, and (3) suggest that boreal fall +IOD SSTs local to the Indian Ocean have a significantly smaller impact on Maritime Continent MJO propagation compared to contemporaneous Pacific SST anomalies which, for October 2006, resemble El Ninõ-like conditions.« less

Quantification of Cannabinoid Content in Cannabis

NASA Astrophysics Data System (ADS)

Tian, Y.; Zhang, F.; Jia, K.; Wen, M.; Yuan, Ch.

2015-09-01

Cannabis is an economically important plant that is used in many fields, in addition to being the most commonly consumed illicit drug worldwide. Monitoring the spatial distribution of cannabis cultivation and judging whether it is drug- or fiber-type cannabis is critical for governments and international communities to understand the scale of the illegal drug trade. The aim of this study was to investigate whether the cannabinoids content in cannabis could be spectrally quantified using a spectrometer and to identify the optimal wavebands for quantifying the cannabinoid content. Spectral reflectance data of dried cannabis leaf samples and the cannabis canopy were measured in the laboratory and in the field, respectively. Correlation analysis and the stepwise multivariate regression method were used to select the optimal wavebands for cannabinoid content quantification based on the laboratory-measured spectral data. The results indicated that the delta-9-tetrahydrocannabinol (THC) content in cannabis leaves could be quantified using laboratory-measured spectral reflectance data and that the 695 nm band is the optimal band for THC content quantification. This study provides prerequisite information for designing spectral equipment to enable immediate quantification of THC content in cannabis and to discriminate drug- from fiber-type cannabis based on THC content quantification in the field.

A Differential Effect of Indian Ocean Dipole and El Niño on Cholera Dynamics in Bangladesh

PubMed Central

Hashizume, Masahiro; Chaves, Luis Fernando; Faruque, A. S. G.; Yunus, Md; Streatfield, Kim; Moji, Kazuhiko

2013-01-01

Background A stationary (i.e., constant through time) association between El Niño Southern Oscillation (ENSO), the Indian Ocean Dipole (IOD) and epidemics of cholera in Bangladesh has been widely assumed. However, whether or not elements of the local climate that are relevant for cholera transmission have stationary signatures of the IOD on their dynamics over different time scales is still not clear. Here we report results on the time-varying relationships between the various remote and local environmental drivers and cholera incidence in Bangladesh. Methodology/Principal Findings We performed a cross wavelet coherency analysis to examine patterns of association between monthly cholera cases in the hospitals in Dhaka and Matlab (1983–2008) and indices for both IOD and ENSO. Our results showed that the strength of both the IOD and ENSO associations with cholera hospitalizations changed across time scales during the study period. In Dhaka, 4-year long coherent cycles were observed between cholera and the index of IOD in 1988–1997. In Matlab, the effect of ENSO was more dominant while there was no evidence for an IOD effect on cholera hospitalizations. Conclusions/Significance Our results call for the consideration of non-stationary, possibly non-linear, patterns of association between cholera hospitalizations and climatic factors in cholera epidemic early warning systems. PMID:23555861

Implant-supported Mandibular Overdentures in Very Old Adults

PubMed Central

Müller, F.; Duvernay, E.; Loup, A.; Vazquez, L.; Herrmann, F.R.; Schimmel, M.

2013-01-01

The purpose of this study was (1) to investigate denture satisfaction following the conversion of existing mandibular complete dentures to implant overdentures (IOD) in very old edentulous patients who depend on help for activities of daily living and (2) to evaluate secondary end points, such as functional, structural, nutritional, and patient-centered aspects. For this randomized clinical trial, 2 interforaminal short implants were placed in the intervention group (n = 16, 85.0 ± 6.19 yrs) to retain mandibular IODs; the control group (n = 18, 84.1 ± 5.55 yrs) received conventional relines. During the first year, no implant was lost; however, 2 patients died. IODs proved more stable, and participants in the intervention group demonstrated significantly higher denture satisfaction as well as an increased oral health–related quality of life compared to the control group. Maximum voluntary bite force improved significantly with IODs, yet the chewing efficiency was not different between groups. Masseter muscle thickness increased with IODs, mainly on the preferred chewing side. Body mass index decreased in both groups, but the decline tended to be smaller in the intervention group; blood markers and the Mini Nutritional Assessment did not confirm this tendency. These results indicate that edentulous patients who depend on help for activities of daily living may benefit from IODs even late in life (ClinicalTrial.gov NCT01928004). PMID:24158342

Development of a Protein Standard Absolute Quantification (PSAQ™) assay for the quantification of Staphylococcus aureus enterotoxin A in serum.

PubMed

Adrait, Annie; Lebert, Dorothée; Trauchessec, Mathieu; Dupuis, Alain; Louwagie, Mathilde; Masselon, Christophe; Jaquinod, Michel; Chevalier, Benoît; Vandenesch, François; Garin, Jérôme; Bruley, Christophe; Brun, Virginie

2012-06-06

Enterotoxin A (SEA) is a staphylococcal virulence factor which is suspected to worsen septic shock prognosis. However, the presence of SEA in the blood of sepsis patients has never been demonstrated. We have developed a mass spectrometry-based assay for the targeted and absolute quantification of SEA in serum. To enhance sensitivity and specificity, we combined an immunoaffinity-based sample preparation with mass spectrometry analysis in the selected reaction monitoring (SRM) mode. Absolute quantification of SEA was performed using the PSAQ™ method (Protein Standard Absolute Quantification), which uses a full-length isotope-labeled SEA as internal standard. The lower limit of detection (LLOD) and lower limit of quantification (LLOQ) were estimated at 352pg/mL and 1057pg/mL, respectively. SEA recovery after immunocapture was determined to be 7.8±1.4%. Therefore, we assumed that less than 1femtomole of each SEA proteotypic peptide was injected on the liquid chromatography column before SRM analysis. From a 6-point titration experiment, quantification accuracy was determined to be 77% and precision at LLOQ was lower than 5%. With this sensitive PSAQ-SRM assay, we expect to contribute to decipher the pathophysiological role of SEA in severe sepsis. This article is part of a Special Issue entitled: Proteomics: The clinical link. Copyright © 2011 Elsevier B.V. All rights reserved.

Colour thresholding and objective quantification in bioimaging

NASA Technical Reports Server (NTRS)

Fermin, C. D.; Gerber, M. A.; Torre-Bueno, J. R.

1992-01-01

Computer imaging is rapidly becoming an indispensable tool for the quantification of variables in research and medicine. Whilst its use in medicine has largely been limited to qualitative observations, imaging in applied basic sciences, medical research and biotechnology demands objective quantification of the variables in question. In black and white densitometry (0-256 levels of intensity) the separation of subtle differences between closely related hues from stains is sometimes very difficult. True-colour and real-time video microscopy analysis offer choices not previously available with monochrome systems. In this paper we demonstrate the usefulness of colour thresholding, which has so far proven indispensable for proper objective quantification of the products of histochemical reactions and/or subtle differences in tissue and cells. In addition, we provide interested, but untrained readers with basic information that may assist decisions regarding the most suitable set-up for a project under consideration. Data from projects in progress at Tulane are shown to illustrate the advantage of colour thresholding over monochrome densitometry and for objective quantification of subtle colour differences between experimental and control samples.

Cues, quantification, and agreement in language comprehension.

PubMed

Tanner, Darren; Bulkes, Nyssa Z

2015-12-01

We investigated factors that affect the comprehension of subject-verb agreement in English, using quantification as a window into the relationship between morphosyntactic processes in language production and comprehension. Event-related brain potentials (ERPs) were recorded while participants read sentences with grammatical and ungrammatical verbs, in which the plurality of the subject noun phrase was either doubly marked (via overt plural quantification and morphological marking on the noun) or singly marked (via only plural morphology on the noun). Both acceptability judgments and the ERP data showed heightened sensitivity to agreement violations when quantification provided an additional cue to the grammatical number of the subject noun phrase, over and above plural morphology. This is consistent with models of grammatical comprehension that emphasize feature prediction in tandem with cue-based memory retrieval. Our results additionally contrast with those of prior studies that showed no effects of plural quantification on agreement in language production. These findings therefore highlight some nontrivial divergences in the cues and mechanisms supporting morphosyntactic processing in language production and comprehension.

Multiplex Droplet Digital PCR Protocols for Quantification of GM Maize Events.

PubMed

Dobnik, David; Spilsberg, Bjørn; Bogožalec Košir, Alexandra; Štebih, Dejan; Morisset, Dany; Holst-Jensen, Arne; Žel, Jana

2018-01-01

The standard-curve based simplex quantitative polymerase chain reaction (qPCR) has been the gold standard for DNA target quantification for more than a decade. The large and growing number of individual analyses needed to test for genetically modified organisms (GMOs) is reducing the cost-effectiveness of qPCR. Droplet digital PCR (ddPCR) enables absolute quantification without standard curves, avoids the amplification efficiency bias observed with qPCR, allows more accurate estimations at low target copy numbers and, in combination with multiplexing, significantly improves cost efficiency. Here we describe two protocols for multiplex quantification of GM maize events: (1) nondiscriminating, with multiplex quantification of targets as a group (12 GM maize lines) and (2) discriminating, with multiplex quantification of individual targets (events). The first enables the quantification of twelve European Union authorized GM maize events as a group with only two assays, but does not permit determination of the individual events present. The second protocol enables the quantification of four individual targets (three GM events and one endogene) in a single reaction. Both protocols can be modified for quantification of any other DNA target.

Automated quantification of myocardial perfusion SPECT using simplified normal limits.

PubMed

Slomka, Piotr J; Nishina, Hidetaka; Berman, Daniel S; Akincioglu, Cigdem; Abidov, Aiden; Friedman, John D; Hayes, Sean W; Germano, Guido

2005-01-01

To simplify development of normal limits for myocardial perfusion SPECT (MPS), we implemented a quantification scheme in which normal limits are derived without visual scoring of abnormal scans or optimization of regional thresholds. Normal limits were derived from same-day TI-201 rest/Tc-99m-sestamibi stress scans of male (n = 40) and female (n = 40) low-likelihood patients. Defect extent, total perfusion deficit (TPD), and regional perfusion extents were derived by comparison to normal limits in polar-map coordinates. MPS scans from 256 consecutive patients without known coronary artery disease, who underwent coronary angiography, were analyzed. The new method of quantification (TPD) was compared with our previously developed quantification system and visual scoring. The receiver operator characteristic area under the curve for detection of 50% or greater stenoses by TPD (0.88 +/- 0.02) was higher than by visual scoring (0.83 +/- 0.03) ( P = .039) or standard quantification (0.82 +/- 0.03) ( P = .004). For detection of 70% or greater stenoses, it was higher for TPD (0.89 +/- 0.02) than for standard quantification (0.85 +/- 0.02) ( P = .014). Sensitivity and specificity were 93% and 79%, respectively, for TPD; 81% and 85%, respectively, for visual scoring; and 80% and 73%, respectively, for standard quantification. The use of stress mode-specific normal limits did not improve performance. Simplified quantification achieves performance better than or equivalent to visual scoring or quantification based on per-segment visual optimization of abnormality thresholds.

Selective Distance-Based K+ Quantification on Paper-Based Microfluidics.

PubMed

Gerold, Chase T; Bakker, Eric; Henry, Charles S

2018-04-03

In this study, paper-based microfluidic devices (μPADs) capable of K + quantification in aqueous samples, as well as in human serum, using both colorimetric and distance-based methods are described. A lipophilic phase containing potassium ionophore I (valinomycin) was utilized to achieve highly selective quantification of K + in the presence of Na + , Li + , and Mg 2+ ions. Successful addition of a suspended lipophilic phase to a wax printed paper-based device is described and offers a solution to current approaches that rely on organic solvents, which damage wax barriers. The approach provides an avenue for future alkali/alkaline quantification utilizing μPADs. Colorimetric spot tests allowed for K + quantification from 0.1-5.0 mM using only 3.00 μL of sample solution. Selective distance-based quantification required small sample volumes (6.00 μL) and gave responses sensitive enough to distinguish between 1.0 and 2.5 mM of sample K + . μPADs using distance-based methods were also capable of differentiating between 4.3 and 6.9 mM K + in human serum samples. Distance-based methods required no digital analysis, electronic hardware, or pumps; any steps required for quantification could be carried out using the naked eye.

Quantification of uncertainties for application in detonation simulation

NASA Astrophysics Data System (ADS)

Zheng, Miao; Ma, Zhibo

2016-06-01

Numerical simulation has become an important means in designing detonation systems, and the quantification of its uncertainty is also necessary to reliability certification. As to quantifying the uncertainty, it is the most important to analyze how the uncertainties occur and develop, and how the simulations develop from benchmark models to new models. Based on the practical needs of engineering and the technology of verification & validation, a framework of QU(quantification of uncertainty) is brought forward in the case that simulation is used on detonation system for scientific prediction. An example is offered to describe the general idea of quantification of simulation uncertainties.

Rapid quantification and sex determination of forensic evidence materials.

PubMed

Andréasson, Hanna; Allen, Marie

2003-11-01

DNA quantification of forensic evidence is very valuable for an optimal use of the available biological material. Moreover, sex determination is of great importance as additional information in criminal investigations as well as in identification of missing persons, no suspect cases, and ancient DNA studies. While routine forensic DNA analysis based on short tandem repeat markers includes a marker for sex determination, analysis of samples containing scarce amounts of DNA is often based on mitochondrial DNA, and sex determination is not performed. In order to allow quantification and simultaneous sex determination on minute amounts of DNA, an assay based on real-time PCR analysis of a marker within the human amelogenin gene has been developed. The sex determination is based on melting curve analysis, while an externally standardized kinetic analysis allows quantification of the nuclear DNA copy number in the sample. This real-time DNA quantification assay has proven to be highly sensitive, enabling quantification of single DNA copies. Although certain limitations were apparent, the system is a rapid, cost-effective, and flexible assay for analysis of forensic casework samples.

Revisiting Cholera-Climate Teleconnections in the Native Homeland: ENSO and other Extremes through the Regional Hydroclimatic Drivers

NASA Astrophysics Data System (ADS)

Akanda, A. S.; Jutla, A.; Huq, A.; Colwell, R. R.

2014-12-01

Cholera is a global disease, with significantly large outbreaks occurring since the 1990s, notably in Sub-Saharan Africa and South Asia and recently in Haiti, in the Caribbean. Critical knowledge gaps remain in the understanding of the annual recurrence in endemic areas and the nature of epidemic outbreaks, especially those that follow extreme hydroclimatic events. Teleconnections with large-scale climate phenomena affecting regional scale hydroclimatic drivers of cholera dynamics remain largely unexplained. For centuries, the Bengal delta region has been strongly influenced by the asymmetric availability of water in the rivers Ganges and the Brahmaputra. As these two major rivers are known to have strong contrasting affects on local cholera dynamics in the region, we argue that the role of El Nino-Southern Oscillation (ENSO), Indian Ocean Dipole (IOD), or other phenomena needs to be interpreted in the context of the seasonal role of individual rivers and subsequent impact on local environmental processes, not as a teleconnection having a remote and unified effect. We present a modified hypothesis that the influences of large-scale climate phenomena such as ENSO and IOD on Bengal cholera can be explicitly identified and incorporated through regional scale hydroclimatic drivers. Here, we provide an analytical review of the literature addressing cholera and climate linkages and present hypotheses, based on recent evidence, and quantification on the role of regional scale hydroclimatic drivers of cholera. We argue that the seasonal changes in precipitation and temperature, and resulting river discharge in the GBM basin region during ENSO and IOD events have a dominant combined effect on the endemic persistence and the epidemic vulnerability to cholera outbreaks in spring and fall seasons, respectively, that is stronger than the effect of localized hydrological and socio-economic sensitivities in Bangladesh. In addition, systematic identification of underlying seasonal

Rotational movements of mandibular two-implant overdentures.

PubMed

Kimoto, Suguru; Pan, Shaoxia; Drolet, Nicolas; Feine, Jocelyne S

2009-08-01

Clinicians have reported that their patients complain that their mandibular two-implant overdentures (IOD) rotate. Therefore, we studied the frequency and severity of rotation of IODs with two-ball attachments, how rotation may influence perceived satisfaction ratings of chewing ability, and the factors that are involved in the rotation of IODs. Seventy-nine participants were recruited and asked to rate their general satisfaction of their IODs, as well as their ability to chew foods, the existence of any mandibular denture rotation, and to what degree denture rotation bothered them. Data on participant sociodemographic, anatomical, and prosthesis characteristics were also collected. Student's t-test and logistic regression analyses were performed to analyze the differences between participants who did (R group) and did not report (NR group) denture rotation. Thirty-seven of 79 participants were aware of rotational movement in their IODs. These patients were significantly less satisfied with their chewing ability than those who felt no rotation (69.1 mm R group vs. 82.9 mm), and discomfort caused by the rotation bothered them moderately (39/100 mm). The multivariate logistic regression analysis revealed that the arrangement of the anterior teeth and the length of the denture are significantly associated with awareness of denture rotation. Thirty-eight percent in the R group and 31% in the NR group had non-scheduled visits. Rotational movement with a mandibular two-IOD has a negative effect on perceived chewing ability and is associated with anterior tooth arrangement and denture length.

Do implant overdentures improve dietary intake? A randomized clinical trial.

PubMed

Hamdan, N M; Gray-Donald, K; Awad, M A; Johnson-Down, L; Wollin, S; Feine, J S

2013-12-01

People wearing mandibular two-implant overdentures (IOD) chew food with less difficulty than those wearing conventional complete dentures (CD). However, there is still controversy over whether or not this results in better dietary intake. In this randomized clinical trials (RCT), the amounts of total dietary fiber (TDF), macronutrients, 9 micronutrients, and energy in diets consumed by persons with IOD and CD were compared. Male and female edentate patients ≥ 65 yrs (n = 255) were randomly divided into 2 groups and assigned to receive a maxillary CD and either a mandibular IOD or a CD. One year following prosthesis delivery, 217 participants (CD = 114, IOD = 103) reported the food and quantities they consumed to a registered dietician through a standard 24-hour dietary recall method. The mean and median values of TDF, macro- and micronutrients, and energy consumed by both groups were calculated and compared analytically. No significant between-group differences were found (ps > .05). Despite quality-of-life benefits from IODs, this adequately powered study reveals no evidence of nutritional advantages for independently living medically healthy edentate elders wearing two-implant mandibular overdentures over those wearing conventional complete dentures in their dietary intake at one year following prosthesis delivery.

Survey of Existing Uncertainty Quantification Capabilities for Army Relevant Problems

DTIC Science & Technology

2017-11-27

ARL-TR-8218•NOV 2017 US Army Research Laboratory Survey of Existing Uncertainty Quantification Capabilities for Army-Relevant Problems by James J...NOV 2017 US Army Research Laboratory Survey of Existing Uncertainty Quantification Capabilities for Army-Relevant Problems by James J Ramsey...Rev. 8/98)    Prescribed by ANSI Std. Z39.18 November 2017 Technical Report Survey of Existing Uncertainty Quantification Capabilities for Army

Critical points of DNA quantification by real-time PCR – effects of DNA extraction method and sample matrix on quantification of genetically modified organisms

PubMed Central

Cankar, Katarina; Štebih, Dejan; Dreo, Tanja; Žel, Jana; Gruden, Kristina

2006-01-01

Background Real-time PCR is the technique of choice for nucleic acid quantification. In the field of detection of genetically modified organisms (GMOs) quantification of biotech products may be required to fulfil legislative requirements. However, successful quantification depends crucially on the quality of the sample DNA analyzed. Methods for GMO detection are generally validated on certified reference materials that are in the form of powdered grain material, while detection in routine laboratories must be performed on a wide variety of sample matrixes. Due to food processing, the DNA in sample matrixes can be present in low amounts and also degraded. In addition, molecules of plant origin or from other sources that affect PCR amplification of samples will influence the reliability of the quantification. Further, the wide variety of sample matrixes presents a challenge for detection laboratories. The extraction method must ensure high yield and quality of the DNA obtained and must be carefully selected, since even components of DNA extraction solutions can influence PCR reactions. GMO quantification is based on a standard curve, therefore similarity of PCR efficiency for the sample and standard reference material is a prerequisite for exact quantification. Little information on the performance of real-time PCR on samples of different matrixes is available. Results Five commonly used DNA extraction techniques were compared and their suitability for quantitative analysis was assessed. The effect of sample matrix on nucleic acid quantification was assessed by comparing 4 maize and 4 soybean matrixes. In addition 205 maize and soybean samples from routine analysis were analyzed for PCR efficiency to assess variability of PCR performance within each sample matrix. Together with the amount of DNA needed for reliable quantification, PCR efficiency is the crucial parameter determining the reliability of quantitative results, therefore it was chosen as the primary

GMO quantification: valuable experience and insights for the future.

PubMed

Milavec, Mojca; Dobnik, David; Yang, Litao; Zhang, Dabing; Gruden, Kristina; Zel, Jana

2014-10-01

Cultivation and marketing of genetically modified organisms (GMOs) have been unevenly adopted worldwide. To facilitate international trade and to provide information to consumers, labelling requirements have been set up in many countries. Quantitative real-time polymerase chain reaction (qPCR) is currently the method of choice for detection, identification and quantification of GMOs. This has been critically assessed and the requirements for the method performance have been set. Nevertheless, there are challenges that should still be highlighted, such as measuring the quantity and quality of DNA, and determining the qPCR efficiency, possible sequence mismatches, characteristics of taxon-specific genes and appropriate units of measurement, as these remain potential sources of measurement uncertainty. To overcome these problems and to cope with the continuous increase in the number and variety of GMOs, new approaches are needed. Statistical strategies of quantification have already been proposed and expanded with the development of digital PCR. The first attempts have been made to use new generation sequencing also for quantitative purposes, although accurate quantification of the contents of GMOs using this technology is still a challenge for the future, and especially for mixed samples. New approaches are needed also for the quantification of stacks, and for potential quantification of organisms produced by new plant breeding techniques.

Genetic Algorithm for Initial Orbit Determination with Too Short Arc

NASA Astrophysics Data System (ADS)

Li, X. R.; Wang, X.

2016-01-01

The sky surveys of space objects have obtained a huge quantity of too-short-arc (TSA) observation data. However, the classical method of initial orbit determination (IOD) can hardly get reasonable results for the TSAs. The IOD is reduced to a two-stage hierarchical optimization problem containing three variables for each stage. Using the genetic algorithm, a new method of the IOD for TSAs is established, through the selection of optimizing variables as well as the corresponding genetic operator for specific problems. Numerical experiments based on the real measurements show that the method can provide valid initial values for the follow-up work.

Oceanic Precondition and Evolution of the Indian Ocean Dipole Events

NASA Astrophysics Data System (ADS)

Horii, T.; Masumoto, Y.; Ueki, I.; Hase, H.; Mizuno, K.

2008-12-01

Indian Ocean Dipole (IOD) is one of the interannual climate variability in the Indian Ocean, associated with the negative (positive) SST anomaly in the eastern (western) equatorial region developing during boreal summer/autumn seasons. Japan Agency for Marine-Earth Science and Technology (JAMSTEC) has been deploying TRITON buoys in the eastern equatorial Indian Ocean since October 2001. Details of subsurface ocean conditions associated with IOD events were observed by the mooring buoys in the eastern equatorial Indian Ocean in 2006, 2007, and 2008. In the 2006 IOD event, large-scale sea surface signals in the tropical Indian Ocean associated with the positive IOD started in August 2006, and the anomalous conditions continued until December 2006. Data from the mooring buoys, however, captured the first appearance of the negative temperature anomaly at the thermocline depth with strong westward current anomalies in May 2006, about three months earlier than the development of the surface signatures. Similar appearance of negative temperature anomalies in the subsurface were also observed in 2007 and 2008, while the amplitude, the timing, and the relation to the surface layer were different among the events. The implications of the subsurface conditions for the occurrences of these IOD events are discussed.

Do Implant Overdentures Improve Dietary Intake? A Randomized Clinical Trial

PubMed Central

Hamdan, N.M.; Gray-Donald, K.; Awad, M.A.; Johnson-Down, L.; Wollin, S.; Feine, J.S.

2013-01-01

People wearing mandibular two-implant overdentures (IOD) chew food with less difficulty than those wearing conventional complete dentures (CD). However, there is still controversy over whether or not this results in better dietary intake. In this randomized clinical trials (RCT), the amounts of total dietary fiber (TDF), macronutrients, 9 micronutrients, and energy in diets consumed by persons with IOD and CD were compared. Male and female edentate patients ≥ 65 yrs (n = 255) were randomly divided into 2 groups and assigned to receive a maxillary CD and either a mandibular IOD or a CD. One year following prosthesis delivery, 217 participants (CD = 114, IOD = 103) reported the food and quantities they consumed to a registered dietician through a standard 24-hour dietary recall method. The mean and median values of TDF, macro- and micronutrients, and energy consumed by both groups were calculated and compared analytically. No significant between-group differences were found (ps > .05). Despite quality-of-life benefits from IODs, this adequately powered study reveals no evidence of nutritional advantages for independently living medically healthy edentate elders wearing two-implant mandibular overdentures over those wearing conventional complete dentures in their dietary intake at one year following prosthesis delivery (International Clinical Trials ISRCTN24273915). PMID:24158335

The role of Indonesian convection in the interaction between the Indian Ocean and ENSO

NASA Astrophysics Data System (ADS)

Wieners, Claudia; Dijkstra, Henk; de Ruijter, Will

2017-04-01

In recent years it has been discussed whether a cool West Indian Ocean (WIO) or negative Indian Ocean Dipole (IOD) in boreal autumn favours El Niño at a lead time of 15 months (Izumo et al, 2010; Wieners et al, 2016). Observational evidence suggests that a cool WIO or negative IOD might be accompanied by easterlies over the West Pacific, though it is hard to disentangle influences of the Indian Ocean and ENSO through data analysis. Such easterlies can enhance the West Pacific Warm Water Volume, thus favouring El Niño development from the following boreal spring onward. However, the Gill response to a cool WIO (negative IOD) forcing would lead to westerly (nearly zero) winds over the WPO. We hypothesise that a cool WIO or negative IOD leads to low-level air convergence and hence enhanced convectional heating over the Maritime Continent (MC), which in turn amplifies the wind convergence such as to cause easterly winds over the West Pacific. This hypothesis is tested by adding a simplified Indian Ocean and a simple convective feedback over the MC to a Zebiak-Cane model. We confirm that for a sufficiently strong convection feedback a cool WIO or negative IOD indeed leads to easterlies over the WPO. The response IO cooling over the whole zonal width of the basin (negative Indian Ocean Basinwide warming / IOB) is still westerly, with the direct Gill response dominating over convection-induced winds. Positive (negative) IOB events typically occur a few months after El Niño (La Niña) - observed correlations are about 0.9 - and cause easterlies (westerlies) over the Pacific, facilitating the switch to the opposite ENSO phase, hence IOB variability dampens the ENSO mode and reduces its period. The IOD, on the other hand, tends to be positive (negative) a few months prior to El Niño (La Niña) and trigger westerlies (easterlies) favouring ENSO development. However, the observed correlation between IOD and ENSO is only about 0.6, i.e. the IOD is less closely liked to the

Recent application of quantification II in Japanese medical research.

PubMed Central

Suzuki, T; Kudo, A

1979-01-01

Hayashi's Quantification II is a method of multivariate discrimination analysis to manipulate attribute data as predictor variables. It is very useful in the medical research field for estimation, diagnosis, prognosis, evaluation of epidemiological factors, and other problems based on multiplicity of attribute data. In Japan, this method is so well known that most of the computer program packages include the Hayashi Quantification, but it seems to be yet unfamiliar with the method for researchers outside Japan. In view of this situation, we introduced 19 selected articles of recent applications of the Quantification II in Japanese medical research. In reviewing these papers, special mention is made to clarify how the researchers were satisfied with findings provided by the method. At the same time, some recommendations are made about terminology and program packages. Also a brief discussion of the background of the quantification methods is given with special reference to the Behaviormetric Society of Japan. PMID:540587

A quantification model for the structure of clay materials.

PubMed

Tang, Liansheng; Sang, Haitao; Chen, Haokun; Sun, Yinlei; Zhang, Longjian

2016-07-04

In this paper, the quantification for clay structure is explicitly explained, and the approach and goals of quantification are also discussed. The authors consider that the purpose of the quantification for clay structure is to determine some parameters that can be used to quantitatively characterize the impact of clay structure on the macro-mechanical behaviour. According to the system theory and the law of energy conservation, a quantification model for the structure characteristics of clay materials is established and three quantitative parameters (i.e., deformation structure potential, strength structure potential and comprehensive structure potential) are proposed. And the corresponding tests are conducted. The experimental results show that these quantitative parameters can accurately reflect the influence of clay structure on the deformation behaviour, strength behaviour and the relative magnitude of structural influence on the above two quantitative parameters, respectively. These quantitative parameters have explicit mechanical meanings, and can be used to characterize the structural influences of clay on its mechanical behaviour.

Artifacts Quantification of Metal Implants in MRI

NASA Astrophysics Data System (ADS)

Vrachnis, I. N.; Vlachopoulos, G. F.; Maris, T. G.; Costaridou, L. I.

2017-11-01

The presence of materials with different magnetic properties, such as metal implants, causes distortion of the magnetic field locally, resulting in signal voids and pile ups, i.e. susceptibility artifacts in MRI. Quantitative and unbiased measurement of the artifact is prerequisite for optimization of acquisition parameters. In this study an image gradient based segmentation method is proposed for susceptibility artifact quantification. The method captures abrupt signal alterations by calculation of the image gradient. Then the artifact is quantified in terms of its extent by an automated cross entropy thresholding method as image area percentage. The proposed method for artifact quantification was tested in phantoms containing two orthopedic implants with significantly different magnetic permeabilities. The method was compared against a method proposed in the literature, considered as a reference, demonstrating moderate to good correlation (Spearman’s rho = 0.62 and 0.802 in case of titanium and stainless steel implants). The automated character of the proposed quantification method seems promising towards MRI acquisition parameter optimization.

On the relationship between the Indian summer monsoon rainfall and the EQUINOO in the CFSv2

NASA Astrophysics Data System (ADS)

Vishnu, S.; Francis, P. A.; Ramakrishna, S. S. V. S.; Shenoi, S. S. C.

2018-03-01

Several recent studies have shown that positive (negative) phase of Equatorial Indian Ocean Oscillation (EQUINOO) is favourable (unfavourable) to the Indian summer monsoon. However, many ocean-atmosphere global coupled models, including the state-of-the-art Climate Forecast System (CFS) version 2 have difficulty in reproducing this link realistically. In this study, we analyze the retrospective forecasts by the CFS model for the period 1982-2010 with an objective to identify the reasons behind the failure of the model to simulate the observed links between Indian summer monsoon and EQUINOO. It is found that, in the model hindcasts, the rainfall in the core monsoon region was mainly due to westward propagating synoptic scale systems, that originated from the vicinity of the tropical convergence zone (TCZ). Our analysis shows that unlike in observations, in the CFS, majority of positive (negative) EQUINOO events are associated with El Niño (La Niña) events in the Pacific. In addition to this, there is a strong link between EQUINOO and Indian Ocean Dipole (IOD) in the model. We show that, during the negative phase of EQUINOO/IOD, northward propagating TCZs remained stationary over the Bay of Bengal for longer period compared to the positive phase of EQUINOO/IOD. As a result, compared to the positive phase of EQUINOO/IOD, during a negative phase of EQUINOO/IOD, more westward propagating synoptic scale systems originated from the vicinity of TCZ and moved on to the core monsoon region, which resulted in higher rainfall over this region in the CFS. We further show that frequent, though short-lived, westward propagating systems, generated near the vicinity of TCZ over the Bay moved onto the mainland were responsible for less number of break monsoon spells during the negative phase of EQUINOO/IOD in the model hindcasts. This study underlines the necessity for improving the skill of the coupled models, particularly CFS model, to simulate the links between EQUINOO/IOD and

Collagen Quantification in Tissue Specimens.

PubMed

Coentro, João Quintas; Capella-Monsonís, Héctor; Graceffa, Valeria; Wu, Zhuning; Mullen, Anne Maria; Raghunath, Michael; Zeugolis, Dimitrios I

2017-01-01

Collagen is the major extracellular protein in mammals. Accurate quantification of collagen is essential in the biomaterials (e.g., reproducible collagen scaffold fabrication), drug discovery (e.g., assessment of collagen in pathophysiologies, such as fibrosis), and tissue engineering (e.g., quantification of cell-synthesized collagen) fields. Although measuring hydroxyproline content is the most widely used method to quantify collagen in biological specimens, the process is very laborious. To this end, the Sircol™ Collagen Assay is widely used due to its inherent simplicity and convenience. However, this method leads to overestimation of collagen content due to the interaction of Sirius red with basic amino acids of non-collagenous proteins. Herein, we describe the addition of an ultrafiltration purification step in the process to accurately determine collagen content in tissues.

Quantitative Proteomics via High Resolution MS Quantification: Capabilities and Limitations

PubMed Central

Higgs, Richard E.; Butler, Jon P.; Han, Bomie; Knierman, Michael D.

2013-01-01

Recent improvements in the mass accuracy and resolution of mass spectrometers have led to renewed interest in label-free quantification using data from the primary mass spectrum (MS1) acquired from data-dependent proteomics experiments. The capacity for higher specificity quantification of peptides from samples enriched for proteins of biological interest offers distinct advantages for hypothesis generating experiments relative to immunoassay detection methods or prespecified peptide ions measured by multiple reaction monitoring (MRM) approaches. Here we describe an evaluation of different methods to post-process peptide level quantification information to support protein level inference. We characterize the methods by examining their ability to recover a known dilution of a standard protein in background matrices of varying complexity. Additionally, the MS1 quantification results are compared to a standard, targeted, MRM approach on the same samples under equivalent instrument conditions. We show the existence of multiple peptides with MS1 quantification sensitivity similar to the best MRM peptides for each of the background matrices studied. Based on these results we provide recommendations on preferred approaches to leveraging quantitative measurements of multiple peptides to improve protein level inference. PMID:23710359

Increased frequency of extreme Indian Ocean Dipole events due to greenhouse warming.

PubMed

Cai, Wenju; Santoso, Agus; Wang, Guojian; Weller, Evan; Wu, Lixin; Ashok, Karumuri; Masumoto, Yukio; Yamagata, Toshio

2014-06-12

The Indian Ocean dipole is a prominent mode of coupled ocean-atmosphere variability, affecting the lives of millions of people in Indian Ocean rim countries. In its positive phase, sea surface temperatures are lower than normal off the Sumatra-Java coast, but higher in the western tropical Indian Ocean. During the extreme positive-IOD (pIOD) events of 1961, 1994 and 1997, the eastern cooling strengthened and extended westward along the equatorial Indian Ocean through strong reversal of both the mean westerly winds and the associated eastward-flowing upper ocean currents. This created anomalously dry conditions from the eastern to the central Indian Ocean along the Equator and atmospheric convergence farther west, leading to catastrophic floods in eastern tropical African countries but devastating droughts in eastern Indian Ocean rim countries. Despite these serious consequences, the response of pIOD events to greenhouse warming is unknown. Here, using an ensemble of climate models forced by a scenario of high greenhouse gas emissions (Representative Concentration Pathway 8.5), we project that the frequency of extreme pIOD events will increase by almost a factor of three, from one event every 17.3 years over the twentieth century to one event every 6.3 years over the twenty-first century. We find that a mean state change--with weakening of both equatorial westerly winds and eastward oceanic currents in association with a faster warming in the western than the eastern equatorial Indian Ocean--facilitates more frequent occurrences of wind and oceanic current reversal. This leads to more frequent extreme pIOD events, suggesting an increasing frequency of extreme climate and weather events in regions affected by the pIOD.

Genetic Algorithm for Initial Orbit Determination with Too Short Arc

NASA Astrophysics Data System (ADS)

Li, Xin-ran; Wang, Xin

2017-01-01

A huge quantity of too-short-arc (TSA) observational data have been obtained in sky surveys of space objects. However, reasonable results for the TSAs can hardly be obtained with the classical methods of initial orbit determination (IOD). In this paper, the IOD is reduced to a two-stage hierarchical optimization problem containing three variables for each stage. Using the genetic algorithm, a new method of the IOD for TSAs is established, through the selections of the optimized variables and the corresponding genetic operators for specific problems. Numerical experiments based on the real measurements show that the method can provide valid initial values for the follow-up work.

Quantification of micro stickies

Treesearch

Mahendra Doshi; Jeffrey Dyer; Salman Aziz; Kristine Jackson; Said M. Abubakr

1997-01-01

The objective of this project was to compare the different methods for the quantification of micro stickies. The hydrophobic materials investigated in this project for the collection of micro stickies were Microfoam* (polypropylene packing material), low density polyethylene film (LDPE), high density polyethylene (HDPE; a flat piece from a square plastic bottle), paper...

Lesion Quantification in Dual-Modality Mammotomography

NASA Astrophysics Data System (ADS)

Li, Heng; Zheng, Yibin; More, Mitali J.; Goodale, Patricia J.; Williams, Mark B.

2007-02-01

This paper describes a novel x-ray/SPECT dual modality breast imaging system that provides 3D structural and functional information. While only a limited number of views on one side of the breast can be acquired due to mechanical and time constraints, we developed a technique to compensate for the limited angle artifact in reconstruction images and accurately estimate both the lesion size and radioactivity concentration. Various angular sampling strategies were evaluated using both simulated and experimental data. It was demonstrated that quantification of lesion size to an accuracy of 10% and quantification of radioactivity to an accuracy of 20% are feasible from limited-angle data acquired with clinically practical dosage and acquisition time

Predictability of the Indian Ocean Dipole in the coupled models

NASA Astrophysics Data System (ADS)

Liu, Huafeng; Tang, Youmin; Chen, Dake; Lian, Tao

2017-03-01

In this study, the Indian Ocean Dipole (IOD) predictability, measured by the Indian Dipole Mode Index (DMI), is comprehensively examined at the seasonal time scale, including its actual prediction skill and potential predictability, using the ENSEMBLES multiple model ensembles and the recently developed information-based theoretical framework of predictability. It was found that all model predictions have useful skill, which is normally defined by the anomaly correlation coefficient larger than 0.5, only at around 2-3 month leads. This is mainly because there are more false alarms in predictions as leading time increases. The DMI predictability has significant seasonal variation, and the predictions whose target seasons are boreal summer (JJA) and autumn (SON) are more reliable than that for other seasons. All of models fail to predict the IOD onset before May and suffer from the winter (DJF) predictability barrier. The potential predictability study indicates that, with the model development and initialization improvement, the prediction of IOD onset is likely to be improved but the winter barrier cannot be overcome. The IOD predictability also has decadal variation, with a high skill during the 1960s and the early 1990s, and a low skill during the early 1970s and early 1980s, which is very consistent with the potential predictability. The main factors controlling the IOD predictability, including its seasonal and decadal variations, are also analyzed in this study.

Regulation of trace elements and redox status in striatum of adult rats by long-term aerobic exercise depends on iron uptakes.

PubMed

Wu, Hua-Bo; Xiao, De-Sheng

2017-03-06

We investigated the effects of aerobic exercise (AE) on trace element contents and redox status in the striatum of rats with different diet iron. Weaned female rats were randomly fed with iron-adequate diet (IAD), iron-deficient diet (IDD), and iron-overloaded diet (IOD). After feeding their respective diet for 1 month, the rats fed with same diet were divided into swimming and maintaining sedentary (S) group. After 3 months, the non-heme iron (NHI), Mn, Cu, and Zn in the striatum were measured. Meanwhile, malonaldehyde acid (MDA), total superoxide dismutase activity, hydroxyl radical scavenging activity, and total antioxidant capacity were also analyzed. As compared with respective S rats, Mn, Cu, and Zn contents were significantly decreased in IDDE, but no significantly changes could be seen in IADE or IODE. A negative correlation of NHI with Cu contents in IDDE and positive correlations of NHI with Cu, or Zn contents in IADE, or with Mn or Cu contents in IODE were observed. In addition, striatum MDA was significantly decreased and anti-oxidative variables were increased in IODE compared to IODS. Our results suggest that the modification of trace elements and redox status in the striatum of rats caused by AE depends on dietary iron contents and that AE may also regulate the metabolic relationship of iron storage with other trace elements. Copyright © 2017 Elsevier B.V. All rights reserved.

Response of near-surface currents in the Indian Ocean to the anomalous atmospheric condition in 2015

NASA Astrophysics Data System (ADS)

Utari, P. A.; Nurkhakim, M. Y.; Setiabudidaya, D.; Iskandar, I.

2018-05-01

Anomalous ocean-atmosphere conditions were detected in the tropical Indian Ocean during boreal spring to boreal winter 2015. It was suggested that the anomalous conditions were characteristics of the positive Indian Ocean Dipole (pIOD) event. The purpose of this investigation was to investigate the response of near-surface currents in the tropical Indian Ocean to the anomalous atmospheric condition in 2015. Near-surface current from OSCAR (Ocean Surface Current Analyses Real Time) reanalysis data combined with the sea surface temperature (SST) data from OISST – NOAA, sea surface height (SSH) and surface winds from the ECMWF were used in this investigation. The analysis showed that the evolution of 2015 pIOD started in June/July, peaked in the September and terminated in late November 2015. Correlated with the evolution of the pIOD, easterly winds anomalies were detected along the equator. As the oceanic response to these easterly wind anomalies, the surface currents anomalously westward during the peak of the pIOD. It was interesting to note that the evolution of 2015 pIOD event was closely related to the ocean wave dynamics as revealed by the SSH data. Downwelling westward propagating Rossby waves were detected in the southwestern tropical Indian Ocean. Once reached the western boundary of the Indian Ocean, they were redirected back into interior Indian Ocean and propagating eastward as the downwelling Kelvin waves.

Protein quantification using a cleavable reporter peptide.

PubMed

Duriez, Elodie; Trevisiol, Stephane; Domon, Bruno

2015-02-06

Peptide and protein quantification based on isotope dilution and mass spectrometry analysis are widely employed for the measurement of biomarkers and in system biology applications. The accuracy and reliability of such quantitative assays depend on the quality of the stable-isotope labeled standards. Although the quantification using stable-isotope labeled peptides is precise, the accuracy of the results can be severely biased by the purity of the internal standards, their stability and formulation, and the determination of their concentration. Here we describe a rapid and cost-efficient method to recalibrate stable isotope labeled peptides in a single LC-MS analysis. The method is based on the equimolar release of a protein reference peptide (used as surrogate for the protein of interest) and a universal reporter peptide during the trypsinization of a concatenated polypeptide standard. The quality and accuracy of data generated with such concatenated polypeptide standards are highlighted by the quantification of two clinically important proteins in urine samples and compared with results obtained with conventional stable isotope labeled reference peptides. Furthermore, the application of the UCRP standards in complex samples is described.

Phylogenetic Quantification of Intra-tumour Heterogeneity

PubMed Central

Schwarz, Roland F.; Trinh, Anne; Sipos, Botond; Brenton, James D.; Goldman, Nick; Markowetz, Florian

2014-01-01

Intra-tumour genetic heterogeneity is the result of ongoing evolutionary change within each cancer. The expansion of genetically distinct sub-clonal populations may explain the emergence of drug resistance, and if so, would have prognostic and predictive utility. However, methods for objectively quantifying tumour heterogeneity have been missing and are particularly difficult to establish in cancers where predominant copy number variation prevents accurate phylogenetic reconstruction owing to horizontal dependencies caused by long and cascading genomic rearrangements. To address these challenges, we present MEDICC, a method for phylogenetic reconstruction and heterogeneity quantification based on a Minimum Event Distance for Intra-tumour Copy-number Comparisons. Using a transducer-based pairwise comparison function, we determine optimal phasing of major and minor alleles, as well as evolutionary distances between samples, and are able to reconstruct ancestral genomes. Rigorous simulations and an extensive clinical study show the power of our method, which outperforms state-of-the-art competitors in reconstruction accuracy, and additionally allows unbiased numerical quantification of tumour heterogeneity. Accurate quantification and evolutionary inference are essential to understand the functional consequences of tumour heterogeneity. The MEDICC algorithms are independent of the experimental techniques used and are applicable to both next-generation sequencing and array CGH data. PMID:24743184

Quantification of protein carbonylation.

PubMed

Wehr, Nancy B; Levine, Rodney L

2013-01-01

Protein carbonylation is the most commonly used measure of oxidative modification of proteins. It is most often measured spectrophotometrically or immunochemically by derivatizing proteins with the classical carbonyl reagent 2,4 dinitrophenylhydrazine (DNPH). We present protocols for the derivatization and quantification of protein carbonylation with these two methods, including a newly described dot blot with greatly increased sensitivity.

Evaluation of digital PCR for absolute RNA quantification.

PubMed

Sanders, Rebecca; Mason, Deborah J; Foy, Carole A; Huggett, Jim F

2013-01-01

Gene expression measurements detailing mRNA quantities are widely employed in molecular biology and are increasingly important in diagnostic fields. Reverse transcription (RT), necessary for generating complementary DNA, can be both inefficient and imprecise, but remains a quintessential RNA analysis tool using qPCR. This study developed a Transcriptomic Calibration Material and assessed the RT reaction using digital (d)PCR for RNA measurement. While many studies characterise dPCR capabilities for DNA quantification, less work has been performed investigating similar parameters using RT-dPCR for RNA analysis. RT-dPCR measurement using three, one-step RT-qPCR kits was evaluated using single and multiplex formats when measuring endogenous and synthetic RNAs. The best performing kit was compared to UV quantification and sensitivity and technical reproducibility investigated. Our results demonstrate assay and kit dependent RT-dPCR measurements differed significantly compared to UV quantification. Different values were reported by different kits for each target, despite evaluation of identical samples using the same instrument. RT-dPCR did not display the strong inter-assay agreement previously described when analysing DNA. This study demonstrates that, as with DNA measurement, RT-dPCR is capable of accurate quantification of low copy RNA targets, but the results are both kit and target dependent supporting the need for calibration controls.

Spatial and Temporal Climatic Variation in Coastal Tanzania

NASA Astrophysics Data System (ADS)

Rohli, R. V.; Ates, S.; Rivera-Monroy, V. H.; Polito, M. J.; Midway, S. R.; Gold, A.; Castañeda-Moya, E.; Uchida, E.; Suwa, M.; Mangora, M. M.

2017-12-01

Climatic controls are particularly important to the natural and human systems in coastal Tanzania, where mangrove vegetation is a major component of world-renowned biodiversity. This research provides an improved understanding of the climatic features and forcing mechanisms that support the critical mangroves of Tanzania and the livelihoods of its populace, using updated and complete datasets. Updated data confirm that coastal Tanzania falls in the tropical wet-dry Köppen-Geiger climatic type, except for the extreme north, where tropical rain forest exists north of Pangani. The northeast monsoon, known as the kaskazi, largely corresponds to the rainy November-December and March-May months. The southeast monsoon - known as the kusi - overlaps with the drier June-September. Results suggest that El Niño-Southern Oscillation (ENSO) and Indian Ocean Dipole (IOD) are key modulators of precipitation variability in the entire area. More specifically, September-November positive precipitation anomalies occur during positive IOD, especially when combined with El Niño, with slightly negative anomalies during negative IOD, especially when combined with La Niña. The rest of the year tends to show similar precipitation during both IOD phases (March-August) or less precipitation during the positive phase (December-February). Because the literature suggests likelihood of more frequent positive IOD mode and a strengthened relationship of these events to warm-ENSO events, changes to the hydrologic cycle in east Africa may be likely in the future, with a potential for an expanded secondary rainy season and a drier "saddle" between the secondary and primary rainy seasons (i.e., December-February). Therefore, future research should investigate in more detail the influence of the IOD and ENSO on various components of the climatic water balance. Results may be useful to earth, environmental, and social scientists as they seek further understanding of the drivers of ecological and

Clinical outcome of double crown-retained implant overdentures with zirconia primary crowns

PubMed Central

Buergers, Ralf; Ziebolz, Dirk; Roediger, Matthias

2015-01-01

PURPOSE This retrospective study aims at the evaluation of implant-supported overdentures (IODs) supported by ceramo-galvanic double crowns (CGDCs: zirconia primary crowns + galvano-formed secondary crown). MATERIALS AND METHODS In a private practice, 14 patients were restored with 18 IODs (mandible: 11, maxilla: 7) retained by CGDCs on 4 - 8 implants and annually evaluated for technical and/or biological failures/complications. RESULTS One of the 86 inserted implants failed during the healing period (cumulative survival rate (CSR) implants: 98.8%). During the prosthetic functional period (mean: 5.9 ± 2.2 years), 1 implant demonstrated an abutment fracture (CSR-abutments: 98.2%), and one case of peri-implantitis was detected. All IODs remained in function (CSR-denture: 100%). A total of 15 technical complications required interventions to maintain function (technical complication rate: 0.178 treatments/patients/year). CONCLUSION Considering the small sample size, the use of CGDCs for the attachment of IODs is possible without an increased risk of technical complications. However, for a final evaluation, results from a larger cohort are required. PMID:26330981

Functional benefits of implants placed during ablative surgery: A 5-year prospective study on the prosthodontic rehabilitation of 56 edentulous oral cancer patients.

PubMed

Wetzels, Jan Willem; Koole, Ron; Meijer, Gert J; de Haan, Anton F J; Merkx, Matthias A W; Speksnijder, Caroline M

2016-04-01

The timing of placement as well as the functional benefit of interforaminal implants in edentulous patients treated for oral cancer is unclear. Fifty-six patients were recruited at 2 institutions. In 1 institution, interforaminal implants were placed during ablative surgery, the other institution used conventional prosthodontics with optional placement of implants postsurgery (postponed-placement). Masticatory performance, bite force, and subjective masticatory function were assessed before and 6 months, 1 year, and 5 years after surgery. Implant-retained overdentures (IODs) demonstrated the highest bite force and the least problems with solid food and food choice. Masticatory performance was equal for IODs and conventional dentures. After 5 years, IODs from patients in the during-ablative-surgery cohort tend to have higher bite force and masticatory performance than those from patients in the postponed-placement cohort. IODs produce the highest overall masticatory function. Implant placement during ablative surgery seems to be functionally beneficial. © 2016 Wiley Periodicals, Inc. Head Neck 38: E2103-E2111, 2016. © 2016 Wiley Periodicals, Inc.

Automated lobar quantification of emphysema in patients with severe COPD.

PubMed

Revel, Marie-Pierre; Faivre, Jean-Baptiste; Remy-Jardin, Martine; Deken, Valérie; Duhamel, Alain; Marquette, Charles-Hugo; Tacelli, Nunzia; Bakai, Anne-Marie; Remy, Jacques

2008-12-01

Automated lobar quantification of emphysema has not yet been evaluated. Unenhanced 64-slice MDCT was performed in 47 patients evaluated before bronchoscopic lung-volume reduction. CT images reconstructed with a standard (B20) and high-frequency (B50) kernel were analyzed using a dedicated prototype software (MevisPULMO) allowing lobar quantification of emphysema extent. Lobar quantification was obtained following (a) a fully automatic delineation of the lobar limits by the software and (b) a semiautomatic delineation with manual correction of the lobar limits when necessary and was compared with the visual scoring of emphysema severity per lobe. No statistically significant difference existed between automated and semiautomated lobar quantification (p > 0.05 in the five lobes), with differences ranging from 0.4 to 3.9%. The agreement between the two methods (intraclass correlation coefficient, ICC) was excellent for left upper lobe (ICC = 0.94), left lower lobe (ICC = 0.98), and right lower lobe (ICC = 0.80). The agreement was good for right upper lobe (ICC = 0.68) and moderate for middle lobe (IC = 0.53). The Bland and Altman plots confirmed these results. A good agreement was observed between the software and visually assessed lobar predominance of emphysema (kappa 0.78; 95% CI 0.64-0.92). Automated and semiautomated lobar quantifications of emphysema are concordant and show good agreement with visual scoring.

STEM VQ Method, Using Scanning Transmission Electron Microscopy (STEM) for Accurate Virus Quantification

DTIC Science & Technology

2017-02-02

Corresponding Author Abstract Accurate virus quantification is sought, but a perfect method still eludes the scientific community. Electron...unlimited. UNCLASSIFIED 2 provides morphology data and counts all viral particles, including partial or noninfectious particles; however, EM methods ...consistent, reproducible virus quantification method called Scanning Transmission Electron Microscopy – Virus Quantification (STEM-VQ) which simplifies

Rapid and Easy Protocol for Quantification of Next-Generation Sequencing Libraries.

PubMed

Hawkins, Steve F C; Guest, Paul C

2018-01-01

The emergence of next-generation sequencing (NGS) over the last 10 years has increased the efficiency of DNA sequencing in terms of speed, ease, and price. However, the exact quantification of a NGS library is crucial in order to obtain good data on sequencing platforms developed by the current market leader Illumina. Different approaches for DNA quantification are available currently and the most commonly used are based on analysis of the physical properties of the DNA through spectrophotometric or fluorometric methods. Although these methods are technically simple, they do not allow exact quantification as can be achieved using a real-time quantitative PCR (qPCR) approach. A qPCR protocol for DNA quantification with applications in NGS library preparation studies is presented here. This can be applied in various fields of study such as medical disorders resulting from nutritional programming disturbances.

AVQS: attack route-based vulnerability quantification scheme for smart grid.

PubMed

Ko, Jongbin; Lim, Hyunwoo; Lee, Seokjun; Shon, Taeshik

2014-01-01

A smart grid is a large, consolidated electrical grid system that includes heterogeneous networks and systems. Based on the data, a smart grid system has a potential security threat in its network connectivity. To solve this problem, we develop and apply a novel scheme to measure the vulnerability in a smart grid domain. Vulnerability quantification can be the first step in security analysis because it can help prioritize the security problems. However, existing vulnerability quantification schemes are not suitable for smart grid because they do not consider network vulnerabilities. We propose a novel attack route-based vulnerability quantification scheme using a network vulnerability score and an end-to-end security score, depending on the specific smart grid network environment to calculate the vulnerability score for a particular attack route. To evaluate the proposed approach, we derive several attack scenarios from the advanced metering infrastructure domain. The experimental results of the proposed approach and the existing common vulnerability scoring system clearly show that we need to consider network connectivity for more optimized vulnerability quantification.

AVQS: Attack Route-Based Vulnerability Quantification Scheme for Smart Grid

PubMed Central

Lim, Hyunwoo; Lee, Seokjun; Shon, Taeshik

2014-01-01

A smart grid is a large, consolidated electrical grid system that includes heterogeneous networks and systems. Based on the data, a smart grid system has a potential security threat in its network connectivity. To solve this problem, we develop and apply a novel scheme to measure the vulnerability in a smart grid domain. Vulnerability quantification can be the first step in security analysis because it can help prioritize the security problems. However, existing vulnerability quantification schemes are not suitable for smart grid because they do not consider network vulnerabilities. We propose a novel attack route-based vulnerability quantification scheme using a network vulnerability score and an end-to-end security score, depending on the specific smart grid network environment to calculate the vulnerability score for a particular attack route. To evaluate the proposed approach, we derive several attack scenarios from the advanced metering infrastructure domain. The experimental results of the proposed approach and the existing common vulnerability scoring system clearly show that we need to consider network connectivity for more optimized vulnerability quantification. PMID:25152923

Comparison of machine learning and semi-quantification algorithms for (I123)FP-CIT classification: the beginning of the end for semi-quantification?

PubMed

Taylor, Jonathan Christopher; Fenner, John Wesley

2017-11-29

Semi-quantification methods are well established in the clinic for assisted reporting of (I123) Ioflupane images. Arguably, these are limited diagnostic tools. Recent research has demonstrated the potential for improved classification performance offered by machine learning algorithms. A direct comparison between methods is required to establish whether a move towards widespread clinical adoption of machine learning algorithms is justified. This study compared three machine learning algorithms with that of a range of semi-quantification methods, using the Parkinson's Progression Markers Initiative (PPMI) research database and a locally derived clinical database for validation. Machine learning algorithms were based on support vector machine classifiers with three different sets of features: Voxel intensities Principal components of image voxel intensities Striatal binding radios from the putamen and caudate. Semi-quantification methods were based on striatal binding ratios (SBRs) from both putamina, with and without consideration of the caudates. Normal limits for the SBRs were defined through four different methods: Minimum of age-matched controls Mean minus 1/1.5/2 standard deviations from age-matched controls Linear regression of normal patient data against age (minus 1/1.5/2 standard errors) Selection of the optimum operating point on the receiver operator characteristic curve from normal and abnormal training data Each machine learning and semi-quantification technique was evaluated with stratified, nested 10-fold cross-validation, repeated 10 times. The mean accuracy of the semi-quantitative methods for classification of local data into Parkinsonian and non-Parkinsonian groups varied from 0.78 to 0.87, contrasting with 0.89 to 0.95 for classifying PPMI data into healthy controls and Parkinson's disease groups. The machine learning algorithms gave mean accuracies between 0.88 to 0.92 and 0.95 to 0.97 for local and PPMI data respectively. Classification

MJO prediction using the sub-seasonal to seasonal forecast model of Beijing Climate Center

NASA Astrophysics Data System (ADS)

Liu, Xiangwen; Wu, Tongwen; Yang, Song; Li, Tim; Jie, Weihua; Zhang, Li; Wang, Zaizhi; Liang, Xiaoyun; Li, Qiaoping; Cheng, Yanjie; Ren, Hongli; Fang, Yongjie; Nie, Suping

2017-05-01

By conducting several sets of hindcast experiments using the Beijing Climate Center Climate System Model, which participates in the Sub-seasonal to Seasonal (S2S) Prediction Project, we systematically evaluate the model's capability in forecasting MJO and its main deficiencies. In the original S2S hindcast set, MJO forecast skill is about 16 days. Such a skill shows significant seasonal-to-interannual variations. It is found that the model-dependent MJO forecast skill is more correlated with the Indian Ocean Dipole (IOD) than with the El Niño-Southern Oscillation. The highest skill is achieved in autumn when the IOD attains its maturity. Extended skill is found when the IOD is in its positive phase. MJO forecast skill's close association with the IOD is partially due to the quickly strengthening relationship between MJO amplitude and IOD intensity as lead time increases to about 15 days, beyond which a rapid weakening of the relationship is shown. This relationship transition may cause the forecast skill to decrease quickly with lead time, and is related to the unrealistic amplitude and phase evolutions of predicted MJO over or near the equatorial Indian Ocean during anomalous IOD phases, suggesting a possible influence of exaggerated IOD variability in the model. The results imply that the upper limit of intraseasonal predictability is modulated by large-scale external forcing background state in the tropical Indian Ocean. Two additional sets of hindcast experiments with improved atmosphere and ocean initial conditions (referred to as S2S_IEXP1 and S2S_IEXP2, respectively) are carried out, and the results show that the overall MJO forecast skill is increased to 21-22 days. It is found that the optimization of initial sea surface temperature condition largely accounts for the increase of the overall MJO forecast skill, even though the improved initial atmosphere conditions also play a role. For the DYNAMO/CINDY field campaign period, the forecast skill increases

Quantification of pericardial effusions by echocardiography and computed tomography.

PubMed

Leibowitz, David; Perlman, Gidon; Planer, David; Gilon, Dan; Berman, Philip; Bogot, Naama

2011-01-15

Echocardiography is a well-accepted tool for the diagnosis and quantification of pericardial effusion (PEff). Given the increasing use of computed tomographic (CT) scanning, more PEffs are being initially diagnosed by computed tomography. No study has compared quantification of PEff by computed tomography and echocardiography. The objective of this study was to assess the accuracy of quantification of PEff by 2-dimensional echocardiography and computed tomography compared to the amount of pericardial fluid drained at pericardiocentesis. We retrospectively reviewed an institutional database to identify patients who underwent chest computed tomography and echocardiography before percutaneous pericardiocentesis with documentation of the amount of fluid withdrawn. Digital 2-dimensional echocardiographic and CT images were retrieved and quantification of PEff volume was performed by applying the formula for the volume of a prolate ellipse, π × 4/3 × maximal long-axis dimension/2 × maximal transverse dimension/2 × maximal anteroposterior dimension/2, to the pericardial sac and to the heart. Nineteen patients meeting study qualifications were entered into the study. The amount of PEff drained was 200 to 1,700 ml (mean 674 ± 340). Echocardiographically calculated pericardial effusion volume correlated relatively well with PEff volume (r = 0.73, p <0.001, mean difference -41 ± 225 ml). There was only moderate correlation between CT volume quantification and actual volume drained (r = 0.4, p = 0.004, mean difference 158 ± 379 ml). In conclusion, echocardiography appears a more accurate imaging technique than computed tomography in quantitative assessment of nonloculated PEffs and should continue to be the primary imaging in these patients. Copyright © 2011 Elsevier Inc. All rights reserved.

Normal Databases for the Relative Quantification of Myocardial Perfusion

PubMed Central

Rubeaux, Mathieu; Xu, Yuan; Germano, Guido; Berman, Daniel S.; Slomka, Piotr J.

2016-01-01

Purpose of review Myocardial perfusion imaging (MPI) with SPECT is performed clinically worldwide to detect and monitor coronary artery disease (CAD). MPI allows an objective quantification of myocardial perfusion at stress and rest. This established technique relies on normal databases to compare patient scans against reference normal limits. In this review, we aim to introduce the process of MPI quantification with normal databases and describe the associated perfusion quantitative measures that are used. Recent findings New equipment and new software reconstruction algorithms have been introduced which require the development of new normal limits. The appearance and regional count variations of normal MPI scan may differ between these new scanners and standard Anger cameras. Therefore, these new systems may require the determination of new normal limits to achieve optimal accuracy in relative myocardial perfusion quantification. Accurate diagnostic and prognostic results rivaling those obtained by expert readers can be obtained by this widely used technique. Summary Throughout this review, we emphasize the importance of the different normal databases and the need for specific databases relative to distinct imaging procedures. use of appropriate normal limits allows optimal quantification of MPI by taking into account subtle image differences due to the hardware and software used, and the population studied. PMID:28138354

Installation Restoration Program. Confirmation/Quantification Stage 1. Phase 2

DTIC Science & Technology

1985-03-07

INSTALLATION RESTORATION PROGRAM i0 PHASE II - CONFIRMATION/QUANTIFICATION 0STAGE 1 KIRTLAND AFB KIRTLAND AFB, NEW MEXICO 87117 IIl PREPARED BY SCIENCE...APPLICATIONS INTERNATIONAL CORPORATION 505 MARQUETTE NW, SUITE 1200 ALBUQUERQUE, NEW MEXICO 871021 5MARCH 1985 FINAL REPORT FROM FEB 1983 TO MAR 1985...QUANTIFICATION STAGE 1 i FINAL REPORT FOR IKIRTLAND AFB KIRTLAND AFB, NEW MEXICO 87117U HEADQUARTERS MILITARY AIRLIFT COMMAND COMMAND SURGEON’S OFFICE (HQ MAC

Quantification Bias Caused by Plasmid DNA Conformation in Quantitative Real-Time PCR Assay

PubMed Central

Lin, Chih-Hui; Chen, Yu-Chieh; Pan, Tzu-Ming

2011-01-01

Quantitative real-time PCR (qPCR) is the gold standard for the quantification of specific nucleic acid sequences. However, a serious concern has been revealed in a recent report: supercoiled plasmid standards cause significant over-estimation in qPCR quantification. In this study, we investigated the effect of plasmid DNA conformation on the quantification of DNA and the efficiency of qPCR. Our results suggest that plasmid DNA conformation has significant impact on the accuracy of absolute quantification by qPCR. DNA standard curves shifted significantly among plasmid standards with different DNA conformations. Moreover, the choice of DNA measurement method and plasmid DNA conformation may also contribute to the measurement error of DNA standard curves. Due to the multiple effects of plasmid DNA conformation on the accuracy of qPCR, efforts should be made to assure the highest consistency of plasmid standards for qPCR. Thus, we suggest that the conformation, preparation, quantification, purification, handling, and storage of standard plasmid DNA should be described and defined in the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) to assure the reproducibility and accuracy of qPCR absolute quantification. PMID:22194997

RNA-Skim: a rapid method for RNA-Seq quantification at transcript level

PubMed Central

Zhang, Zhaojun; Wang, Wei

2014-01-01

Motivation: RNA-Seq technique has been demonstrated as a revolutionary means for exploring transcriptome because it provides deep coverage and base pair-level resolution. RNA-Seq quantification is proven to be an efficient alternative to Microarray technique in gene expression study, and it is a critical component in RNA-Seq differential expression analysis. Most existing RNA-Seq quantification tools require the alignments of fragments to either a genome or a transcriptome, entailing a time-consuming and intricate alignment step. To improve the performance of RNA-Seq quantification, an alignment-free method, Sailfish, has been recently proposed to quantify transcript abundances using all k-mers in the transcriptome, demonstrating the feasibility of designing an efficient alignment-free method for transcriptome quantification. Even though Sailfish is substantially faster than alternative alignment-dependent methods such as Cufflinks, using all k-mers in the transcriptome quantification impedes the scalability of the method. Results: We propose a novel RNA-Seq quantification method, RNA-Skim, which partitions the transcriptome into disjoint transcript clusters based on sequence similarity, and introduces the notion of sig-mers, which are a special type of k-mers uniquely associated with each cluster. We demonstrate that the sig-mer counts within a cluster are sufficient for estimating transcript abundances with accuracy comparable with any state-of-the-art method. This enables RNA-Skim to perform transcript quantification on each cluster independently, reducing a complex optimization problem into smaller optimization tasks that can be run in parallel. As a result, RNA-Skim uses <4% of the k-mers and <10% of the CPU time required by Sailfish. It is able to finish transcriptome quantification in <10 min per sample by using just a single thread on a commodity computer, which represents >100 speedup over the state-of-the-art alignment-based methods, while delivering

Relative quantification of biomarkers using mixed-isotope labeling coupled with MS

PubMed Central

Chapman, Heidi M; Schutt, Katherine L; Dieter, Emily M; Lamos, Shane M

2013-01-01

The identification and quantification of important biomarkers is a critical first step in the elucidation of biological systems. Biomarkers take many forms as cellular responses to stimuli and can be manifested during transcription, translation, and/or metabolic processing. Increasingly, researchers have relied upon mixed-isotope labeling (MIL) coupled with MS to perform relative quantification of biomarkers between two or more biological samples. MIL effectively tags biomarkers of interest for ease of identification and quantification within the mass spectrometer by using isotopic labels that introduce a heavy and light form of the tag. In addition to MIL coupled with MS, a number of other approaches have been used to quantify biomarkers including protein gel staining, enzymatic labeling, metabolic labeling, and several label-free approaches that generate quantitative data from the MS signal response. This review focuses on MIL techniques coupled with MS for the quantification of protein and small-molecule biomarkers. PMID:23157360

pyQms enables universal and accurate quantification of mass spectrometry data.

PubMed

Leufken, Johannes; Niehues, Anna; Sarin, L Peter; Wessel, Florian; Hippler, Michael; Leidel, Sebastian A; Fufezan, Christian

2017-10-01

Quantitative mass spectrometry (MS) is a key technique in many research areas (1), including proteomics, metabolomics, glycomics, and lipidomics. Because all of the corresponding molecules can be described by chemical formulas, universal quantification tools are highly desirable. Here, we present pyQms, an open-source software for accurate quantification of all types of molecules measurable by MS. pyQms uses isotope pattern matching that offers an accurate quality assessment of all quantifications and the ability to directly incorporate mass spectrometer accuracy. pyQms is, due to its universal design, applicable to every research field, labeling strategy, and acquisition technique. This opens ultimate flexibility for researchers to design experiments employing innovative and hitherto unexplored labeling strategies. Importantly, pyQms performs very well to accurately quantify partially labeled proteomes in large scale and high throughput, the most challenging task for a quantification algorithm. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Quantification of Efficiency of Beneficiation of Lunar Regolith

NASA Technical Reports Server (NTRS)

Trigwell, Steve; Lane, John; Captain, James; Weis, Kyle; Quinn, Jacqueline; Watanabe, Fumiya

2011-01-01

Electrostatic beneficiation of lunar regolith is being researched at Kennedy Space Center to enhance the ilmenite concentration of the regolith for the production of oxygen in in-situ resource utilization on the lunar surface. Ilmenite enrichment of up to 200% was achieved using lunar simulants. For the most accurate quantification of the regolith particles, standard petrographic methods are typically followed, but in order to optimize the process, many hundreds of samples were generated in this study that made the standard analysis methods time prohibitive. In the current studies, X-ray photoelectron spectroscopy (XPS) and Secondary Electron microscopy/Energy Dispersive Spectroscopy (SEM/EDS) were used that could automatically, and quickly, analyze many separated fractions of lunar simulant. In order to test the accuracy of the quantification, test mixture samples of known quantities of ilmenite (2, 5, 10, and 20 wt%) in silica (pure quartz powder), were analyzed by XPS and EDS. The results showed that quantification for low concentrations of ilmenite in silica could be accurately achieved by both XPS and EDS, knowing the limitations of the techniques. 1

Assessment of cardiac fibrosis: a morphometric method comparison for collagen quantification.

PubMed

Schipke, Julia; Brandenberger, Christina; Rajces, Alexandra; Manninger, Martin; Alogna, Alessio; Post, Heiner; Mühlfeld, Christian

2017-04-01

Fibrotic remodeling of the heart is a frequent condition linked to various diseases and cardiac dysfunction. Collagen quantification is an important objective in cardiac fibrosis research; however, a variety of different histological methods are currently used that may differ in accuracy. Here, frequently applied collagen quantification techniques were compared. A porcine model of early stage heart failure with preserved ejection fraction was used as an example. Semiautomated threshold analyses were imprecise, mainly due to inclusion of noncollagen structures or failure to detect certain collagen deposits. In contrast, collagen assessment by automated image analysis and light microscopy (LM)-stereology was more sensitive. Depending on the quantification method, the amount of estimated collagen varied and influenced intergroup comparisons. PicroSirius Red, Masson's trichrome, and Azan staining protocols yielded similar results, whereas the measured collagen area increased with increasing section thickness. Whereas none of the LM-based methods showed significant differences between the groups, electron microscopy (EM)-stereology revealed a significant collagen increase between cardiomyocytes in the experimental group, but not at other localizations. In conclusion, in contrast to the staining protocol, section thickness and the quantification method being used directly influence the estimated collagen content and thus, possibly, intergroup comparisons. EM in combination with stereology is a precise and sensitive method for collagen quantification if certain prerequisites are considered. For subtle fibrotic alterations, consideration of collagen localization may be necessary. Among LM methods, LM-stereology and automated image analysis are appropriate to quantify fibrotic changes, the latter depending on careful control of algorithm and comparable section staining. NEW & NOTEWORTHY Direct comparison of frequently applied histological fibrosis assessment techniques

Microbial quantification in activated sludge: the hits and misses.

PubMed

Hall, S J; Keller, J; Blackall, L L

2003-01-01

Since the implementation of the activated sludge process for treating wastewater, there has been a reliance on chemical and physical parameters to monitor the system. However, in biological nutrient removal (BNR) processes, the microorganisms responsible for some of the transformations should be used to monitor the processes with the overall goal to achieve better treatment performance. The development of in situ identification and rapid quantification techniques for key microorganisms involved in BNR are required to achieve this goal. This study explored the quantification of Nitrospira, a key organism in the oxidation of nitrite to nitrate in BNR. Two molecular genetic microbial quantification techniques were evaluated: real-time polymerase chain reaction (PCR) and fluorescence in situ hybridisation (FISH) followed by digital image analysis. A correlation between the Nitrospira quantitative data and the nitrate production rate, determined in batch tests, was attempted. The disadvantages and advantages of both methods will be discussed.

freeQuant: A Mass Spectrometry Label-Free Quantification Software Tool for Complex Proteome Analysis.

PubMed

Deng, Ning; Li, Zhenye; Pan, Chao; Duan, Huilong

2015-01-01

Study of complex proteome brings forward higher request for the quantification method using mass spectrometry technology. In this paper, we present a mass spectrometry label-free quantification tool for complex proteomes, called freeQuant, which integrated quantification with functional analysis effectively. freeQuant consists of two well-integrated modules: label-free quantification and functional analysis with biomedical knowledge. freeQuant supports label-free quantitative analysis which makes full use of tandem mass spectrometry (MS/MS) spectral count, protein sequence length, shared peptides, and ion intensity. It adopts spectral count for quantitative analysis and builds a new method for shared peptides to accurately evaluate abundance of isoforms. For proteins with low abundance, MS/MS total ion count coupled with spectral count is included to ensure accurate protein quantification. Furthermore, freeQuant supports the large-scale functional annotations for complex proteomes. Mitochondrial proteomes from the mouse heart, the mouse liver, and the human heart were used to evaluate the usability and performance of freeQuant. The evaluation showed that the quantitative algorithms implemented in freeQuant can improve accuracy of quantification with better dynamic range.

Quantification of Fibrosis and Osteosclerosis in Myeloproliferative Neoplasms: A Computer-Assisted Image Study

PubMed Central

Teman, Carolin J.; Wilson, Andrew R.; Perkins, Sherrie L.; Hickman, Kimberly; Prchal, Josef T.; Salama, Mohamed E.

2010-01-01

Evaluation of bone marrow fibrosis and osteosclerosis in myeloproliferative neoplasms (MPN) is subject to interobserver inconsistency. Performance data for currently utilized fibrosis grading systems are lacking, and classification scales for osteosclerosis do not exist. Digital imaging can serve as a quantification method for fibrosis and osteosclerosis. We used digital imaging techniques for trabecular area assessment and reticulin-fiber quantification. Patients with all Philadelphia negative MPN subtypes had higher trabecular volume than controls (p ≤0.0015). Results suggest that the degree of osteosclerosis helps differentiate primary myelofibrosis from other MPN. Numerical quantification of fibrosis highly correlated with subjective scores, and interobserver correlation was satisfactory. Digital imaging provides accurate quantification for osteosclerosis and fibrosis. PMID:20122729

Single cell genomic quantification by non-fluorescence nonlinear microscopy

NASA Astrophysics Data System (ADS)

Kota, Divya; Liu, Jing

2017-02-01

Human epidermal growth receptor 2 (Her2) is a gene which plays a major role in breast cancer development. The quantification of Her2 expression in single cells is limited by several drawbacks in existing fluorescence-based single molecule techniques, such as low signal-to-noise ratio (SNR), strong autofluorescence and background signals from biological components. For rigorous genomic quantification, a robust method of orthogonal detection is highly desirable and we demonstrated it by two non-fluorescent imaging techniques -transient absorption microscopy (TAM) and second harmonic generation (SHG). In TAM, gold nanoparticles (AuNPs) are chosen as an orthogonal probes for detection of single molecules which gives background-free quantifications of single mRNA transcript. In SHG, emission from barium titanium oxide (BTO) nanoprobes was demonstrated which allows stable signal beyond the autofluorescence window. Her2 mRNA was specifically labeled with nanoprobes which are conjugated with antibodies or oligonucleotides and quantified at single copy sensitivity in the cancer cells and tissues. Furthermore, a non-fluorescent super-resolution concept, named as second harmonic super-resolution microscopy (SHaSM), was proposed to quantify individual Her2 transcripts in cancer cells beyond the diffraction limit. These non-fluorescent imaging modalities will provide new dimensions in biomarker quantification at single molecule sensitivity in turbid biological samples, offering a strong cross-platform strategy for clinical monitoring at single cell resolution.

Quantification of Training and Competition Loads in Endurance Sports: Methods and Applications.

PubMed

Mujika, Iñigo

2017-04-01

Training quantification is basic to evaluate an endurance athlete's responses to training loads, ensure adequate stress/recovery balance, and determine the relationship between training and performance. Quantifying both external and internal workload is important, because external workload does not measure the biological stress imposed by the exercise sessions. Generally used quantification methods include retrospective questionnaires, diaries, direct observation, and physiological monitoring, often based on the measurement of oxygen uptake, heart rate, and blood lactate concentration. Other methods in use in endurance sports include speed measurement and the measurement of power output, made possible by recent technological advances such as power meters in cycling and triathlon. Among subjective methods of quantification, rating of perceived exertion stands out because of its wide use. Concurrent assessments of the various quantification methods allow researchers and practitioners to evaluate stress/recovery balance, adjust individual training programs, and determine the relationships between external load, internal load, and athletes' performance. This brief review summarizes the most relevant external- and internal-workload-quantification methods in endurance sports and provides practical examples of their implementation to adjust the training programs of elite athletes in accordance with their individualized stress/recovery balance.

In-Gel Stable-Isotope Labeling (ISIL): a strategy for mass spectrometry-based relative quantification.

PubMed

Asara, John M; Zhang, Xiang; Zheng, Bin; Christofk, Heather H; Wu, Ning; Cantley, Lewis C

2006-01-01

Most proteomics approaches for relative quantification of protein expression use a combination of stable-isotope labeling and mass spectrometry. Traditionally, researchers have used difference gel electrophoresis (DIGE) from stained 1D and 2D gels for relative quantification. While differences in protein staining intensity can often be visualized, abundant proteins can obscure less abundant proteins, and quantification of post-translational modifications is difficult. A method is presented for quantifying changes in the abundance of a specific protein or changes in specific modifications of a protein using In-gel Stable-Isotope Labeling (ISIL). Proteins extracted from any source (tissue, cell line, immunoprecipitate, etc.), treated under two experimental conditions, are resolved in separate lanes by gel electrophoresis. The regions of interest (visualized by staining) are reacted separately with light versus heavy isotope-labeled reagents, and the gel slices are then mixed and digested with proteases. The resulting peptides are then analyzed by LC-MS to determine relative abundance of light/heavy isotope pairs and analyzed by LC-MS/MS for identification of sequence and modifications. The strategy compares well with other relative quantification strategies, and in silico calculations reveal its effectiveness as a global relative quantification strategy. An advantage of ISIL is that visualization of gel differences can be used as a first quantification step followed by accurate and sensitive protein level stable-isotope labeling and mass spectrometry-based relative quantification.

Water mass characteristic in the outflow region of the Indonesian throughflow during and post 2016 negative Indian ocean dipole event

NASA Astrophysics Data System (ADS)

Bayhaqi, A.; Iskandar, I.; Surinati, D.; Budiman, A. S.; Wardhana, A. K.; Dirhamsyah; Yuan, D.; Lestari, D. O.

2018-05-01

Strong El Niño and positive Indian Ocean Dipole (pIOD) events in 2015/2016 followed by relatively strong negative Indian Ocean Dipole (nIOD) and weak La Niña in 2016 events have affected hydrography conditions in the Indonesian Throughflow (ITF) region. Two research cruises were conducted using RV Baruna Jaya VIII in August and November 2016. These cruises aim to evaluate possible impact of those two climate mode events on the water mass characteristic in the outflow region of the ITF. Hydrographic data from those two cruises were combined with the sea surface temperature (SST) from the Advanced Very High Resolution Radiometer (AVHRR) and surface wind data from the European Centre for Medium-Range Weather Forecasts (ECMWF). The results showed that in the 2016 anomaly year, the cooler sea surface temperature was observed during the negative IOD (nIOD) event while the warmer temperature was found in the post of nIOD event. The observed water mass characteristics in the outflow region of the ITF revealed that the upper layer was dominated by the Indian Ocean water mass, while the Pacific Ocean water mass was observed in the deeper layer. The observed current data across the Sumba Strait showed that the South Java Coastal Current (SJCC) was observed in the upper layer, propagating eastward toward the Savu Sea. A few days later, the observed currents in the upper layer of the Ombai Strait revealed the ITF flow towards the Indian Ocean. Meanwhile, the lower layer showed an eastward flow towards the Ombai Strait.

The use of self-quantification systems for personal health information: big data management activities and prospects.

PubMed

Almalki, Manal; Gray, Kathleen; Sanchez, Fernando Martin

2015-01-01

Self-quantification is seen as an emerging paradigm for health care self-management. Self-quantification systems (SQS) can be used for tracking, monitoring, and quantifying health aspects including mental, emotional, physical, and social aspects in order to gain self-knowledge. However, there has been a lack of a systematic approach for conceptualising and mapping the essential activities that are undertaken by individuals who are using SQS in order to improve health outcomes. In this paper, we propose a new model of personal health information self-quantification systems (PHI-SQS). PHI-SQS model describes two types of activities that individuals go through during their journey of health self-managed practice, which are 'self-quantification' and 'self-activation'. In this paper, we aimed to examine thoroughly the first type of activity in PHI-SQS which is 'self-quantification'. Our objectives were to review the data management processes currently supported in a representative set of self-quantification tools and ancillary applications, and provide a systematic approach for conceptualising and mapping these processes with the individuals' activities. We reviewed and compared eleven self-quantification tools and applications (Zeo Sleep Manager, Fitbit, Actipressure, MoodPanda, iBGStar, Sensaris Senspod, 23andMe, uBiome, Digifit, BodyTrack, and Wikilife), that collect three key health data types (Environmental exposure, Physiological patterns, Genetic traits). We investigated the interaction taking place at different data flow stages between the individual user and the self-quantification technology used. We found that these eleven self-quantification tools and applications represent two major tool types (primary and secondary self-quantification systems). In each type, the individuals experience different processes and activities which are substantially influenced by the technologies' data management capabilities. Self-quantification in personal health maintenance

Clinical applications of MS-based protein quantification.

PubMed

Sabbagh, Bassel; Mindt, Sonani; Neumaier, Michael; Findeisen, Peter

2016-04-01

Mass spectrometry-based assays are increasingly important in clinical laboratory medicine and nowadays are already commonly used in several areas of routine diagnostics. These include therapeutic drug monitoring, toxicology, endocrinology, pediatrics, and microbiology. Accordingly, some of the most common analyses are therapeutic drug monitoring of immunosuppressants, vitamin D, steroids, newborn screening, and bacterial identification. However, MS-based quantification of peptides and proteins for routine diagnostic use is rather rare up to now despite excellent analytical specificity and good sensitivity. Here, we want to give an overview over current fit-for-purpose assays for MS-based protein quantification. Advantages as well as challenges of this approach will be discussed with focus on feasibility for routine diagnostic use. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantification and Formalization of Security

DTIC Science & Technology

2010-02-01

Quantification of Information Flow . . . . . . . . . . . . . . . . . . 30 2.4 Language Semantics . . . . . . . . . . . . . . . . . . . . . . . . . . 46...system behavior observed by users holding low clearances. This policy, or a variant of it, is enforced by many pro- gramming language -based mechanisms...illustrates with a particular programming language (while-programs plus probabilistic choice). The model is extended in §2.5 to programs in which

Quantification is Neither Necessary Nor Sufficient for Measurement

NASA Astrophysics Data System (ADS)

Mari, Luca; Maul, Andrew; Torres Irribarra, David; Wilson, Mark

2013-09-01

Being an infrastructural, widespread activity, measurement is laden with stereotypes. Some of these concern the role of measurement in the relation between quality and quantity. In particular, it is sometimes argued or assumed that quantification is necessary for measurement; it is also sometimes argued or assumed that quantification is sufficient for or synonymous with measurement. To assess the validity of these positions the concepts of measurement and quantitative evaluation should be independently defined and their relationship analyzed. We contend that the defining characteristic of measurement should be the structure of the process, not a feature of its results. Under this perspective, quantitative evaluation is neither sufficient nor necessary for measurement.

Detection and quantification of proteins and cells by use of elemental mass spectrometry: progress and challenges.

PubMed

Yan, Xiaowen; Yang, Limin; Wang, Qiuquan

2013-07-01

Much progress has been made in identification of the proteins in proteomes, and quantification of these proteins has attracted much interest. In addition to popular tandem mass spectrometric methods based on soft ionization, inductively coupled plasma mass spectrometry (ICPMS), a typical example of mass spectrometry based on hard ionization, usually used for analysis of elements, has unique advantages in absolute quantification of proteins by determination of an element with a definite stoichiometry in a protein or attached to the protein. In this Trends article, we briefly describe state-of-the-art ICPMS-based methods for quantification of proteins, emphasizing protein-labeling and element-tagging strategies developed on the basis of chemically selective reactions and/or biospecific interactions. Recent progress from protein to cell quantification by use of ICPMS is also discussed, and the possibilities and challenges of ICPMS-based protein quantification for universal, selective, or targeted quantification of proteins and cells in a biological sample are also discussed critically. We believe ICPMS-based protein quantification will become ever more important in targeted quantitative proteomics and bioanalysis in the near future.

Recent advances in stable isotope labeling based techniques for proteome relative quantification.

PubMed

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

2014-10-24

The large scale relative quantification of all proteins expressed in biological samples under different states is of great importance for discovering proteins with important biological functions, as well as screening disease related biomarkers and drug targets. Therefore, the accurate quantification of proteins at proteome level has become one of the key issues in protein science. Herein, the recent advances in stable isotope labeling based techniques for proteome relative quantification were reviewed, from the aspects of metabolic labeling, chemical labeling and enzyme-catalyzed labeling. Furthermore, the future research direction in this field was prospected. Copyright © 2014 Elsevier B.V. All rights reserved.

Quantification of DNA using the luminescent oxygen channeling assay.

PubMed

Patel, R; Pollner, R; de Keczer, S; Pease, J; Pirio, M; DeChene, N; Dafforn, A; Rose, S

2000-09-01

Simplified and cost-effective methods for the detection and quantification of nucleic acid targets are still a challenge in molecular diagnostics. Luminescent oxygen channeling assay (LOCI(TM)) latex particles can be conjugated to synthetic oligodeoxynucleotides and hybridized, via linking probes, to different DNA targets. These oligomer-conjugated LOCI particles survive thermocycling in a PCR reaction and allow quantified detection of DNA targets in both real-time and endpoint formats. The endpoint DNA quantification format utilized two sensitizer bead types that are sensitive to separate illumination wavelengths. These two bead types were uniquely annealed to target or control amplicons, and separate illuminations generated time-resolved chemiluminescence, which distinguished the two amplicon types. In the endpoint method, ratios of the two signals allowed determination of the target DNA concentration over a three-log range. The real-time format allowed quantification of the DNA target over a six-log range with a linear relationship between threshold cycle and log of the number of DNA targets. This is the first report of the use of an oligomer-labeled latex particle assay capable of producing DNA quantification and sequence-specific chemiluminescent signals in a homogeneous format. It is also the first report of the generation of two signals from a LOCI assay. The methods described here have been shown to be easily adaptable to new DNA targets because of the generic nature of the oligomer-labeled LOCI particles.

Recurrence quantification analysis of electrically evoked surface EMG signal.

PubMed

Liu, Chunling; Wang, Xu

2005-01-01

Recurrence Plot is a quite useful tool used in time-series analysis, in particular for measuring unstable periodic orbits embedded in a chaotic dynamical system. This paper introduced the structures of the Recurrence Plot and the ways of the plot coming into being. Then the way of the quantification of the Recurrence Plot is defined. In this paper, one of the possible applications of Recurrence Quantification Analysis (RQA) strategy to the analysis of electrical stimulation evoked surface EMG. The result shows the percent determination is increased along with stimulation intensity.

The NASA Langley Multidisciplinary Uncertainty Quantification Challenge

NASA Technical Reports Server (NTRS)

Crespo, Luis G.; Kenny, Sean P.; Giesy, Daniel P.

2014-01-01

This paper presents the formulation of an uncertainty quantification challenge problem consisting of five subproblems. These problems focus on key aspects of uncertainty characterization, sensitivity analysis, uncertainty propagation, extreme-case analysis, and robust design.

1H NMR quantification in very dilute toxin solutions: application to anatoxin-a analysis.

PubMed

Dagnino, Denise; Schripsema, Jan

2005-08-01

A complete procedure is described for the extraction, detection and quantification of anatoxin-a in biological samples. Anatoxin-a is extracted from biomass by a routine acid base extraction. The extract is analysed by GC-MS, without the need of derivatization, with a detection limit of 0.5 ng. A method was developed for the accurate quantification of anatoxin-a in the standard solution to be used for the calibration of the GC analysis. 1H NMR allowed the accurate quantification of microgram quantities of anatoxin-a. The accurate quantification of compounds in standard solutions is rarely discussed, but for compounds like anatoxin-a (toxins with prices in the range of a million dollar a gram), of which generally only milligram quantities or less are available, this factor in the quantitative analysis is certainly not trivial. The method that was developed can easily be adapted for the accurate quantification of other toxins in very dilute solutions.

The use of self-quantification systems for personal health information: big data management activities and prospects

PubMed Central

2015-01-01

Background Self-quantification is seen as an emerging paradigm for health care self-management. Self-quantification systems (SQS) can be used for tracking, monitoring, and quantifying health aspects including mental, emotional, physical, and social aspects in order to gain self-knowledge. However, there has been a lack of a systematic approach for conceptualising and mapping the essential activities that are undertaken by individuals who are using SQS in order to improve health outcomes. In this paper, we propose a new model of personal health information self-quantification systems (PHI-SQS). PHI-SQS model describes two types of activities that individuals go through during their journey of health self-managed practice, which are 'self-quantification' and 'self-activation'. Objectives In this paper, we aimed to examine thoroughly the first type of activity in PHI-SQS which is 'self-quantification'. Our objectives were to review the data management processes currently supported in a representative set of self-quantification tools and ancillary applications, and provide a systematic approach for conceptualising and mapping these processes with the individuals' activities. Method We reviewed and compared eleven self-quantification tools and applications (Zeo Sleep Manager, Fitbit, Actipressure, MoodPanda, iBGStar, Sensaris Senspod, 23andMe, uBiome, Digifit, BodyTrack, and Wikilife), that collect three key health data types (Environmental exposure, Physiological patterns, Genetic traits). We investigated the interaction taking place at different data flow stages between the individual user and the self-quantification technology used. Findings We found that these eleven self-quantification tools and applications represent two major tool types (primary and secondary self-quantification systems). In each type, the individuals experience different processes and activities which are substantially influenced by the technologies' data management capabilities. Conclusions

[DNA quantification of blood samples pre-treated with pyramidon].

PubMed

Zhu, Chuan-Hong; Zheng, Dao-Li; Ni, Rao-Zhi; Wang, Hai-Sheng; Ning, Ping; Fang, Hui; Liu, Yan

2014-06-01

To study DNA quantification and STR typing of samples pre-treated with pyramidon. The blood samples of ten unrelated individuals were anticoagulated in EDTA. The blood stains were made on the filter paper. The experimental groups were divided into six groups in accordance with the storage time, 30 min, 1 h, 3 h, 6 h, 12 h and 24h after pre-treated with pyramidon. DNA was extracted by three methods: magnetic bead-based extraction, QIAcube DNA purification method and Chelex-100 method. The quantification of DNA was made by fluorescent quantitative PCR. STR typing was detected by PCR-STR fluorescent technology. In the same DNA extraction method, the sample DNA decreased gradually with times after pre-treatment with pyramidon. In the same storage time, the DNA quantification in different extraction methods had significant differences. Sixteen loci DNA typing were detected in 90.56% of samples. Pyramidon pre-treatment could cause DNA degradation, but effective STR typing can be achieved within 24 h. The magnetic bead-based extraction is the best method for STR profiling and DNA extraction.

Standardless quantification by parameter optimization in electron probe microanalysis

NASA Astrophysics Data System (ADS)

Limandri, Silvina P.; Bonetto, Rita D.; Josa, Víctor Galván; Carreras, Alejo C.; Trincavelli, Jorge C.

2012-11-01

A method for standardless quantification by parameter optimization in electron probe microanalysis is presented. The method consists in minimizing the quadratic differences between an experimental spectrum and an analytical function proposed to describe it, by optimizing the parameters involved in the analytical prediction. This algorithm, implemented in the software POEMA (Parameter Optimization in Electron Probe Microanalysis), allows the determination of the elemental concentrations, along with their uncertainties. The method was tested in a set of 159 elemental constituents corresponding to 36 spectra of standards (mostly minerals) that include trace elements. The results were compared with those obtained with the commercial software GENESIS Spectrum® for standardless quantification. The quantifications performed with the method proposed here are better in the 74% of the cases studied. In addition, the performance of the method proposed is compared with the first principles standardless analysis procedure DTSA for a different data set, which excludes trace elements. The relative deviations with respect to the nominal concentrations are lower than 0.04, 0.08 and 0.35 for the 66% of the cases for POEMA, GENESIS and DTSA, respectively.

Lamb Wave Damage Quantification Using GA-Based LS-SVM.

PubMed

Sun, Fuqiang; Wang, Ning; He, Jingjing; Guan, Xuefei; Yang, Jinsong

2017-06-12

Lamb waves have been reported to be an efficient tool for non-destructive evaluations (NDE) for various application scenarios. However, accurate and reliable damage quantification using the Lamb wave method is still a practical challenge, due to the complex underlying mechanism of Lamb wave propagation and damage detection. This paper presents a Lamb wave damage quantification method using a least square support vector machine (LS-SVM) and a genetic algorithm (GA). Three damage sensitive features, namely, normalized amplitude, phase change, and correlation coefficient, were proposed to describe changes of Lamb wave characteristics caused by damage. In view of commonly used data-driven methods, the GA-based LS-SVM model using the proposed three damage sensitive features was implemented to evaluate the crack size. The GA method was adopted to optimize the model parameters. The results of GA-based LS-SVM were validated using coupon test data and lap joint component test data with naturally developed fatigue cracks. Cases of different loading and manufacturer were also included to further verify the robustness of the proposed method for crack quantification.

Lamb Wave Damage Quantification Using GA-Based LS-SVM

PubMed Central

Sun, Fuqiang; Wang, Ning; He, Jingjing; Guan, Xuefei; Yang, Jinsong

2017-01-01

Lamb waves have been reported to be an efficient tool for non-destructive evaluations (NDE) for various application scenarios. However, accurate and reliable damage quantification using the Lamb wave method is still a practical challenge, due to the complex underlying mechanism of Lamb wave propagation and damage detection. This paper presents a Lamb wave damage quantification method using a least square support vector machine (LS-SVM) and a genetic algorithm (GA). Three damage sensitive features, namely, normalized amplitude, phase change, and correlation coefficient, were proposed to describe changes of Lamb wave characteristics caused by damage. In view of commonly used data-driven methods, the GA-based LS-SVM model using the proposed three damage sensitive features was implemented to evaluate the crack size. The GA method was adopted to optimize the model parameters. The results of GA-based LS-SVM were validated using coupon test data and lap joint component test data with naturally developed fatigue cracks. Cases of different loading and manufacturer were also included to further verify the robustness of the proposed method for crack quantification. PMID:28773003

Consistency of flow quantifications in tridirectional phase-contrast MRI

NASA Astrophysics Data System (ADS)

Unterhinninghofen, R.; Ley, S.; Dillmann, R.

2009-02-01

Tridirectionally encoded phase-contrast MRI is a technique to non-invasively acquire time-resolved velocity vector fields of blood flow. These may not only be used to analyze pathological flow patterns, but also to quantify flow at arbitrary positions within the acquired volume. In this paper we examine the validity of this approach by analyzing the consistency of related quantifications instead of comparing it with an external reference measurement. Datasets of the thoracic aorta were acquired from 6 pigs, 1 healthy volunteer and 3 patients with artificial aortic valves. Using in-house software an elliptical flow quantification plane was placed manually at 6 positions along the descending aorta where it was rotated to 5 different angles. For each configuration flow was computed based on the original data and data that had been corrected for phase offsets. Results reveal that quantifications are more dependent on changes in position than on changes in angle. Phase offset correction considerably reduces this dependency. Overall consistency is good with a maximum variation coefficient of 9.9% and a mean variation coefficient of 7.2%.

Improved Strategies and Optimization of Calibration Models for Real-time PCR Absolute Quantification

EPA Science Inventory

Real-time PCR absolute quantification applications rely on the use of standard curves to make estimates of DNA target concentrations in unknown samples. Traditional absolute quantification approaches dictate that a standard curve must accompany each experimental run. However, t...

Automated quantification of renal interstitial fibrosis for computer-aided diagnosis: A comprehensive tissue structure segmentation method.

PubMed

Tey, Wei Keat; Kuang, Ye Chow; Ooi, Melanie Po-Leen; Khoo, Joon Joon

2018-03-01

Interstitial fibrosis in renal biopsy samples is a scarring tissue structure that may be visually quantified by pathologists as an indicator to the presence and extent of chronic kidney disease. The standard method of quantification by visual evaluation presents reproducibility issues in the diagnoses. This study proposes an automated quantification system for measuring the amount of interstitial fibrosis in renal biopsy images as a consistent basis of comparison among pathologists. The system extracts and segments the renal tissue structures based on colour information and structural assumptions of the tissue structures. The regions in the biopsy representing the interstitial fibrosis are deduced through the elimination of non-interstitial fibrosis structures from the biopsy area and quantified as a percentage of the total area of the biopsy sample. A ground truth image dataset has been manually prepared by consulting an experienced pathologist for the validation of the segmentation algorithms. The results from experiments involving experienced pathologists have demonstrated a good correlation in quantification result between the automated system and the pathologists' visual evaluation. Experiments investigating the variability in pathologists also proved the automated quantification error rate to be on par with the average intra-observer variability in pathologists' quantification. Interstitial fibrosis in renal biopsy samples is a scarring tissue structure that may be visually quantified by pathologists as an indicator to the presence and extent of chronic kidney disease. The standard method of quantification by visual evaluation presents reproducibility issues in the diagnoses due to the uncertainties in human judgement. An automated quantification system for accurately measuring the amount of interstitial fibrosis in renal biopsy images is presented as a consistent basis of comparison among pathologists. The system identifies the renal tissue structures

On the Confounding Effect of Temperature on Chemical Shift-Encoded Fat Quantification

PubMed Central

Hernando, Diego; Sharma, Samir D.; Kramer, Harald; Reeder, Scott B.

2014-01-01

Purpose To characterize the confounding effect of temperature on chemical shift-encoded (CSE) fat quantification. Methods The proton resonance frequency of water, unlike triglycerides, depends on temperature. This leads to a temperature dependence of the spectral models of fat (relative to water) that are commonly used by CSE-MRI methods. Simulation analysis was performed for 1.5 Tesla CSE fat–water signals at various temperatures and echo time combinations. Oil–water phantoms were constructed and scanned at temperatures between 0 and 40°C using spectroscopy and CSE imaging at three echo time combinations. An explanted human liver, rejected for transplantation due to steatosis, was scanned using spectroscopy and CSE imaging. Fat–water reconstructions were performed using four different techniques: magnitude and complex fitting, with standard or temperature-corrected signal modeling. Results In all experiments, magnitude fitting with standard signal modeling resulted in large fat quantification errors. Errors were largest for echo time combinations near TEinit ≈ 1.3 ms, ΔTE ≈ 2.2 ms. Errors in fat quantification caused by temperature-related frequency shifts were smaller with complex fitting, and were avoided using a temperature-corrected signal model. Conclusion Temperature is a confounding factor for fat quantification. If not accounted for, it can result in large errors in fat quantifications in phantom and ex vivo acquisitions. PMID:24123362

Influence of 1997/98 and 2006/2007 Indian Ocean Dipole on Phytoplankton Composition in the Eastern Tropical Indian Ocean

NASA Astrophysics Data System (ADS)

Mahapatra, K.; Okada, Y.

2016-02-01

The influence of Indian Ocean Dipole (IOD) events of varied intensity co-occurred with El Niño/Southern Oscillation (ENSO) in 1997/98 and 2006/2007 on phytoplankton functional types (PFTs) was assessed in the eastern tropical Indian Ocean using the NASA Ocean Biogeochemical Model (NOBM) and particle size distribution (PSD) parameters retrieved from satellite derived ocean color data. Response of the PFTs to the IOD events of 1997/98 and 2006/2007 was varied in term of magnitude and duration. Nitrate, chlorophyll and 2 PFTs (diatoms and chlorophytes) out of 4 PFTs (Diatoms, Chlorophytes, Coccolithophores and Cyanobacteria) were strongly correlated with the Dipole Mode Indices. The NOBM provided insight to the course of events leading to perturbations and evolution of biogeochemical processes associated with the IOD in a multi-phytoplankton context, against the backdrop of circulation and turbulence dynamics, irradiance availability, and the interaction among different PFTs. Different phases of the IOD cycle were well captured in the evolution of phytoplankton dynamics. Satellite-based retrievals of PSD parameters further characterized the specific biogeochemical setup that facilitated the PFTs to thrive and cross-dominate each other. We examined the potential impact of the IOD/ENSO events on the PFT-specific primary production. Significant correlation was noticed between DMI and PFT-specific primary production of diatoms and chlorophytes. We highlighted the need (1) to develop regional biogeochemical models to overcome the gaps in our understanding and elucidate the precise mechanism that drive the biogeochemical fluctuations in the region (2) to pursue further research on phenological aspects of PFTs to understand potential impact of climatological change on phytoplankton community and on annually recurring cycle of pelagic trophodynamics and ecosystem functions.

SST cooling along coastal Java and Sumatra during positive Indian Ocean Dipole events

NASA Astrophysics Data System (ADS)

Delman, A. S.; McClean, J.; Sprintall, J.; Talley, L. D.; Bryan, F.; Johnson, B. K.; Carton, J.

2016-02-01

The evolution of positive Indian Ocean Dipole (pIOD) events is driven in part by anomalous SST cooling near the coasts of Java and Sumatra. However, the mechanisms and timeline of surface temperature changes near these two islands are distinct. Satellite data and mixed layer budgets in a forced ocean model simulation with 0.1° spatial resolution were used to characterize the dominant influences on SST in each region during pIOD events. Along the south coast of Java, where upwelling from southeasterly trade winds happens seasonally in June-September, strengthening/weakening of the trade winds has little effect on the interannual variability of SST. Instead, remotely-forced upwelling Kelvin waves are the primary mechanism for producing anomalous Java SST cooling in the early stages of a pIOD event. Other mechanisms that affect Java SST anomalies include inflows from the interior Indonesian Seas, mesoscale eddies, and air-sea heat fluxes; these influences can hasten the decay of cool Java SST anomalies and therefore may impact the strength and duration of pIOD events. Along the west coast of Sumatra, surface cooling is initially delayed by a deeper thermocline and a salinity-stratified barrier layer. Hence upwelling Kelvin waves do not substantially affect SST near Sumatra during the first 2-3 months of Java SST cooling; however, they do help drive surface cooling near Sumatra once the barrier layer has been sufficiently eroded by waters of decreasing temperature and increasing salinity. Upwelling Kelvin wave activity in the equatorial Indian Ocean starting in April is also shown to be a robust predictor of pIOD events later in the calendar year.

Quantification of confocal images of biofilms grown on irregular surfaces

PubMed Central

Ross, Stacy Sommerfeld; Tu, Mai Han; Falsetta, Megan L.; Ketterer, Margaret R.; Kiedrowski, Megan R.; Horswill, Alexander R.; Apicella, Michael A.; Reinhardt, Joseph M.; Fiegel, Jennifer

2014-01-01

Bacterial biofilms grow on many types of surfaces, including flat surfaces such as glass and metal and irregular surfaces such as rocks, biological tissues and polymers. While laser scanning confocal microscopy can provide high-resolution images of biofilms grown on any surface, quantification of biofilm-associated bacteria is currently limited to bacteria grown on flat surfaces. This can limit researchers studying irregular surfaces to qualitative analysis or quantification of only the total bacteria in an image. In this work, we introduce a new algorithm called modified connected volume filtration (MCVF) to quantify bacteria grown on top of an irregular surface that is fluorescently labeled or reflective. Using the MCVF algorithm, two new quantification parameters are introduced. The modified substratum coverage parameter enables quantification of the connected-biofilm bacteria on top of the surface and on the imaging substratum. The utility of MCVF and the modified substratum coverage parameter were shown with Pseudomonas aeruginosa and Staphylococcus aureus biofilms grown on human airway epithelial cells. A second parameter, the percent association, provides quantified data on the colocalization of the bacteria with a labeled component, including bacteria within a labeled tissue. The utility of quantifying the bacteria associated with the cell cytoplasm was demonstrated with Neisseria gonorrhoeae biofilms grown on cervical epithelial cells. This algorithm provides more flexibility and quantitative ability to researchers studying biofilms grown on a variety of irregular substrata. PMID:24632515

Quantification of taurine in energy drinks using ¹H NMR.

PubMed

Hohmann, Monika; Felbinger, Christine; Christoph, Norbert; Wachter, Helmut; Wiest, Johannes; Holzgrabe, Ulrike

2014-05-01

The consumption of so called energy drinks is increasing, especially among adolescents. These beverages commonly contain considerable amounts of the amino sulfonic acid taurine, which is related to a magnitude of various physiological effects. The customary method to control the legal limit of taurine in energy drinks is LC-UV/vis with postcolumn derivatization using ninhydrin. In this paper we describe the quantification of taurine in energy drinks by (1)H NMR as an alternative to existing methods of quantification. Variation of pH values revealed the separation of a distinct taurine signal in (1)H NMR spectra, which was applied for integration and quantification. Quantification was performed using external calibration (R(2)>0.9999; linearity verified by Mandel's fitting test with a 95% confidence level) and PULCON. Taurine concentrations in 20 different energy drinks were analyzed by both using (1)H NMR and LC-UV/vis. The deviation between (1)H NMR and LC-UV/vis results was always below the expanded measurement uncertainty of 12.2% for the LC-UV/vis method (95% confidence level) and at worst 10.4%. Due to the high accordance to LC-UV/vis data and adequate recovery rates (ranging between 97.1% and 108.2%), (1)H NMR measurement presents a suitable method to quantify taurine in energy drinks. Copyright © 2013 Elsevier B.V. All rights reserved.

SMOS reveals the signature of Indian Ocean Dipole events

NASA Astrophysics Data System (ADS)

Durand, Fabien; Alory, Gaël; Dussin, Raphaël; Reul, Nicolas

2013-12-01

The tropical Indian Ocean experiences an interannual mode of climatic variability, known as the Indian Ocean Dipole (IOD). The signature of this variability in ocean salinity is hypothesized based on modeling and assimilation studies, on account of scanty observations. Soil Moisture and Ocean Salinity (SMOS) satellite has been designed to take up the challenge of sea surface salinity remote sensing. We show that SMOS data can be used to infer the pattern of salinity variability linked with the IOD events. The core of maximum variability is located in the central tropical basin, south of the equator. This region is anomalously salty during the 2010 negative IOD event, and anomalously fresh during the 2011 positive IOD event. The peak-to-peak anomaly exceeds one salinity unit, between late 2010 and late 2011. In conjunction with other observational datasets, SMOS data allow us to draw the salt budget of the area. It turns out that the horizontal advection is the main driver of salinity anomalies. This finding is confirmed by the analysis of the outputs of a numerical model. This study shows that the advent of SMOS makes it feasible the quantitative assessment of the mechanisms of ocean surface salinity variability in the tropical basins, at interannual timescales.

Practical quantification of necrosis in histological whole-slide images.

PubMed

Homeyer, André; Schenk, Andrea; Arlt, Janine; Dahmen, Uta; Dirsch, Olaf; Hahn, Horst K

2013-06-01

Since the histological quantification of necrosis is a common task in medical research and practice, we evaluate different image analysis methods for quantifying necrosis in whole-slide images. In a practical usage scenario, we assess the impact of different classification algorithms and feature sets on both accuracy and computation time. We show how a well-chosen combination of multiresolution features and an efficient postprocessing step enables the accurate quantification necrosis in gigapixel images in less than a minute. The results are general enough to be applied to other areas of histological image analysis as well. Copyright © 2013 Elsevier Ltd. All rights reserved.

Integrated protocol for reliable and fast quantification and documentation of electrophoresis gels.

PubMed

Rehbein, Peter; Schwalbe, Harald

2015-06-01

Quantitative analysis of electrophoresis gels is an important part in molecular cloning, as well as in protein expression and purification. Parallel quantifications in yield and purity can be most conveniently obtained from densitometric analysis. This communication reports a comprehensive, reliable and simple protocol for gel quantification and documentation, applicable for single samples and with special features for protein expression screens. As major component of the protocol, the fully annotated code of a proprietary open source computer program for semi-automatic densitometric quantification of digitized electrophoresis gels is disclosed. The program ("GelQuant") is implemented for the C-based macro-language of the widespread integrated development environment of IGOR Pro. Copyright © 2014 Elsevier Inc. All rights reserved.

Multiscale recurrence quantification analysis of order recurrence plots

NASA Astrophysics Data System (ADS)

Xu, Mengjia; Shang, Pengjian; Lin, Aijing

2017-03-01

In this paper, we propose a new method of multiscale recurrence quantification analysis (MSRQA) to analyze the structure of order recurrence plots. The MSRQA is based on order patterns over a range of time scales. Compared with conventional recurrence quantification analysis (RQA), the MSRQA can show richer and more recognizable information on the local characteristics of diverse systems which successfully describes their recurrence properties. Both synthetic series and stock market indexes exhibit their properties of recurrence at large time scales that quite differ from those at a single time scale. Some systems present more accurate recurrence patterns under large time scales. It demonstrates that the new approach is effective for distinguishing three similar stock market systems and showing some inherent differences.

Superposition Quantification

NASA Astrophysics Data System (ADS)

Chang, Li-Na; Luo, Shun-Long; Sun, Yuan

2017-11-01

The principle of superposition is universal and lies at the heart of quantum theory. Although ever since the inception of quantum mechanics a century ago, superposition has occupied a central and pivotal place, rigorous and systematic studies of the quantification issue have attracted significant interests only in recent years, and many related problems remain to be investigated. In this work we introduce a figure of merit which quantifies superposition from an intuitive and direct perspective, investigate its fundamental properties, connect it to some coherence measures, illustrate it through several examples, and apply it to analyze wave-particle duality. Supported by Science Challenge Project under Grant No. TZ2016002, Laboratory of Computational Physics, Institute of Applied Physics and Computational Mathematics, Beijing, Key Laboratory of Random Complex Structures and Data Science, Chinese Academy of Sciences, Grant under No. 2008DP173182

HPLC Quantification of astaxanthin and canthaxanthin in Salmonidae eggs.

PubMed

Tzanova, Milena; Argirova, Mariana; Atanasov, Vasil

2017-04-01

Astaxanthin and canthaxanthin are naturally occurring antioxidants referred to as xanthophylls. They are used as food additives in fish farms to improve the organoleptic qualities of salmonid products and to prevent reproductive diseases. This study reports the development and single-laboratory validation of a rapid method for quantification of astaxanthin and canthaxanthin in eggs of rainbow trout (Oncorhynchus mykiss) and brook trout (Salvelinus fontinalis М.). An advantage of the proposed method is the perfect combination of selective extraction of the xanthophylls and analysis of the extract by high-performance liquid chromatography and photodiode array detection. The method validation was carried out in terms of linearity, accuracy, precision, recovery and limits of detection and quantification. The method was applied for simultaneous quantification of the two xanthophylls in eggs of rainbow trout and brook trout after their selective extraction. The results show that astaxanthin accumulations in salmonid fish eggs are larger than those of canthaxanthin. As the levels of these two xanthophylls affect fish fertility, this method can be used to improve the nutritional quality and to minimize the occurrence of the M74 syndrome in fish populations. Copyright © 2016 John Wiley & Sons, Ltd.

Model Uncertainty Quantification Methods In Data Assimilation

NASA Astrophysics Data System (ADS)

Pathiraja, S. D.; Marshall, L. A.; Sharma, A.; Moradkhani, H.

2017-12-01

Data Assimilation involves utilising observations to improve model predictions in a seamless and statistically optimal fashion. Its applications are wide-ranging; from improving weather forecasts to tracking targets such as in the Apollo 11 mission. The use of Data Assimilation methods in high dimensional complex geophysical systems is an active area of research, where there exists many opportunities to enhance existing methodologies. One of the central challenges is in model uncertainty quantification; the outcome of any Data Assimilation study is strongly dependent on the uncertainties assigned to both observations and models. I focus on developing improved model uncertainty quantification methods that are applicable to challenging real world scenarios. These include developing methods for cases where the system states are only partially observed, where there is little prior knowledge of the model errors, and where the model error statistics are likely to be highly non-Gaussian.

Real-time quantitative PCR for retrovirus-like particle quantification in CHO cell culture.

PubMed

de Wit, C; Fautz, C; Xu, Y

2000-09-01

Chinese hamster ovary (CHO) cells have been widely used to manufacture recombinant proteins intended for human therapeutic uses. Retrovirus-like particles, which are apparently defective and non-infectious, have been detected in all CHO cells by electron microscopy (EM). To assure viral safety of CHO cell-derived biologicals, quantification of retrovirus-like particles in production cell culture and demonstration of sufficient elimination of such retrovirus-like particles by the down-stream purification process are required for product market registration worldwide. EM, with a detection limit of 1x10(6) particles/ml, is the standard retrovirus-like particle quantification method. The whole process, which requires a large amount of sample (3-6 litres), is labour intensive, time consuming, expensive, and subject to significant assay variability. In this paper, a novel real-time quantitative PCR assay (TaqMan assay) has been developed for the quantification of retrovirus-like particles. Each retrovirus particle contains two copies of the viral genomic particle RNA (pRNA) molecule. Therefore, quantification of retrovirus particles can be achieved by quantifying the pRNA copy number, i.e. every two copies of retroviral pRNA is equivalent to one retrovirus-like particle. The TaqMan assay takes advantage of the 5'-->3' exonuclease activity of Taq DNA polymerase and utilizes the PRISM 7700 Sequence Detection System of PE Applied Biosystems (Foster City, CA, U.S.A.) for automated pRNA quantification through a dual-labelled fluorogenic probe. The TaqMan quantification technique is highly comparable to the EM analysis. In addition, it offers significant advantages over the EM analysis, such as a higher sensitivity of less than 600 particles/ml, greater accuracy and reliability, higher sample throughput, more flexibility and lower cost. Therefore, the TaqMan assay should be used as a substitute for EM analysis for retrovirus-like particle quantification in CHO cell

Matrix suppression as a guideline for reliable quantification of peptides by matrix-assisted laser desorption ionization.

PubMed

Ahn, Sung Hee; Bae, Yong Jin; Moon, Jeong Hee; Kim, Myung Soo

2013-09-17

We propose to divide matrix suppression in matrix-assisted laser desorption ionization into two parts, normal and anomalous. In quantification of peptides, the normal effect can be accounted for by constructing the calibration curve in the form of peptide-to-matrix ion abundance ratio versus concentration. The anomalous effect forbids reliable quantification and is noticeable when matrix suppression is larger than 70%. With this 70% rule, matrix suppression becomes a guideline for reliable quantification, rather than a nuisance. A peptide in a complex mixture can be quantified even in the presence of large amounts of contaminants, as long as matrix suppression is below 70%. The theoretical basis for the quantification method using a peptide as an internal standard is presented together with its weaknesses. A systematic method to improve quantification of high concentration analytes has also been developed.

Detection and quantification of beef and pork materials in meat products by duplex droplet digital PCR.

PubMed

Cai, Yicun; He, Yuping; Lv, Rong; Chen, Hongchao; Wang, Qiang; Pan, Liangwen

2017-01-01

Meat products often consist of meat from multiple animal species, and inaccurate food product adulteration and mislabeling can negatively affect consumers. Therefore, a cost-effective and reliable method for identification and quantification of animal species in meat products is required. In this study, we developed a duplex droplet digital PCR (dddPCR) detection and quantification system to simultaneously identify and quantify the source of meat in samples containing a mixture of beef (Bos taurus) and pork (Sus scrofa) in a single digital PCR reaction tube. Mixed meat samples of known composition were used to test the accuracy and applicability of this method. The limit of detection (LOD) and the limit of quantification (LOQ) of this detection and quantification system were also identified. We conclude that our dddPCR detection and quantification system is suitable for quality control and routine analyses of meat products.

Mathematical and Computational Foundations of Recurrence Quantifications

NASA Astrophysics Data System (ADS)

Marwan, Norbert; Webber, Charles L.

Real-world systems possess deterministic trajectories, phase singularities and noise. Dynamic trajectories have been studied in temporal and frequency domains, but these are linear approaches. Basic to the field of nonlinear dynamics is the representation of trajectories in phase space. A variety of nonlinear tools such as the Lyapunov exponent, Kolmogorov-Sinai entropy, correlation dimension, etc. have successfully characterized trajectories in phase space, provided the systems studied were stationary in time. Ubiquitous in nature, however, are systems that are nonlinear and nonstationary, existing in noisy environments all of which are assumption breaking to otherwise powerful linear tools. What has been unfolding over the last quarter of a century, however, is the timely discovery and practical demonstration that the recurrences of system trajectories in phase space can provide important clues to the system designs from which they derive. In this chapter we will introduce the basics of recurrence plots (RP) and their quantification analysis (RQA). We will begin by summarizing the concept of phase space reconstructions. Then we will provide the mathematical underpinnings of recurrence plots followed by the details of recurrence quantifications. Finally, we will discuss computational approaches that have been implemented to make recurrence strategies feasible and useful. As computers become faster and computer languages advance, younger generations of researchers will be stimulated and encouraged to capture nonlinear recurrence patterns and quantification in even better formats. This particular branch of nonlinear dynamics remains wide open for the definition of new recurrence variables and new applications untouched to date.

Spatial and seasonal responses of precipitation in the Ganges and Brahmaputra river basins to ENSO and Indian Ocean dipole modes: implications for flooding and drought

USGS Publications Warehouse

Pervez, Md Shahriar; Henebry, Geoffry M.

2015-01-01

We evaluated the spatial and seasonal responses of precipitation in the Ganges and Brahmaputra basins as modulated by the El Niño Southern Oscillation (ENSO) and Indian Ocean Dipole (IOD) modes using Global Precipitation Climatology Centre (GPCC) full data reanalysis of monthly global land-surface precipitation data from 1901 to 2010 with a spatial resolution of 0.5° × 0.5°. The GPCC monthly total precipitation climatology targeting the period 1951–2000 was used to compute gridded monthly anomalies for the entire time period. The gridded monthly anomalies were averaged for the years influenced by combinations of climate modes. Occurrences of El Niño alone significantly reduce (88% of the long-term average (LTA)) precipitation during the monsoon months in the western and southeastern Ganges Basin. In contrast, occurrences of La Niña and co-occurrences of La Niña and negative IOD events significantly enhance (110 and 109% of LTA in the Ganges and Brahmaputra Basin, respectively) precipitation across both basins. When El Niño co-occurs with positive IOD events, the impacts of El Niño on the basins' precipitation diminishes. When there is no active ENSO or IOD events (occurring in 41 out of 110 years), precipitation remains below average (95% of LTA) in the agriculturally intensive areas of Haryana, Uttar Pradesh, Rajasthan, Madhya Pradesh, and Western Nepal in the Ganges Basin, whereas precipitation remains average to above average (104% of LTA) across the Brahmaputra Basin. This pattern implies that a regular water deficit is likely, especially in the Ganges Basin, with implications for the agriculture sector due to its reliance on consistent rainfall for successful production. Historically, major droughts occurred during El Niño and co-occurrences of El Niño and positive IOD events, while major flooding occurred during La Niña and co-occurrences of La Niña and negative IOD events in the basins. This observational analysis will facilitate well

Dynamical analysis of the Indian Ocean climate network and its correlation with Australian Millennium Drought

NASA Astrophysics Data System (ADS)

Carpi, Laura; Masoller, Cristina; Díaz-Guilera, Albert; Ravetti, Martín G.

2015-04-01

During the period between the mid-1990s and late 2000s Australia had suffered one of the worst droughts on record. Severe rainfall deficits affected great part of southeast Australia, causing widespread drought conditions and catastrophic bushfires. The "Millennium Drought", as it was called, was unusual in terms of its severity, duration and extent, leaving important environmental and financial damages. One of the most important drivers of Australia climate variability is the Indian Ocean dipole (IOD), that is a coupled ocean and atmosphere phenomenon in the equatorial Indian Ocean. The IOD is measured by an index (DMI) that is the difference between sea surface temperature (SST) anomalies in the western and eastern equatorial Indian Ocean. Its positive phase is characterized by lower than normal sea surface temperatures in the tropical eastern coast, and higher than normal in the tropical western Indian Ocean. Extreme positive IOD (pIOD) events are associated to severe droughts in countries located over the eastern Indian Ocean, and to severe floods in the western tropical ones. Recent research works projected that the frequency of extreme pIOD events will increase significantly over the twenty-first century and consequently, the frequency of extreme climate conditions in the zones affected by it. In this work we study the dynamics of the Indian Ocean for the period of 1979-2014, by using climate networks of skin temperature and humidity (reanalysis data). Annual networks are constructed by creating links when the Pearson correlation coefficient between two nodes is greater than a specific value. The distance distribution Pd(k), that indicates the fraction of pairs of nodes at distance k, is computed to characterize the dynamics of the network by using Information Theory quantifiers. We found a clear change in the Indian Ocean dynamics and an increment in the network's similarities quantified by the Jensen-Shannon divergence in the late 1990s. We speculate that

Intraseasonal SST-precipitation coupling during the Indian Summer Monsoon, and its modulation by the Indian Ocean Dipole

NASA Astrophysics Data System (ADS)

Jongaramrungruang, S.; Seo, H.; Ummenhofer, C.

2016-02-01

The Indian Summer Monsoon (ISM) plays a crucial role in shaping the large proportion of the total precipitation over the Indian subcontinent each year. The ISM rainfall exhibits a particularly strong intraseasonal variability, that has profound socioeconomic consequences, such as agricultural planning and flood preparation. However, our understanding of the variability on this time scale is still limited due to sparse data availability in the past. In this study, we used a combination of state-of-the-art high-resolution satellite estimate of rainfall, objectively analyzed surface flux, as well as atmospheric reanalysis product to investigate the nature of the ISM intraseasonal rainfall variability and how it varies year to year. The emphasis is placed on the Bay of Bengal (BoB) where the intraseasonal ocean-atmosphere coupling is most prominent. Results show that the maximum warming of SST leads the onset of heavy precipitation event by 3-5 days, and that surface heat flux and surface wind speed are weak prior to the rain but amplifies and peaks after the rain reaches its maximum. Furthermore, the Indian Ocean Dipole (IOD) significantly affects the observed intraseasonal SST-precipitation relationship. The pre-convection SST warming is stronger and more pronounced during the negative phase of the IOD, while the signal is weaker and less organized in the positive phase. This is explained by the column-integrated moisture budget analysis which reveals that, during the ISM heavy rainfall in the BoB, there is more moisture interchange in the form of enhanced vertical advection from the ocean to atmosphere in negative IOD years as compared to positive IOD years. Knowing the distinction of ISM variabilities during opposite phases of the IOD will help contribute to a more reliable prediction of ISM activities.

A non-stationary relationship between global climate phenomena and human plague incidence in Madagascar.

PubMed

Kreppel, Katharina S; Caminade, Cyril; Telfer, Sandra; Rajerison, Minoarison; Rahalison, Lila; Morse, Andy; Baylis, Matthew

2014-10-01

Plague, a zoonosis caused by Yersinia pestis, is found in Asia and the Americas, but predominantly in Africa, with the island of Madagascar reporting almost one third of human cases worldwide. Plague's occurrence is affected by local climate factors which in turn are influenced by large-scale climate phenomena such as the El Niño Southern Oscillation (ENSO). The effects of ENSO on regional climate are often enhanced or reduced by a second large-scale climate phenomenon, the Indian Ocean Dipole (IOD). It is known that ENSO and the IOD interact as drivers of disease. Yet the impacts of these phenomena in driving plague dynamics via their effect on regional climate, and specifically contributing to the foci of transmission on Madagascar, are unknown. Here we present the first analysis of the effects of ENSO and IOD on plague in Madagascar. We use a forty-eight year monthly time-series of reported human plague cases from 1960 to 2008. Using wavelet analysis, we show that over the last fifty years there have been complex non-stationary associations between ENSO/IOD and the dynamics of plague in Madagascar. We demonstrate that ENSO and IOD influence temperature in Madagascar and that temperature and plague cycles are associated. The effects on plague appear to be mediated more by temperature, but precipitation also undoubtedly influences plague in Madagascar. Our results confirm a relationship between plague anomalies and an increase in the intensity of ENSO events and precipitation. This work widens the understanding of how climate factors acting over different temporal scales can combine to drive local disease dynamics. Given the association of increasing ENSO strength and plague anomalies in Madagascar it may in future be possible to forecast plague outbreaks in Madagascar. The study gives insight into the complex and changing relationship between climate factors and plague in Madagascar.

Quantification of L-Citrulline and other physiologic amino acids in watermelon and selected cucurbits

USDA-ARS?s Scientific Manuscript database

High performance liquid chromatography of dabsyl derivatives of amino acids was employed for quantification of physiologic amino acids in cucurbits. This method is particularly useful because the dabsyl derivatives of glutamine and citrulline are sufficiently separated to allow quantification of ea...

Protein, enzyme and carbohydrate quantification using smartphone through colorimetric digitization technique.

PubMed

Dutta, Sibasish; Saikia, Gunjan Prasad; Sarma, Dhruva Jyoti; Gupta, Kuldeep; Das, Priyanka; Nath, Pabitra

2017-05-01

In this paper the utilization of smartphone as a detection platform for colorimetric quantification of biological macromolecules has been demonstrated. Using V-channel of HSV color space, the quantification of BSA protein, catalase enzyme and carbohydrate (using D-glucose) have been successfully investigated. A custom designed android application has been developed for estimating the total concentration of biological macromolecules. The results have been compared with that of a standard spectrophotometer which is generally used for colorimetric quantification in laboratory settings by measuring its absorbance at a specific wavelength. The results obtained with the designed sensor is found to be similar when compared with the spectrophotometer data. The designed sensor is low cost, robust and we envision that it could promote diverse fields of bio-analytical investigations. Schematic illustration of the smartphone sensing mechanism for colorimetric analysis of biomolecular samples. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantification of trace metals in water using complexation and filter concentration.

PubMed

Dolgin, Bella; Bulatov, Valery; Japarov, Julia; Elish, Eyal; Edri, Elad; Schechter, Israel

2010-06-15

Various metals undergo complexation with organic reagents, resulting in colored products. In practice, their molar absorptivities allow for quantification in the ppm range. However, a proper pre-concentration of the colored complex on paper filter lowers the quantification limit to the low ppb range. In this study, several pre-concentration techniques have been examined and compared: filtering the already complexed mixture, complexation on filter, and dipping of dye-covered filter in solution. The best quantification has been based on the ratio of filter reflectance at a certain wavelength to that at zero metal concentration. The studied complex formations (Ni ions with TAN and Cd ions with PAN) involve production of nanoparticle suspensions, which are associated with complicated kinetics. The kinetics of the complexation of Ni ions with TAN has been investigated and optimum timing could be found. Kinetic optimization in regard to some interferences has also been suggested.

Nitric Oxide Analyzer Quantification of Plant S-Nitrosothiols.

PubMed

Hussain, Adil; Yun, Byung-Wook; Loake, Gary J

2018-01-01

Nitric oxide (NO) is a small diatomic molecule that regulates multiple physiological processes in animals, plants, and microorganisms. In animals, it is involved in vasodilation and neurotransmission and is present in exhaled breath. In plants, it regulates both plant immune function and numerous developmental programs. The high reactivity and short half-life of NO and cross-reactivity of its various derivatives make its quantification difficult. Different methods based on calorimetric, fluorometric, and chemiluminescent detection of NO and its derivatives are available, but all of them have significant limitations. Here we describe a method for the chemiluminescence-based quantification of NO using ozone-chemiluminescence technology in plants. This approach provides a sensitive, robust, and flexible approach for determining the levels of NO and its signaling products, protein S-nitrosothiols.

Parsing and Quantification of Raw Orbitrap Mass Spectrometer Data Using RawQuant.

PubMed

Kovalchik, Kevin A; Moggridge, Sophie; Chen, David D Y; Morin, Gregg B; Hughes, Christopher S

2018-06-01

Effective analysis of protein samples by mass spectrometry (MS) requires careful selection and optimization of a range of experimental parameters. As the output from the primary detection device, the "raw" MS data file can be used to gauge the success of a given sample analysis. However, the closed-source nature of the standard raw MS file can complicate effective parsing of the data contained within. To ease and increase the range of analyses possible, the RawQuant tool was developed to enable parsing of raw MS files derived from Thermo Orbitrap instruments to yield meta and scan data in an openly readable text format. RawQuant can be commanded to export user-friendly files containing MS 1 , MS 2 , and MS 3 metadata as well as matrices of quantification values based on isobaric tagging approaches. In this study, the utility of RawQuant is demonstrated in several scenarios: (1) reanalysis of shotgun proteomics data for the identification of the human proteome, (2) reanalysis of experiments utilizing isobaric tagging for whole-proteome quantification, and (3) analysis of a novel bacterial proteome and synthetic peptide mixture for assessing quantification accuracy when using isobaric tags. Together, these analyses successfully demonstrate RawQuant for the efficient parsing and quantification of data from raw Thermo Orbitrap MS files acquired in a range of common proteomics experiments. In addition, the individual analyses using RawQuant highlights parametric considerations in the different experimental sets and suggests targetable areas to improve depth of coverage in identification-focused studies and quantification accuracy when using isobaric tags.

Uncertainty Quantification in Alchemical Free Energy Methods.

PubMed

Bhati, Agastya P; Wan, Shunzhou; Hu, Yuan; Sherborne, Brad; Coveney, Peter V

2018-06-12

Alchemical free energy methods have gained much importance recently from several reports of improved ligand-protein binding affinity predictions based on their implementation using molecular dynamics simulations. A large number of variants of such methods implementing different accelerated sampling techniques and free energy estimators are available, each claimed to be better than the others in its own way. However, the key features of reproducibility and quantification of associated uncertainties in such methods have barely been discussed. Here, we apply a systematic protocol for uncertainty quantification to a number of popular alchemical free energy methods, covering both absolute and relative free energy predictions. We show that a reliable measure of error estimation is provided by ensemble simulation-an ensemble of independent MD simulations-which applies irrespective of the free energy method. The need to use ensemble methods is fundamental and holds regardless of the duration of time of the molecular dynamics simulations performed.

Modeling qRT-PCR dynamics with application to cancer biomarker quantification.

PubMed

Chervoneva, Inna; Freydin, Boris; Hyslop, Terry; Waldman, Scott A

2017-01-01

Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is widely used for molecular diagnostics and evaluating prognosis in cancer. The utility of mRNA expression biomarkers relies heavily on the accuracy and precision of quantification, which is still challenging for low abundance transcripts. The critical step for quantification is accurate estimation of efficiency needed for computing a relative qRT-PCR expression. We propose a new approach to estimating qRT-PCR efficiency based on modeling dynamics of polymerase chain reaction amplification. In contrast, only models for fluorescence intensity as a function of polymerase chain reaction cycle have been used so far for quantification. The dynamics of qRT-PCR efficiency is modeled using an ordinary differential equation model, and the fitted ordinary differential equation model is used to obtain effective polymerase chain reaction efficiency estimates needed for efficiency-adjusted quantification. The proposed new qRT-PCR efficiency estimates were used to quantify GUCY2C (Guanylate Cyclase 2C) mRNA expression in the blood of colorectal cancer patients. Time to recurrence and GUCY2C expression ratios were analyzed in a joint model for survival and longitudinal outcomes. The joint model with GUCY2C quantified using the proposed polymerase chain reaction efficiency estimates provided clinically meaningful results for association between time to recurrence and longitudinal trends in GUCY2C expression.

Finite element analysis and clinical complications in mandibular implant-overdentures opposing maxillary dentures.

PubMed

Khuder, Tameem; Yunus, Norsiah; Sulaiman, Eshamsul; Dabbagh, Ali

2017-11-01

Denture fracture is a common clinical complication caused by improper material selection, design, or fabrication technique. This study aimed to investigate the effect of two attachment systems on fracture risk of the implant-overdentures (IOD) via finite element analysis (FEA), using the force distributions obtained from patients' occlusal analyses and to compare the obtained results with the clinical complications associated with these attachments. A three-dimensional jaw model comprised of the edentulous bones was constructed. Three types of mandibular prostheses including complete denture (CD) (model LCD), IOD with Locator attachment (model LID-L), and IOD with telescopic attachment (model LID-T), as well as a maxillary CD (model UCD) were assembled. The vertical occlusal forces at anterior and posterior quadrants were obtained from the patients wearing mandibular CDs or IODs. The FEA results were further compared with the mechanical failures of different prostheses observed at patient recalls. In overall, the fracture risk of mandibular prostheses was lower than the maxillary compartments. The UCD opposing LCD underwent higher strains than that opposing LID-L and LID-T, which was mostly concentrated at the anterior mid-palatal polished surface. On the other hand, LID-L showed the lowest strain, followed by LID-T, and LCD. The obtained results were consistent with the clinical complications observed in the patient recalls. Copyright © 2017 Elsevier Ltd. All rights reserved.

A refined methodology for modeling volume quantification performance in CT

NASA Astrophysics Data System (ADS)

Chen, Baiyu; Wilson, Joshua; Samei, Ehsan

2014-03-01

The utility of CT lung nodule volume quantification technique depends on the precision of the quantification. To enable the evaluation of quantification precision, we previously developed a mathematical model that related precision to image resolution and noise properties in uniform backgrounds in terms of an estimability index (e'). The e' was shown to predict empirical precision across 54 imaging and reconstruction protocols, but with different correlation qualities for FBP and iterative reconstruction (IR) due to the non-linearity of IR impacted by anatomical structure. To better account for the non-linearity of IR, this study aimed to refine the noise characterization of the model in the presence of textured backgrounds. Repeated scans of an anthropomorphic lung phantom were acquired. Subtracted images were used to measure the image quantum noise, which was then used to adjust the noise component of the e' calculation measured from a uniform region. In addition to the model refinement, the validation of the model was further extended to 2 nodule sizes (5 and 10 mm) and 2 segmentation algorithms. Results showed that the magnitude of IR's quantum noise was significantly higher in structured backgrounds than in uniform backgrounds (ASiR, 30-50%; MBIR, 100-200%). With the refined model, the correlation between e' values and empirical precision no longer depended on reconstruction algorithm. In conclusion, the model with refined noise characterization relfected the nonlinearity of iterative reconstruction in structured background, and further showed successful prediction of quantification precision across a variety of nodule sizes, dose levels, slice thickness, reconstruction algorithms, and segmentation software.

Recurrence quantification as potential bio-markers for diagnosis of pre-cancer

NASA Astrophysics Data System (ADS)

Mukhopadhyay, Sabyasachi; Pratiher, Sawon; Barman, Ritwik; Pratiher, Souvik; Pradhan, Asima; Ghosh, Nirmalya; Panigrahi, Prasanta K.

2017-03-01

In this paper, the spectroscopy signals have been analyzed in recurrence plots (RP), and extract recurrence quantification analysis (RQA) parameters from the RP in order to classify the tissues into normal and different precancerous grades. Three RQA parameters have been quantified in order to extract the important features in the spectroscopy data. These features have been fed to different classifiers for classification. Simulation results validate the efficacy of the recurrence quantification as potential bio-markers for diagnosis of pre-cancer.

Generic method for the absolute quantification of glutathione S-conjugates: Application to the conjugates of acetaminophen, clozapine and diclofenac.

PubMed

den Braver, Michiel W; Vermeulen, Nico P E; Commandeur, Jan N M

2017-03-01

Modification of cellular macromolecules by reactive drug metabolites is considered to play an important role in the initiation of tissue injury by many drugs. Detection and identification of reactive intermediates is often performed by analyzing the conjugates formed after trapping by glutathione (GSH). Although sensitivity of modern mass spectrometrical methods is extremely high, absolute quantification of GSH-conjugates is critically dependent on the availability of authentic references. Although 1 H NMR is currently the method of choice for quantification of metabolites formed biosynthetically, its intrinsically low sensitivity can be a limiting factor in quantification of GSH-conjugates which generally are formed at low levels. In the present study, a simple but sensitive and generic method for absolute quantification of GSH-conjugates is presented. The method is based on quantitative alkaline hydrolysis of GSH-conjugates and subsequent quantification of glutamic acid and glycine by HPLC after precolumn derivatization with o-phthaldialdehyde/N-acetylcysteine (OPA/NAC). Because of the lower stability of the glycine OPA/NAC-derivate, quantification of the glutamic acid OPA/NAC-derivate appeared most suitable for quantification of GSH-conjugates. The novel method was used to quantify the concentrations of GSH-conjugates of diclofenac, clozapine and acetaminophen and quantification was consistent with 1 H NMR, but with a more than 100-fold lower detection limit for absolute quantification. Copyright © 2017. Published by Elsevier B.V.

Sulfur-based absolute quantification of proteins using isotope dilution inductively coupled plasma mass spectrometry

NASA Astrophysics Data System (ADS)

Lee, Hyun-Seok; Heun Kim, Sook; Jeong, Ji-Seon; Lee, Yong-Moon; Yim, Yong-Hyeon

2015-10-01

An element-based reductive approach provides an effective means of realizing International System of Units (SI) traceability for high-purity biological standards. Here, we develop an absolute protein quantification method using double isotope dilution (ID) inductively coupled plasma mass spectrometry (ICP-MS) combined with microwave-assisted acid digestion for the first time. We validated the method and applied it to certify the candidate protein certified reference material (CRM) of human growth hormone (hGH). The concentration of hGH was determined by analysing the total amount of sulfur in hGH. Next, the size-exclusion chromatography method was used with ICP-MS to characterize and quantify sulfur-containing impurities. By subtracting the contribution of sulfur-containing impurities from the total sulfur content in the hGH CRM, we obtained a SI-traceable certification value. The quantification result obtained with the present method based on sulfur analysis was in excellent agreement with the result determined via a well-established protein quantification method based on amino acid analysis using conventional acid hydrolysis combined with an ID liquid chromatography-tandem mass spectrometry. The element-based protein quantification method developed here can be generally used for SI-traceable absolute quantification of proteins, especially pure-protein standards.

A multicenter study benchmarks software tools for label-free proteome quantification.

PubMed

Navarro, Pedro; Kuharev, Jörg; Gillet, Ludovic C; Bernhardt, Oliver M; MacLean, Brendan; Röst, Hannes L; Tate, Stephen A; Tsou, Chih-Chiang; Reiter, Lukas; Distler, Ute; Rosenberger, George; Perez-Riverol, Yasset; Nesvizhskii, Alexey I; Aebersold, Ruedi; Tenzer, Stefan

2016-11-01

Consistent and accurate quantification of proteins by mass spectrometry (MS)-based proteomics depends on the performance of instruments, acquisition methods and data analysis software. In collaboration with the software developers, we evaluated OpenSWATH, SWATH 2.0, Skyline, Spectronaut and DIA-Umpire, five of the most widely used software methods for processing data from sequential window acquisition of all theoretical fragment-ion spectra (SWATH)-MS, which uses data-independent acquisition (DIA) for label-free protein quantification. We analyzed high-complexity test data sets from hybrid proteome samples of defined quantitative composition acquired on two different MS instruments using different SWATH isolation-window setups. For consistent evaluation, we developed LFQbench, an R package, to calculate metrics of precision and accuracy in label-free quantitative MS and report the identification performance, robustness and specificity of each software tool. Our reference data sets enabled developers to improve their software tools. After optimization, all tools provided highly convergent identification and reliable quantification performance, underscoring their robustness for label-free quantitative proteomics.

Radio-frequency energy quantification in magnetic resonance imaging

NASA Astrophysics Data System (ADS)

Alon, Leeor

Mapping of radio frequency (RF) energy deposition has been challenging for 50+ years, especially, when scanning patients in the magnetic resonance imaging (MRI) environment. As result, electromagnetic simulation software is often used for estimating the specific absorption rate (SAR), the rate of RF energy deposition in tissue. The thesis work presents challenges associated with aligning information provided by electromagnetic simulation and MRI experiments. As result of the limitations of simulations, experimental methods for the quantification of SAR were established. A system for quantification of the total RF energy deposition was developed for parallel transmit MRI (a system that uses multiple antennas to excite and image the body). The system is capable of monitoring and predicting channel-by-channel RF energy deposition, whole body SAR and capable of tracking potential hardware failures that occur in the transmit chain and may cause the deposition of excessive energy into patients. Similarly, we demonstrated that local RF power deposition can be mapped and predicted for parallel transmit systems based on a series of MRI temperature mapping acquisitions. Resulting from the work, we developed tools for optimal reconstruction temperature maps from MRI acquisitions. The tools developed for temperature mapping paved the way for utilizing MRI as a diagnostic tool for evaluation of RF/microwave emitting device safety. Quantification of the RF energy was demonstrated for both MRI compatible and non-MRI-compatible devices (such as cell phones), while having the advantage of being noninvasive, of providing millimeter resolution and high accuracy.

Theoretical limitations of quantification for noncompetitive sandwich immunoassays.

PubMed

Woolley, Christine F; Hayes, Mark A; Mahanti, Prasun; Douglass Gilman, S; Taylor, Tom

2015-11-01

Immunoassays exploit the highly selective interaction between antibodies and antigens to provide a vital method for biomolecule detection at low concentrations. Developers and practitioners of immunoassays have long known that non-specific binding often restricts immunoassay limits of quantification (LOQs). Aside from non-specific binding, most efforts by analytical chemists to reduce the LOQ for these techniques have focused on improving the signal amplification methods and minimizing the limitations of the detection system. However, with detection technology now capable of sensing single-fluorescence molecules, this approach is unlikely to lead to dramatic improvements in the future. Here, fundamental interactions based on the law of mass action are analytically connected to signal generation, replacing the four- and five-parameter fittings commercially used to approximate sigmoidal immunoassay curves and allowing quantitative consideration of non-specific binding and statistical limitations in order to understand the ultimate detection capabilities of immunoassays. The restrictions imposed on limits of quantification by instrumental noise, non-specific binding, and counting statistics are discussed based on equilibrium relations for a sandwich immunoassay. Understanding the maximal capabilities of immunoassays for each of these regimes can greatly assist in the development and evaluation of immunoassay platforms. While many studies suggest that single molecule detection is possible through immunoassay techniques, here, it is demonstrated that the fundamental limit of quantification (precision of 10 % or better) for an immunoassay is approximately 131 molecules and this limit is based on fundamental and unavoidable statistical limitations.

PSEA-Quant: a protein set enrichment analysis on label-free and label-based protein quantification data.

PubMed

Lavallée-Adam, Mathieu; Rauniyar, Navin; McClatchy, Daniel B; Yates, John R

2014-12-05

The majority of large-scale proteomics quantification methods yield long lists of quantified proteins that are often difficult to interpret and poorly reproduced. Computational approaches are required to analyze such intricate quantitative proteomics data sets. We propose a statistical approach to computationally identify protein sets (e.g., Gene Ontology (GO) terms) that are significantly enriched with abundant proteins with reproducible quantification measurements across a set of replicates. To this end, we developed PSEA-Quant, a protein set enrichment analysis algorithm for label-free and label-based protein quantification data sets. It offers an alternative approach to classic GO analyses, models protein annotation biases, and allows the analysis of samples originating from a single condition, unlike analogous approaches such as GSEA and PSEA. We demonstrate that PSEA-Quant produces results complementary to GO analyses. We also show that PSEA-Quant provides valuable information about the biological processes involved in cystic fibrosis using label-free protein quantification of a cell line expressing a CFTR mutant. Finally, PSEA-Quant highlights the differences in the mechanisms taking place in the human, rat, and mouse brain frontal cortices based on tandem mass tag quantification. Our approach, which is available online, will thus improve the analysis of proteomics quantification data sets by providing meaningful biological insights.

PSEA-Quant: A Protein Set Enrichment Analysis on Label-Free and Label-Based Protein Quantification Data

PubMed Central

2015-01-01

The majority of large-scale proteomics quantification methods yield long lists of quantified proteins that are often difficult to interpret and poorly reproduced. Computational approaches are required to analyze such intricate quantitative proteomics data sets. We propose a statistical approach to computationally identify protein sets (e.g., Gene Ontology (GO) terms) that are significantly enriched with abundant proteins with reproducible quantification measurements across a set of replicates. To this end, we developed PSEA-Quant, a protein set enrichment analysis algorithm for label-free and label-based protein quantification data sets. It offers an alternative approach to classic GO analyses, models protein annotation biases, and allows the analysis of samples originating from a single condition, unlike analogous approaches such as GSEA and PSEA. We demonstrate that PSEA-Quant produces results complementary to GO analyses. We also show that PSEA-Quant provides valuable information about the biological processes involved in cystic fibrosis using label-free protein quantification of a cell line expressing a CFTR mutant. Finally, PSEA-Quant highlights the differences in the mechanisms taking place in the human, rat, and mouse brain frontal cortices based on tandem mass tag quantification. Our approach, which is available online, will thus improve the analysis of proteomics quantification data sets by providing meaningful biological insights. PMID:25177766

WE-AB-204-05: Harmonizing PET/CT Quantification in Multicenter Studies: A Case Study

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

Marques da Silva, A; Fischer, A

2015-06-15

Purpose: To present the implementation of a strategy to harmonize FDG PET/CT quantification (SUV), performed with different scanner models and manufacturers. Methods: The strategy was based on Boellaard (2011) and EARL FDG-PET/CT accreditation program, that propose quality control measurements for harmonizing scanner performance. A NEMA IEC Body phantom study was performed using four different devices: PHP-1 (Gemini TF Base, Philips); PHP-2 (Gemini GXL, Philips); GEH (Discovery 600, General Electric); SMS (Biograph Hi-Rez 16, Siemens). The SUV Recovery Coefficient (RC) was calculated using the clinical protocol and other clinically relevant reconstruction parameters. The most appropriate reconstruction parameters (MARP) for SUV harmonization,more » in each scanner, are those which achieve EARL harmonizing standards. They were identified using the lowest root mean square errors (RMSE). To evaluate the strategy’s effectiveness, the Maximum Differences (MD) between the clinical and MARP RC values were calculated. Results: The reconstructions parameters that obtained the lowest RMSE are: FBP 5mm (PHP-1); LOR-RAMLA 2i0.008l (PHP-2); VuePointHD 2i32s10mm (GEH); and FORE+OSEM 4i8s6mm (SMS). Thus, to ensure that quantitative PET image measurements are interchangeable between these sites, images must be reconstructed with the above-mentioned parameters. Although, a decoupling between the best image for PET/CT qualitative analysis and the best image for quantification studies was observed. The MD showed that the strategy was effective in reducing the variability of SUV quantification for small structures (<17mm). Conclusion: The harmonization strategy of the SUV quantification implemented with these devices was effective in reducing the variability of small structures quantification, minimizing the inter-scanner and inter-institution differences in quantification. However, it is essential that, in addition to the harmonization of quantification, the standardization of

Absolute quantification by droplet digital PCR versus analog real-time PCR

PubMed Central

Hindson, Christopher M; Chevillet, John R; Briggs, Hilary A; Gallichotte, Emily N; Ruf, Ingrid K; Hindson, Benjamin J; Vessella, Robert L; Tewari, Muneesh

2014-01-01

Nanoliter-sized droplet technology paired with digital PCR (ddPCR) holds promise for highly precise, absolute nucleic acid quantification. Our comparison of microRNA quantification by ddPCR and real-time PCR revealed greater precision (coefficients of variation decreased by 37–86%) and improved day-to-day reproducibility (by a factor of seven) of ddPCR but with comparable sensitivity. When we applied ddPCR to serum microRNA biomarker analysis, this translated to superior diagnostic performance for identifying individuals with cancer. PMID:23995387

Carbon Nanotubes Released from an Epoxy-Based Nanocomposite: Quantification and Particle Toxicity.

PubMed

Schlagenhauf, Lukas; Buerki-Thurnherr, Tina; Kuo, Yu-Ying; Wichser, Adrian; Nüesch, Frank; Wick, Peter; Wang, Jing

2015-09-01

Studies combining both the quantification of free nanoparticle release and the toxicological investigations of the released particles from actual nanoproducts in a real-life exposure scenario are urgently needed, yet very rare. Here, a new measurement method was established to quantify the amount of free-standing and protruding multiwalled carbon nanotubes (MWCNTs) in the respirable fraction of particles abraded from a MWCNT-epoxy nanocomposite. The quantification approach involves the prelabeling of MWCNTs with lead ions, nanocomposite production, abrasion and collection of the inhalable particle fraction, and quantification of free-standing and protruding MWCNTs by measuring the concentration of released lead ions. In vitro toxicity studies for genotoxicity, reactive oxygen species formation, and cell viability were performed using A549 human alveolar epithelial cells and THP-1 monocyte-derived macrophages. The quantification experiment revealed that in the respirable fraction of the abraded particles, approximately 4000 ppm of the MWCNTs were released as exposed MWCNTs (which could contact lung cells upon inhalation) and approximately 40 ppm as free-standing MWCNTs in the worst-case scenario. The release of exposed MWCNTs was lower for nanocomposites containing agglomerated MWCNTs. The toxicity tests revealed that the abraded particles did not induce any acute cytotoxic effects.

A Bayes network approach to uncertainty quantification in hierarchically developed computational models

DOE PAGES

Urbina, Angel; Mahadevan, Sankaran; Paez, Thomas L.

2012-03-01

Here, performance assessment of complex systems is ideally accomplished through system-level testing, but because they are expensive, such tests are seldom performed. On the other hand, for economic reasons, data from tests on individual components that are parts of complex systems are more readily available. The lack of system-level data leads to a need to build computational models of systems and use them for performance prediction in lieu of experiments. Because their complexity, models are sometimes built in a hierarchical manner, starting with simple components, progressing to collections of components, and finally, to the full system. Quantification of uncertainty inmore » the predicted response of a system model is required in order to establish confidence in the representation of actual system behavior. This paper proposes a framework for the complex, but very practical problem of quantification of uncertainty in system-level model predictions. It is based on Bayes networks and uses the available data at multiple levels of complexity (i.e., components, subsystem, etc.). Because epistemic sources of uncertainty were shown to be secondary, in this application, aleatoric only uncertainty is included in the present uncertainty quantification. An example showing application of the techniques to uncertainty quantification of measures of response of a real, complex aerospace system is included.« less

Mass Spectrometric Quantification of N-Linked Glycans by Reference to Exogenous Standards.

PubMed

Mehta, Nickita; Porterfield, Mindy; Struwe, Weston B; Heiss, Christian; Azadi, Parastoo; Rudd, Pauline M; Tiemeyer, Michael; Aoki, Kazuhiro

2016-09-02

Environmental and metabolic processes shape the profile of glycoprotein glycans expressed by cells, whether in culture, developing tissues, or mature organisms. Quantitative characterization of glycomic changes associated with these conditions has been achieved historically by reductive coupling of oligosaccharides to various fluorophores following release from glycoprotein and subsequent HPLC or capillary electrophoretic separation. Such labeling-based approaches provide a robust means of quantifying glycan amount based on fluorescence yield. Mass spectrometry, on the other hand, has generally been limited to relative quantification in which the contribution of the signal intensity for an individual glycan is expressed as a percent of the signal intensity summed over the total profile. Relative quantification has been valuable for highlighting changes in glycan expression between samples; sensitivity is high, and structural information can be derived by fragmentation. We have investigated whether MS-based glycomics is amenable to absolute quantification by referencing signal intensities to well-characterized oligosaccharide standards. We report the qualification of a set of N-linked oligosaccharide standards by NMR, HPLC, and MS. We also demonstrate the dynamic range, sensitivity, and recovery from complex biological matrices for these standards in their permethylated form. Our results indicate that absolute quantification for MS-based glycomic analysis is reproducible and robust utilizing currently available glycan standards.

Accurate Quantification of Cardiovascular Biomarkers in Serum Using Protein Standard Absolute Quantification (PSAQ™) and Selected Reaction Monitoring*

PubMed Central

Huillet, Céline; Adrait, Annie; Lebert, Dorothée; Picard, Guillaume; Trauchessec, Mathieu; Louwagie, Mathilde; Dupuis, Alain; Hittinger, Luc; Ghaleh, Bijan; Le Corvoisier, Philippe; Jaquinod, Michel; Garin, Jérôme; Bruley, Christophe; Brun, Virginie

2012-01-01

Development of new biomarkers needs to be significantly accelerated to improve diagnostic, prognostic, and toxicity monitoring as well as therapeutic follow-up. Biomarker evaluation is the main bottleneck in this development process. Selected Reaction Monitoring (SRM) combined with stable isotope dilution has emerged as a promising option to speed this step, particularly because of its multiplexing capacities. However, analytical variabilities because of upstream sample handling or incomplete trypsin digestion still need to be resolved. In 2007, we developed the PSAQ™ method (Protein Standard Absolute Quantification), which uses full-length isotope-labeled protein standards to quantify target proteins. In the present study we used clinically validated cardiovascular biomarkers (LDH-B, CKMB, myoglobin, and troponin I) to demonstrate that the combination of PSAQ and SRM (PSAQ-SRM) allows highly accurate biomarker quantification in serum samples. A multiplex PSAQ-SRM assay was used to quantify these biomarkers in clinical samples from myocardial infarction patients. Good correlation between PSAQ-SRM and ELISA assay results was found and demonstrated the consistency between these analytical approaches. Thus, PSAQ-SRM has the capacity to improve both accuracy and reproducibility in protein analysis. This will be a major contribution to efficient biomarker development strategies. PMID:22080464

Emphysema quantification from CT scans using novel application of diaphragm curvature estimation: comparison with standard quantification methods and pulmonary function data

NASA Astrophysics Data System (ADS)

Keller, Brad M.; Reeves, Anthony P.; Yankelevitz, David F.; Henschke, Claudia I.; Barr, R. Graham

2009-02-01

Emphysema is a disease of the lungs that destroys the alveolar air sacs and induces long-term respiratory dysfunction. CT scans allow for the imaging of the anatomical basis of emphysema and quantification of the underlying disease state. Several measures have been introduced for the quantification emphysema directly from CT data; most,however, are based on the analysis of density information provided by the CT scans, which vary by scanner and can be hard to standardize across sites and time. Given that one of the anatomical variations associated with the progression of emphysema is the flatting of the diaphragm due to the loss of elasticity in the lung parenchyma, curvature analysis of the diaphragm would provide information about emphysema from CT. Therefore, we propose a new, non-density based measure of the curvature of the diaphragm that would allow for further quantification methods in a robust manner. To evaluate the new method, 24 whole-lung scans were analyzed using the ratios of the lung height and diaphragm width to diaphragm height as curvature estimates as well as using the emphysema index as comparison. Pearson correlation coefficients showed a strong trend of several of the proposed diaphragm curvature measures to have higher correlations, of up to r=0.57, with DLCO% and VA than did the emphysema index. Furthermore, we found emphysema index to have only a 0.27 correlation to the proposed measures, indicating that the proposed measures evaluate different aspects of the disease.

Surface Enhanced Raman Spectroscopy (SERS) methods for endpoint and real-time quantification of miRNA assays

NASA Astrophysics Data System (ADS)

Restaino, Stephen M.; White, Ian M.

2017-03-01

Surface Enhanced Raman spectroscopy (SERS) provides significant improvements over conventional methods for single and multianalyte quantification. Specifically, the spectroscopic fingerprint provided by Raman scattering allows for a direct multiplexing potential far beyond that of fluorescence and colorimetry. Additionally, SERS generates a comparatively low financial and spatial footprint compared with common fluorescence based systems. Despite the advantages of SERS, it has remained largely an academic pursuit. In the field of biosensing, techniques to apply SERS to molecular diagnostics are constantly under development but, most often, assay protocols are redesigned around the use of SERS as a quantification method and ultimately complicate existing protocols. Our group has sought to rethink common SERS methodologies in order to produce translational technologies capable of allowing SERS to compete in the evolving, yet often inflexible biosensing field. This work will discuss the development of two techniques for quantification of microRNA, a promising biomarker for homeostatic and disease conditions ranging from cancer to HIV. First, an inkjet-printed paper SERS sensor has been developed to allow on-demand production of a customizable and multiplexable single-step lateral flow assay for miRNA quantification. Second, as miRNA concentrations commonly exist in relatively low concentrations, amplification methods (e.g. PCR) are therefore required to facilitate quantification. This work presents a novel miRNA assay alongside a novel technique for quantification of nuclease driven nucleic acid amplification strategies that will allow SERS to be used directly with common amplification strategies for quantification of miRNA and other nucleic acid biomarkers.

A phase quantification method based on EBSD data for a continuously cooled microalloyed steel

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

Zhao, H.; Wynne, B.P.; Palmiere, E.J., E-mail: e.j

2017-01-15

Mechanical properties of steels depend on the phase constitutions of the final microstructures which can be related to the processing parameters. Therefore, accurate quantification of different phases is necessary to investigate the relationships between processing parameters, final microstructures and mechanical properties. Point counting on micrographs observed by optical or scanning electron microscopy is widely used as a phase quantification method, and different phases are discriminated according to their morphological characteristics. However, it is difficult to differentiate some of the phase constituents with similar morphology. Differently, for EBSD based phase quantification methods, besides morphological characteristics, other parameters derived from the orientationmore » information can also be used for discrimination. In this research, a phase quantification method based on EBSD data in the unit of grains was proposed to identify and quantify the complex phase constitutions of a microalloyed steel subjected to accelerated coolings. Characteristics of polygonal ferrite/quasi-polygonal ferrite, acicular ferrite and bainitic ferrite on grain averaged misorientation angles, aspect ratios, high angle grain boundary fractions and grain sizes were analysed and used to develop the identification criteria for each phase. Comparing the results obtained by this EBSD based method and point counting, it was found that this EBSD based method can provide accurate and reliable phase quantification results for microstructures with relatively slow cooling rates. - Highlights: •A phase quantification method based on EBSD data in the unit of grains was proposed. •The critical grain area above which GAM angles are valid parameters was obtained. •Grain size and grain boundary misorientation were used to identify acicular ferrite. •High cooling rates deteriorate the accuracy of this EBSD based method.« less

Event-specific real-time detection and quantification of genetically modified Roundup Ready soybean.

PubMed

Huang, Chia-Chia; Pan, Tzu-Ming

2005-05-18

The event-specific real-time detection and quantification of Roundup Ready soybean (RRS) using an ABI PRISM 7700 sequence detection system with light upon extension (LUX) primer was developed in this study. The event-specific primers were designed, targeting the junction of the RRS 5' integration site and the endogenous gene lectin1. Then, a standard reference plasmid was constructed that carried both of the targeted sequences for quantitative analysis. The detection limit of the LUX real-time PCR system was 0.05 ng of 100% RRS genomic DNA, which was equal to 20.5 copies. The range of quantification was from 0.1 to 100%. The sensitivity and range of quantification successfully met the requirement of the labeling rules in the European Union and Taiwan.

GC-MS quantification of suspected volatile allergens in fragrances. 2. Data treatment strategies and method performances.

PubMed

Bassereau, Maud; Chaintreau, Alain; Duperrex, Stéphanie; Joulain, Daniel; Leijs, Hans; Loesing, Gerd; Owen, Neil; Sherlock, Alan; Schippa, Christine; Thorel, Pierre-Jean; Vey, Matthias

2007-01-10

The performances of the GC-MS determination of suspected allergens in fragrance concentrates have been investigated. The limit of quantification was experimentally determined (10 mg/L), and the variability was investigated for three different data treatment strategies: (1) two columns and three quantification ions; (2) two columns and one quantification ion; and (3) one column and three quantification ions. The first strategy best minimizes the risk of determination bias due to coelutions. This risk was evaluated by calculating the probability of coeluting a suspected allergen with perfume constituents exhibiting ions in common. For hydroxycitronellal, when using a two-column strategy, this may statistically occur more than once every 36 analyses for one ion or once every 144 analyses for three ions in common.

In vivo behavior of NTBI revealed by automated quantification system.

PubMed

Ito, Satoshi; Ikuta, Katsuya; Kato, Daisuke; Lynda, Addo; Shibusa, Kotoe; Niizeki, Noriyasu; Toki, Yasumichi; Hatayama, Mayumi; Yamamoto, Masayo; Shindo, Motohiro; Iizuka, Naomi; Kohgo, Yutaka; Fujiya, Mikihiro

2016-08-01

Non-Tf-bound iron (NTBI), which appears in serum in iron overload, is thought to contribute to organ damage; the monitoring of serum NTBI levels may therefore be clinically useful in iron-overloaded patients. However, NTBI quantification methods remain complex, limiting their use in clinical practice. To overcome the technical difficulties often encountered, we recently developed a novel automated NTBI quantification system capable of measuring large numbers of samples. In the present study, we investigated the in vivo behavior of NTBI in human and animal serum using this newly established automated system. Average NTBI in healthy volunteers was 0.44 ± 0.076 μM (median 0.45 μM, range 0.28-0.66 μM), with no significant difference between sexes. Additionally, serum NTBI rapidly increased after iron loading, followed by a sudden disappearance. NTBI levels also decreased in inflammation. The results indicate that NTBI is a unique marker of iron metabolism, unlike other markers of iron metabolism, such as serum ferritin. Our new automated NTBI quantification method may help to reveal the clinical significance of NTBI and contribute to our understanding of iron overload.

Strawberry: Fast and accurate genome-guided transcript reconstruction and quantification from RNA-Seq.

PubMed

Liu, Ruolin; Dickerson, Julie

2017-11-01

We propose a novel method and software tool, Strawberry, for transcript reconstruction and quantification from RNA-Seq data under the guidance of genome alignment and independent of gene annotation. Strawberry consists of two modules: assembly and quantification. The novelty of Strawberry is that the two modules use different optimization frameworks but utilize the same data graph structure, which allows a highly efficient, expandable and accurate algorithm for dealing large data. The assembly module parses aligned reads into splicing graphs, and uses network flow algorithms to select the most likely transcripts. The quantification module uses a latent class model to assign read counts from the nodes of splicing graphs to transcripts. Strawberry simultaneously estimates the transcript abundances and corrects for sequencing bias through an EM algorithm. Based on simulations, Strawberry outperforms Cufflinks and StringTie in terms of both assembly and quantification accuracies. Under the evaluation of a real data set, the estimated transcript expression by Strawberry has the highest correlation with Nanostring probe counts, an independent experiment measure for transcript expression. Strawberry is written in C++14, and is available as open source software at https://github.com/ruolin/strawberry under the MIT license.

Literacy and Language Education: The Quantification of Learning

ERIC Educational Resources Information Center

Gibb, Tara

2015-01-01

This chapter describes international policy contexts of adult literacy and language assessment and the shift toward standardization through measurement tools. It considers the implications the quantification of learning outcomes has for pedagogy and practice and for the social inclusion of transnational migrants.

How to Make Data a Blessing to Parametric Uncertainty Quantification and Reduction?

NASA Astrophysics Data System (ADS)

Ye, M.; Shi, X.; Curtis, G. P.; Kohler, M.; Wu, J.

2013-12-01

In a Bayesian point of view, probability of model parameters and predictions are conditioned on data used for parameter inference and prediction analysis. It is critical to use appropriate data for quantifying parametric uncertainty and its propagation to model predictions. However, data are always limited and imperfect. When a dataset cannot properly constrain model parameters, it may lead to inaccurate uncertainty quantification. While in this case data appears to be a curse to uncertainty quantification, a comprehensive modeling analysis may help understand the cause and characteristics of parametric uncertainty and thus turns data into a blessing. In this study, we illustrate impacts of data on uncertainty quantification and reduction using an example of surface complexation model (SCM) developed to simulate uranyl (U(VI)) adsorption. The model includes two adsorption sites, referred to as strong and weak sites. The amount of uranium adsorption on these sites determines both the mean arrival time and the long tail of the breakthrough curves. There is one reaction on the weak site but two reactions on the strong site. The unknown parameters include fractions of the total surface site density of the two sites and surface complex formation constants of the three reactions. A total of seven experiments were conducted with different geochemical conditions to estimate these parameters. The experiments with low initial concentration of U(VI) result in a large amount of parametric uncertainty. A modeling analysis shows that it is because the experiments cannot distinguish the relative adsorption affinity of the strong and weak sites on uranium adsorption. Therefore, the experiments with high initial concentration of U(VI) are needed, because in the experiments the strong site is nearly saturated and the weak site can be determined. The experiments with high initial concentration of U(VI) are a blessing to uncertainty quantification, and the experiments with low initial

Compositional Solution Space Quantification for Probabilistic Software Analysis

NASA Technical Reports Server (NTRS)

Borges, Mateus; Pasareanu, Corina S.; Filieri, Antonio; d'Amorim, Marcelo; Visser, Willem

2014-01-01

Probabilistic software analysis aims at quantifying how likely a target event is to occur during program execution. Current approaches rely on symbolic execution to identify the conditions to reach the target event and try to quantify the fraction of the input domain satisfying these conditions. Precise quantification is usually limited to linear constraints, while only approximate solutions can be provided in general through statistical approaches. However, statistical approaches may fail to converge to an acceptable accuracy within a reasonable time. We present a compositional statistical approach for the efficient quantification of solution spaces for arbitrarily complex constraints over bounded floating-point domains. The approach leverages interval constraint propagation to improve the accuracy of the estimation by focusing the sampling on the regions of the input domain containing the sought solutions. Preliminary experiments show significant improvement on previous approaches both in results accuracy and analysis time.

Quantification of prebiotics in commercial infant formulas.

PubMed

Sabater, Carlos; Prodanov, Marin; Olano, Agustín; Corzo, Nieves; Montilla, Antonia

2016-03-01

Since breastfeeding is not always possible, infant formulas (IFs) are supplemented with prebiotic oligosaccharides, such as galactooligosaccharides (GOS) and/or fructooligosaccharides (FOS) to exert similar effects to those of the breast milk. Nowadays, a great number of infant formulas enriched with prebiotics are disposal in the market, however there are scarce data about their composition. In this study, the combined use of two chromatographic methods (GC-FID and HPLC-RID) for the quantification of carbohydrates present in commercial infant formulas have been used. According to the results obtained by GC-FID for products containing prebiotics, the content of FOS, GOS and GOS/FOS was in the ranges of 1.6-5.0, 1.7-3.2, and 0.08-0.25/2.3-3.8g/100g of product, respectively. HPLC-RID analysis allowed quantification of maltodextrins with degree of polymerization (DP) up to 19. The methodology proposed here may be used for routine quality control of infant formula and other food ingredients containing prebiotics. Copyright © 2015 Elsevier Ltd. All rights reserved.

Improving microstructural quantification in FIB/SEM nanotomography.

PubMed

Taillon, Joshua A; Pellegrinelli, Christopher; Huang, Yi-Lin; Wachsman, Eric D; Salamanca-Riba, Lourdes G

2018-01-01

FIB/SEM nanotomography (FIB-nt) is a powerful technique for the determination and quantification of the three-dimensional microstructure in subsurface features. Often times, the microstructure of a sample is the ultimate determiner of the overall performance of a system, and a detailed understanding of its properties is crucial in advancing the materials engineering of a resulting device. While the FIB-nt technique has developed significantly in the 15 years since its introduction, advanced nanotomographic analysis is still far from routine, and a number of challenges remain in data acquisition and post-processing. In this work, we present a number of techniques to improve the quality of the acquired data, together with easy-to-implement methods to obtain "advanced" microstructural quantifications. The techniques are applied to a solid oxide fuel cell cathode of interest to the electrochemistry community, but the methodologies are easily adaptable to a wide range of material systems. Finally, results from an analyzed sample are presented as a practical example of how these techniques can be implemented. Copyright © 2017 Elsevier B.V. All rights reserved.

Self-digitization microfluidic chip for absolute quantification of mRNA in single cells.

PubMed

Thompson, Alison M; Gansen, Alexander; Paguirigan, Amy L; Kreutz, Jason E; Radich, Jerald P; Chiu, Daniel T

2014-12-16

Quantification of mRNA in single cells provides direct insight into how intercellular heterogeneity plays a role in disease progression and outcomes. Quantitative polymerase chain reaction (qPCR), the current gold standard for evaluating gene expression, is insufficient for providing absolute measurement of single-cell mRNA transcript abundance. Challenges include difficulties in handling small sample volumes and the high variability in measurements. Microfluidic digital PCR provides far better sensitivity for minute quantities of genetic material, but the typical format of this assay does not allow for counting of the absolute number of mRNA transcripts samples taken from single cells. Furthermore, a large fraction of the sample is often lost during sample handling in microfluidic digital PCR. Here, we report the absolute quantification of single-cell mRNA transcripts by digital, one-step reverse transcription PCR in a simple microfluidic array device called the self-digitization (SD) chip. By performing the reverse transcription step in digitized volumes, we find that the assay exhibits a linear signal across a wide range of total RNA concentrations and agrees well with standard curve qPCR. The SD chip is found to digitize a high percentage (86.7%) of the sample for single-cell experiments. Moreover, quantification of transferrin receptor mRNA in single cells agrees well with single-molecule fluorescence in situ hybridization experiments. The SD platform for absolute quantification of single-cell mRNA can be optimized for other genes and may be useful as an independent control method for the validation of mRNA quantification techniques.

Quantification of brain lipids by FTIR spectroscopy and partial least squares regression

NASA Astrophysics Data System (ADS)

Dreissig, Isabell; Machill, Susanne; Salzer, Reiner; Krafft, Christoph

2009-01-01

Brain tissue is characterized by high lipid content. Its content decreases and the lipid composition changes during transformation from normal brain tissue to tumors. Therefore, the analysis of brain lipids might complement the existing diagnostic tools to determine the tumor type and tumor grade. Objective of this work is to extract lipids from gray matter and white matter of porcine brain tissue, record infrared (IR) spectra of these extracts and develop a quantification model for the main lipids based on partial least squares (PLS) regression. IR spectra of the pure lipids cholesterol, cholesterol ester, phosphatidic acid, phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, phosphatidylinositol, sphingomyelin, galactocerebroside and sulfatide were used as references. Two lipid mixtures were prepared for training and validation of the quantification model. The composition of lipid extracts that were predicted by the PLS regression of IR spectra was compared with lipid quantification by thin layer chromatography.

A Java program for LRE-based real-time qPCR that enables large-scale absolute quantification.

PubMed

Rutledge, Robert G

2011-03-02

Linear regression of efficiency (LRE) introduced a new paradigm for real-time qPCR that enables large-scale absolute quantification by eliminating the need for standard curves. Developed through the application of sigmoidal mathematics to SYBR Green I-based assays, target quantity is derived directly from fluorescence readings within the central region of an amplification profile. However, a major challenge of implementing LRE quantification is the labor intensive nature of the analysis. Utilizing the extensive resources that are available for developing Java-based software, the LRE Analyzer was written using the NetBeans IDE, and is built on top of the modular architecture and windowing system provided by the NetBeans Platform. This fully featured desktop application determines the number of target molecules within a sample with little or no intervention by the user, in addition to providing extensive database capabilities. MS Excel is used to import data, allowing LRE quantification to be conducted with any real-time PCR instrument that provides access to the raw fluorescence readings. An extensive help set also provides an in-depth introduction to LRE, in addition to guidelines on how to implement LRE quantification. The LRE Analyzer provides the automated analysis and data storage capabilities required by large-scale qPCR projects wanting to exploit the many advantages of absolute quantification. Foremost is the universal perspective afforded by absolute quantification, which among other attributes, provides the ability to directly compare quantitative data produced by different assays and/or instruments. Furthermore, absolute quantification has important implications for gene expression profiling in that it provides the foundation for comparing transcript quantities produced by any gene with any other gene, within and between samples.

Digital Quantification of Proteins and mRNA in Single Mammalian Cells.

PubMed

Albayrak, Cem; Jordi, Christian A; Zechner, Christoph; Lin, Jing; Bichsel, Colette A; Khammash, Mustafa; Tay, Savaş

2016-03-17

Absolute quantification of macromolecules in single cells is critical for understanding and modeling biological systems that feature cellular heterogeneity. Here we show extremely sensitive and absolute quantification of both proteins and mRNA in single mammalian cells by a very practical workflow that combines proximity ligation assay (PLA) and digital PCR. This digital PLA method has femtomolar sensitivity, which enables the quantification of very small protein concentration changes over its entire 3-log dynamic range, a quality necessary for accounting for single-cell heterogeneity. We counted both endogenous (CD147) and exogenously expressed (GFP-p65) proteins from hundreds of single cells and determined the correlation between CD147 mRNA and the protein it encodes. Using our data, a stochastic two-state model of the central dogma was constructed and verified using joint mRNA/protein distributions, allowing us to estimate transcription burst sizes and extrinsic noise strength and calculate the transcription and translation rate constants in single mammalian cells. Copyright © 2016 Elsevier Inc. All rights reserved.

UV-Vis as quantification tool for solubilized lignin following a single-shot steam process.

PubMed

Lee, Roland A; Bédard, Charles; Berberi, Véronique; Beauchet, Romain; Lavoie, Jean-Michel

2013-09-01

In this short communication, UV/Vis was used as an analytical tool for the quantification of lignin concentrations in aqueous mediums. A significant correlation was determined between absorbance and concentration of lignin in solution. For this study, lignin was produced from different types of biomasses (willow, aspen, softwood, canary grass and hemp) using steam processes. Quantification was performed at 212, 225, 237, 270, 280 and 287 nm. UV-Vis quantification of lignin was found suitable for different types of biomass making this a timesaving analytical system that could lead to uses as Process Analytical Tool (PAT) in biorefineries utilizing steam processes or comparable approaches. Copyright © 2013 Elsevier Ltd. All rights reserved.

Metering error quantification under voltage and current waveform distortion

NASA Astrophysics Data System (ADS)

Wang, Tao; Wang, Jia; Xie, Zhi; Zhang, Ran

2017-09-01

With integration of more and more renewable energies and distortion loads into power grid, the voltage and current waveform distortion results in metering error in the smart meters. Because of the negative effects on the metering accuracy and fairness, it is an important subject to study energy metering combined error. In this paper, after the comparing between metering theoretical value and real recorded value under different meter modes for linear and nonlinear loads, a quantification method of metering mode error is proposed under waveform distortion. Based on the metering and time-division multiplier principles, a quantification method of metering accuracy error is proposed also. Analyzing the mode error and accuracy error, a comprehensive error analysis method is presented which is suitable for new energy and nonlinear loads. The proposed method has been proved by simulation.

Species identification and quantification in meat and meat products using droplet digital PCR (ddPCR).

PubMed

Floren, C; Wiedemann, I; Brenig, B; Schütz, E; Beck, J

2015-04-15

Species fraud and product mislabelling in processed food, albeit not being a direct health issue, often results in consumer distrust. Therefore methods for quantification of undeclared species are needed. Targeting mitochondrial DNA, e.g. CYTB gene, for species quantification is unsuitable, due to a fivefold inter-tissue variation in mtDNA content per cell resulting in either an under- (-70%) or overestimation (+160%) of species DNA contents. Here, we describe a reliable two-step droplet digital PCR (ddPCR) assay targeting the nuclear F2 gene for precise quantification of cattle, horse, and pig in processed meat products. The ddPCR assay is advantageous over qPCR showing a limit of quantification (LOQ) and detection (LOD) in different meat products of 0.01% and 0.001%, respectively. The specificity was verified in 14 different species. Hence, determining F2 in food by ddPCR can be recommended for quality assurance and control in production systems. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Good quantification practices of flavours and fragrances by mass spectrometry.

PubMed

Begnaud, Frédéric; Chaintreau, Alain

2016-10-28

Over the past 15 years, chromatographic techniques with mass spectrometric detection have been increasingly used to monitor the rapidly expanded list of regulated flavour and fragrance ingredients. This trend entails a need for good quantification practices suitable for complex media, especially for multi-analytes. In this article, we present experimental precautions needed to perform the analyses and ways to process the data according to the most recent approaches. This notably includes the identification of analytes during their quantification and method validation, when applied to real matrices, based on accuracy profiles. A brief survey of application studies based on such practices is given.This article is part of the themed issue 'Quantitative mass spectrometry'. © 2016 The Authors.

A Constrained Genetic Algorithm with Adaptively Defined Fitness Function in MRS Quantification

NASA Astrophysics Data System (ADS)

Papakostas, G. A.; Karras, D. A.; Mertzios, B. G.; Graveron-Demilly, D.; van Ormondt, D.

MRS Signal quantification is a rather involved procedure and has attracted the interest of the medical engineering community, regarding the development of computationally efficient methodologies. Significant contributions based on Computational Intelligence tools, such as Neural Networks (NNs), demonstrated a good performance but not without drawbacks already discussed by the authors. On the other hand preliminary application of Genetic Algorithms (GA) has already been reported in the literature by the authors regarding the peak detection problem encountered in MRS quantification using the Voigt line shape model. This paper investigates a novel constrained genetic algorithm involving a generic and adaptively defined fitness function which extends the simple genetic algorithm methodology in case of noisy signals. The applicability of this new algorithm is scrutinized through experimentation in artificial MRS signals interleaved with noise, regarding its signal fitting capabilities. Although extensive experiments with real world MRS signals are necessary, the herein shown performance illustrates the method's potential to be established as a generic MRS metabolites quantification procedure.

Quaternary ammonium isobaric tag for a relative and absolute quantification of peptides.

PubMed

Setner, Bartosz; Stefanowicz, Piotr; Szewczuk, Zbigniew

2018-02-01

Isobaric labeling quantification of peptides has become a method of choice for mass spectrometry-based proteomics studies. However, despite of wide variety of commercially available isobaric tags, none of the currently available methods offers significant improvement of sensitivity of detection during MS experiment. Recently, many strategies were applied to increase the ionization efficiency of peptides involving chemical modifications introducing quaternary ammonium fixed charge. Here, we present a novel quaternary ammonium-based isobaric tag for relative and absolute quantification of peptides (QAS-iTRAQ 2-plex). Upon collisional activation, the new stable benzylic-type cationic reporter ion is liberated from the tag. Deuterium atoms were used to offset the differential masses of a reporter group. We tested the applicability of QAS-iTRAQ 2-plex reagent on a series of model peptides as well as bovine serum albumin tryptic digest. Obtained results suggest usefulness of this isobaric ionization tag for relative and absolute quantification of peptides. Copyright © 2017 John Wiley & Sons, Ltd.

Photoacoustic bio-quantification of graphene based nanomaterials at a single cell level (Conference Presentation)

NASA Astrophysics Data System (ADS)

Nedosekin, Dmitry A.; Nolan, Jacqueline; Biris, Alexandru S.; Zharov, Vladimir P.

2017-03-01

Arkansas Nanomedicine Center at the University of Arkansas for Medical Sciences in collaboration with other Arkansas Universities and the FDA-based National Center of Toxicological Research in Jefferson, AR is developing novel techniques for rapid quantification of graphene-based nanomaterials (GBNs) in various biological samples. All-carbon GBNs have wide range of potential applications in industry, agriculture, food processing and medicine; however, quantification of GBNs is difficult in carbon reach biological tissues. The accurate quantification of GBNs is essential for research on material toxicity and the development of GBNs-based drug delivery platforms. We have developed microscopy and cytometry platforms for detection and quantification of GBNs in single cells, tissue and blood samples using photoacoustic contrast of GBNs. We demonstrated PA quantification of individual graphene uptake by single cells. High-resolution PA microscopy provided mapping of GBN distribution within live cells to establish correlation with intracellular toxic phenomena using apoptotic and necrotic assays. This new methodology and corresponding technical platform provide the insight on possible toxicological risks of GBNs at singe cells levels. In addition, in vivo PA image flow cytometry demonstrated the capability to monitor of GBNs pharmacokinetics in mouse model and to map the resulting biodistribution of GBNs in mouse tissues. The integrated PA platform provided an unprecedented sensitivity toward GBNs and allowed to enhance conventional toxicology research by providing a direct correlation between uptake of GBNs at a single cell level and cell viability status.

Lowering the quantification limit of the QubitTM RNA HS assay using RNA spike-in.

PubMed

Li, Xin; Ben-Dov, Iddo Z; Mauro, Maurizio; Williams, Zev

2015-05-06

RNA quantification is often a prerequisite for most RNA analyses such as RNA sequencing. However, the relatively low sensitivity and large sample consumption of traditional RNA quantification methods such as UV spectrophotometry and even the much more sensitive fluorescence-based RNA quantification assays, such as the Qubit™ RNA HS Assay, are often inadequate for measuring minute levels of RNA isolated from limited cell and tissue samples and biofluids. Thus, there is a pressing need for a more sensitive method to reliably and robustly detect trace levels of RNA without interference from DNA. To improve the quantification limit of the Qubit™ RNA HS Assay, we spiked-in a known quantity of RNA to achieve the minimum reading required by the assay. Samples containing trace amounts of RNA were then added to the spike-in and measured as a reading increase over RNA spike-in baseline. We determined the accuracy and precision of reading increases between 1 and 20 pg/μL as well as RNA-specificity in this range, and compared to those of RiboGreen(®), another sensitive fluorescence-based RNA quantification assay. We then applied Qubit™ Assay with RNA spike-in to quantify plasma RNA samples. RNA spike-in improved the quantification limit of the Qubit™ RNA HS Assay 5-fold, from 25 pg/μL down to 5 pg/μL while maintaining high specificity to RNA. This enabled quantification of RNA with original concentration as low as 55.6 pg/μL compared to 250 pg/μL for the standard assay and decreased sample consumption from 5 to 1 ng. Plasma RNA samples that were not measurable by the Qubit™ RNA HS Assay were measurable by our modified method. The Qubit™ RNA HS Assay with RNA spike-in is able to quantify RNA with high specificity at 5-fold lower concentration and uses 5-fold less sample quantity than the standard Qubit™ Assay.

Sensitive Targeted Quantification of ERK Phosphorylation Dynamics and Stoichiometry in Human Cells without Affinity Enrichment

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

Shi, Tujin; Gao, Yuqian; Gaffrey, Matthew J.

2014-12-17

Mass spectrometry-based targeted quantification is a promising technology for site-specific quantification of posttranslational modifications (PTMs). However, a major constraint of most targeted MS approaches is the limited sensitivity for quantifying low-abundance PTMs, requiring the use of affinity reagents to enrich specific PTMs. Herein, we demonstrate the direct site-specific quantification of ERK phosphorylation isoforms (pT, pY, pTpY) and their relative stoichiometries using a highly sensitive targeted MS approach termed high-pressure, high-resolution separations with intelligent selection and multiplexing (PRISM). PRISM provides effective enrichment of target peptides within a given fraction from complex biological matrix with minimal sample losses, followed by selected reactionmore » monitoring (SRM) quantification. The PRISM-SRM approach enabled direct quantification of ERK phosphorylation in human mammary epithelial cells (HMEC) from as little as 25 µg tryptic peptides from whole cell lysates. Compared to immobilized metal-ion affinity chromatography, PRISM provided >10-fold improvement in signal intensities, presumably due to the better peptide recovery of PRISM for handling small size samples. This approach was applied to quantify ERK phosphorylation dynamics in HMEC treated by different doses of EGF at both the peak activation (10 min) and steady state (2 h). At 10 min, the maximal ERK activation was observed with 0.3 ng/mL dose, whereas the maximal steady state level of ERK activation at 2 h was at 3 ng/ml dose, corresponding to 1200 and 9000 occupied receptors, respectively. At 10 min, the maximally activated pTpY isoform represented ~40% of total ERK, falling to less than 10% at 2 h. The time course and dose-response profiles of individual phosphorylated ERK isoforms indicated that singly phosphorylated pT-ERK never increases significantly, while the increase of pY-ERK paralleled that of pTpY-ERK. This data supports for a processive, rather than

A Java Program for LRE-Based Real-Time qPCR that Enables Large-Scale Absolute Quantification

PubMed Central

Rutledge, Robert G.

2011-01-01

Background Linear regression of efficiency (LRE) introduced a new paradigm for real-time qPCR that enables large-scale absolute quantification by eliminating the need for standard curves. Developed through the application of sigmoidal mathematics to SYBR Green I-based assays, target quantity is derived directly from fluorescence readings within the central region of an amplification profile. However, a major challenge of implementing LRE quantification is the labor intensive nature of the analysis. Findings Utilizing the extensive resources that are available for developing Java-based software, the LRE Analyzer was written using the NetBeans IDE, and is built on top of the modular architecture and windowing system provided by the NetBeans Platform. This fully featured desktop application determines the number of target molecules within a sample with little or no intervention by the user, in addition to providing extensive database capabilities. MS Excel is used to import data, allowing LRE quantification to be conducted with any real-time PCR instrument that provides access to the raw fluorescence readings. An extensive help set also provides an in-depth introduction to LRE, in addition to guidelines on how to implement LRE quantification. Conclusions The LRE Analyzer provides the automated analysis and data storage capabilities required by large-scale qPCR projects wanting to exploit the many advantages of absolute quantification. Foremost is the universal perspective afforded by absolute quantification, which among other attributes, provides the ability to directly compare quantitative data produced by different assays and/or instruments. Furthermore, absolute quantification has important implications for gene expression profiling in that it provides the foundation for comparing transcript quantities produced by any gene with any other gene, within and between samples. PMID:21407812

Quantification of sterol lipids in plants by quadrupole time-of-flight mass spectrometry

PubMed Central

Wewer, Vera; Dombrink, Isabel; vom Dorp, Katharina; Dörmann, Peter

2011-01-01

Glycerolipids, sphingolipids, and sterol lipids constitute the major lipid classes in plants. Sterol lipids are composed of free and conjugated sterols, i.e., sterol esters, sterol glycosides, and acylated sterol glycosides. Sterol lipids play crucial roles during adaption to abiotic stresses and plant-pathogen interactions. Presently, no comprehensive method for sterol lipid quantification in plants is available. We used nanospray ionization quadrupole-time-of-flight mass spectrometry (Q-TOF MS) to resolve and identify the molecular species of all four sterol lipid classes from Arabidopsis thaliana. Free sterols were derivatized with chlorobetainyl chloride. Sterol esters, sterol glycosides, and acylated sterol glycosides were ionized as ammonium adducts. Quantification of molecular species was achieved in the positive mode after fragmentation in the presence of internal standards. The amounts of sterol lipids quantified by Q-TOF MS/MS were validated by comparison with results obtained with TLC/GC. Quantification of sterol lipids from leaves and roots of phosphate-deprived A. thaliana plants revealed changes in the amounts and molecular species composition. The Q-TOF method is far more sensitive than GC or HPLC. Therefore, Q-TOF MS/MS provides a comprehensive strategy for sterol lipid quantification that can be adapted to other tandem mass spectrometers. PMID:21382968

Quantification of lithium at ppm level in geological samples using nuclear reaction analysis.

PubMed

De La Rosa, Nathaly; Kristiansson, Per; Nilsson, E J Charlotta; Ros, Linus; Pallon, Jan; Skogby, Henrik

2018-01-01

Proton-induced reaction (p,α) is one type of nuclear reaction analysis (NRA) suitable especially for light element quantification. In the case of lithium quantification presented in this work, accelerated protons with an energy about of 850 keV were used to induce the 7 Li(p,α) 4 He reaction in standard reference and geological samples such as tourmaline and other Li-minerals. It is shown that this technique for lithium quantification allowed for measurement of concentrations down below one ppm. The possibility to relate the lithium content with the boron content in a single analysis was also demonstrated using tourmaline samples, both in absolute concentration and in lateral distribution. In addition, Particle induced X-ray emission (PIXE) was utilized as a complementary IBA technique for simultaneous mapping of elements heavier than sodium.

Simultaneous digital quantification and fluorescence-based size characterization of massively parallel sequencing libraries.

PubMed

Laurie, Matthew T; Bertout, Jessica A; Taylor, Sean D; Burton, Joshua N; Shendure, Jay A; Bielas, Jason H

2013-08-01

Due to the high cost of failed runs and suboptimal data yields, quantification and determination of fragment size range are crucial steps in the library preparation process for massively parallel sequencing (or next-generation sequencing). Current library quality control methods commonly involve quantification using real-time quantitative PCR and size determination using gel or capillary electrophoresis. These methods are laborious and subject to a number of significant limitations that can make library calibration unreliable. Herein, we propose and test an alternative method for quality control of sequencing libraries using droplet digital PCR (ddPCR). By exploiting a correlation we have discovered between droplet fluorescence and amplicon size, we achieve the joint quantification and size determination of target DNA with a single ddPCR assay. We demonstrate the accuracy and precision of applying this method to the preparation of sequencing libraries.

Tropical Indian Ocean Variability Driving Southeast Australian Droughts

NASA Astrophysics Data System (ADS)

Ummenhofer, C. C.; England, M. H.; McIntosh, P. C.; Meyers, G. A.; Pook, M. J.; Risbey, J. S.; Sen Gupta, A.; Taschetto, A. S.

2009-04-01

Variability in the tropical Indian Ocean has widespread effects on rainfall in surrounding countries, including East Africa, India and Indonesia. The leading mode of tropical Indian Ocean variability, the Indian Ocean Dipole (IOD), is a coupled ocean-atmosphere mode characterized by sea surface temperature (SST) anomalies of opposite sign in the east and west of the basin with an associated large-scale atmospheric re-organisation. Earlier work has often focused on the positive phase of the IOD. However, we show here that the negative IOD phase is an important driver of regional rainfall variability and multi-year droughts. For southeastern Australia, we show that it is actually a lack of the negative IOD phase, rather than the positive IOD phase or Pacific variability, that provides the most robust explanation for recent drought conditions. Since 1995, a large region of Australia has been gripped by the most severe drought in living memory, the so-called "Big Dry". The ramifications for affected regions are dire, with acute water shortages for rural and metropolitan areas, record agricultural losses, the drying-out of two of Australia's major river systems and far-reaching ecosystem damage. Yet the drought's origins have remained elusive. For Southeast Australia, we show that the "Big Dry" and other iconic 20th Century droughts, including the Federation Drought (1895-1902) and World War II drought (1937-1945), are driven by tropical Indian Ocean variability, not Pacific Ocean conditions as traditionally assumed. Specifically, a conspicuous absence of characteristic Indian Ocean temperature conditions that are conducive to enhanced tropical moisture transport has deprived southeastern Australia of its normal rainfall quota. In the case of the "Big Dry", its unprecedented intensity is also related to recent above-average temperatures. Implications of recent non-uniform warming trends in the Indian Ocean and how that might affect ocean characteristics and climate in

A Non-Stationary Relationship between Global Climate Phenomena and Human Plague Incidence in Madagascar

PubMed Central

Kreppel, Katharina S.; Caminade, Cyril; Telfer, Sandra; Rajerison, Minoarison; Rahalison, Lila; Morse, Andy; Baylis, Matthew

2014-01-01

Background Plague, a zoonosis caused by Yersinia pestis, is found in Asia and the Americas, but predominantly in Africa, with the island of Madagascar reporting almost one third of human cases worldwide. Plague's occurrence is affected by local climate factors which in turn are influenced by large-scale climate phenomena such as the El Niño Southern Oscillation (ENSO). The effects of ENSO on regional climate are often enhanced or reduced by a second large-scale climate phenomenon, the Indian Ocean Dipole (IOD). It is known that ENSO and the IOD interact as drivers of disease. Yet the impacts of these phenomena in driving plague dynamics via their effect on regional climate, and specifically contributing to the foci of transmission on Madagascar, are unknown. Here we present the first analysis of the effects of ENSO and IOD on plague in Madagascar. Methodology/principal findings We use a forty-eight year monthly time-series of reported human plague cases from 1960 to 2008. Using wavelet analysis, we show that over the last fifty years there have been complex non-stationary associations between ENSO/IOD and the dynamics of plague in Madagascar. We demonstrate that ENSO and IOD influence temperature in Madagascar and that temperature and plague cycles are associated. The effects on plague appear to be mediated more by temperature, but precipitation also undoubtedly influences plague in Madagascar. Our results confirm a relationship between plague anomalies and an increase in the intensity of ENSO events and precipitation. Conclusions/significance This work widens the understanding of how climate factors acting over different temporal scales can combine to drive local disease dynamics. Given the association of increasing ENSO strength and plague anomalies in Madagascar it may in future be possible to forecast plague outbreaks in Madagascar. The study gives insight into the complex and changing relationship between climate factors and plague in Madagascar. PMID

Process Contributions to Cool Java SST Anomalies at the Onset of Positive Indian Ocean Dipole Events

NASA Astrophysics Data System (ADS)

Delman, A. S.; McClean, J.; Sprintall, J.; Talley, L. D.

2016-12-01

The seasonal upwelling region along the south coast of Java is the first area to exhibit the negative SST anomalies associated with positive Indian Ocean Dipole (pIOD) events. The seasonal cooling in austral winter is driven by local wind forcing; however, recent observational studies have suggested that the anomalous Java cooling that starts during May-July of pIOD years is driven largely by intraseasonal wind variability along the equator, which forces upwelling Kelvin waves that propagate to the coast of Java. Using observations and an eddy-active ocean GCM simulation, the impacts of local wind stress and remotely-forced Kelvin waves are assessed and compared to the effects of mesoscale eddies and outflows from nearby Lombok Strait. A Kelvin wave coefficient computed from altimetry data shows anomalous levels of upwelling Kelvin wave activity during May-July of all pIOD years, indicating that Kelvin waves are an important and perhaps necessary precondition for pIOD events. Correlation analyses also suggest that flows through Lombok Strait and winds along the Indonesian Throughflow may be influential, though their impacts are more difficult to isolate. Composite temperature budgets from the ocean GCM indicate that advection and diabatic vertical mixing are the primary mechanisms for anomalous mixed layer cooling south of Java. The advection term is further decomposed by linearly regressing model velocity and temperature anomalies onto indices representing each process. According to this process decomposition, the local wind stress and Kelvin waves together account for most of the anomalous advective cooling, though the anomalous cooling effect of local wind stress may be overestimated in the model due to wind and stratification biases. The process decomposition also shows a very modest warming effect from mesoscale eddies. These results demonstrate both the IOD's resemblance to ENSO in the importance of Kelvin waves for its evolution, and notable differences from

Localized 2D COSY sequences: Method and experimental evaluation for a whole metabolite quantification approach

NASA Astrophysics Data System (ADS)

Martel, Dimitri; Tse Ve Koon, K.; Le Fur, Yann; Ratiney, Hélène

2015-11-01

Two-dimensional spectroscopy offers the possibility to unambiguously distinguish metabolites by spreading out the multiplet structure of J-coupled spin systems into a second dimension. Quantification methods that perform parametric fitting of the 2D MRS signal have recently been proposed for resolved PRESS (JPRESS) but not explicitly for Localized Correlation Spectroscopy (LCOSY). Here, through a whole metabolite quantification approach, correlation spectroscopy quantification performances are studied. The ability to quantify metabolite relaxation constant times is studied for three localized 2D MRS sequences (LCOSY, LCTCOSY and the JPRESS) in vitro on preclinical MR systems. The issues encountered during implementation and quantification strategies are discussed with the help of the Fisher matrix formalism. The described parameterized models enable the computation of the lower bound for error variance - generally known as the Cramér Rao bounds (CRBs), a standard of precision - on the parameters estimated from these 2D MRS signal fittings. LCOSY has a theoretical net signal loss of two per unit of acquisition time compared to JPRESS. A rapid analysis could point that the relative CRBs of LCOSY compared to JPRESS (expressed as a percentage of the concentration values) should be doubled but we show that this is not necessarily true. Finally, the LCOSY quantification procedure has been applied on data acquired in vivo on a mouse brain.

Global Sensitivity Analysis and Estimation of Model Error, Toward Uncertainty Quantification in Scramjet Computations

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

Huan, Xun; Safta, Cosmin; Sargsyan, Khachik

The development of scramjet engines is an important research area for advancing hypersonic and orbital flights. Progress toward optimal engine designs requires accurate flow simulations together with uncertainty quantification. However, performing uncertainty quantification for scramjet simulations is challenging due to the large number of uncertain parameters involved and the high computational cost of flow simulations. These difficulties are addressed in this paper by developing practical uncertainty quantification algorithms and computational methods, and deploying them in the current study to large-eddy simulations of a jet in crossflow inside a simplified HIFiRE Direct Connect Rig scramjet combustor. First, global sensitivity analysis ismore » conducted to identify influential uncertain input parameters, which can help reduce the system’s stochastic dimension. Second, because models of different fidelity are used in the overall uncertainty quantification assessment, a framework for quantifying and propagating the uncertainty due to model error is presented. In conclusion, these methods are demonstrated on a nonreacting jet-in-crossflow test problem in a simplified scramjet geometry, with parameter space up to 24 dimensions, using static and dynamic treatments of the turbulence subgrid model, and with two-dimensional and three-dimensional geometries.« less

Global Sensitivity Analysis and Estimation of Model Error, Toward Uncertainty Quantification in Scramjet Computations

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

Huan, Xun; Safta, Cosmin; Sargsyan, Khachik

The development of scramjet engines is an important research area for advancing hypersonic and orbital flights. Progress toward optimal engine designs requires accurate flow simulations together with uncertainty quantification. However, performing uncertainty quantification for scramjet simulations is challenging due to the large number of uncertain parameters involved and the high computational cost of flow simulations. These difficulties are addressed in this paper by developing practical uncertainty quantification algorithms and computational methods, and deploying them in the current study to large-eddy simulations of a jet in crossflow inside a simplified HIFiRE Direct Connect Rig scramjet combustor. First, global sensitivity analysis ismore » conducted to identify influential uncertain input parameters, which can help reduce the system’s stochastic dimension. Second, because models of different fidelity are used in the overall uncertainty quantification assessment, a framework for quantifying and propagating the uncertainty due to model error is presented. Finally, these methods are demonstrated on a nonreacting jet-in-crossflow test problem in a simplified scramjet geometry, with parameter space up to 24 dimensions, using static and dynamic treatments of the turbulence subgrid model, and with two-dimensional and three-dimensional geometries.« less

Global Sensitivity Analysis and Estimation of Model Error, Toward Uncertainty Quantification in Scramjet Computations

NASA Astrophysics Data System (ADS)

Huan, Xun; Safta, Cosmin; Sargsyan, Khachik; Geraci, Gianluca; Eldred, Michael S.; Vane, Zachary P.; Lacaze, Guilhem; Oefelein, Joseph C.; Najm, Habib N.

2018-03-01

The development of scramjet engines is an important research area for advancing hypersonic and orbital flights. Progress toward optimal engine designs requires accurate flow simulations together with uncertainty quantification. However, performing uncertainty quantification for scramjet simulations is challenging due to the large number of uncertain parameters involved and the high computational cost of flow simulations. These difficulties are addressed in this paper by developing practical uncertainty quantification algorithms and computational methods, and deploying them in the current study to large-eddy simulations of a jet in crossflow inside a simplified HIFiRE Direct Connect Rig scramjet combustor. First, global sensitivity analysis is conducted to identify influential uncertain input parameters, which can help reduce the systems stochastic dimension. Second, because models of different fidelity are used in the overall uncertainty quantification assessment, a framework for quantifying and propagating the uncertainty due to model error is presented. These methods are demonstrated on a nonreacting jet-in-crossflow test problem in a simplified scramjet geometry, with parameter space up to 24 dimensions, using static and dynamic treatments of the turbulence subgrid model, and with two-dimensional and three-dimensional geometries.

Global Sensitivity Analysis and Estimation of Model Error, Toward Uncertainty Quantification in Scramjet Computations

DOE PAGES

Huan, Xun; Safta, Cosmin; Sargsyan, Khachik; ...

2018-02-09

The development of scramjet engines is an important research area for advancing hypersonic and orbital flights. Progress toward optimal engine designs requires accurate flow simulations together with uncertainty quantification. However, performing uncertainty quantification for scramjet simulations is challenging due to the large number of uncertain parameters involved and the high computational cost of flow simulations. These difficulties are addressed in this paper by developing practical uncertainty quantification algorithms and computational methods, and deploying them in the current study to large-eddy simulations of a jet in crossflow inside a simplified HIFiRE Direct Connect Rig scramjet combustor. First, global sensitivity analysis ismore » conducted to identify influential uncertain input parameters, which can help reduce the system’s stochastic dimension. Second, because models of different fidelity are used in the overall uncertainty quantification assessment, a framework for quantifying and propagating the uncertainty due to model error is presented. In conclusion, these methods are demonstrated on a nonreacting jet-in-crossflow test problem in a simplified scramjet geometry, with parameter space up to 24 dimensions, using static and dynamic treatments of the turbulence subgrid model, and with two-dimensional and three-dimensional geometries.« less

Quantification of complex modular architecture in plants.

PubMed

Reeb, Catherine; Kaandorp, Jaap; Jansson, Fredrik; Puillandre, Nicolas; Dubuisson, Jean-Yves; Cornette, Raphaël; Jabbour, Florian; Coudert, Yoan; Patiño, Jairo; Flot, Jean-François; Vanderpoorten, Alain

2018-04-01

Morphometrics, the assignment of quantities to biological shapes, is a powerful tool to address taxonomic, evolutionary, functional and developmental questions. We propose a novel method for shape quantification of complex modular architecture in thalloid plants, whose extremely reduced morphologies, combined with the lack of a formal framework for thallus description, have long rendered taxonomic and evolutionary studies extremely challenging. Using graph theory, thalli are described as hierarchical series of nodes and edges, allowing for accurate, homologous and repeatable measurements of widths, lengths and angles. The computer program MorphoSnake was developed to extract the skeleton and contours of a thallus and automatically acquire, at each level of organization, width, length, angle and sinuosity measurements. Through the quantification of leaf architecture in Hymenophyllum ferns (Polypodiopsida) and a fully worked example of integrative taxonomy in the taxonomically challenging thalloid liverwort genus Riccardia, we show that MorphoSnake is applicable to all ramified plants. This new possibility of acquiring large numbers of quantitative traits in plants with complex modular architectures opens new perspectives of applications, from the development of rapid species identification tools to evolutionary analyses of adaptive plasticity. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

Colorimetric Quantification and in Situ Detection of Collagen

ERIC Educational Resources Information Center

Esteban, Francisco J.; del Moral, Maria L.; Sanchez-Lopez, Ana M.; Blanco, Santos; Jimenez, Ana; Hernandez, Raquel; Pedrosa, Juan A.; Peinado, Maria A.

2005-01-01

A simple multidisciplinary and inexpensive laboratory exercise is proposed, in which the undergraduate student may correlate biochemical and anatomical findings. The entire practical session can be completed in one 2.5-3 hour laboratory period, and consists of the quantification of collagen and total protein content from tissue sections--without…

Accurate proteome-wide protein quantification from high-resolution 15N mass spectra

PubMed Central

2011-01-01

In quantitative mass spectrometry-based proteomics, the metabolic incorporation of a single source of 15N-labeled nitrogen has many advantages over using stable isotope-labeled amino acids. However, the lack of a robust computational framework for analyzing the resulting spectra has impeded wide use of this approach. We have addressed this challenge by introducing a new computational methodology for analyzing 15N spectra in which quantification is integrated with identification. Application of this method to an Escherichia coli growth transition reveals significant improvement in quantification accuracy over previous methods. PMID:22182234

Uncertainty quantification and sensitivity analysis with CASL Core Simulator VERA-CS

DOE PAGES

Brown, C. S.; Zhang, Hongbin

2016-05-24

Uncertainty quantification and sensitivity analysis are important for nuclear reactor safety design and analysis. A 2x2 fuel assembly core design was developed and simulated by the Virtual Environment for Reactor Applications, Core Simulator (VERA-CS) coupled neutronics and thermal-hydraulics code under development by the Consortium for Advanced Simulation of Light Water Reactors (CASL). An approach to uncertainty quantification and sensitivity analysis with VERA-CS was developed and a new toolkit was created to perform uncertainty quantification and sensitivity analysis with fourteen uncertain input parameters. Furthermore, the minimum departure from nucleate boiling ratio (MDNBR), maximum fuel center-line temperature, and maximum outer clad surfacemore » temperature were chosen as the selected figures of merit. Pearson, Spearman, and partial correlation coefficients were considered for all of the figures of merit in sensitivity analysis and coolant inlet temperature was consistently the most influential parameter. We used parameters as inputs to the critical heat flux calculation with the W-3 correlation were shown to be the most influential on the MDNBR, maximum fuel center-line temperature, and maximum outer clad surface temperature.« less

Plasma protein absolute quantification by nano-LC Q-TOF UDMSE for clinical biomarker verification

PubMed Central

ILIES, MARIA; IUGA, CRISTINA ADELA; LOGHIN, FELICIA; DHOPLE, VISHNU MUKUND; HAMMER, ELKE

2017-01-01

Background and aims Proteome-based biomarker studies are targeting proteins that could serve as diagnostic, prognosis, and prediction molecules. In the clinical routine, immunoassays are currently used for the absolute quantification of such biomarkers, with the major limitation that only one molecule can be targeted per assay. The aim of our study was to test a mass spectrometry based absolute quantification method for the verification of plasma protein sets which might serve as reliable biomarker panels for the clinical practice. Methods Six EDTA plasma samples were analyzed after tryptic digestion using a high throughput data independent acquisition nano-LC Q-TOF UDMSE proteomics approach. Synthetic Escherichia coli standard peptides were spiked in each sample for the absolute quantification. Data analysis was performed using ProgenesisQI v2.0 software (Waters Corporation). Results Our method ensured absolute quantification of 242 non redundant plasma proteins in a single run analysis. The dynamic range covered was 105. 86% were represented by classical plasma proteins. The overall median coefficient of variation was 0.36, while a set of 63 proteins was found to be highly stable. Absolute protein concentrations strongly correlated with values reviewed in the literature. Conclusions Nano-LC Q-TOF UDMSE proteomic analysis can be used for a simple and rapid determination of absolute amounts of plasma proteins. A large number of plasma proteins could be analyzed, while a wide dynamic range was covered with low coefficient of variation at protein level. The method proved to be a reliable tool for the quantification of protein panel for biomarker verification in the clinical practice. PMID:29151793

Current position of high-resolution MS for drug quantification in clinical & forensic toxicology.

PubMed

Meyer, Markus R; Helfer, Andreas G; Maurer, Hans H

2014-08-01

This paper reviews high-resolution MS approaches published from January 2011 until March 2014 for the quantification of drugs (of abuse) and/or their metabolites in biosamples using LC-MS with time-of-flight or Orbitrap™ mass analyzers. Corresponding approaches are discussed including sample preparation and mass spectral settings. The advantages and limitations of high-resolution MS for drug quantification, as well as the demand for a certain resolution or a specific mass accuracy are also explored.

Quantification of HCV RNA in Clinical Specimens by Branched DNA (bDNA) Technology.

PubMed

Wilber, J C; Urdea, M S

1999-01-01

The diagnosis and monitoring of hepatitis C virus (HCV) infection have been aided by the development of HCV RNA quantification assays A direct measure of viral load, HCV RNA quantification has the advantage of providing information on viral kinetics and provides unique insight into the disease process. Branched DNA (bDNA) signal amplification technology provides a novel approach for the direct quantification of HCV RNA in patient specimens. The bDNA assay measures HCV RNA at physiological levels by boosting the reporter signal, rather than by replicating target sequences as the means of detection, and thus avoids the errors inherent in the extraction and amplification of target sequences. Inherently quantitative and nonradioactive, the bDNA assay is amenable to routine use in a clinical research setting, and has been used by several groups to explore the natural history, pathogenesis, and treatment of HCV infection.

Uncertainty quantification metrics for whole product life cycle cost estimates in aerospace innovation

NASA Astrophysics Data System (ADS)

Schwabe, O.; Shehab, E.; Erkoyuncu, J.

2015-08-01

The lack of defensible methods for quantifying cost estimate uncertainty over the whole product life cycle of aerospace innovations such as propulsion systems or airframes poses a significant challenge to the creation of accurate and defensible cost estimates. Based on the axiomatic definition of uncertainty as the actual prediction error of the cost estimate, this paper provides a comprehensive overview of metrics used for the uncertainty quantification of cost estimates based on a literature review, an evaluation of publicly funded projects such as part of the CORDIS or Horizon 2020 programs, and an analysis of established approaches used by organizations such NASA, the U.S. Department of Defence, the ESA, and various commercial companies. The metrics are categorized based on their foundational character (foundations), their use in practice (state-of-practice), their availability for practice (state-of-art) and those suggested for future exploration (state-of-future). Insights gained were that a variety of uncertainty quantification metrics exist whose suitability depends on the volatility of available relevant information, as defined by technical and cost readiness level, and the number of whole product life cycle phases the estimate is intended to be valid for. Information volatility and number of whole product life cycle phases can hereby be considered as defining multi-dimensional probability fields admitting various uncertainty quantification metric families with identifiable thresholds for transitioning between them. The key research gaps identified were the lacking guidance grounded in theory for the selection of uncertainty quantification metrics and lacking practical alternatives to metrics based on the Central Limit Theorem. An innovative uncertainty quantification framework consisting of; a set-theory based typology, a data library, a classification system, and a corresponding input-output model are put forward to address this research gap as the basis

Hemispheric specialization in quantification processes.

PubMed

Pasini, M; Tessari, A

2001-01-01

Three experiments were carried out to study hemispheric specialization for subitizing (the rapid enumeration of small patterns) and counting (the serial quantification process based on some formal principles). The experiments consist of numerosity identification of dot patterns presented in one visual field, with a tachistoscopic technique, or eye movements monitored through glasses, and comparison between centrally presented dot patterns and lateralized tachistoscopically presented digits. Our experiments show left visual field advantage in the identification and comparison tasks in the subitizing range, whereas right visual field advantage has been found in the comparison task for the counting range.

Quantification of Fluorine Content in AFFF Concentrates

DTIC Science & Technology

2017-09-29

and quantitative integrations, a 100 ppm spectral window (FIDRes 0.215 Hz) was scanned using the following acquisition parameters: acquisition time ...Naval Research Laboratory Washington, DC 20375-5320 NRL/MR/6120--17-9752 Quantification of Fluorine Content in AFFF Concentrates September 29, 2017...collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing data sources

Neutron-Encoded Protein Quantification by Peptide Carbamylation

NASA Astrophysics Data System (ADS)

Ulbrich, Arne; Merrill, Anna E.; Hebert, Alexander S.; Westphall, Michael S.; Keller, Mark P.; Attie, Alan D.; Coon, Joshua J.

2014-01-01

We describe a chemical tag for duplex proteome quantification using neutron encoding (NeuCode). The method utilizes the straightforward, efficient, and inexpensive carbamylation reaction. We demonstrate the utility of NeuCode carbamylation by accurately measuring quantitative ratios from tagged yeast lysates mixed in known ratios and by applying this method to quantify differential protein expression in mice fed a either control or high-fat diet.

The positive Indian Ocean Dipole-like response in the tropical Indian Ocean to global warming

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

Luo, Yiyong; Lu, Jian; Liu, Fukai

Climate models project a positive Indian Ocean Dipole (pIOD)-like SST response in the tropical Indian Ocean to global warming. By employing the Community Earth System Model (CESM) and applying an overriding technique to its ocean component Parallel Ocean Program version 2 (POP2), this study investigates the similarity and difference of the formation mechanisms for the changes in the tropical Indian Ocean during the pIOD versus global warming. Results show that their formation processes and related seasonality are quite similar; in particular, the Bjerknes feedback is the leading mechanism in producing the anomalous cooling over the eastern tropics in both cases.more » Some differences are also found, including that the cooling effect of the vertical advection over the eastern tropical Indian Ocean is dominated by the anomalous vertical velocity during the pIOD while it is dominated by the anomalous upper-ocean stratification under global warming. Lastly, these findings above are further examined with an analysis of the mixed layer heat budget.« less

The positive Indian Ocean Dipole-like response in the tropical Indian Ocean to global warming

DOE PAGES

Luo, Yiyong; Lu, Jian; Liu, Fukai; ...

2016-02-04

Climate models project a positive Indian Ocean Dipole (pIOD)-like SST response in the tropical Indian Ocean to global warming. By employing the Community Earth System Model (CESM) and applying an overriding technique to its ocean component Parallel Ocean Program version 2 (POP2), this study investigates the similarity and difference of the formation mechanisms for the changes in the tropical Indian Ocean during the pIOD versus global warming. Results show that their formation processes and related seasonality are quite similar; in particular, the Bjerknes feedback is the leading mechanism in producing the anomalous cooling over the eastern tropics in both cases.more » Some differences are also found, including that the cooling effect of the vertical advection over the eastern tropical Indian Ocean is dominated by the anomalous vertical velocity during the pIOD while it is dominated by the anomalous upper-ocean stratification under global warming. Lastly, these findings above are further examined with an analysis of the mixed layer heat budget.« less

Development of a Framework for Model-Based Analysis, Uncertainty Quantification, and Robust Control Design of Nonlinear Smart Composite Systems

DTIC Science & Technology

2015-06-04

control, vibration and noise control, health monitoring, and energy harvesting . However, these advantages come at the cost of rate-dependent hysteresis...configuration used for energy harvesting . Uncertainty Quantification Uncertainty quantification is pursued in two steps: (i) determination of densities...Crews and R.C. Smith, “Quantification of parameter and model uncertainty for shape mem- ory alloy bending actuators,” Journal of Intelligent material

Metal Stable Isotope Tagging: Renaissance of Radioimmunoassay for Multiplex and Absolute Quantification of Biomolecules.

PubMed

Liu, Rui; Zhang, Shixi; Wei, Chao; Xing, Zhi; Zhang, Sichun; Zhang, Xinrong

2016-05-17

The unambiguous quantification of biomolecules is of great significance in fundamental biological research as well as practical clinical diagnosis. Due to the lack of a detectable moiety, the direct and highly sensitive quantification of biomolecules is often a "mission impossible". Consequently, tagging strategies to introduce detectable moieties for labeling target biomolecules were invented, which had a long and significant impact on studies of biomolecules in the past decades. For instance, immunoassays have been developed with radioisotope tagging by Yalow and Berson in the late 1950s. The later languishment of this technology can be almost exclusively ascribed to the use of radioactive isotopes, which led to the development of nonradioactive tagging strategy-based assays such as enzyme-linked immunosorbent assay, fluorescent immunoassay, and chemiluminescent and electrochemiluminescent immunoassay. Despite great success, these strategies suffered from drawbacks such as limited spectral window capacity for multiplex detection and inability to provide absolute quantification of biomolecules. After recalling the sequences of tagging strategies, an apparent question is why not use stable isotopes from the start? A reasonable explanation is the lack of reliable means for accurate and precise quantification of stable isotopes at that time. The situation has changed greatly at present, since several atomic mass spectrometric measures for metal stable isotopes have been developed. Among the newly developed techniques, inductively coupled plasma mass spectrometry is an ideal technique to determine metal stable isotope-tagged biomolecules, for its high sensitivity, wide dynamic linear range, and more importantly multiplex and absolute quantification ability. Since the first published report by our group, metal stable isotope tagging has become a revolutionary technique and gained great success in biomolecule quantification. An exciting research highlight in this area

Methods for quantification of soil-transmitted helminths in environmental media: current techniques and recent advances

PubMed Central

Collender, Philip A.; Kirby, Amy E.; Addiss, David G.; Freeman, Matthew C.; Remais, Justin V.

2015-01-01

Limiting the environmental transmission of soil-transmitted helminths (STH), which infect 1.5 billion people worldwide, will require sensitive, reliable, and cost effective methods to detect and quantify STH in the environment. We review the state of the art of STH quantification in soil, biosolids, water, produce, and vegetation with respect to four major methodological issues: environmental sampling; recovery of STH from environmental matrices; quantification of recovered STH; and viability assessment of STH ova. We conclude that methods for sampling and recovering STH require substantial advances to provide reliable measurements for STH control. Recent innovations in the use of automated image identification and developments in molecular genetic assays offer considerable promise for improving quantification and viability assessment. PMID:26440788

Antibody-free PRISM-SRM for multiplexed protein quantification: Is this the new competition for immunoassays in bioanalysis?

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

Shi, Tujin; Qian, Weijun

2013-02-01

Highly sensitive technologies for multiplexed quantification of a large number of candidate proteins will play an increasingly important role in clinical biomarker discovery, systems biology, and general biomedical research. Herein we introduce the new PRISM-SRM technology, which represents a highly sensitive multiplexed quantification technology capable of simultaneous quantification of many low-abundance proteins without the need of affinity reagents. The versatility of antibody-free PRISM-SRM for quantifying various types of targets including protein isoforms, protein modifications, metabolites, and others, thus offering new competition with immunoassays.

Advanced Technologies and Methodology for Automated Ultrasonic Testing Systems Quantification

DOT National Transportation Integrated Search

2011-04-29

For automated ultrasonic testing (AUT) detection and sizing accuracy, this program developed a methodology for quantification of AUT systems, advancing and quantifying AUT systems imagecapture capabilities, quantifying the performance of multiple AUT...

The Qiagen Investigator® Quantiplex HYres as an alternative kit for DNA quantification.

PubMed

Frégeau, Chantal J; Laurin, Nancy

2015-05-01

The Investigator® Quantiplex HYres kit was evaluated as a potential replacement for dual DNA quantification of casework samples. This kit was determined to be highly sensitive with a limit of quantification and limit of detection of 0.0049ng/μL and 0.0003ng/μL, respectively, for both human and male DNA, using full or half reaction volumes. It was also accurate in assessing the amount of male DNA present in 96 mock and actual casework male:female mixtures (various ratios) processed in this exercise. The close correlation between the male/human DNA ratios expressed in percentages derived from the Investigator® Quantiplex HYres quantification results and the male DNA proportion calculated in mixed AmpFlSTR® Profiler® Plus or AmpFlSTR® Identifiler® Plus profiles, using the Amelogenin Y peak and STR loci, allowed guidelines to be developed to facilitate decisions regarding when to submit samples to Y-STR rather than autosomal STR profiling. The internal control (IC) target was shown to be more sensitive to inhibitors compared to the human and male DNA targets included in the Investigator® Quantiplex HYres kit serving as a good quality assessor of DNA extracts. The new kit met our criteria of enhanced sensitivity, accuracy, consistency, reliability and robustness for casework DNA quantification. Crown Copyright © 2015. Published by Elsevier Ireland Ltd. All rights reserved.

A multi-center study benchmarks software tools for label-free proteome quantification

PubMed Central

Gillet, Ludovic C; Bernhardt, Oliver M.; MacLean, Brendan; Röst, Hannes L.; Tate, Stephen A.; Tsou, Chih-Chiang; Reiter, Lukas; Distler, Ute; Rosenberger, George; Perez-Riverol, Yasset; Nesvizhskii, Alexey I.; Aebersold, Ruedi; Tenzer, Stefan

2016-01-01

The consistent and accurate quantification of proteins by mass spectrometry (MS)-based proteomics depends on the performance of instruments, acquisition methods and data analysis software. In collaboration with the software developers, we evaluated OpenSWATH, SWATH2.0, Skyline, Spectronaut and DIA-Umpire, five of the most widely used software methods for processing data from SWATH-MS (sequential window acquisition of all theoretical fragment ion spectra), a method that uses data-independent acquisition (DIA) for label-free protein quantification. We analyzed high-complexity test datasets from hybrid proteome samples of defined quantitative composition acquired on two different MS instruments using different SWATH isolation windows setups. For consistent evaluation we developed LFQbench, an R-package to calculate metrics of precision and accuracy in label-free quantitative MS, and report the identification performance, robustness and specificity of each software tool. Our reference datasets enabled developers to improve their software tools. After optimization, all tools provided highly convergent identification and reliable quantification performance, underscoring their robustness for label-free quantitative proteomics. PMID:27701404

Experimental validation of 2D uncertainty quantification for DIC.

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

Reu, Phillip L.

Because digital image correlation (DIC) has become such an important and standard tool in the toolbox of experimental mechanicists, a complete uncertainty quantification of the method is needed. It should be remembered that each DIC setup and series of images will have a unique uncertainty based on the calibration quality and the image and speckle quality of the analyzed images. Any pretest work done with a calibrated DIC stereo-rig to quantify the errors using known shapes and translations, while useful, do not necessarily reveal the uncertainty of a later test. This is particularly true with high-speed applications where actual testmore » images are often less than ideal. Work has previously been completed on the mathematical underpinnings of DIC uncertainty quantification and is already published, this paper will present corresponding experimental work used to check the validity of the uncertainty equations.« less

The role of PET quantification in cardiovascular imaging.

PubMed

Slomka, Piotr; Berman, Daniel S; Alexanderson, Erick; Germano, Guido

2014-08-01

Positron Emission Tomography (PET) has several clinical and research applications in cardiovascular imaging. Myocardial perfusion imaging with PET allows accurate global and regional measurements of myocardial perfusion, myocardial blood flow and function at stress and rest in one exam. Simultaneous assessment of function and perfusion by PET with quantitative software is currently the routine practice. Combination of ejection fraction reserve with perfusion information may improve the identification of severe disease. The myocardial viability can be estimated by quantitative comparison of fluorodeoxyglucose ( 18 FDG) and rest perfusion imaging. The myocardial blood flow and coronary flow reserve measurements are becoming routinely included in the clinical assessment due to enhanced dynamic imaging capabilities of the latest PET/CT scanners. Absolute flow measurements allow evaluation of the coronary microvascular dysfunction and provide additional prognostic and diagnostic information for coronary disease. Standard quantitative approaches to compute myocardial blood flow from kinetic PET data in automated and rapid fashion have been developed for 13 N-ammonia, 15 O-water and 82 Rb radiotracers. The agreement between software methods available for such analysis is excellent. Relative quantification of 82 Rb PET myocardial perfusion, based on comparisons to normal databases, demonstrates high performance for the detection of obstructive coronary disease. New tracers, such as 18 F-flurpiridaz may allow further improvements in the disease detection. Computerized analysis of perfusion at stress and rest reduces the variability of the assessment as compared to visual analysis. PET quantification can be enhanced by precise coregistration with CT angiography. In emerging clinical applications, the potential to identify vulnerable plaques by quantification of atherosclerotic plaque uptake of 18 FDG and 18 F-sodium fluoride tracers in carotids, aorta and coronary arteries

An assessment of Indian monsoon seasonal forecasts and mechanisms underlying monsoon interannual variability in the Met Office GloSea5-GC2 system

NASA Astrophysics Data System (ADS)

Johnson, Stephanie J.; Turner, Andrew; Woolnough, Steven; Martin, Gill; MacLachlan, Craig

2017-03-01

We assess Indian summer monsoon seasonal forecasts in GloSea5-GC2, the Met Office fully coupled subseasonal to seasonal ensemble forecasting system. Using several metrics, GloSea5-GC2 shows similar skill to other state-of-the-art seasonal forecast systems. The prediction skill of the large-scale South Asian monsoon circulation is higher than that of Indian monsoon rainfall. Using multiple linear regression analysis we evaluate relationships between Indian monsoon rainfall and five possible drivers of monsoon interannual variability. Over the time period studied (1992-2011), the El Niño-Southern Oscillation (ENSO) and the Indian Ocean dipole (IOD) are the most important of these drivers in both observations and GloSea5-GC2. Our analysis indicates that ENSO and its teleconnection with Indian rainfall are well represented in GloSea5-GC2. However, the relationship between the IOD and Indian rainfall anomalies is too weak in GloSea5-GC2, which may be limiting the prediction skill of the local monsoon circulation and Indian rainfall. We show that this weak relationship likely results from a coupled mean state bias that limits the impact of anomalous wind forcing on SST variability, resulting in erroneous IOD SST anomalies. Known difficulties in representing convective precipitation over India may also play a role. Since Indian rainfall responds weakly to the IOD, it responds more consistently to ENSO than in observations. Our assessment identifies specific coupled biases that are likely limiting GloSea5-GC2 Indian summer monsoon seasonal prediction skill, providing targets for model improvement.

Four human Plasmodium species quantification using droplet digital PCR.

PubMed

Srisutham, Suttipat; Saralamba, Naowarat; Malleret, Benoit; Rénia, Laurent; Dondorp, Arjen M; Imwong, Mallika

2017-01-01

Droplet digital polymerase chain reaction (ddPCR) is a partial PCR based on water-oil emulsion droplet technology. It is a highly sensitive method for detecting and delineating minor alleles from complex backgrounds and provides absolute quantification of DNA targets. The ddPCR technology has been applied for detection of many pathogens. Here the sensitive assay utilizing ddPCR for detection and quantification of Plasmodium species was investigated. The assay was developed for two levels of detection, genus specific for all Plasmodium species and for specific Plasmodium species detection. The ddPCR assay was developed based on primers and probes specific to the Plasmodium genus 18S rRNA gene. Using ddPCR for ultra-sensitive P. falciparum assessment, the lower level of detection from concentrated DNA obtained from a high volume (1 mL) blood sample was 11 parasites/mL. For species identification, in particular for samples with mixed infections, a duplex reaction was developed for detection and quantification P. falciparum/ P. vivax and P. malariae/ P. ovale. Amplification of each Plasmodium species in the duplex reaction showed equal sensitivity to singleplex single species detection. The duplex ddPCR assay had higher sensitivity to identify minor species in 32 subpatent parasitaemia samples from Cambodia, and performed better than real-time PCR. The ddPCR assay shows high sensitivity to assess very low parasitaemia of all human Plasmodium species. This provides a useful research tool for studying the role of the asymptomatic parasite reservoir for transmission in regions aiming for malaria elimination.

Whole farm quantification of GHG emissions within smallholder farms in developing countries

NASA Astrophysics Data System (ADS)

Seebauer, Matthias

2014-03-01

The IPCC has compiled the best available scientific methods into published guidelines for estimating greenhouse gas emissions and emission removals from the land-use sector. In order to evaluate existing GHG quantification tools to comprehensively quantify GHG emissions and removals in smallholder conditions, farm scale quantification was tested with farm data from Western Kenya. After conducting a cluster analysis to identify different farm typologies GHG quantification was exercised using the VCS SALM methodology complemented with IPCC livestock emission factors and the cool farm tool. The emission profiles of four farm clusters representing the baseline conditions in the year 2009 are compared with 2011 where farmers adopted sustainable land management practices (SALM). The results demonstrate the variation in both the magnitude of the estimated GHG emissions per ha between different smallholder farm typologies and the emissions estimated by applying two different accounting tools. The farm scale quantification further shows that the adoption of SALM has a significant impact on emission reduction and removals and the mitigation benefits range between 4 and 6.5 tCO2 ha-1 yr-1 with significantly different mitigation benefits depending on typologies of the crop-livestock systems, their different agricultural practices, as well as adoption rates of improved practices. However, the inherent uncertainty related to the emission factors applied by accounting tools has substantial implications for reported agricultural emissions. With regard to uncertainty related to activity data, the assessment confirms the high variability within different farm types as well as between different parameters surveyed to comprehensively quantify GHG emissions within smallholder farms.

Quantification of source uncertainties in Seismic Probabilistic Tsunami Hazard Analysis (SPTHA)

NASA Astrophysics Data System (ADS)

Selva, J.; Tonini, R.; Molinari, I.; Tiberti, M. M.; Romano, F.; Grezio, A.; Melini, D.; Piatanesi, A.; Basili, R.; Lorito, S.

2016-06-01

We propose a procedure for uncertainty quantification in Probabilistic Tsunami Hazard Analysis (PTHA), with a special emphasis on the uncertainty related to statistical modelling of the earthquake source in Seismic PTHA (SPTHA), and on the separate treatment of subduction and crustal earthquakes (treated as background seismicity). An event tree approach and ensemble modelling are used in spite of more classical approaches, such as the hazard integral and the logic tree. This procedure consists of four steps: (1) exploration of aleatory uncertainty through an event tree, with alternative implementations for exploring epistemic uncertainty; (2) numerical computation of tsunami generation and propagation up to a given offshore isobath; (3) (optional) site-specific quantification of inundation; (4) simultaneous quantification of aleatory and epistemic uncertainty through ensemble modelling. The proposed procedure is general and independent of the kind of tsunami source considered; however, we implement step 1, the event tree, specifically for SPTHA, focusing on seismic source uncertainty. To exemplify the procedure, we develop a case study considering seismic sources in the Ionian Sea (central-eastern Mediterranean Sea), using the coasts of Southern Italy as a target zone. The results show that an efficient and complete quantification of all the uncertainties is feasible even when treating a large number of potential sources and a large set of alternative model formulations. We also find that (i) treating separately subduction and background (crustal) earthquakes allows for optimal use of available information and for avoiding significant biases; (ii) both subduction interface and crustal faults contribute to the SPTHA, with different proportions that depend on source-target position and tsunami intensity; (iii) the proposed framework allows sensitivity and deaggregation analyses, demonstrating the applicability of the method for operational assessments.

Novel Techniques for Quantification of Correlation Between Primary Liquid Jet Breakup and Downstream Spray Characteristics

DTIC Science & Technology

2016-05-08

unlimited. 5 1. Introduction Several liquid -fuelled combustion systems, such as liquid propellant rocket engines and gas turbines...AFRL-AFOSR-JP-TR-2016-0084 Novel techniques for quantification of correlation between primary liquid jet breakup and downstream spray characteristics...to 17 Apr 2016 4.  TITLE AND SUBTITLE Novel techniques for quantification of correlation between primary liquid jet breakup and downstream spray

Novel Techniques for Quantification of Correlation Between Primary Liquid Jet Breakup and Downstream Spray Characteristics

DTIC Science & Technology

2016-10-05

unlimited. 5 1. Introduction Several liquid -fuelled combustion systems, such as liquid propellant rocket engines and gas turbines...AFRL-AFOSR-JP-TR-2016-0084 Novel techniques for quantification of correlation between primary liquid jet breakup and downstream spray characteristics...to 17 Apr 2016 4.  TITLE AND SUBTITLE Novel techniques for quantification of correlation between primary liquid jet breakup and downstream spray

Automated Quantification of Pneumothorax in CT

PubMed Central

Do, Synho; Salvaggio, Kristen; Gupta, Supriya; Kalra, Mannudeep; Ali, Nabeel U.; Pien, Homer

2012-01-01

An automated, computer-aided diagnosis (CAD) algorithm for the quantification of pneumothoraces from Multidetector Computed Tomography (MDCT) images has been developed. Algorithm performance was evaluated through comparison to manual segmentation by expert radiologists. A combination of two-dimensional and three-dimensional processing techniques was incorporated to reduce required processing time by two-thirds (as compared to similar techniques). Volumetric measurements on relative pneumothorax size were obtained and the overall performance of the automated method shows an average error of just below 1%. PMID:23082091

Methods for Quantification of Soil-Transmitted Helminths in Environmental Media: Current Techniques and Recent Advances.

PubMed

Collender, Philip A; Kirby, Amy E; Addiss, David G; Freeman, Matthew C; Remais, Justin V

2015-12-01

Limiting the environmental transmission of soil-transmitted helminths (STHs), which infect 1.5 billion people worldwide, will require sensitive, reliable, and cost-effective methods to detect and quantify STHs in the environment. We review the state-of-the-art of STH quantification in soil, biosolids, water, produce, and vegetation with regard to four major methodological issues: environmental sampling; recovery of STHs from environmental matrices; quantification of recovered STHs; and viability assessment of STH ova. We conclude that methods for sampling and recovering STHs require substantial advances to provide reliable measurements for STH control. Recent innovations in the use of automated image identification and developments in molecular genetic assays offer considerable promise for improving quantification and viability assessment. Copyright © 2015 Elsevier Ltd. All rights reserved.

Virus detection and quantification using electrical parameters

NASA Astrophysics Data System (ADS)

Ahmad, Mahmoud Al; Mustafa, Farah; Ali, Lizna M.; Rizvi, Tahir A.

2014-10-01

Here we identify and quantitate two similar viruses, human and feline immunodeficiency viruses (HIV and FIV), suspended in a liquid medium without labeling, using a semiconductor technique. The virus count was estimated by calculating the impurities inside a defined volume by observing the change in electrical parameters. Empirically, the virus count was similar to the absolute value of the ratio of the change of the virus suspension dopant concentration relative to the mock dopant over the change in virus suspension Debye volume relative to mock Debye volume. The virus type was identified by constructing a concentration-mobility relationship which is unique for each kind of virus, allowing for a fast (within minutes) and label-free virus quantification and identification. For validation, the HIV and FIV virus preparations were further quantified by a biochemical technique and the results obtained by both approaches corroborated well. We further demonstrate that the electrical technique could be applied to accurately measure and characterize silica nanoparticles that resemble the virus particles in size. Based on these results, we anticipate our present approach to be a starting point towards establishing the foundation for label-free electrical-based identification and quantification of an unlimited number of viruses and other nano-sized particles.

Fully automated system for the quantification of human osteoarthritic knee joint effusion volume using magnetic resonance imaging.

PubMed

Li, Wei; Abram, François; Pelletier, Jean-Pierre; Raynauld, Jean-Pierre; Dorais, Marc; d'Anjou, Marc-André; Martel-Pelletier, Johanne

2010-01-01

Joint effusion is frequently associated with osteoarthritis (OA) flare-up and is an important marker of therapeutic response. This study aimed at developing and validating a fully automated system based on magnetic resonance imaging (MRI) for the quantification of joint effusion volume in knee OA patients. MRI examinations consisted of two axial sequences: a T2-weighted true fast imaging with steady-state precession and a T1-weighted gradient echo. An automated joint effusion volume quantification system using MRI was developed and validated (a) with calibrated phantoms (cylinder and sphere) and effusion from knee OA patients; (b) with assessment by manual quantification; and (c) by direct aspiration. Twenty-five knee OA patients with joint effusion were included in the study. The automated joint effusion volume quantification was developed as a four stage sequencing process: bone segmentation, filtering of unrelated structures, segmentation of joint effusion, and subvoxel volume calculation. Validation experiments revealed excellent coefficients of variation with the calibrated cylinder (1.4%) and sphere (0.8%) phantoms. Comparison of the OA knee joint effusion volume assessed by the developed automated system and by manual quantification was also excellent (r = 0.98; P < 0.0001), as was the comparison with direct aspiration (r = 0.88; P = 0.0008). The newly developed fully automated MRI-based system provided precise quantification of OA knee joint effusion volume with excellent correlation with data from phantoms, a manual system, and joint aspiration. Such an automated system will be instrumental in improving the reproducibility/reliability of the evaluation of this marker in clinical application.

In-line multipoint near-infrared spectroscopy for moisture content quantification during freeze-drying.

PubMed

Kauppinen, Ari; Toiviainen, Maunu; Korhonen, Ossi; Aaltonen, Jaakko; Järvinen, Kristiina; Paaso, Janne; Juuti, Mikko; Ketolainen, Jarkko

2013-02-19

During the past decade, near-infrared (NIR) spectroscopy has been applied for in-line moisture content quantification during a freeze-drying process. However, NIR has been used as a single-vial technique and thus is not representative of the entire batch. This has been considered as one of the main barriers for NIR spectroscopy becoming widely used in process analytical technology (PAT) for freeze-drying. Clearly it would be essential to monitor samples that reliably represent the whole batch. The present study evaluated multipoint NIR spectroscopy for in-line moisture content quantification during a freeze-drying process. Aqueous sucrose solutions were used as model formulations. NIR data was calibrated to predict the moisture content using partial least-squares (PLS) regression with Karl Fischer titration being used as a reference method. PLS calibrations resulted in root-mean-square error of prediction (RMSEP) values lower than 0.13%. Three noncontact, diffuse reflectance NIR probe heads were positioned on the freeze-dryer shelf to measure the moisture content in a noninvasive manner, through the side of the glass vials. The results showed that the detection of unequal sublimation rates within a freeze-dryer shelf was possible with the multipoint NIR system in use. Furthermore, in-line moisture content quantification was reliable especially toward the end of the process. These findings indicate that the use of multipoint NIR spectroscopy can achieve representative quantification of moisture content and hence a drying end point determination to a desired residual moisture level.

Development and validation of an open source quantification tool for DSC-MRI studies.

PubMed

Gordaliza, P M; Mateos-Pérez, J M; Montesinos, P; Guzmán-de-Villoria, J A; Desco, M; Vaquero, J J

2015-03-01

This work presents the development of an open source tool for the quantification of dynamic susceptibility-weighted contrast-enhanced (DSC) perfusion studies. The development of this tool is motivated by the lack of open source tools implemented on open platforms to allow external developers to implement their own quantification methods easily and without the need of paying for a development license. This quantification tool was developed as a plugin for the ImageJ image analysis platform using the Java programming language. A modular approach was used in the implementation of the components, in such a way that the addition of new methods can be done without breaking any of the existing functionalities. For the validation process, images from seven patients with brain tumors were acquired and quantified with the presented tool and with a widely used clinical software package. The resulting perfusion parameters were then compared. Perfusion parameters and the corresponding parametric images were obtained. When no gamma-fitting is used, an excellent agreement with the tool used as a gold-standard was obtained (R(2)>0.8 and values are within 95% CI limits in Bland-Altman plots). An open source tool that performs quantification of perfusion studies using magnetic resonance imaging has been developed and validated using a clinical software package. It works as an ImageJ plugin and the source code has been published with an open source license. Copyright © 2015 Elsevier Ltd. All rights reserved.

Quantification of Noise Sources in EMI Surveys

DTIC Science & Technology

2012-04-09

Naval Research Laboratory Washington, DC 20375-5320 NRL/MR/ 6110 --12-9400 Quantification of Noise Sources in EMI Surveys ESTCP MR-0508 Final Guidance...NUMBER 2 . REPORT TYPE1. REPORT DATE (DD-MM-YYYY) 4. TITLE AND SUBTITLE 6. AUTHOR(S) 8. PERFORMING ORGANIZATION REPORT NUMBER 7. PERFORMING...Barrow,‡ Jonathan T. Miller,‡ and Thomas H. Bell,‡ Naval Research Laboratory, Code 6110 4555 Overlook Avenue, SW Washington, DC 20375-5320 NRL/MR

Leveraging transcript quantification for fast computation of alternative splicing profiles.

PubMed

Alamancos, Gael P; Pagès, Amadís; Trincado, Juan L; Bellora, Nicolás; Eyras, Eduardo

2015-09-01

Alternative splicing plays an essential role in many cellular processes and bears major relevance in the understanding of multiple diseases, including cancer. High-throughput RNA sequencing allows genome-wide analyses of splicing across multiple conditions. However, the increasing number of available data sets represents a major challenge in terms of computation time and storage requirements. We describe SUPPA, a computational tool to calculate relative inclusion values of alternative splicing events, exploiting fast transcript quantification. SUPPA accuracy is comparable and sometimes superior to standard methods using simulated as well as real RNA-sequencing data compared with experimentally validated events. We assess the variability in terms of the choice of annotation and provide evidence that using complete transcripts rather than more transcripts per gene provides better estimates. Moreover, SUPPA coupled with de novo transcript reconstruction methods does not achieve accuracies as high as using quantification of known transcripts, but remains comparable to existing methods. Finally, we show that SUPPA is more than 1000 times faster than standard methods. Coupled with fast transcript quantification, SUPPA provides inclusion values at a much higher speed than existing methods without compromising accuracy, thereby facilitating the systematic splicing analysis of large data sets with limited computational resources. The software is implemented in Python 2.7 and is available under the MIT license at https://bitbucket.org/regulatorygenomicsupf/suppa. © 2015 Alamancos et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Semi-automated quantification and neuroanatomical mapping of heterogeneous cell populations.

PubMed

Mendez, Oscar A; Potter, Colin J; Valdez, Michael; Bello, Thomas; Trouard, Theodore P; Koshy, Anita A

2018-07-15

Our group studies the interactions between cells of the brain and the neurotropic parasite Toxoplasma gondii. Using an in vivo system that allows us to permanently mark and identify brain cells injected with Toxoplasma protein, we have identified that Toxoplasma-injected neurons (TINs) are heterogeneously distributed throughout the brain. Unfortunately, standard methods to quantify and map heterogeneous cell populations onto a reference brain atlas are time consuming and prone to user bias. We developed a novel MATLAB-based semi-automated quantification and mapping program to allow the rapid and consistent mapping of heterogeneously distributed cells on to the Allen Institute Mouse Brain Atlas. The system uses two-threshold background subtraction to identify and quantify cells of interest. We demonstrate that we reliably quantify and neuroanatomically localize TINs with low intra- or inter-observer variability. In a follow up experiment, we show that specific regions of the mouse brain are enriched with TINs. The procedure we use takes advantage of simple immunohistochemistry labeling techniques, use of a standard microscope with a motorized stage, and low cost computing that can be readily obtained at a research institute. To our knowledge there is no other program that uses such readily available techniques and equipment for mapping heterogeneous populations of cells across the whole mouse brain. The quantification method described here allows reliable visualization, quantification, and mapping of heterogeneous cell populations in immunolabeled sections across whole mouse brains. Copyright © 2018 Elsevier B.V. All rights reserved.

Subnuclear foci quantification using high-throughput 3D image cytometry

NASA Astrophysics Data System (ADS)

Wadduwage, Dushan N.; Parrish, Marcus; Choi, Heejin; Engelward, Bevin P.; Matsudaira, Paul; So, Peter T. C.

2015-07-01

Ionising radiation causes various types of DNA damages including double strand breaks (DSBs). DSBs are often recognized by DNA repair protein ATM which forms gamma-H2AX foci at the site of the DSBs that can be visualized using immunohistochemistry. However most of such experiments are of low throughput in terms of imaging and image analysis techniques. Most of the studies still use manual counting or classification. Hence they are limited to counting a low number of foci per cell (5 foci per nucleus) as the quantification process is extremely labour intensive. Therefore we have developed a high throughput instrumentation and computational pipeline specialized for gamma-H2AX foci quantification. A population of cells with highly clustered foci inside nuclei were imaged, in 3D with submicron resolution, using an in-house developed high throughput image cytometer. Imaging speeds as high as 800 cells/second in 3D were achieved by using HiLo wide-field depth resolved imaging and a remote z-scanning technique. Then the number of foci per cell nucleus were quantified using a 3D extended maxima transform based algorithm. Our results suggests that while most of the other 2D imaging and manual quantification studies can count only up to about 5 foci per nucleus our method is capable of counting more than 100. Moreover we show that 3D analysis is significantly superior compared to the 2D techniques.

Tutorial examples for uncertainty quantification methods.

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

De Bord, Sarah

2015-08-01

This report details the work accomplished during my 2015 SULI summer internship at Sandia National Laboratories in Livermore, CA. During this internship, I worked on multiple tasks with the common goal of making uncertainty quantification (UQ) methods more accessible to the general scientific community. As part of my work, I created a comprehensive numerical integration example to incorporate into the user manual of a UQ software package. Further, I developed examples involving heat transfer through a window to incorporate into tutorial lectures that serve as an introduction to UQ methods.

Uncertainty Quantification of CFD Data Generated for a Model Scramjet Isolator Flowfield

NASA Technical Reports Server (NTRS)

Baurle, R. A.; Axdahl, E. L.

2017-01-01

Computational fluid dynamics is now considered to be an indispensable tool for the design and development of scramjet engine components. Unfortunately, the quantification of uncertainties is rarely addressed with anything other than sensitivity studies, so the degree of confidence associated with the numerical results remains exclusively with the subject matter expert that generated them. This practice must be replaced with a formal uncertainty quantification process for computational fluid dynamics to play an expanded role in the system design, development, and flight certification process. Given the limitations of current hypersonic ground test facilities, this expanded role is believed to be a requirement by some in the hypersonics community if scramjet engines are to be given serious consideration as a viable propulsion system. The present effort describes a simple, relatively low cost, nonintrusive approach to uncertainty quantification that includes the basic ingredients required to handle both aleatoric (random) and epistemic (lack of knowledge) sources of uncertainty. The nonintrusive nature of the approach allows the computational fluid dynamicist to perform the uncertainty quantification with the flow solver treated as a "black box". Moreover, a large fraction of the process can be automated, allowing the uncertainty assessment to be readily adapted into the engineering design and development workflow. In the present work, the approach is applied to a model scramjet isolator problem where the desire is to validate turbulence closure models in the presence of uncertainty. In this context, the relevant uncertainty sources are determined and accounted for to allow the analyst to delineate turbulence model-form errors from other sources of uncertainty associated with the simulation of the facility flow.

Rapid Quantification of Low-Viscosity Acetyl-Triacylglycerols Using Electrospray Ionization Mass Spectrometry.

PubMed

Bansal, Sunil; Durrett, Timothy P

2016-09-01

Acetyl-triacylglycerols (acetyl-TAG) possess an sn-3 acetate group, which confers useful chemical and physical properties to these unusual triacylglycerols (TAG). Current methods for quantification of acetyl-TAG are time consuming and do not provide any information on the molecular species profile. Electrospray ionization mass spectrometry (ESI-MS)-based methods can overcome these drawbacks. However, the ESI-MS signal intensity for TAG depends on the aliphatic chain length and unsaturation index of the molecule. Therefore response factors for different molecular species need to be determined before any quantification. The effects of the chain length and the number of double-bonds of the sn-1/2 acyl groups on the signal intensity for the neutral loss of short chain length sn-3 groups were quantified using a series of synthesized sn-3 specific structured TAG. The signal intensity for the neutral loss of the sn-3 acyl group was found to negatively correlated with the aliphatic chain length and unsaturation index of the sn-1/2 acyl groups. The signal intensity of the neutral loss of the sn-3 acyl group was also negatively correlated with the size of that chain. Further, the position of the group undergoing neutral loss was also important, with the signal from an sn-2 acyl group much lower than that from one located at sn-3. Response factors obtained from these analyses were used to develop a method for the absolute quantification of acetyl-TAG. The increased sensitivity of this ESI-MS-based approach allowed successful quantification of acetyl-TAG in various biological settings, including the products of in vitro enzyme activity assays.

Multiplex electrochemical DNA platform for femtomolar-level quantification of genetically modified soybean.

PubMed

Manzanares-Palenzuela, C Lorena; de-Los-Santos-Álvarez, Noemí; Lobo-Castañón, María Jesús; López-Ruiz, Beatriz

2015-06-15

Current EU regulations on the mandatory labeling of genetically modified organisms (GMOs) with a minimum content of 0.9% would benefit from the availability of reliable and rapid methods to detect and quantify DNA sequences specific for GMOs. Different genosensors have been developed to this aim, mainly intended for GMO screening. A remaining challenge, however, is the development of genosensing platforms for GMO quantification, which should be expressed as the number of event-specific DNA sequences per taxon-specific sequences. Here we report a simple and sensitive multiplexed electrochemical approach for the quantification of Roundup-Ready Soybean (RRS). Two DNA sequences, taxon (lectin) and event-specific (RR), are targeted via hybridization onto magnetic beads. Both sequences are simultaneously detected by performing the immobilization, hybridization and labeling steps in a single tube and parallel electrochemical readout. Hybridization is performed in a sandwich format using signaling probes labeled with fluorescein isothiocyanate (FITC) or digoxigenin (Dig), followed by dual enzymatic labeling using Fab fragments of anti-Dig and anti-FITC conjugated to peroxidase or alkaline phosphatase, respectively. Electrochemical measurement of the enzyme activity is finally performed on screen-printed carbon electrodes. The assay gave a linear range of 2-250 pM for both targets, with LOD values of 650 fM (160 amol) and 190 fM (50 amol) for the event-specific and the taxon-specific targets, respectively. Results indicate that the method could be applied for GMO quantification below the European labeling threshold level (0.9%), offering a general approach for the rapid quantification of specific GMO events in foods. Copyright © 2015 Elsevier B.V. All rights reserved.

Critical aspects of data analysis for quantification in laser-induced breakdown spectroscopy

NASA Astrophysics Data System (ADS)

Motto-Ros, V.; Syvilay, D.; Bassel, L.; Negre, E.; Trichard, F.; Pelascini, F.; El Haddad, J.; Harhira, A.; Moncayo, S.; Picard, J.; Devismes, D.; Bousquet, B.

2018-02-01

In this study, a collaborative contest focused on LIBS data processing has been conducted in an original way since the participants did not share the same samples to be analyzed on their own LIBS experiments but a set of LIBS spectra obtained from one single experiment. Each participant was asked to provide the predicted concentrations of several elements for two glass samples. The analytical contest revealed a wide diversity of results among participants, even when the same spectral lines were considered for the analysis. Then, a parametric study was conducted to investigate the influence of each step during the data processing. This study was based on several analytical figures of merit such as the determination coefficient, uncertainty, limit of quantification and prediction ability (i.e., trueness). Then, it was possible to interpret the results provided by the participants, emphasizing the fact that the type of data extraction, baseline modeling as well as the calibration model play key roles in the quantification performance of the technique. This work provides a set of recommendations based on a systematic evaluation of the quantification procedure with the aim of optimizing the methodological steps toward the standardization of LIBS.

USACM Thematic Workshop On Uncertainty Quantification And Data-Driven Modeling.

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

Stewart, James R.

The USACM Thematic Workshop on Uncertainty Quantification and Data-Driven Modeling was held on March 23-24, 2017, in Austin, TX. The organizers of the technical program were James R. Stewart of Sandia National Laboratories and Krishna Garikipati of University of Michigan. The administrative organizer was Ruth Hengst, who serves as Program Coordinator for the USACM. The organization of this workshop was coordinated through the USACM Technical Thrust Area on Uncertainty Quantification and Probabilistic Analysis. The workshop website (http://uqpm2017.usacm.org) includes the presentation agenda as well as links to several of the presentation slides (permission to access the presentations was granted by eachmore » of those speakers, respectively). Herein, this final report contains the complete workshop program that includes the presentation agenda, the presentation abstracts, and the list of posters.« less

An Uncertainty Quantification Framework for Prognostics and Condition-Based Monitoring

NASA Technical Reports Server (NTRS)

Sankararaman, Shankar; Goebel, Kai

2014-01-01

This paper presents a computational framework for uncertainty quantification in prognostics in the context of condition-based monitoring of aerospace systems. The different sources of uncertainty and the various uncertainty quantification activities in condition-based prognostics are outlined in detail, and it is demonstrated that the Bayesian subjective approach is suitable for interpreting uncertainty in online monitoring. A state-space model-based framework for prognostics, that can rigorously account for the various sources of uncertainty, is presented. Prognostics consists of two important steps. First, the state of the system is estimated using Bayesian tracking, and then, the future states of the system are predicted until failure, thereby computing the remaining useful life of the system. The proposed framework is illustrated using the power system of a planetary rover test-bed, which is being developed and studied at NASA Ames Research Center.

qPCR-based mitochondrial DNA quantification: Influence of template DNA fragmentation on accuracy

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

Jackson, Christopher B., E-mail: Christopher.jackson@insel.ch; Gallati, Sabina, E-mail: sabina.gallati@insel.ch; Schaller, Andre, E-mail: andre.schaller@insel.ch

2012-07-06

Highlights: Black-Right-Pointing-Pointer Serial qPCR accurately determines fragmentation state of any given DNA sample. Black-Right-Pointing-Pointer Serial qPCR demonstrates different preservation of the nuclear and mitochondrial genome. Black-Right-Pointing-Pointer Serial qPCR provides a diagnostic tool to validate the integrity of bioptic material. Black-Right-Pointing-Pointer Serial qPCR excludes degradation-induced erroneous quantification. -- Abstract: Real-time PCR (qPCR) is the method of choice for quantification of mitochondrial DNA (mtDNA) by relative comparison of a nuclear to a mitochondrial locus. Quantitative abnormal mtDNA content is indicative of mitochondrial disorders and mostly confines in a tissue-specific manner. Thus handling of degradation-prone bioptic material is inevitable. We established a serialmore » qPCR assay based on increasing amplicon size to measure degradation status of any DNA sample. Using this approach we can exclude erroneous mtDNA quantification due to degraded samples (e.g. long post-exicision time, autolytic processus, freeze-thaw cycles) and ensure abnormal DNA content measurements (e.g. depletion) in non-degraded patient material. By preparation of degraded DNA under controlled conditions using sonification and DNaseI digestion we show that erroneous quantification is due to the different preservation qualities of the nuclear and the mitochondrial genome. This disparate degradation of the two genomes results in over- or underestimation of mtDNA copy number in degraded samples. Moreover, as analysis of defined archival tissue would allow to precise the molecular pathomechanism of mitochondrial disorders presenting with abnormal mtDNA content, we compared fresh frozen (FF) with formalin-fixed paraffin-embedded (FFPE) skeletal muscle tissue of the same sample. By extrapolation of measured decay constants for nuclear DNA ({lambda}{sub nDNA}) and mtDNA ({lambda}{sub mtDNA}) we present an approach to possibly correct

A validated Fourier transform infrared spectroscopy method for quantification of total lactones in Inula racemosa and Andrographis paniculata.

PubMed

Shivali, Garg; Praful, Lahorkar; Vijay, Gadgil

2012-01-01

Fourier transform infrared (FT-IR) spectroscopy is a technique widely used for detection and quantification of various chemical moieties. This paper describes the use of the FT-IR spectroscopy technique for the quantification of total lactones present in Inula racemosa and Andrographis paniculata. To validate the FT-IR spectroscopy method for quantification of total lactones in I. racemosa and A. paniculata. Dried and powdered I. racemosa roots and A. paniculata plant were extracted with ethanol and dried to remove ethanol completely. The ethanol extract was analysed in a KBr pellet by FT-IR spectroscopy. The FT-IR spectroscopy method was validated and compared with a known spectrophotometric method for quantification of lactones in A. paniculata. By FT-IR spectroscopy, the amount of total lactones was found to be 2.12 ± 0.47% (n = 3) in I. racemosa and 8.65 ± 0.51% (n = 3) in A. paniculata. The method showed comparable results with a known spectrophotometric method used for quantification of such lactones: 8.42 ± 0.36% (n = 3) in A. paniculata. Limits of detection and quantification for isoallantolactone were 1 µg and 10 µg respectively; for andrographolide they were 1.5 µg and 15 µg respectively. Recoveries were over 98%, with good intra- and interday repeatability: RSD ≤ 2%. The FT-IR spectroscopy method proved linear, accurate, precise and specific, with low limits of detection and quantification, for estimation of total lactones, and is less tedious than the UV spectrophotometric method for the compounds tested. This validated FT-IR spectroscopy method is readily applicable for the quality control of I. racemosa and A. paniculata. Copyright © 2011 John Wiley & Sons, Ltd.

18O-labeled proteome reference as global internal standards for targeted quantification by selected reaction monitoring-mass spectrometry.

PubMed

Kim, Jong-Seo; Fillmore, Thomas L; Liu, Tao; Robinson, Errol; Hossain, Mahmud; Champion, Boyd L; Moore, Ronald J; Camp, David G; Smith, Richard D; Qian, Wei-Jun

2011-12-01

Selected reaction monitoring (SRM)-MS is an emerging technology for high throughput targeted protein quantification and verification in biomarker discovery studies; however, the cost associated with the application of stable isotope-labeled synthetic peptides as internal standards can be prohibitive for screening a large number of candidate proteins as often required in the preverification phase of discovery studies. Herein we present a proof of concept study using an (18)O-labeled proteome reference as global internal standards (GIS) for SRM-based relative quantification. The (18)O-labeled proteome reference (or GIS) can be readily prepared and contains a heavy isotope ((18)O)-labeled internal standard for every possible tryptic peptide. Our results showed that the percentage of heavy isotope ((18)O) incorporation applying an improved protocol was >99.5% for most peptides investigated. The accuracy, reproducibility, and linear dynamic range of quantification were further assessed based on known ratios of standard proteins spiked into the labeled mouse plasma reference. Reliable quantification was observed with high reproducibility (i.e. coefficient of variance <10%) for analyte concentrations that were set at 100-fold higher or lower than those of the GIS based on the light ((16)O)/heavy ((18)O) peak area ratios. The utility of (18)O-labeled GIS was further illustrated by accurate relative quantification of 45 major human plasma proteins. Moreover, quantification of the concentrations of C-reactive protein and prostate-specific antigen was illustrated by coupling the GIS with standard additions of purified protein standards. Collectively, our results demonstrated that the use of (18)O-labeled proteome reference as GIS provides a convenient, low cost, and effective strategy for relative quantification of a large number of candidate proteins in biological or clinical samples using SRM.

Advancing agricultural greenhouse gas quantification*

NASA Astrophysics Data System (ADS)

Olander, Lydia; Wollenberg, Eva; Tubiello, Francesco; Herold, Martin

2013-03-01

1. Introduction Better information on greenhouse gas (GHG) emissions and mitigation potential in the agricultural sector is necessary to manage these emissions and identify responses that are consistent with the food security and economic development priorities of countries. Critical activity data (what crops or livestock are managed in what way) are poor or lacking for many agricultural systems, especially in developing countries. In addition, the currently available methods for quantifying emissions and mitigation are often too expensive or complex or not sufficiently user friendly for widespread use. The purpose of this focus issue is to capture the state of the art in quantifying greenhouse gases from agricultural systems, with the goal of better understanding our current capabilities and near-term potential for improvement, with particular attention to quantification issues relevant to smallholders in developing countries. This work is timely in light of international discussions and negotiations around how agriculture should be included in efforts to reduce and adapt to climate change impacts, and considering that significant climate financing to developing countries in post-2012 agreements may be linked to their increased ability to identify and report GHG emissions (Murphy et al 2010, CCAFS 2011, FAO 2011). 2. Agriculture and climate change mitigation The main agricultural GHGs—methane and nitrous oxide—account for 10%-12% of anthropogenic emissions globally (Smith et al 2008), or around 50% and 60% of total anthropogenic methane and nitrous oxide emissions, respectively, in 2005. Net carbon dioxide fluxes between agricultural land and the atmosphere linked to food production are relatively small, although significant carbon emissions are associated with degradation of organic soils for plantations in tropical regions (Smith et al 2007, FAO 2012). Population growth and shifts in dietary patterns toward more meat and dairy consumption will lead to

Uncertainty Quantification for Robust Control of Wind Turbines using Sliding Mode Observer

NASA Astrophysics Data System (ADS)

Schulte, Horst

2016-09-01

A new quantification method of uncertain models for robust wind turbine control using sliding-mode techniques is presented with the objective to improve active load mitigation. This approach is based on the so-called equivalent output injection signal, which corresponds to the average behavior of the discontinuous switching term, establishing and maintaining a motion on a so-called sliding surface. The injection signal is directly evaluated to obtain estimates of the uncertainty bounds of external disturbances and parameter uncertainties. The applicability of the proposed method is illustrated by the quantification of a four degree-of-freedom model of the NREL 5MW reference turbine containing uncertainties.

Simultaneous quantification and semi-quantification of ginkgolic acids and their metabolites in rat plasma by UHPLC-LTQ-Orbitrap-MS and its application to pharmacokinetics study.

PubMed

Qian, Yiyun; Zhu, Zhenhua; Duan, Jin-Ao; Guo, Sheng; Shang, Erxin; Tao, Jinhua; Su, Shulan; Guo, Jianming

2017-01-15

A highly sensitive method using ultra-high-pressure liquid chromatography coupled with linear ion trap-Orbitrap tandem mass spectrometry (UHPLC-LTQ-Orbitrap-MS) has been developed and validated for the simultaneous identification and quantification of ginkgolic acids and semi-quantification of their metabolites in rat plasma. For the five selected ginkgolic acids, the method was found to be with good linearities (r>0.9991), good intra- and inter-day precisions (RSD<15%), and good accuracies (RE, from -10.33% to 4.92%) as well. Extraction recoveries, matrix effects and stabilities for rat plasm samples were within the required limits. The validated method was successfully applied to investigate the pharmacokinetics of the five ginkgolic acids in rat plasma after oral administration of 3 dosage groups (900mg/kg, 300mg/kg and 100mg/kg). Meanwhile, six metabolites of GA (15:1) and GA (17:1) were identified by comparison of MS data with reported values. The results of validation in terms of linear ranges, precisions and stabilities were established for semi-quantification of metabolites. The curves of relative changes of these metabolites during the metabolic process were constructed by plotting the peak area ratios of metabolites to salicylic acid (internal standard, IS), respectively. Double peaks were observed in all 3 dose groups. Different type of metabolites and different dosage of each metabolite both resulted in different T max . Copyright © 2016 Elsevier B.V. All rights reserved.

New approach for the quantification of processed animal proteins in feed using light microscopy.

PubMed

Veys, P; Baeten, V

2010-07-01

A revision of European Union's total feed ban on animal proteins in feed will need robust quantification methods, especially for control analyses, if tolerance levels are to be introduced, as for fishmeal in ruminant feed. In 2006, a study conducted by the Community Reference Laboratory for Animal Proteins in feedstuffs (CRL-AP) demonstrated the deficiency of the official quantification method based on light microscopy. The study concluded that the method had to be revised. This paper puts forward an improved quantification method based on three elements: (1) the preparation of permanent slides with an optical adhesive preserving all morphological markers of bones necessary for accurate identification and precision counting; (2) the use of a counting grid eyepiece reticle; and (3) new definitions for correction factors for the estimated portions of animal particles in the sediment. This revised quantification method was tested on feeds adulterated at different levels with bovine meat and bone meal (MBM) and fishmeal, and it proved to be effortless to apply. The results obtained were very close to the expected values of contamination levels for both types of adulteration (MBM or fishmeal). Calculated values were not only replicable, but also reproducible. The advantages of the new approach, including the benefits of the optical adhesive used for permanent slide mounting and the experimental conditions that need to be met to implement the new method correctly, are discussed.

Data-Independent MS/MS Quantification of Neuropeptides for Determination of Putative Feeding-Related Neurohormones in Microdialysate

PubMed Central

2015-01-01

Food consumption is an important behavior that is regulated by an intricate array of neuropeptides (NPs). Although many feeding-related NPs have been identified in mammals, precise mechanisms are unclear and difficult to study in mammals, as current methods are not highly multiplexed and require extensive a priori knowledge about analytes. New advances in data-independent acquisition (DIA) MS/MS and the open-source quantification software Skyline have opened up the possibility to identify hundreds of compounds and quantify them from a single DIA MS/MS run. An untargeted DIA MSE quantification method using Skyline software for multiplexed, discovery-driven quantification was developed and found to produce linear calibration curves for peptides at physiologically relevant concentrations using a protein digest as internal standard. By using this method, preliminary relative quantification of the crab Cancer borealis neuropeptidome (<2 kDa, 137 peptides from 18 families) was possible in microdialysates from 8 replicate feeding experiments. Of these NPs, 55 were detected with an average mass error below 10 ppm. The time-resolved profiles of relative concentration changes for 6 are shown, and there is great potential for the use of this method in future experiments to aid in correlation of NP changes with behavior. This work presents an unbiased approach to winnowing candidate NPs related to a behavior of interest in a functionally relevant manner, and demonstrates the success of such a UPLC-MSE quantification method using the open source software Skyline. PMID:25552291

Data-independent MS/MS quantification of neuropeptides for determination of putative feeding-related neurohormones in microdialysate.

PubMed

Schmerberg, Claire M; Liang, Zhidan; Li, Lingjun

2015-01-21

Food consumption is an important behavior that is regulated by an intricate array of neuropeptides (NPs). Although many feeding-related NPs have been identified in mammals, precise mechanisms are unclear and difficult to study in mammals, as current methods are not highly multiplexed and require extensive a priori knowledge about analytes. New advances in data-independent acquisition (DIA) MS/MS and the open-source quantification software Skyline have opened up the possibility to identify hundreds of compounds and quantify them from a single DIA MS/MS run. An untargeted DIA MS(E) quantification method using Skyline software for multiplexed, discovery-driven quantification was developed and found to produce linear calibration curves for peptides at physiologically relevant concentrations using a protein digest as internal standard. By using this method, preliminary relative quantification of the crab Cancer borealis neuropeptidome (<2 kDa, 137 peptides from 18 families) was possible in microdialysates from 8 replicate feeding experiments. Of these NPs, 55 were detected with an average mass error below 10 ppm. The time-resolved profiles of relative concentration changes for 6 are shown, and there is great potential for the use of this method in future experiments to aid in correlation of NP changes with behavior. This work presents an unbiased approach to winnowing candidate NPs related to a behavior of interest in a functionally relevant manner, and demonstrates the success of such a UPLC-MS(E) quantification method using the open source software Skyline.

Secondary Students' Quantification of Ratio and Rate: A Framework for Reasoning about Change in Covarying Quantities

ERIC Educational Resources Information Center

Johnson, Heather Lynn

2015-01-01

Contributing to a growing body of research addressing secondary students' quantitative and covariational reasoning, the multiple case study reported in this article investigated secondary students' quantification of ratio and rate. This article reports results from a study investigating students' quantification of rate and ratio as…

Computational analysis of PET by AIBL (CapAIBL): a cloud-based processing pipeline for the quantification of PET images

NASA Astrophysics Data System (ADS)

Bourgeat, Pierrick; Dore, Vincent; Fripp, Jurgen; Villemagne, Victor L.; Rowe, Chris C.; Salvado, Olivier

2015-03-01

With the advances of PET tracers for β-Amyloid (Aβ) detection in neurodegenerative diseases, automated quantification methods are desirable. For clinical use, there is a great need for PET-only quantification method, as MR images are not always available. In this paper, we validate a previously developed PET-only quantification method against MR-based quantification using 6 tracers: 18F-Florbetaben (N=148), 18F-Florbetapir (N=171), 18F-NAV4694 (N=47), 18F-Flutemetamol (N=180), 11C-PiB (N=381) and 18F-FDG (N=34). The results show an overall mean absolute percentage error of less than 5% for each tracer. The method has been implemented as a remote service called CapAIBL (http://milxcloud.csiro.au/capaibl). PET images are uploaded to a cloud platform where they are spatially normalised to a standard template and quantified. A report containing global as well as local quantification, along with surface projection of the β-Amyloid deposition is automatically generated at the end of the pipeline and emailed to the user.

Fully automated system for the quantification of human osteoarthritic knee joint effusion volume using magnetic resonance imaging

PubMed Central

2010-01-01

Introduction Joint effusion is frequently associated with osteoarthritis (OA) flare-up and is an important marker of therapeutic response. This study aimed at developing and validating a fully automated system based on magnetic resonance imaging (MRI) for the quantification of joint effusion volume in knee OA patients. Methods MRI examinations consisted of two axial sequences: a T2-weighted true fast imaging with steady-state precession and a T1-weighted gradient echo. An automated joint effusion volume quantification system using MRI was developed and validated (a) with calibrated phantoms (cylinder and sphere) and effusion from knee OA patients; (b) with assessment by manual quantification; and (c) by direct aspiration. Twenty-five knee OA patients with joint effusion were included in the study. Results The automated joint effusion volume quantification was developed as a four stage sequencing process: bone segmentation, filtering of unrelated structures, segmentation of joint effusion, and subvoxel volume calculation. Validation experiments revealed excellent coefficients of variation with the calibrated cylinder (1.4%) and sphere (0.8%) phantoms. Comparison of the OA knee joint effusion volume assessed by the developed automated system and by manual quantification was also excellent (r = 0.98; P < 0.0001), as was the comparison with direct aspiration (r = 0.88; P = 0.0008). Conclusions The newly developed fully automated MRI-based system provided precise quantification of OA knee joint effusion volume with excellent correlation with data from phantoms, a manual system, and joint aspiration. Such an automated system will be instrumental in improving the reproducibility/reliability of the evaluation of this marker in clinical application. PMID:20846392

QconCATs: design and expression of concatenated protein standards for multiplexed protein quantification.

PubMed

Simpson, Deborah M; Beynon, Robert J

2012-09-01

Systems biology requires knowledge of the absolute amounts of proteins in order to model biological processes and simulate the effects of changes in specific model parameters. Quantification concatamers (QconCATs) are established as a method to provide multiplexed absolute peptide standards for a set of target proteins in isotope dilution standard experiments. Two or more quantotypic peptides representing each of the target proteins are concatenated into a designer gene that is metabolically labelled with stable isotopes in Escherichia coli or other cellular or cell-free systems. Co-digestion of a known amount of QconCAT with the target proteins generates a set of labelled reference peptide standards for the unlabelled analyte counterparts, and by using an appropriate mass spectrometry platform, comparison of the intensities of the peptide ratios delivers absolute quantification of the encoded peptides and in turn the target proteins for which they are surrogates. In this review, we discuss the criteria and difficulties associated with surrogate peptide selection and provide examples in the design of QconCATs for quantification of the proteins of the nuclear factor κB pathway.

Quantification of free circulating tumor DNA as a diagnostic marker for breast cancer.

PubMed

Catarino, Raquel; Ferreira, Maria M; Rodrigues, Helena; Coelho, Ana; Nogal, Ana; Sousa, Abreu; Medeiros, Rui

2008-08-01

To determine whether the amounts of circulating DNA could discriminate between breast cancer patients and healthy individuals by using real-time PCR quantification methodology. Our standard protocol for quantification of cell-free plasma DNA involved 175 consecutive patients with breast cancer and 80 healthy controls. We found increased levels of circulating DNA in breast cancer patients compared to control individuals (105.2 vs. 77.06 ng/mL, p < 0.001). We also found statistically significant differences in circulating DNA amounts in patients before and after breast surgery (105.2 vs. 59.0 ng/mL, p = 0.001). Increased plasma cell-free DNA concentration was a strong risk factor for breast cancer, conferring an increased risk for the presence of this disease (OR, 12.32; 95% CI, 2.09-52.28; p < 0.001). Quantification of circulating DNA by real-time PCR may be a good and simple tool for detection of breast cancer with a potential to clinical applicability together with other current methods used for monitoring the disease.

Universal Quantification in a Constraint-Based Planner

NASA Technical Reports Server (NTRS)

Golden, Keith; Frank, Jeremy; Clancy, Daniel (Technical Monitor)

2002-01-01

Constraints and universal quantification are both useful in planning, but handling universally quantified constraints presents some novel challenges. We present a general approach to proving the validity of universally quantified constraints. The approach essentially consists of checking that the constraint is not violated for all members of the universe. We show that this approach can sometimes be applied even when variable domains are infinite, and we present some useful special cases where this can be done efficiently.

Century scale climatic rhythms in the equatorial Indian Ocean during the late Quaternary: Faunal and geochemical proxies from the Maldivian Archipelago

NASA Astrophysics Data System (ADS)

Sarkar, S.; Gupta, A. K.

2012-04-01

The equatorial Indian Ocean is swept by the Indian Ocean equatorial westerlies (IEW) which are strong during monsoon transitions in April-May and October-November, driving Eastward Equatorial Current (EEC) in the upper ocean. This study is based on the biogenic sediments from Ocean Drilling Program (ODP) Hole 716A, recovered beneath the narrow equatorial track (7 Degree North to 7 Degree South) along which the IEW prevail. We analyzed 300 Kyr record of benthic and planktic foraminifera, pteropods combined with stable isotope values measured on planktic foraminifer Globigerinoides ruber from 451 core samples to understand paleoceanographic and paleoclimatic changes in the equatorial Indian Ocean during the late Quaternary (~450 - 150 Kyrs). Factor and cluster analyses of the 53 highest-ranked benthic foraminiferal species enabled to identify five biofacies, indicating varied nature of deep-sea environments during the late Quaternary, with a major shift across the middle Brunhes epoch (across Marine Isotope Stage 9 and 8). Biofacies Robulus nicobarensis - Trifarina reussi (Rn-Tr), Uvigerina porrecta - Reussella simplex (Upo-Rs) and Cymbaloporetta squammosa - Bolivinita sp. (Cs-Bsp) document high organic flux with low oxygen paleoenvironment dominating before the mid-Brunhes event, similar to Globigerina bulloides population, while benthic foraminiferal biofacies Hoeglundina elegans - Miliolinella subrotunda (He-Ms) and Uvigerina peregrina - Quinqueloculina seminulum (Upe-Qs) record high seasonality in food supply with well-oxygenated deep water after ~300 Kyr. These changes are also visible in planktic foraminifera and pteropod record. In the present day, the strength of the IEW is inversely related to the Indian Ocean Dipole (IOD). The IEW weakened across MIS 9/8 during which time the IOD strengthened, causing heavy rains and floods over the equatorial East Africa and deficient rainfall over Australasia. The proxy response changed from low to high frequency cycles

Multi-decadal trend and space-time variability of sea level over the Indian Ocean since the 1950s: impact of decadal climate modes

NASA Astrophysics Data System (ADS)

Han, W.; Stammer, D.; Meehl, G. A.; Hu, A.; Sienz, F.

2016-12-01

Sea level varies on decadal and multi-decadal timescales over the Indian Ocean. The variations are not spatially uniform, and can deviate considerably from the global mean sea level rise (SLR) due to various geophysical processes. One of these processes is the change of ocean circulation, which can be partly attributed to natural internal modes of climate variability. Over the Indian Ocean, the most influential climate modes on decadal and multi-decadal timescales are the Interdecadal Pacific Oscillation (IPO) and decadal variability of the Indian Ocean dipole (IOD). Here, we first analyze observational datasets to investigate the impacts of IPO and IOD on spatial patterns of decadal and interdecadal (hereafter decal) sea level variability & multi-decadal trend over the Indian Ocean since the 1950s, using a new statistical approach of Bayesian Dynamical Linear regression Model (DLM). The Bayesian DLM overcomes the limitation of "time-constant (static)" regression coefficients in conventional multiple linear regression model, by allowing the coefficients to vary with time and therefore measuring "time-evolving (dynamical)" relationship between climate modes and sea level. For the multi-decadal sea level trend since the 1950s, our results show that climate modes and non-climate modes (the part that cannot be explained by climate modes) have comparable contributions in magnitudes but with different spatial patterns, with each dominating different regions of the Indian Ocean. For decadal variability, climate modes are the major contributors for sea level variations over most region of the tropical Indian Ocean. The relative importance of IPO and decadal variability of IOD, however, varies spatially. For example, while IOD decadal variability dominates IPO in the eastern equatorial basin (85E-100E, 5S-5N), IPO dominates IOD in causing sea level variations in the tropical southwest Indian Ocean (45E-65E, 12S-2S). To help decipher the possible contribution of external

Identification and absolute quantification of enzymes in laundry detergents by liquid chromatography tandem mass spectrometry.

PubMed

Gaubert, Alexandra; Jeudy, Jérémy; Rougemont, Blandine; Bordes, Claire; Lemoine, Jérôme; Casabianca, Hervé; Salvador, Arnaud

2016-07-01

In a stricter legislative context, greener detergent formulations are developed. In this way, synthetic surfactants are frequently replaced by bio-sourced surfactants and/or used at lower concentrations in combination with enzymes. In this paper, a LC-MS/MS method was developed for the identification and quantification of enzymes in laundry detergents. Prior to the LC-MS/MS analyses, a specific sample preparation protocol was developed due to matrix complexity (high surfactant percentages). Then for each enzyme family mainly used in detergent formulations (protease, amylase, cellulase, and lipase), specific peptides were identified on a high resolution platform. A LC-MS/MS method was then developed in selected reaction monitoring (SRM) MS mode for the light and corresponding heavy peptides. The method was linear on the peptide concentration ranges 25-1000 ng/mL for protease, lipase, and cellulase; 50-1000 ng/mL for amylase; and 5-1000 ng/mL for cellulase in both water and laundry detergent matrices. The application of the developed analytical strategy to real commercial laundry detergents enabled enzyme identification and absolute quantification. For the first time, identification and absolute quantification of enzymes in laundry detergent was realized by LC-MS/MS in a single run. Graphical Abstract Identification and quantification of enzymes by LC-MS/MS.

Application of synchrotron radiation computed microtomography for quantification of bone microstructure in human and rat bones

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

Parreiras Nogueira, Liebert; Barroso, Regina Cely; Pereira de Almeida, Andre

2012-05-17

This work aims to evaluate histomorphometric quantification by synchrotron radiation computed microto-mography in bones of human and rat specimens. Bones specimens are classified as normal and pathological (for human samples) and irradiated and non-irradiated samples (for rat ones). Human bones are specimens which were affected by some injury, or not. Rat bones are specimens which were irradiated, simulating radiotherapy procedures, or not. Images were obtained on SYRMEP beamline at the Elettra Synchrotron Laboratory in Trieste, Italy. The system generated 14 {mu}m tomographic images. The quantification of bone structures were performed directly by the 3D rendered images using a home-made software.more » Resolution yielded was excellent what facilitate quantification of bone microstructures.« less

Tropospheric biennial oscillation and south Asian summer monsoon rainfall in a coupled model

NASA Astrophysics Data System (ADS)

Konda, Gopinadh; Chowdary, J. S.; Srinivas, G.; Gnanaseelan, C.; Parekh, Anant; Attada, Raju; Rama Krishna, S. S. V. S.

2018-06-01

In this study Tropospheric Biennial Oscillation (TBO) and south Asian summer monsoon rainfall are examined in the National Centers for Environmental Prediction (NCEP) Climate Forecast System (CFSv2) hindcast. High correlation between the observations and model TBO index suggests that the model is able to capture most of the TBO years. Spatial patterns of rainfall anomalies associated with positive TBO over the south Asian region are better represented in the model as in the observations. However, the model predicted rainfall anomaly patterns associated with negative TBO years are improper and magnitudes are underestimated compared to the observations. It is noted that positive (negative) TBO is associated with La Niña (El Niño) like Sea surface temperature (SST) anomalies in the model. This leads to the fact that model TBO is El Niño-Southern Oscillation (ENSO) driven, while in the observations Indian Ocean Dipole (IOD) also plays a role in the negative TBO phase. Detailed analysis suggests that the negative TBO rainfall anomaly pattern in the model is highly influenced by improper teleconnections allied to IOD. Unlike in the observations, rainfall anomalies over the south Asian region are anti-correlated with IOD index in CFSv2. Further, summer monsoon rainfall over south Asian region is highly correlated with IOD western pole than eastern pole in CFSv2 in contrast to the observations. Altogether, the present study highlights the importance of improving Indian Ocean SST teleconnections to south Asian summer rainfall in the model by enhancing the predictability of TBO. This in turn would improve monsoon rainfall prediction skill of the model.

Decoding the drivers of bank erosion on the Mekong river: The roles of the Asian monsoon, tropical storms, and snowmelt.

PubMed

Darby, Stephen E; Leyland, Julian; Kummu, Matti; Räsänen, Timo A; Lauri, Hannu

2013-04-01

We evaluate links between climate and simulated river bank erosion for one of the world's largest rivers, the Mekong. We employ a process-based model to reconstruct multidecadal time series of bank erosion at study sites within the Mekong's two main hydrological response zones, defining a new parameter, accumulated excess runoff (AER), pertinent to bank erosion. We employ a hydrological model to isolate how snowmelt, tropical storms and monsoon precipitation each contribute to AER and thus modeled bank erosion. Our results show that melt (23.9% at the upstream study site, declining to 11.1% downstream) and tropical cyclones (17.5% and 26.4% at the upstream and downstream sites, respectively) both force significant fractions of bank erosion on the Mekong. We also show (i) small, but significant, declines in AER and hence assumed bank erosion during the 20th century, and; (ii) that significant correlations exist between AER and the Indian Ocean Dipole (IOD) and El Niño Southern Oscillation (ENSO). Of these modes of climate variability, we find that IOD events exert a greater control on simulated bank erosion than ENSO events; but the influences of both ENSO and IOD when averaged over several decades are found to be relatively weak. However, importantly, relationships between ENSO, IOD, and AER and hence inferred river bank erosion are not time invariant. Specifically, we show that there is an intense and prolonged epoch of strong coherence between ENSO and AER from the early 1980s to present, such that in recent decades derived Mekong River bank erosion has been more strongly affected by ENSO.

Decoding the drivers of bank erosion on the Mekong river: The roles of the Asian monsoon, tropical storms, and snowmelt

PubMed Central

Darby, Stephen E; Leyland, Julian; Kummu, Matti; Räsänen, Timo A; Lauri, Hannu

2013-01-01

We evaluate links between climate and simulated river bank erosion for one of the world's largest rivers, the Mekong. We employ a process-based model to reconstruct multidecadal time series of bank erosion at study sites within the Mekong's two main hydrological response zones, defining a new parameter, accumulated excess runoff (AER), pertinent to bank erosion. We employ a hydrological model to isolate how snowmelt, tropical storms and monsoon precipitation each contribute to AER and thus modeled bank erosion. Our results show that melt (23.9% at the upstream study site, declining to 11.1% downstream) and tropical cyclones (17.5% and 26.4% at the upstream and downstream sites, respectively) both force significant fractions of bank erosion on the Mekong. We also show (i) small, but significant, declines in AER and hence assumed bank erosion during the 20th century, and; (ii) that significant correlations exist between AER and the Indian Ocean Dipole (IOD) and El Niño Southern Oscillation (ENSO). Of these modes of climate variability, we find that IOD events exert a greater control on simulated bank erosion than ENSO events; but the influences of both ENSO and IOD when averaged over several decades are found to be relatively weak. However, importantly, relationships between ENSO, IOD, and AER and hence inferred river bank erosion are not time invariant. Specifically, we show that there is an intense and prolonged epoch of strong coherence between ENSO and AER from the early 1980s to present, such that in recent decades derived Mekong River bank erosion has been more strongly affected by ENSO. PMID:23926362

Quantification of the benefits of access management for Kentucky : final report.

DOT National Transportation Integrated Search

2006-07-01

This report describes the benefits quantification performed for the proposed access management plan for Kentucky. This study evaluates the capacity, safety and economic impacts associated with access management programs. The proposed Kentucky access ...

Weakening of the relationship between the Indian Ocean Dipole and the ENSO in recent decades

NASA Astrophysics Data System (ADS)

Choi, Jun-Young; Ham, Yoo-Geun; Kug, Jong-Seong

2016-04-01

This study reports, on the 20th century the relationship between the El Nino Southern Oscillation (ENSO) and the Indian Ocean Dipole (IOD) was weaker then late 1990s. We shows that 15-yr moving correlation between the Nino3.4 index during the December to February (DJF) and IOD index during the September to November (SON) season. At this results we divided previous decades (1979 to 1998) and late decades (1999 to 2014). The correlation coefficient was 0.64 in the previous decades and 0.21 in the late decades. Late decades was suddenly weaker then previous decades. Because, there is a big difference between previous decades and late decades in the ENSO regressed precipitation anomaly spatial distribution during the El Nino developing the MAM season. There was existed positive precipitation anomalies over the off-equatorial western Pacific. It was induced the cross-equatorial southerly flow over the eastern Indian Ocean and maritime continent. It means cross-equatorial southerly flow was key point to understanding ENSO-IOD coupling system. In addition, using the climate models participated in Coupled Model Intercomparison Project phase 5 (CMIP5) supports the observational results.

Normative biometrics for fetal ocular growth using volumetric MRI reconstruction.

PubMed

Velasco-Annis, Clemente; Gholipour, Ali; Afacan, Onur; Prabhu, Sanjay P; Estroff, Judy A; Warfield, Simon K

2015-04-01

To determine normative ranges for fetal ocular biometrics between 19 and 38 weeks gestational age (GA) using volumetric MRI reconstruction. The 3D images of 114 healthy fetuses between 19 and 38 weeks GA were created using super-resolution volume reconstructions from MRI slice acquisitions. These 3D images were semi-automatically segmented to measure fetal orbit volume, binocular distance (BOD), interocular distance (IOD), and ocular diameter (OD). All biometry correlated with GA (Volume, Pearson's correlation coefficient (CC) = 0.9680; BOD, CC = 0.9552; OD, CC = 0.9445; and IOD, CC = 0.8429), and growth curves were plotted against linear and quadratic growth models. Regression analysis showed quadratic models to best fit BOD, IOD, and OD and a linear model to best fit volume. Orbital volume had the greatest correlation with GA, although BOD and OD also showed strong correlation. The normative data found in this study may be helpful for the detection of congenital fetal anomalies with more consistent measurements than are currently available. © 2015 John Wiley & Sons, Ltd. © 2015 John Wiley & Sons, Ltd.

Evolution and impact of the 2016 negative Indian Ocean Dipole

NASA Astrophysics Data System (ADS)

Iskandar, I.; Lestari, D. O.; Utari, P. A.; Supardi; Rozirwan; Khakim, M. Y. N.; Poerwono, P.; Setiabudidaya, D.

2018-03-01

Strong negative Indian Ocean Dipole (IOD) event took place in the tropical Indian Ocean during 2016. Based on the Dipole Mode Index (DMI), the event has shown two peaks: in July and September. It is shown that the second peak was stronger than the first peak. Evolution of the event has started in May, reached its first peak in July, weaken in August, but rebounded and came to its second peak in September. The event was terminated in November. Robust sea surface temperature (SST) dipole patterns were observed during both peaks. In July, the SST anomaly in the eastern (western) pole of the IOD reached +1°C (-1.5°C). Meanwhile, during the second peak of the event, the SST anomaly in the eastern (western) pole of the IOD rose (fall) to nearly +2.5°C (-1°C). As a consequence, strong convective activities were observed over the maritime continent causing heavy rainfall during the peak of the event. On the other hand, there was a significant reduce of the rainfall over the eastern Africa during the peak of the event.

Distribution of Monoclonal Antibody Subgroups and Sequence-Based Types among Legionella pneumophila Serogroup 1 Isolates Derived from Cooling Tower Water, Bathwater, and Soil in Japan

PubMed Central

Kikukawa, Kiyomi; Helbig, Jürgen H.; Kaneko, Satoko; Suzuki-Hashimoto, Atsuko; Furuhata, Katsunori; Chang, Bin; Murai, Miyo; Ichinose, Masayuki; Ohnishi, Makoto; Kura, Fumiaki

2012-01-01

Legionella pneumophila serogroup (SG) 1 is the most frequent cause of legionellosis. This study analyzed environmental isolates of L. pneumophila SG 1 in Japan using monoclonal antibody (MAb) typing and sequence-based typing (SBT). Samples were analyzed from bathwater (BW; n = 50), cooling tower water (CT; n = 50), and soil (SO; n = 35). The distribution of MAb types varied by source, with the most prevalent types being Bellingham (42%), Oxford (72%), and OLDA (51%) in BW, CT, and SO, respectively. The ratios of MAb 3/1 positive isolates were 26, 2, and 14% from BW, CT, and SO, respectively. The environmental isolates from BW, CT, and SO were divided into 34 sequence types (STs; index of discrimination [IOD] = 0.973), 8 STs (IOD = 0.448), and 11 STs (IOD = 0.879), respectively. Genetic variation among CT isolates was smaller than seen in BW and SO. ST1 accounted for 74% of the CT isolates. The only common STs between (i) BW and CT, (ii) BW and SO, and (iii) CT and SO were ST1, ST129, and ST48, respectively, suggesting that each environment constitutes an independent habitat. PMID:22492442

Distribution of monoclonal antibody subgroups and sequence-based types among Legionella pneumophila serogroup 1 isolates derived from cooling tower water, bathwater, and soil in Japan.

PubMed

Amemura-Maekawa, Junko; Kikukawa, Kiyomi; Helbig, Jürgen H; Kaneko, Satoko; Suzuki-Hashimoto, Atsuko; Furuhata, Katsunori; Chang, Bin; Murai, Miyo; Ichinose, Masayuki; Ohnishi, Makoto; Kura, Fumiaki

2012-06-01

Legionella pneumophila serogroup (SG) 1 is the most frequent cause of legionellosis. This study analyzed environmental isolates of L. pneumophila SG 1 in Japan using monoclonal antibody (MAb) typing and sequence-based typing (SBT). Samples were analyzed from bathwater (BW; n = 50), cooling tower water (CT; n = 50), and soil (SO; n = 35). The distribution of MAb types varied by source, with the most prevalent types being Bellingham (42%), Oxford (72%), and OLDA (51%) in BW, CT, and SO, respectively. The ratios of MAb 3/1 positive isolates were 26, 2, and 14% from BW, CT, and SO, respectively. The environmental isolates from BW, CT, and SO were divided into 34 sequence types (STs; index of discrimination [IOD] = 0.973), 8 STs (IOD = 0.448), and 11 STs (IOD = 0.879), respectively. Genetic variation among CT isolates was smaller than seen in BW and SO. ST1 accounted for 74% of the CT isolates. The only common STs between (i) BW and CT, (ii) BW and SO, and (iii) CT and SO were ST1, ST129, and ST48, respectively, suggesting that each environment constitutes an independent habitat.

Targeted Proteomic Quantification on Quadrupole-Orbitrap Mass Spectrometer*

PubMed Central

Gallien, Sebastien; Duriez, Elodie; Crone, Catharina; Kellmann, Markus; Moehring, Thomas; Domon, Bruno

2012-01-01

There is an immediate need for improved methods to systematically and precisely quantify large sets of peptides in complex biological samples. To date protein quantification in biological samples has been routinely performed on triple quadrupole instruments operated in selected reaction monitoring mode (SRM), and two major challenges remain. Firstly, the number of peptides to be included in one survey experiment needs to be increased to routinely reach several hundreds, and secondly, the degree of selectivity should be improved so as to reliably discriminate the targeted analytes from background interferences. High resolution and accurate mass (HR/AM) analysis on the recently developed Q-Exactive mass spectrometer can potentially address these issues. This instrument presents a unique configuration: it is constituted of an orbitrap mass analyzer equipped with a quadrupole mass filter as the front-end for precursor ion mass selection. This configuration enables new quantitative methods based on HR/AM measurements, including targeted analysis in MS mode (single ion monitoring) and in MS/MS mode (parallel reaction monitoring). The ability of the quadrupole to select a restricted m/z range allows one to overcome the dynamic range limitations associated with trapping devices, and the MS/MS mode provides an additional stage of selectivity. When applied to targeted protein quantification in urine samples and benchmarked with the reference SRM technique, the quadrupole-orbitrap instrument exhibits similar or better performance in terms of selectivity, dynamic range, and sensitivity. This high performance is further enhanced by leveraging the multiplexing capability of the instrument to design novel acquisition methods and apply them to large targeted proteomic studies for the first time, as demonstrated on 770 tryptic yeast peptides analyzed in one 60-min experiment. The increased quality of quadrupole-orbitrap data has the potential to improve existing protein

Evaluation of the reliability of maize reference assays for GMO quantification.

PubMed

Papazova, Nina; Zhang, David; Gruden, Kristina; Vojvoda, Jana; Yang, Litao; Buh Gasparic, Meti; Blejec, Andrej; Fouilloux, Stephane; De Loose, Marc; Taverniers, Isabel

2010-03-01

A reliable PCR reference assay for relative genetically modified organism (GMO) quantification must be specific for the target taxon and amplify uniformly along the commercialised varieties within the considered taxon. Different reference assays for maize (Zea mays L.) are used in official methods for GMO quantification. In this study, we evaluated the reliability of eight existing maize reference assays, four of which are used in combination with an event-specific polymerase chain reaction (PCR) assay validated and published by the Community Reference Laboratory (CRL). We analysed the nucleotide sequence variation in the target genomic regions in a broad range of transgenic and conventional varieties and lines: MON 810 varieties cultivated in Spain and conventional varieties from various geographical origins and breeding history. In addition, the reliability of the assays was evaluated based on their PCR amplification performance. A single base pair substitution, corresponding to a single nucleotide polymorphism (SNP) reported in an earlier study, was observed in the forward primer of one of the studied alcohol dehydrogenase 1 (Adh1) (70) assays in a large number of varieties. The SNP presence is consistent with a poor PCR performance observed for this assay along the tested varieties. The obtained data show that the Adh1 (70) assay used in the official CRL NK603 assay is unreliable. Based on our results from both the nucleotide stability study and the PCR performance test, we can conclude that the Adh1 (136) reference assay (T25 and Bt11 assays) as well as the tested high mobility group protein gene assay, which also form parts of CRL methods for quantification, are highly reliable. Despite the observed uniformity in the nucleotide sequence of the invertase gene assay, the PCR performance test reveals that this target sequence might occur in more than one copy. Finally, although currently not forming a part of official quantification methods, zein and SSIIb

Quantification and characterization of Si in Pinus Insignis Dougl by TXRF

NASA Astrophysics Data System (ADS)

Navarro, Henry; Bennun, Leonardo; Marcó, Lué M.

2015-03-01

A simple quantification of silicon is described, in woods such as Pinus Insigne Dougl obtained from the 8th region of Bío-Bío, 37°15″ South-73°19″ West, Chile. The samples were prepared through fractional calcination, and the ashes were directly analyzed by total reflection X-ray fluorescence (TXRF) technique. The analysis of 16 samples that were calcined is presented. The samples were weighed on plastic reflectors in a microbalance with sensitivity of 0.1 µg. Later, the samples were irradiated in a TXRF PICOFOX spectrometer, for 350 and 700 s. To each sample, cobalt was added as an internal standard. Concentrations of silicon over the 1 % in each sample and the self-absorption effect on the quantification were observed, in masses higher than 100 μg.

Quantification of Wine Mixtures with an Electronic Nose and a Human Panel

PubMed Central

Aleixandre, Manuel; Cabellos, Juan M.; Arroyo, Teresa; Horrillo, M. C.

2018-01-01

In this work, an electronic nose and a human panel were used for the quantification of wines formed by binary mixtures of four white grape varieties and two varieties of red wines at different percentages (from 0 to 100% in 10% steps for the electronic nose and from 0 to 100% in 25% steps for the human panel). The wines were prepared using the traditional method with commercial yeasts. Both techniques were able to quantify the mixtures tested, but it is important to note that the technology of the electronic nose is faster, simpler, and more objective than the human panel. In addition, better results of quantification were also obtained using the electronic nose. PMID:29484296

Quantification of Wine Mixtures with an Electronic Nose and a Human Panel.

PubMed

Aleixandre, Manuel; Cabellos, Juan M; Arroyo, Teresa; Horrillo, M C

2018-01-01

In this work, an electronic nose and a human panel were used for the quantification of wines formed by binary mixtures of four white grape varieties and two varieties of red wines at different percentages (from 0 to 100% in 10% steps for the electronic nose and from 0 to 100% in 25% steps for the human panel). The wines were prepared using the traditional method with commercial yeasts. Both techniques were able to quantify the mixtures tested, but it is important to note that the technology of the electronic nose is faster, simpler, and more objective than the human panel. In addition, better results of quantification were also obtained using the electronic nose.

Operational quantification of continuous-variable correlations.

PubMed

Rodó, Carles; Adesso, Gerardo; Sanpera, Anna

2008-03-21

We quantify correlations (quantum and/or classical) between two continuous-variable modes as the maximal number of correlated bits extracted via local quadrature measurements. On Gaussian states, such "bit quadrature correlations" majorize entanglement, reducing to an entanglement monotone for pure states. For non-Gaussian states, such as photonic Bell states, photon-subtracted states, and mixtures of Gaussian states, the bit correlations are shown to be a monotonic function of the negativity. This quantification yields a feasible, operational way to measure non-Gaussian entanglement in current experiments by means of direct homodyne detection, without a complete state tomography.

Uncertainty quantification for PZT bimorph actuators

NASA Astrophysics Data System (ADS)

Bravo, Nikolas; Smith, Ralph C.; Crews, John

2018-03-01

In this paper, we discuss the development of a high fidelity model for a PZT bimorph actuator used for micro-air vehicles, which includes the Robobee. We developed a high-fidelity model for the actuator using the homogenized energy model (HEM) framework, which quantifies the nonlinear, hysteretic, and rate-dependent behavior inherent to PZT in dynamic operating regimes. We then discussed an inverse problem on the model. We included local and global sensitivity analysis of the parameters in the high-fidelity model. Finally, we will discuss the results of Bayesian inference and uncertainty quantification on the HEM.

Recommendations for Improving Identification and Quantification in Non-Targeted, GC-MS-Based Metabolomic Profiling of Human Plasma

PubMed Central

Wang, Hanghang; Muehlbauer, Michael J.; O’Neal, Sara K.; Newgard, Christopher B.; Hauser, Elizabeth R.; Shah, Svati H.

2017-01-01

The field of metabolomics as applied to human disease and health is rapidly expanding. In recent efforts of metabolomics research, greater emphasis has been placed on quality control and method validation. In this study, we report an experience with quality control and a practical application of method validation. Specifically, we sought to identify and modify steps in gas chromatography-mass spectrometry (GC-MS)-based, non-targeted metabolomic profiling of human plasma that could influence metabolite identification and quantification. Our experimental design included two studies: (1) a limiting-dilution study, which investigated the effects of dilution on analyte identification and quantification; and (2) a concentration-specific study, which compared the optimal plasma extract volume established in the first study with the volume used in the current institutional protocol. We confirmed that contaminants, concentration, repeatability and intermediate precision are major factors influencing metabolite identification and quantification. In addition, we established methods for improved metabolite identification and quantification, which were summarized to provide recommendations for experimental design of GC-MS-based non-targeted profiling of human plasma. PMID:28841195

Comparative study between extraction techniques and column separation for the quantification of sinigrin and total isothiocyanates in mustard seed.

PubMed

Cools, Katherine; Terry, Leon A

2012-07-15

Glucosinolates are β-thioglycosides which are found naturally in Cruciferae including the genus Brassica. When enzymatically hydrolysed, glucosinolates yield isothiocyanates and give a pungent taste. Both glucosinolates and isothiocyanates have been linked with anticancer activity as well as antifungal and antibacterial properties and therefore the quantification of these compounds is scientifically important. A wide range of literature exists on glucosinolates, however the extraction and quantification procedures differ greatly resulting in discrepancies between studies. The aim of this study was therefore to compare the most popular extraction procedures to identify the most efficacious method and whether each extraction can also be used for the quantification of total isothiocyanates. Four extraction techniques were compared for the quantification of sinigrin from mustard cv. Centennial (Brassica juncea L.) seed; boiling water, boiling 50% (v/v) aqueous acetonitrile, boiling 100% methanol and 70% (v/v) aqueous methanol at 70 °C. Prior to injection into the HPLC, the extractions which involved solvents (acetonitrile or methanol) were freeze-dried and resuspended in water. To identify whether the same extract could be used to measure total isothiocyanates, a dichloromethane extraction was carried out on the sinigrin extracts. For the quantification of sinigrin alone, boiling 50% (v/v) acetonitrile was found to be the most efficacious extraction solvent of the four tested yielding 15% more sinigrin than the water extraction. However, the removal of the acetonitrile by freeze-drying had a negative impact on the isothiocyanate content. Quantification of both sinigrin and total isothiocyanates was possible when the sinigrin was extracted using boiling water. Two columns were compared for the quantification of sinigrin revealing the Zorbax Eclipse to be the best column using this particular method. Copyright © 2012 Elsevier B.V. All rights reserved.

Aeroelastic Uncertainty Quantification Studies Using the S4T Wind Tunnel Model

NASA Technical Reports Server (NTRS)

Nikbay, Melike; Heeg, Jennifer

2017-01-01

This paper originates from the joint efforts of an aeroelastic study team in the Applied Vehicle Technology Panel from NATO Science and Technology Organization, with the Task Group number AVT-191, titled "Application of Sensitivity Analysis and Uncertainty Quantification to Military Vehicle Design." We present aeroelastic uncertainty quantification studies using the SemiSpan Supersonic Transport wind tunnel model at the NASA Langley Research Center. The aeroelastic study team decided treat both structural and aerodynamic input parameters as uncertain and represent them as samples drawn from statistical distributions, propagating them through aeroelastic analysis frameworks. Uncertainty quantification processes require many function evaluations to asses the impact of variations in numerous parameters on the vehicle characteristics, rapidly increasing the computational time requirement relative to that required to assess a system deterministically. The increased computational time is particularly prohibitive if high-fidelity analyses are employed. As a remedy, the Istanbul Technical University team employed an Euler solver in an aeroelastic analysis framework, and implemented reduced order modeling with Polynomial Chaos Expansion and Proper Orthogonal Decomposition to perform the uncertainty propagation. The NASA team chose to reduce the prohibitive computational time by employing linear solution processes. The NASA team also focused on determining input sample distributions.

Systematic Errors in Peptide and Protein Identification and Quantification by Modified Peptides*

PubMed Central

Bogdanow, Boris; Zauber, Henrik; Selbach, Matthias

2016-01-01

The principle of shotgun proteomics is to use peptide mass spectra in order to identify corresponding sequences in a protein database. The quality of peptide and protein identification and quantification critically depends on the sensitivity and specificity of this assignment process. Many peptides in proteomic samples carry biochemical modifications, and a large fraction of unassigned spectra arise from modified peptides. Spectra derived from modified peptides can erroneously be assigned to wrong amino acid sequences. However, the impact of this problem on proteomic data has not yet been investigated systematically. Here we use combinations of different database searches to show that modified peptides can be responsible for 20–50% of false positive identifications in deep proteomic data sets. These false positive hits are particularly problematic as they have significantly higher scores and higher intensities than other false positive matches. Furthermore, these wrong peptide assignments lead to hundreds of false protein identifications and systematic biases in protein quantification. We devise a “cleaned search” strategy to address this problem and show that this considerably improves the sensitivity and specificity of proteomic data. In summary, we show that modified peptides cause systematic errors in peptide and protein identification and quantification and should therefore be considered to further improve the quality of proteomic data annotation. PMID:27215553

Quantification of plasma exosome is a potential prognostic marker for esophageal squamous cell carcinoma.

PubMed

Matsumoto, Yasunori; Kano, Masayuki; Akutsu, Yasunori; Hanari, Naoyuki; Hoshino, Isamu; Murakami, Kentaro; Usui, Akihiro; Suito, Hiroshi; Takahashi, Masahiko; Otsuka, Ryota; Xin, Hu; Komatsu, Aki; Iida, Keiko; Matsubara, Hisahiro

2016-11-01

Exosomes play important roles in cancer progression. Although its contents (e.g., proteins and microRNAs) have been focused on in cancer research, particularly as potential diagnostic markers, the exosome behavior and methods for exosome quantification remain unclear. In the present study, we analyzed the tumor-derived exosome behavior and assessed the quantification of exosomes in patient plasma as a biomarker for esophageal squamous cell carcinoma (ESCC). A CD63-GFP expressing human ESCC cell line (TE2-CD63-GFP) was made by transfection, and mouse subcutaneous tumor models were established. Fluorescence imaging was performed on tumors and plasma exosomes harvested from mice. GFP-positive small vesicles were confirmed in the plasma obtained from TE2-CD63-GFP tumor-bearing mice. Patient plasma was collected in Chiba University Hospital (n=86). Exosomes were extracted from 100 µl of the plasma and quantified by acetylcholinesterase (AChE) activity. The relationship between exosome quantification and the patient clinical characteristics was assessed. The quantification of exosomes isolated from the patient plasma revealed that esophageal cancer patients (n=66) expressed higher exosome levels than non-malignant patients (n=20) (P=0.0002). Although there was no correlation between the tumor progression and the exosome levels, exosome number was the independent prognostic marker and low levels of exosome predicted a poor prognosis (P=0.03). In conclusion, exosome levels may be useful as an independent prognostic factor for ESCC patients.

Detection and Quantification of Cannabinoids in Extracts of Cannabis sativa Roots Using LC-MS/MS.

PubMed

Gul, Waseem; Gul, Shahbaz W; Chandra, Suman; Lata, Hemant; Ibrahim, Elsayed A; ElSohly, Mahmoud A

2018-03-01

A liquid chromatography-tandem mass spectrometry single-laboratory validation was performed for the detection and quantification of the 10 major cannabinoids of cannabis, namely, (-)- trans -Δ 9 -tetrahydrocannabinol, cannabidiol, cannabigerol, cannabichromene, tetrahydrocannabivarian, cannabinol, (-)- trans -Δ 8 -tetrahydrocannabinol, cannabidiolic acid, cannabigerolic acid, and Δ 9 -tetrahydrocannabinolic acid-A, in the root extract of Cannabis sativa . Acetonitrile : methanol (80 : 20, v/v) was used for extraction; d 3 -cannabidiol and d 3 - tetrahydrocannabinol were used as the internal standards. All 10 cannabinoids showed a good regression relationship with r 2  > 0.99. The validated method is simple, sensitive, and reproducible and is therefore suitable for the detection and quantification of these cannabinoids in extracts of cannabis roots. To our knowledge, this is the first report for the quantification of cannabinoids in cannabis roots. Georg Thieme Verlag KG Stuttgart · New York.

Identification and Quantification Soil Redoximorphic Features by Digital Image Processing

USDA-ARS?s Scientific Manuscript database

Soil redoximorphic features (SRFs) have provided scientists and land managers with insight into relative soil moisture for approximately 60 years. The overall objective of this study was to develop a new method of SRF identification and quantification from soil cores using a digital camera and imag...

Quantification of maltol in Korean ginseng (Panax ginseng) products by high-performance liquid chromatography-diode array detector

PubMed Central

Jeong, Hyun Cheol; Hong, Hee-Do; Kim, Young-Chan; Rhee, Young Kyoung; Choi, Sang Yoon; Kim, Kyung-Tack; Kim, Sung Soo; Lee, Young-Chul; Cho, Chang-Won

2015-01-01

Background: Maltol, as a type of phenolic compounds, is produced by the browning reaction during the high-temperature treatment of ginseng. Thus, maltol can be used as a marker for the quality control of various ginseng products manufactured by high-temperature treatment including red ginseng. For the quantification of maltol in Korean ginseng products, an effective high-performance liquid chromatography-diode array detector (HPLC-DAD) method was developed. Materials and Methods: The HPLC-DAD method for maltol quantification coupled with a liquid-liquid extraction (LLE) method was developed and validated in terms of linearity, precision, and accuracy. An HPLC separation was performed on a C18 column. Results: The LLE methods and HPLC running conditions for maltol quantification were optimized. The calibration curve of the maltol exhibited good linearity (R2 = 1.00). The limit of detection value of maltol was 0.26 μg/mL, and the limit of quantification value was 0.79 μg/mL. The relative standard deviations (RSDs) of the data of the intra- and inter-day experiments were <1.27% and 0.61%, respectively. The results of the recovery test were 101.35–101.75% with an RSD value of 0.21–1.65%. The developed method was applied successfully to quantify the maltol in three ginseng products manufactured by different methods. Conclusion: The results of validation demonstrated that the proposed HPLC-DAD method was useful for the quantification of maltol in various ginseng products. PMID:26246746

Comparative quantification of dietary supplemented neural creatine concentrations with (1)H-MRS peak fitting and basis spectrum methods.

PubMed

Turner, Clare E; Russell, Bruce R; Gant, Nicholas

2015-11-01

Magnetic resonance spectroscopy (MRS) is an analytical procedure that can be used to non-invasively measure the concentration of a range of neural metabolites. Creatine is an important neurometabolite with dietary supplementation offering therapeutic potential for neurological disorders with dysfunctional energetic processes. Neural creatine concentrations can be probed using proton MRS and quantified using a range of software packages based on different analytical methods. This experiment examines the differences in quantification performance of two commonly used analysis packages following a creatine supplementation strategy with potential therapeutic application. Human participants followed a seven day dietary supplementation regime in a placebo-controlled, cross-over design interspersed with a five week wash-out period. Spectroscopy data were acquired the day immediately following supplementation and analyzed with two commonly-used software packages which employ vastly different quantification methods. Results demonstrate that neural creatine concentration was augmented following creatine supplementation when analyzed using the peak fitting method of quantification (105.9%±10.1). In contrast, no change in neural creatine levels were detected with supplementation when analysis was conducted using the basis spectrum method of quantification (102.6%±8.6). Results suggest that software packages that employ the peak fitting procedure for spectral quantification are possibly more sensitive to subtle changes in neural creatine concentrations. The relative simplicity of the spectroscopy sequence and the data analysis procedure suggest that peak fitting procedures may be the most effective means of metabolite quantification when detection of subtle alterations in neural metabolites is necessary. The straightforward technique can be used on a clinical magnetic resonance imaging system. Copyright © 2015 Elsevier Inc. All rights reserved.

Multiple products monitoring as a robust approach for peptide quantification.

PubMed

Baek, Je-Hyun; Kim, Hokeun; Shin, Byunghee; Yu, Myeong-Hee

2009-07-01

Quantification of target peptides and proteins is crucial for biomarker discovery. Approaches such as selected reaction monitoring (SRM) and multiple reaction monitoring (MRM) rely on liquid chromatography and mass spectrometric analysis of defined peptide product ions. These methods are not very widespread because the determination of quantifiable product ion using either SRM or MRM is a very time-consuming process. We developed a novel approach for quantifying target peptides without such an arduous process of ion selection. This method is based on monitoring multiple product ions (multiple products monitoring: MpM) from full-range MS2 spectra of a target precursor. The MpM method uses a scoring system that considers both the absolute intensities of product ions and the similarities between the query MS2 spectrum and the reference MS2 spectrum of the target peptide. Compared with conventional approaches, MpM greatly improves sensitivity and selectivity of peptide quantification using an ion-trap mass spectrometer.

Quantification of cardiolipin by liquid chromatography-electrospray ionization mass spectrometry.

PubMed

Garrett, Teresa A; Kordestani, Reza; Raetz, Christian R H

2007-01-01

Cardiolipin (CL), a tetra-acylated glycerophospholipid composed of two phosphatidyl moieties linked by a bridging glycerol, plays an important role in mitochondrial function in eukaryotic cells. Alterations to the content and acylation state of CL cause mitochondrial dysfunction and may be associated with pathologies such as ischemia, hypothyrodism, aging, and heart failure. The structure of CL is very complex because of microheterogeneity among its four acyl chains. Here we have developed a method for the quantification of CL molecular species by liquid chromatography-electrospray ionization mass spectrometry. We quantify the [M-2H](2-) ion of a CL of a given molecular formula and identify the CLs by their total number of carbons and unsaturations in the acyl chains. This method, developed using mouse macrophage RAW 264.7 tumor cells, is broadly applicable to other cell lines, tissues, bacteria and yeast. Furthermore, this method could be used for the quantification of lyso-CLs and bis-lyso-CLs.

Immobilized Metal Affinity Chromatography Coupled to Multiple Reaction Monitoring Enables Reproducible Quantification of Phospho-signaling*

PubMed Central

Kennedy, Jacob J.; Yan, Ping; Zhao, Lei; Ivey, Richard G.; Voytovich, Uliana J.; Moore, Heather D.; Lin, Chenwei; Pogosova-Agadjanyan, Era L.; Stirewalt, Derek L.; Reding, Kerryn W.; Whiteaker, Jeffrey R.; Paulovich, Amanda G.

2016-01-01

A major goal in cell signaling research is the quantification of phosphorylation pharmacodynamics following perturbations. Traditional methods of studying cellular phospho-signaling measure one analyte at a time with poor standardization, rendering them inadequate for interrogating network biology and contributing to the irreproducibility of preclinical research. In this study, we test the feasibility of circumventing these issues by coupling immobilized metal affinity chromatography (IMAC)-based enrichment of phosphopeptides with targeted, multiple reaction monitoring (MRM) mass spectrometry to achieve precise, specific, standardized, multiplex quantification of phospho-signaling responses. A multiplex immobilized metal affinity chromatography- multiple reaction monitoring assay targeting phospho-analytes responsive to DNA damage was configured, analytically characterized, and deployed to generate phospho-pharmacodynamic curves from primary and immortalized human cells experiencing genotoxic stress. The multiplexed assays demonstrated linear ranges of ≥3 orders of magnitude, median lower limit of quantification of 0.64 fmol on column, median intra-assay variability of 9.3%, median inter-assay variability of 12.7%, and median total CV of 16.0%. The multiplex immobilized metal affinity chromatography- multiple reaction monitoring assay enabled robust quantification of 107 DNA damage-responsive phosphosites from human cells following DNA damage. The assays have been made publicly available as a resource to the community. The approach is generally applicable, enabling wide interrogation of signaling networks. PMID:26621847

Breast density quantification with cone-beam CT: A post-mortem study

PubMed Central

Johnson, Travis; Ding, Huanjun; Le, Huy Q.; Ducote, Justin L.; Molloi, Sabee

2014-01-01

Forty post-mortem breasts were imaged with a flat-panel based cone-beam x-ray CT system at 50 kVp. The feasibility of breast density quantification has been investigated using standard histogram thresholding and an automatic segmentation method based on the fuzzy c-means algorithm (FCM). The breasts were chemically decomposed into water, lipid, and protein immediately after image acquisition was completed. The percent fibroglandular volume (%FGV) from chemical analysis was used as the gold standard for breast density comparison. Both image-based segmentation techniques showed good precision in breast density quantification with high linear coefficients between the right and left breast of each pair. When comparing with the gold standard using %FGV from chemical analysis, Pearson’s r-values were estimated to be 0.983 and 0.968 for the FCM clustering and the histogram thresholding techniques, respectively. The standard error of the estimate (SEE) was also reduced from 3.92% to 2.45% by applying the automatic clustering technique. The results of the postmortem study suggested that breast tissue can be characterized in terms of water, lipid and protein contents with high accuracy by using chemical analysis, which offers a gold standard for breast density studies comparing different techniques. In the investigated image segmentation techniques, the FCM algorithm had high precision and accuracy in breast density quantification. In comparison to conventional histogram thresholding, it was more efficient and reduced inter-observer variation. PMID:24254317

Mixture quantification using PLS in plastic scintillation measurements.

PubMed

Bagán, H; Tarancón, A; Rauret, G; García, J F

2011-06-01

This article reports the capability of plastic scintillation (PS) combined with multivariate calibration (Partial least squares; PLS) to detect and quantify alpha and beta emitters in mixtures. While several attempts have been made with this purpose in mind using liquid scintillation (LS), no attempt was done using PS that has the great advantage of not producing mixed waste after the measurements are performed. Following this objective, ternary mixtures of alpha and beta emitters ((241)Am, (137)Cs and (90)Sr/(90)Y) have been quantified. Procedure optimisation has evaluated the use of the net spectra or the sample spectra, the inclusion of different spectra obtained at different values of the Pulse Shape Analysis parameter and the application of the PLS1 or PLS2 algorithms. The conclusions show that the use of PS+PLS2 applied to the sample spectra, without the use of any pulse shape discrimination, allows quantification of the activities with relative errors less than 10% in most of the cases. This procedure not only allows quantification of mixtures but also reduces measurement time (no blanks are required) and the application of this procedure does not require detectors that include the pulse shape analysis parameter. Copyright © 2011 Elsevier Ltd. All rights reserved.

Targeted Quantification of Isoforms of a Thylakoid-Bound Protein: MRM Method Development.

PubMed

Bru-Martínez, Roque; Martínez-Márquez, Ascensión; Morante-Carriel, Jaime; Sellés-Marchart, Susana; Martínez-Esteso, María José; Pineda-Lucas, José Luis; Luque, Ignacio

2018-01-01

Targeted mass spectrometric methods such as selected/multiple reaction monitoring (SRM/MRM) have found intense application in protein detection and quantification which competes with classical immunoaffinity techniques. It provides a universal procedure to develop a fast, highly specific, sensitive, accurate, and cheap methodology for targeted detection and quantification of proteins based on the direct analysis of their surrogate peptides typically generated by tryptic digestion. This methodology can be advantageously applied in the field of plant proteomics and particularly for non-model species since immunoreagents are scarcely available. Here, we describe the issues to take into consideration in order to develop a MRM method to detect and quantify isoforms of the thylakoid-bound protein polyphenol oxidase from the non-model and database underrepresented species Eriobotrya japonica Lindl.

Uncertainty quantification in nanomechanical measurements using the atomic force microscope

Treesearch

Ryan Wagner; Robert Moon; Jon Pratt; Gordon Shaw; Arvind Raman

2011-01-01

Quantifying uncertainty in measured properties of nanomaterials is a prerequisite for the manufacture of reliable nanoengineered materials and products. Yet, rigorous uncertainty quantification (UQ) is rarely applied for material property measurements with the atomic force microscope (AFM), a widely used instrument that can measure properties at nanometer scale...

Interferences in the direct quantification of bisphenol S in paper by means of thermochemolysis.

PubMed

Becerra, Valentina; Odermatt, Jürgen

2013-02-01

This article analyses the interferences in the quantification of traces of bisphenol S in paper by applying the direct analytical method "analytical pyrolysis gas chromatography mass spectrometry" (Py-GC/MS) in conjunction with on-line derivatisation with tetramethylammonium hydroxide (TMAH). As the analytes are simultaneously analysed with the matrix, the interferences derive from the matrix. The investigated interferences are found in the analysis of paper samples, which include bisphenol S derivative compounds. As the free bisphenol S is the hydrolysis product of the bisphenol S derivative compounds, the detected amount of bisphenol S in the sample may be overestimated. It is found that the formation of free bisphenol S from the bisphenol S derivative compounds is enhanced in the presence of tetramethylammonium hydroxide (TMAH) under pyrolytic conditions. In order to avoid the formation of bisphenol S trimethylsulphonium hydroxide (TMSH) is introduced. Different parameters are optimised in the development of the quantification method with TMSH. The quantification method based on TMSH thermochemolysis has been validated in terms of reproducibility and accuracy. Copyright © 2012 Elsevier B.V. All rights reserved.

Multivariate Analysis for Quantification of Plutonium(IV) in Nitric Acid Based on Absorption Spectra

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

Lines, Amanda M.; Adami, Susan R.; Sinkov, Sergey I.

Development of more effective, reliable, and fast methods for monitoring process streams is a growing opportunity for analytical applications. Many fields can benefit from on-line monitoring, including the nuclear fuel cycle where improved methods for monitoring radioactive materials will facilitate maintenance of proper safeguards and ensure safe and efficient processing of materials. On-line process monitoring with a focus on optical spectroscopy can provide a fast, non-destructive method for monitoring chemical species. However, identification and quantification of species can be hindered by the complexity of the solutions if bands overlap or show condition-dependent spectral features. Plutonium (IV) is one example ofmore » a species which displays significant spectral variation with changing nitric acid concentration. Single variate analysis (i.e. Beer’s Law) is difficult to apply to the quantification of Pu(IV) unless the nitric acid concentration is known and separate calibration curves have been made for all possible acid strengths. Multivariate, or chemometric, analysis is an approach that allows for the accurate quantification of Pu(IV) without a priori knowledge of nitric acid concentration.« less

Convex geometry of quantum resource quantification

NASA Astrophysics Data System (ADS)

Regula, Bartosz

2018-01-01

We introduce a framework unifying the mathematical characterisation of different measures of general quantum resources and allowing for a systematic way to define a variety of faithful quantifiers for any given convex quantum resource theory. The approach allows us to describe many commonly used measures such as matrix norm-based quantifiers, robustness measures, convex roof-based measures, and witness-based quantifiers together in a common formalism based on the convex geometry of the underlying sets of resource-free states. We establish easily verifiable criteria for a measure to possess desirable properties such as faithfulness and strong monotonicity under relevant free operations, and show that many quantifiers obtained in this framework indeed satisfy them for any considered quantum resource. We derive various bounds and relations between the measures, generalising and providing significantly simplified proofs of results found in the resource theories of quantum entanglement and coherence. We also prove that the quantification of resources in this framework simplifies for pure states, allowing us to obtain more easily computable forms of the considered measures, and show that many of them are in fact equal on pure states. Further, we investigate the dual formulation of resource quantifiers, which provide a characterisation of the sets of resource witnesses. We present an explicit application of the results to the resource theories of multi-level coherence, entanglement of Schmidt number k, multipartite entanglement, as well as magic states, providing insight into the quantification of the four resources by establishing novel quantitative relations and introducing new quantifiers, such as a measure of entanglement of Schmidt number k which generalises the convex roof-extended negativity, a measure of k-coherence which generalises the \

The effect of applied transducer force on acoustic radiation force impulse quantification within the left lobe of the liver.

PubMed

Porra, Luke; Swan, Hans; Ho, Chien

2015-08-01

Introduction: Acoustic Radiation Force Impulse (ARFI) Quantification measures shear wave velocities (SWVs) within the liver. It is a reliable method for predicting the severity of liver fibrosis and has the potential to assess fibrosis in any part of the liver, but previous research has found ARFI quantification in the right lobe more accurate than in the left lobe. A lack of standardised applied transducer force when performing ARFI quantification in the left lobe of the liver may account for some of this inaccuracy. The research hypothesis of this present study predicted that an increase in applied transducer force would result in an increase in SWVs measured. Methods: ARFI quantification within the left lobe of the liver was performed within a group of healthy volunteers (n = 28). During each examination, each participant was subjected to ARFI quantification at six different levels of transducer force applied to the epigastric abdominal wall. Results: A repeated measures ANOVA test showed that ARFI quantification was significantly affected by applied transducer force (p = 0.002). Significant pairwise comparisons using Bonferroni correction for multiple comparisons showed that with an increase in applied transducer force, there was a decrease in SWVs. Conclusion: Applied transducer force has a significant effect on SWVs within the left lobe of the liver and it may explain some of the less accurate and less reliable results in previous studies where transducer force was not taken into consideration. Future studies in the left lobe of the liver should take this into account and control for applied transducer force.

Simultaneous quantification of flavonoids and triterpenoids in licorice using HPLC.

PubMed

Wang, Yuan-Chuen; Yang, Yi-Shan

2007-05-01

Numerous bioactive compounds are present in licorice (Glycyrrhizae Radix), including flavonoids and triterpenoids. In this study, a reversed-phase high-performance liquid chromatography (HPLC) method for simultaneous quantification of three flavonoids (liquiritin, liquiritigenin and isoliquiritigenin) and four triterpenoids (glycyrrhizin, 18alpha-glycyrrhetinic acid, 18beta-glycyrrhetinic acid and 18beta-glycyrrhetinic acid methyl ester) from licorice was developed, and further, to quantify these 7 compounds from 20 different licorice samples. Specifically, the reverse-phase HPLC was performed with a gradient mobile phase composed of 25 mM phosphate buffer (pH 2.5)-acetonitrile featuring gradient elution steps as follows: 0 min, 100:0; 10 min, 80:20; 50 min, 70:30; 73 min, 50:50; 110 min, 50:50; 125 min, 20:80; 140 min, 20:80, and peaks were detected at 254 nm. By using our technique, a rather good specificity was obtained regarding to the separation of these seven compounds. The regression coefficient for the linear equations for the seven compounds lay between 0.9978 and 0.9992. The limits of detection and quantification lay in the range of 0.044-0.084 and 0.13-0.25 microg/ml, respectively. The relative recovery rates for the seven compounds lay between 96.63+/-2.43 and 103.55+/-2.77%. Coefficient variation for intra-day and inter-day precisions lay in the range of 0.20-1.84 and 0.28-1.86%, respectively. Based upon our validation results, this analytical technique is a convenient method to simultaneous quantify numerous bioactive compounds derived from licorice, featuring good quantification parameters, accuracy and precision.

Applicability of plasmid calibrant pTC1507 in quantification of TC1507 maize: an interlaboratory study.

PubMed

Meng, Yanan; Liu, Xin; Wang, Shu; Zhang, Dabing; Yang, Litao

2012-01-11

To enforce the labeling regulations of genetically modified organisms (GMOs), the application of DNA plasmids as calibrants is becoming essential for the practical quantification of GMOs. This study reports the construction of plasmid pTC1507 for a quantification assay of genetically modified (GM) maize TC1507 and the collaborative ring trial in international validation of its applicability as a plasmid calibrant. pTC1507 includes one event-specific sequence of TC1507 maize and one unique sequence of maize endogenous gene zSSIIb. A total of eight GMO detection laboratories worldwide were invited to join the validation process, and test results were returned from all eight participants. Statistical analysis of the returned results showed that real-time PCR assays using pTC1507 as calibrant in both GM event-specific and endogenous gene quantifications had high PCR efficiency (ranging from 0.80 to 1.15) and good linearity (ranging from 0.9921 to 0.9998). In a quantification assay of five blind samples, the bias between the test values and true values ranged from 2.6 to 24.9%. All results indicated that the developed pTC1507 plasmid is applicable for the quantitative analysis of TC1507 maize and can be used as a suitable substitute for dried powder certified reference materials (CRMs).

Direct liquid chromatography method for the simultaneous quantification of hydroxytyrosol and tyrosol in red wines.

PubMed

Piñeiro, Zulema; Cantos-Villar, Emma; Palma, Miguel; Puertas, Belen

2011-11-09

A validated HPLC method with fluorescence detection for the simultaneous quantification of hydroxytyrosol and tyrosol in red wines is described. Detection conditions for both compounds were optimized (excitation at 279 and 278 and emission at 631 and 598 nm for hydroxytyrosol and tyrosol, respectively). The validation of the analytical method was based on selectivity, linearity, robustness, detection and quantification limits, repeatability, and recovery. The detection and quantification limits in red wines were set at 0.023 and 0.076 mg L(-1) for hydroxytyrosol and at 0.007 and 0.024 mg L(-1) for tyrosol determination, respectively. Precision values, both within-day and between-day (n = 5), remained below 3% for both compounds. In addition, a fractional factorial experimental design was developed to analyze the influence of six different conditions on analysis. The final optimized HPLC-fluorescence method allowed the analysis of 30 nonpretreated Spanish red wines to evaluate their hydroxytyrosol and tyrosol contents.

A new background subtraction method for Western blot densitometry band quantification through image analysis software.

PubMed

Gallo-Oller, Gabriel; Ordoñez, Raquel; Dotor, Javier

2018-06-01

Since its first description, Western blot has been widely used in molecular labs. It constitutes a multistep method that allows the detection and/or quantification of proteins from simple to complex protein mixtures. Western blot quantification method constitutes a critical step in order to obtain accurate and reproducible results. Due to the technical knowledge required for densitometry analysis together with the resources availability, standard office scanners are often used for the imaging acquisition of developed Western blot films. Furthermore, the use of semi-quantitative software as ImageJ (Java-based image-processing and analysis software) is clearly increasing in different scientific fields. In this work, we describe the use of office scanner coupled with the ImageJ software together with a new image background subtraction method for accurate Western blot quantification. The proposed method represents an affordable, accurate and reproducible approximation that could be used in the presence of limited resources availability. Copyright © 2018 Elsevier B.V. All rights reserved.

Powder X-ray diffraction method for the quantification of cocrystals in the crystallization mixture.

PubMed

Padrela, Luis; de Azevedo, Edmundo Gomes; Velaga, Sitaram P

2012-08-01

The solid state purity of cocrystals critically affects their performance. Thus, it is important to accurately quantify the purity of cocrystals in the final crystallization product. The aim of this study was to develop a powder X-ray diffraction (PXRD) quantification method for investigating the purity of cocrystals. The method developed was employed to study the formation of indomethacin-saccharin (IND-SAC) cocrystals by mechanochemical methods. Pure IND-SAC cocrystals were geometrically mixed with 1:1 w/w mixture of indomethacin/saccharin in various proportions. An accurately measured amount (550 mg) of the mixture was used for the PXRD measurements. The most intense, non-overlapping, characteristic diffraction peak of IND-SAC was used to construct the calibration curve in the range 0-100% (w/w). This calibration model was validated and used to monitor the formation of IND-SAC cocrystals by liquid-assisted grinding (LAG). The IND-SAC cocrystal calibration curve showed excellent linearity (R(2) = 0.9996) over the entire concentration range, displaying limit of detection (LOD) and limit of quantification (LOQ) values of 1.23% (w/w) and 3.74% (w/w), respectively. Validation results showed excellent correlations between actual and predicted concentrations of IND-SAC cocrystals (R(2) = 0.9981). The accuracy and reliability of the PXRD quantification method depend on the methods of sample preparation and handling. The crystallinity of the IND-SAC cocrystals was higher when larger amounts of methanol were used in the LAG method. The PXRD quantification method is suitable and reliable for verifying the purity of cocrystals in the final crystallization product.

Detection and Quantification of Human Fecal Pollution with Real-Time PCR

EPA Science Inventory

ABSTRACT Assessment of health risk and fecal bacteria loads associated with human fecal pollution requires a reliable host-specific genetic marker and a rapid quantification method. We report the development of quantitative PCR assays for enumeration of two recently described ...

A tool for selective inline quantification of co-eluting proteins in chromatography using spectral analysis and partial least squares regression.

PubMed

Brestrich, Nina; Briskot, Till; Osberghaus, Anna; Hubbuch, Jürgen

2014-07-01

Selective quantification of co-eluting proteins in chromatography is usually performed by offline analytics. This is time-consuming and can lead to late detection of irregularities in chromatography processes. To overcome this analytical bottleneck, a methodology for selective protein quantification in multicomponent mixtures by means of spectral data and partial least squares regression was presented in two previous studies. In this paper, a powerful integration of software and chromatography hardware will be introduced that enables the applicability of this methodology for a selective inline quantification of co-eluting proteins in chromatography. A specific setup consisting of a conventional liquid chromatography system, a diode array detector, and a software interface to Matlab® was developed. The established tool for selective inline quantification was successfully applied for a peak deconvolution of a co-eluting ternary protein mixture consisting of lysozyme, ribonuclease A, and cytochrome c on SP Sepharose FF. Compared to common offline analytics based on collected fractions, no loss of information regarding the retention volumes and peak flanks was observed. A comparison between the mass balances of both analytical methods showed, that the inline quantification tool can be applied for a rapid determination of pool yields. Finally, the achieved inline peak deconvolution was successfully applied to make product purity-based real-time pooling decisions. This makes the established tool for selective inline quantification a valuable approach for inline monitoring and control of chromatographic purification steps and just in time reaction on process irregularities. © 2014 Wiley Periodicals, Inc.

MRI-based methods for quantification of the cerebral metabolic rate of oxygen

PubMed Central

Rodgers, Zachary B; Detre, John A

2016-01-01

The brain depends almost entirely on oxidative metabolism to meet its significant energy requirements. As such, the cerebral metabolic rate of oxygen (CMRO2) represents a key measure of brain function. Quantification of CMRO2 has helped elucidate brain functional physiology and holds potential as a clinical tool for evaluating neurological disorders including stroke, brain tumors, Alzheimer’s disease, and obstructive sleep apnea. In recent years, a variety of magnetic resonance imaging (MRI)-based CMRO2 quantification methods have emerged. Unlike positron emission tomography – the current “gold standard” for measurement and mapping of CMRO2 – MRI is non-invasive, relatively inexpensive, and ubiquitously available in modern medical centers. All MRI-based CMRO2 methods are based on modeling the effect of paramagnetic deoxyhemoglobin on the magnetic resonance signal. The various methods can be classified in terms of the MRI contrast mechanism used to quantify CMRO2: T2*, T2′, T2, or magnetic susceptibility. This review article provides an overview of MRI-based CMRO2 quantification techniques. After a brief historical discussion motivating the need for improved CMRO2 methodology, current state-of-the-art MRI-based methods are critically appraised in terms of their respective tradeoffs between spatial resolution, temporal resolution, and robustness, all of critical importance given the spatially heterogeneous and temporally dynamic nature of brain energy requirements. PMID:27089912

miR-MaGiC improves quantification accuracy for small RNA-seq.

PubMed

Russell, Pamela H; Vestal, Brian; Shi, Wen; Rudra, Pratyaydipta D; Dowell, Robin; Radcliffe, Richard; Saba, Laura; Kechris, Katerina

2018-05-15

Many tools have been developed to profile microRNA (miRNA) expression from small RNA-seq data. These tools must contend with several issues: the small size of miRNAs, the small number of unique miRNAs, the fact that similar miRNAs can be transcribed from multiple loci, and the presence of miRNA isoforms known as isomiRs. Methods failing to address these issues can return misleading information. We propose a novel quantification method designed to address these concerns. We present miR-MaGiC, a novel miRNA quantification method, implemented as a cross-platform tool in Java. miR-MaGiC performs stringent mapping to a core region of each miRNA and defines a meaningful set of target miRNA sequences by collapsing the miRNA space to "functional groups". We hypothesize that these two features, mapping stringency and collapsing, provide more optimal quantification to a more meaningful unit (i.e., miRNA family). We test miR-MaGiC and several published methods on 210 small RNA-seq libraries, evaluating each method's ability to accurately reflect global miRNA expression profiles. We define accuracy as total counts close to the total number of input reads originating from miRNAs. We find that miR-MaGiC, which incorporates both stringency and collapsing, provides the most accurate counts.

Quantification of chitinase and thaumatin-like proteins in grape juices and wines.

PubMed

Le Bourse, D; Conreux, A; Villaume, S; Lameiras, P; Nuzillard, J-M; Jeandet, P

2011-09-01

Chitinases and thaumatin-like proteins are important grape proteins as they have a great influence on wine quality. The quantification of these proteins in grape juices and wines, along with their purification, is therefore crucial to study their intrinsic characteristics and the exact role they play in wines. The main isoforms of these two proteins from Chardonnay grape juice were thus purified by liquid chromatography. Two fast protein liquid chromatography (FLPC) steps allowed the fractionation and purification of the juice proteins, using cation exchange and hydrophobic interaction media. A further high-performance liquid chromatography (HPLC) step was used to achieve higher purity levels. Fraction assessment was achieved by mass spectrometry. Fraction purity was determined by HPLC to detect the presence of protein contaminants, and by nuclear magnetic resonance (NMR) spectroscopy to detect the presence of organic contaminants. Once pure fractions of lyophilized chitinase and thaumatin-like protein were obtained, ultra-HPLC (UHPLC) and enzyme-linked immunosorbent assay (ELISA) calibration curves were constructed. The quantification of these proteins in different grape juice and wine samples was thus achieved for the first time with both techniques through comparison with the purified protein calibration curve. UHPLC and ELISA showed very consistent results (less than 16% deviation for both proteins) and either could be considered to provide an accurate and reliable quantification of proteins in the oenology field.

Quantification of mixed chimerism by real time PCR on whole blood-impregnated FTA cards.

PubMed

Pezzoli, N; Silvy, M; Woronko, A; Le Treut, T; Lévy-Mozziconacci, A; Reviron, D; Gabert, J; Picard, C

2007-09-01

This study has investigated quantification of chimerism in sex-mismatched transplantations by quantitative real time PCR (RQ-PCR) using FTA paper for blood sampling. First, we demonstrate that the quantification of DNA from EDTA-blood which has been deposit on FTA card is accurate and reproducible. Secondly, we show that fraction of recipient cells detected by RQ-PCR was concordant between the FTA and salting-out method, reference DNA extraction method. Furthermore, the sensitivity of detection of recipient cells is relatively similar with the two methods. Our results show that this innovative method can be used for MC assessment by RQ-PCR.

Effects of local and regional climatic fluctuations on dengue outbreaks in southern Taiwan.

PubMed

Chuang, Ting-Wu; Chaves, Luis Fernando; Chen, Po-Jiang

2017-01-01

Southern Taiwan has been a hotspot for dengue fever transmission since 1998. During 2014 and 2015, Taiwan experienced unprecedented dengue outbreaks and the causes are poorly understood. This study aims to investigate the influence of regional and local climate conditions on the incidence of dengue fever in Taiwan, as well as to develop a climate-based model for future forecasting. Historical time-series data on dengue outbreaks in southern Taiwan from 1998 to 2015 were investigated. Local climate variables were analyzed using a distributed lag non-linear model (DLNM), and the model of best fit was used to predict dengue incidence between 2013 and 2015. The cross-wavelet coherence approach was used to evaluate the regional El Niño Southern Oscillation (ENSO) and Indian Ocean Dipole (IOD) effects on dengue incidence and local climate variables. The DLNM results highlighted the important non-linear and lag effects of minimum temperature and precipitation. Minimum temperature above 23°C or below 17°C can increase dengue incidence rate with lag effects of 10 to 15 weeks. Moderate to high precipitation can increase dengue incidence rates with a lag of 10 or 20 weeks. The model of best fit successfully predicted dengue transmission between 2013 and 2015. The prediction accuracy ranged from 0.7 to 0.9, depending on the number of weeks ahead of the prediction. ENSO and IOD were associated with nonstationary inter-annual patterns of dengue transmission. IOD had a greater impact on the seasonality of local climate conditions. Our findings suggest that dengue transmission can be affected by regional and local climatic fluctuations in southern Taiwan. The climate-based model developed in this study can provide important information for dengue early warning systems in Taiwan. Local climate conditions might be influenced by ENSO and IOD, to result in unusual dengue outbreaks.

Indian Ocean and Indian summer monsoon: relationships without ENSO in ocean-atmosphere coupled simulations

NASA Astrophysics Data System (ADS)

Crétat, Julien; Terray, Pascal; Masson, Sébastien; Sooraj, K. P.; Roxy, Mathew Koll

2017-08-01

The relationship between the Indian Ocean and the Indian summer monsoon (ISM) and their respective influence over the Indo-Western North Pacific (WNP) region are examined in the absence of El Niño Southern Oscillation (ENSO) in two partially decoupled global experiments. ENSO is removed by nudging the tropical Pacific simulated sea surface temperature (SST) toward SST climatology from either observations or a fully coupled control run. The control reasonably captures the observed relationships between ENSO, ISM and the Indian Ocean Dipole (IOD). Despite weaker amplitude, IODs do exist in the absence of ENSO and are triggered by a boreal spring ocean-atmosphere coupled mode over the South-East Indian Ocean similar to that found in the presence of ENSO. These pure IODs significantly affect the tropical Indian Ocean throughout boreal summer, inducing a significant modulation of both the local Walker and Hadley cells. This meridional circulation is masked in the presence of ENSO. However, these pure IODs do not significantly influence the Indian subcontinent rainfall despite overestimated SST variability in the eastern equatorial Indian Ocean compared to observations. On the other hand, they promote a late summer cross-equatorial quadrupole rainfall pattern linking the tropical Indian Ocean with the WNP, inducing important zonal shifts of the Walker circulation despite the absence of ENSO. Surprisingly, the interannual ISM rainfall variability is barely modified and the Indian Ocean does not force the monsoon circulation when ENSO is removed. On the contrary, the monsoon circulation significantly forces the Arabian Sea and Bay of Bengal SSTs, while its connection with the western tropical Indian Ocean is clearly driven by ENSO in our numerical framework. Convection and diabatic heating associated with above-normal ISM induce a strong response over the WNP, even in the absence of ENSO, favoring moisture convergence over India.

Multiplex quantification of 12 European Union authorized genetically modified maize lines with droplet digital polymerase chain reaction.

PubMed

Dobnik, David; Spilsberg, Bjørn; Bogožalec Košir, Alexandra; Holst-Jensen, Arne; Žel, Jana

2015-08-18

Presence of genetically modified organisms (GMO) in food and feed products is regulated in many countries. The European Union (EU) has implemented a threshold for labeling of products containing more than 0.9% of authorized GMOs per ingredient. As the number of GMOs has increased over time, standard-curve based simplex quantitative polymerase chain reaction (qPCR) analyses are no longer sufficiently cost-effective, despite widespread use of initial PCR based screenings. Newly developed GMO detection methods, also multiplex methods, are mostly focused on screening and detection but not quantification. On the basis of droplet digital PCR (ddPCR) technology, multiplex assays for quantification of all 12 EU authorized GM maize lines (per April first 2015) were developed. Because of high sequence similarity of some of the 12 GM targets, two separate multiplex assays were needed. In both assays (4-plex and 10-plex), the transgenes were labeled with one fluorescence reporter and the endogene with another (GMO concentration = transgene/endogene ratio). It was shown that both multiplex assays produce specific results and that performance parameters such as limit of quantification, repeatability, and trueness comply with international recommendations for GMO quantification methods. Moreover, for samples containing GMOs, the throughput and cost-effectiveness is significantly improved compared to qPCR. Thus, it was concluded that the multiplex ddPCR assays could be applied for routine quantification of 12 EU authorized GM maize lines. In case of new authorizations, the events can easily be added to the existing multiplex assays. The presented principle of quantitative multiplexing can be applied to any other domain.

Quantification of extracellular matrix expansion by CMR in infiltrative heart disease.

PubMed

Mongeon, François-Pierre; Jerosch-Herold, Michael; Coelho-Filho, Otávio Rizzi; Blankstein, Ron; Falk, Rodney H; Kwong, Raymond Y

2012-09-01

The aim of this study was to perform direct quantification of myocardial extracellular volume fraction (ECF) with T1-weighted cardiac magnetic resonance (CMR) imaging in patients suspected to have infiltrative heart disease. Infiltrative heart disease refers to accumulation of abnormal substances within the myocardium. Qualitative assessment of late gadolinium enhancement (LGE) remains the most commonly used method for CMR evaluation of patients suspected with myocardial infiltration. This technique is widely available and can be performed in a reproducible and standardized manner. However, the degree of extracellular matrix expansion due to myocardial infiltration in the intercellular space has, to date, not been amenable to noninvasive quantification with LGE. We performed 3-T CMR in 38 patients (mean age 68 ± 15 years) who were referred for assessment of infiltrative heart disease and also in 9 healthy volunteers as control subjects. The T1 quantification by Look-Locker gradient-echo before and after contrast determined segmental myocardial partition coefficients. The ECF was obtained by referencing the tissue partition coefficient for gadolinium to the plasma volume fraction in blood, derived from serum hematocrit. Cine CMR and LGE imaging in matching locations were also performed. Seventeen patients (45%) had cardiac amyloidosis (CA) (biopsy-confirmed or clinically highly probable), 20 (53%) had a non-amyloid cardiomyopathy, and 1 had lysosomal storage disease. Median global ECF was substantially higher in CA patients (0.49) compared with non-amyloid cardiomyopathy patients (0.33, p < 0.0001) and volunteers (0.24, p = 0.0001). The ECF strongly correlated with visually assessed segmental LGE (r = 0.80, p < 0.0001) and LV mass index (r = 0.69, p < 0.0001), reflecting severity of myocardial infiltration. In patients with CA, ECF was highest in segments with LGE, although it remained elevated in segments without qualitative LGE. The CMR ECF quantification

Uncertainty Quantification in Aeroelasticity

NASA Astrophysics Data System (ADS)

Beran, Philip; Stanford, Bret; Schrock, Christopher

2017-01-01

Physical interactions between a fluid and structure, potentially manifested as self-sustained or divergent oscillations, can be sensitive to many parameters whose values are uncertain. Of interest here are aircraft aeroelastic interactions, which must be accounted for in aircraft certification and design. Deterministic prediction of these aeroelastic behaviors can be difficult owing to physical and computational complexity. New challenges are introduced when physical parameters and elements of the modeling process are uncertain. By viewing aeroelasticity through a nondeterministic prism, where key quantities are assumed stochastic, one may gain insights into how to reduce system uncertainty, increase system robustness, and maintain aeroelastic safety. This article reviews uncertainty quantification in aeroelasticity using traditional analytical techniques not reliant on computational fluid dynamics; compares and contrasts this work with emerging methods based on computational fluid dynamics, which target richer physics; and reviews the state of the art in aeroelastic optimization under uncertainty. Barriers to continued progress, for example, the so-called curse of dimensionality, are discussed.

Simple and Inexpensive Quantification of Ammonia in Whole Blood

PubMed Central

Ayyub, Omar B.; Behrens, Adam M.; Heligman, Brian T.; Natoli, Mary E.; Ayoub, Joseph J.; Cunningham, Gary; Summar, Marshall; Kofinas, Peter

2015-01-01

Quantification of ammonia in whole blood has applications in the diagnosis and management of many hepatic diseases, including cirrhosis and rare urea cycle disorders, amounting to more than 5 million patients in the United States. Current techniques for ammonia measurement suffer from limited range, poor resolution, false positives or large, complex sensor set-ups. Here we demonstrate a technique utilizing inexpensive reagents and simple methods for quantifying ammonia in 100 μl of whole blood. The sensor comprises a modified form of the indophenol reaction, which resists sources of destructive interference in blood, in conjunction with a cation-exchange membrane. The presented sensing scheme is selective against other amine containing molecules such as amino acids and has a shelf life of at least 50 days. Additionally, the resulting system has high sensitivity and allows for the accurate reliable quantification of ammonia in whole human blood samples at a minimum range of 25 to 500 μM, which is clinically for rare hyperammonemic disorders and liver disease. Furthermore, concentrations of 50 and 100 μM ammonia could be reliably discerned with p=0.0001. PMID:25936660

Iron deposition quantification: Applications in the brain and liver.

PubMed

Yan, Fuhua; He, Naying; Lin, Huimin; Li, Ruokun

2018-06-13

Iron has long been implicated in many neurological and other organ diseases. It is known that over and above the normal increases in iron with age, in certain diseases there is an excessive iron accumulation in the brain and liver. MRI is a noninvasive means by which to image the various structures in the brain in three dimensions and quantify iron over the volume of the object of interest. The quantification of iron can provide information about the severity of iron-related diseases as well as quantify changes in iron for patient follow-up and treatment monitoring. This article provides an overview of current MRI-based methods for iron quantification, specifically for the brain and liver, including: signal intensity ratio, R 2 , R2*, R2', phase, susceptibility weighted imaging and quantitative susceptibility mapping (QSM). Although there are numerous approaches to measuring iron, R 2 and R2* are currently preferred methods in imaging the liver and QSM has become the preferred approach for imaging iron in the brain. 5 Technical Efficacy: Stage 5 J. Magn. Reson. Imaging 2018. © 2018 International Society for Magnetic Resonance in Medicine.

Samplers for evaluation and quantification of ultra-low volume space sprays

USDA-ARS?s Scientific Manuscript database

A field study was conducted to investigate the suitability of sampling devices for quantification of spray deposition from ULV space sprays. Five different samplers were included in an experiment conducted in an open grassy field. Samplers included horizontally stretched stationary cotton ribbon at ...

DETECTION AND QUANTIFICATION OF COW FECAL POLLUTION WITH REAL-TIME PCR

EPA Science Inventory

Assessment of health risk and fecal bacteria loads associated with cow fecal pollution requires a reliable host-specific genetic marker and a rapid quantification method. We report the development of quantitative PCR assays for enumeration of two recently described cow-specific g...

MS/MS library facilitated MRM quantification of native peptides prepared by denaturing ultrafiltration

PubMed Central

2012-01-01

Naturally occurring native peptides provide important information about physiological states of an organism and its changes in disease conditions but protocols and methods for assessing their abundance are not well-developed. In this paper, we describe a simple procedure for the quantification of non-tryptic peptides in body fluids. The workflow includes an enrichment step followed by two-dimensional fractionation of native peptides and MS/MS data management facilitating the design and validation of LC- MRM MS assays. The added value of the workflow is demonstrated in the development of a triplex LC-MRM MS assay used for quantification of peptides potentially associated with the progression of liver disease to hepatocellular carcinoma. PMID:22304756

Analysis of laser fluorosensor systems for remote algae detection and quantification

NASA Technical Reports Server (NTRS)

Browell, E. V.

1977-01-01

The development and performance of single- and multiple-wavelength laser fluorosensor systems for use in the remote detection and quantification of algae are discussed. The appropriate equation for the fluorescence power received by a laser fluorosensor system is derived in detail. Experimental development of a single wavelength system and a four wavelength system, which selectively excites the algae contained in the four primary algal color groups, is reviewed, and test results are presented. A comprehensive error analysis is reported which evaluates the uncertainty in the remote determination of the chlorophyll a concentration contained in algae by single- and multiple-wavelength laser fluorosensor systems. Results of the error analysis indicate that the remote quantification of chlorophyll a by a laser fluorosensor system requires optimum excitation wavelength(s), remote measurement of marine attenuation coefficients, and supplemental instrumentation to reduce uncertainties in the algal fluorescence cross sections.

Experimental validation of 2D uncertainty quantification for digital image correlation.

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

Reu, Phillip L.

Because digital image correlation (DIC) has become such an important and standard tool in the toolbox of experimental mechanicists, a complete uncertainty quantification of the method is needed. It should be remembered that each DIC setup and series of images will have a unique uncertainty based on the calibration quality and the image and speckle quality of the analyzed images. Any pretest work done with a calibrated DIC stereo-rig to quantify the errors using known shapes and translations, while useful, do not necessarily reveal the uncertainty of a later test. This is particularly true with high-speed applications where actual testmore » images are often less than ideal. Work has previously been completed on the mathematical underpinnings of DIC uncertainty quantification and is already published, this paper will present corresponding experimental work used to check the validity of the uncertainty equations.« less

Targeted quantification of low ng/mL level proteins in human serum without immunoaffinity depletion

PubMed Central

Shi, Tujin; Sun, Xuefei; Gao, Yuqian; Fillmore, Thomas L.; Schepmoes, Athena A.; Zhao, Rui; He, Jintang; Moore, Ronald J.; Kagan, Jacob; Rodland, Karin D.; Liu, Tao; Liu, Alvin Y.; Smith, Richard D.; Tang, Keqi; Camp, David G.; Qian, Wei-Jun

2013-01-01

We recently reported an antibody-free targeted protein quantification strategy, termed high-pressure, high-resolution separations with intelligent selection and multiplexing (PRISM) for achieving significantly enhanced sensitivity using selected reaction monitoring (SRM) mass spectrometry. Integrating PRISM with front-end IgY14 immunoaffinity depletion, sensitive detection of targeted proteins at 50–100 pg/mL levels in human blood plasma/serum was demonstrated. However, immunoaffinity depletion is often associated with undesired losses of target proteins of interest. Herein we report further evaluation of PRISM-SRM quantification of low-abundance serum proteins without immunoaffinity depletion. Limits of quantification (LOQ) at low ng/mL levels with a median coefficient of variation (CV) of ~12% were achieved for proteins spiked into human female serum. PRISM-SRM provided >100-fold improvement in the LOQ when compared to conventional LC-SRM measurements. PRISM-SRM was then applied to measure several low-abundance endogenous serum proteins, including prostate-specific antigen (PSA), in clinical prostate cancer patient sera. PRISM-SRM enabled confident detection of all target endogenous serum proteins except the low pg/mL-level cardiac troponin T. A correlation coefficient >0.99 was observed for PSA between the results from PRISM-SRM and immunoassays. Our results demonstrate that PRISM-SRM can successful quantify low ng/mL proteins in human plasma or serum without depletion. We anticipate broad applications for PRISM-SRM quantification of low-abundance proteins in candidate biomarker verification and systems biology studies. PMID:23763644

Exploiting multicompartment effects in triple-echo steady-state T2 mapping for fat fraction quantification.

PubMed

Liu, Dian; Steingoetter, Andreas; Curcic, Jelena; Kozerke, Sebastian

2018-01-01

To investigate and exploit the effect of intravoxel off-resonance compartments in the triple-echo steady-state (TESS) sequence without fat suppression for T 2 mapping and to leverage the results for fat fraction quantification. In multicompartment tissue, where at least one compartment is excited off-resonance, the total signal exhibits periodic modulations as a function of echo time (TE). Simulated multicompartment TESS signals were synthesized at various TEs. Fat emulsion phantoms were prepared and scanned at the same TE combinations using TESS. In vivo knee data were obtained with TESS to validate the simulations. The multicompartment effect was exploited for fat fraction quantification in the stomach by acquiring TESS signals at two TE combinations. Simulated and measured multicompartment signal intensities were in good agreement. Multicompartment effects caused erroneous T 2 offsets, even at low water-fat ratios. The choice of TE caused T 2 variations of as much as 28% in cartilage. The feasibility of fat fraction quantification to monitor the decrease of fat content in the stomach during digestion is demonstrated. Intravoxel off-resonance compartments are a confounding factor for T 2 quantification using TESS, causing errors that are dependent on the TE. At the same time, off-resonance effects may allow for efficient fat fraction mapping using steady-state imaging. Magn Reson Med 79:423-429, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Fast microwave-assisted extraction of rotenone for its quantification in seeds of yam bean (Pachyrhizus sp.).

PubMed

Lautié, Emmanuelle; Rasse, Catherine; Rozet, Eric; Mourgues, Claire; Vanhelleputte, Jean-Paul; Quetin-Leclercq, Joëlle

2013-02-01

The aim of this study was to find if fast microwave-assisted extraction could be an alternative to the conventional Soxhlet extraction for the quantification of rotenone in yam bean seeds by SPE and HPLC-UV. For this purpose, an experimental design was used to determine the optimal conditions of the microwave extraction. Then the values of the quantification on three accessions from two different species of yam bean seeds were compared using the two different kinds of extraction. A microwave extraction of 11 min at 55°C using methanol/dichloromethane (50:50) allowed rotenone extraction either equivalently or more efficiently than the 8-h-Soxhlet extraction method and was less sensitive to moisture content. The selectivity, precision, trueness, accuracy, and limit of quantification of the method with microwave extraction were also demonstrated. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Contrast-enhanced ultrasonography for the detection of joint vascularity in arthritis--subjective grading versus computer-aided objective quantification.

PubMed

Klauser, A S; Franz, M; Bellmann Weiler, R; Gruber, J; Hartig, F; Mur, E; Wick, M C; Jaschke, W

2011-12-01

To compare joint inflammation assessment using subjective grading of power Doppler ultrasonography (PDUS) and contrast-enhanced ultrasonography (CEUS) versus computer-aided objective CEUS quantification. 37 joints of 28 patients with arthritis of different etiologies underwent B-mode ultrasonography, PDUS, and CEUS using a second-generation contrast agent. Synovial thickness, extent of vascularized pannus and intensity of vascularization were included in a 4-point PDUS and CEUS grading system. Subjective CEUS and PDUS scores were compared to computer-aided objective CEUS quantification using Qontrast® software for the calculation of the signal intensity (SI) and the ratio of SI for contrast enhancement. The interobserver agreement for subjective scoring was good to excellent (κ = 0.8 - 1.0; P < 0.0001). Computer-aided objective CEUS quantification correlated statistically significantly with subjective CEUS (P < 0.001) and PDUS grading (P < 0.05). The Qontrast® SI ratio correlated with subjective CEUS (P < 0.02) and PDUS grading (P < 0.03). Clinical activity did not correlate with vascularity or synovial thickening (P = N. S.) and no correlation between synovial thickening and vascularity extent could be found, neither using PDUS nor CEUS (P = N. S.). Both subjective CEUS grading and objective CEUS quantification are valuable for assessing joint vascularity in arthritis and computer-aided CEUS quantification may be a suitable objective tool for therapy follow-up in arthritis. © Georg Thieme Verlag KG Stuttgart · New York.

Large differences in land use emission quantifications implied by definition discrepancies

NASA Astrophysics Data System (ADS)

Stocker, B. D.; Joos, F.

2015-03-01

The quantification of CO2 emissions from anthropogenic land use and land use change (eLUC) is essential to understand the drivers of the atmospheric CO2 increase and to inform climate change mitigation policy. Reported values in synthesis reports are commonly derived from different approaches (observation-driven bookkeeping and process-modelling) but recent work has emphasized that inconsistencies between methods may imply substantial differences in eLUC estimates. However, a consistent quantification is lacking and no concise modelling protocol for the separation of primary and secondary components of eLUC has been established. Here, we review the conceptual differences of eLUC quantification methods and apply an Earth System Model to demonstrate that what is claimed to represent total eLUC differs by up to ~20% when quantified from ESM vs. offline vegetation models. Under a future business-as-usual scenario, differences tend to increase further due to slowing land conversion rates and an increasing impact of altered environmental conditions on land-atmosphere fluxes. We establish how coupled Earth System Models may be applied to separate component fluxes of eLUC arising from the replacement of potential C sinks/sources and the land use feedback and show that secondary fluxes derived from offline vegetation models are conceptually and quantitatively not identical to either, nor their sum. Therefore, we argue that synthesis studies and global carbon budget accountings should resort to the "least common denominator" of different methods, following the bookkeeping approach where only primary land use emissions are quantified under the assumption of constant environmental boundary conditions.

Person-generated Data in Self-quantification. A Health Informatics Research Program.

PubMed

Gray, Kathleen; Martin-Sanchez, Fernando J; Lopez-Campos, Guillermo H; Almalki, Manal; Merolli, Mark

2017-01-09

The availability of internet-connected mobile, wearable and ambient consumer technologies, direct-to-consumer e-services and peer-to-peer social media sites far outstrips evidence about the efficiency, effectiveness and efficacy of using them in healthcare applications. The aim of this paper is to describe one approach to build a program of health informatics research, so as to generate rich and robust evidence about health data and information processing in self-quantification and associated healthcare and health outcomes. The paper summarises relevant health informatics research approaches in the literature and presents an example of developing a program of research in the Health and Biomedical Informatics Centre (HaBIC) at the University of Melbourne. The paper describes this program in terms of research infrastructure, conceptual models, research design, research reporting and knowledge sharing. The paper identifies key outcomes from integrative and multiple-angle approaches to investigating the management of information and data generated by use of this Centre's collection of wearable, mobiles and other devices in health self-monitoring experiments. These research results offer lessons for consumers, developers, clinical practitioners and biomedical and health informatics researchers. Health informatics is increasingly called upon to make sense of emerging self-quantification and other digital health phenomena that are well beyond the conventions of healthcare in which the field of informatics originated and consolidated. To make a substantial contribution to optimise the aims, processes and outcomes of health self-quantification needs further work at scale in multi-centre collaborations for this Centre and for health informatics researchers generally.

Direct Quantification of Methane Emissions Across the Supply Chain: Identification of Mitigation Targets

NASA Astrophysics Data System (ADS)

Darzi, M.; Johnson, D.; Heltzel, R.; Clark, N.

2017-12-01

Researchers at West Virginia University's Center for Alternative Fuels, Engines, and Emissions have recently participated in a variety of studies targeted at direction quantification of methane emissions from across the natural gas supply chain. These studies included assessing methane emissions from heavy-duty vehicles and their fuel stations, active unconventional well sites - during both development and production, natural gas compression and storage facilities, natural gas engines - both large and small, two- and four-stroke, and low-throughput equipment associated with coal bed methane wells. Engine emissions were sampled using conventional instruments such as Fourier transform infrared spectrometers and heated flame ionization detection analyzers. However, to accurately quantify a wide range of other sources beyond the tailpipe (both leaks and losses), a full flow sampling system was developed, which included an integrated cavity-enhanced absorption spectrometer. Through these direct quantification efforts and analysis major sources of methane emissions were identified. Technological solutions and best practices exist or could be developed to reduce methane emissions by focusing on the "lowest-hanging fruit." For example, engine crankcases from across the supply chain should employ vent mitigation systems to reduce methane and other emissions. An overview of the direct quantification system and various campaign measurements results will be presented along with the identification of other targets for additional mitigation.

Highly sensitive quantification for human plasma-targeted metabolomics using an amine derivatization reagent.

PubMed

Arashida, Naoko; Nishimoto, Rumi; Harada, Masashi; Shimbo, Kazutaka; Yamada, Naoyuki

2017-02-15

Amino acids and their related metabolites play important roles in various physiological processes and have consequently become biomarkers for diseases. However, accurate quantification methods have only been established for major compounds, such as amino acids and a limited number of target metabolites. We previously reported a highly sensitive high-throughput method for the simultaneous quantification of amines using 3-aminopyridyl-N-succinimidyl carbamate as a derivatization reagent combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS). Herein, we report the successful development of a practical and accurate LC-MS/MS method to analyze low concentrations of 40 physiological amines in 19 min. Thirty-five of these amines showed good linearity, limits of quantification, accuracy, precision, and recovery characteristics in plasma, with scheduled selected reaction monitoring acquisitions. Plasma samples from 10 healthy volunteers were evaluated using our newly developed method. The results revealed that 27 amines were detected in one of the samples, and that 24 of these compounds could be quantified. Notably, this new method successfully quantified metabolites with high accuracy across three orders of magnitude, with lowest and highest averaged concentrations of 31.7 nM (for spermine) and 18.3 μM (for α-aminobutyric acid), respectively. Copyright © 2016 Elsevier B.V. All rights reserved.

ICPP: Identification and Quantification of Elementary Plasma Surface Processes during thin Film Growth

NASA Astrophysics Data System (ADS)

Keudell, A. V.

2000-10-01

The quantification of elementary plasma surface processes in glow discharges used for thin film deposition, is mandatory for a complete description of these low temperature plasmas. Since the surface to volume ratio in these discharge systems is often large, all particle densities in the discharge can be strongly influenced by any surface reactions. The identification and quantification of these surface processes will be illustrated for the plasma deposition of amorphous hydrogenated carbon films. A variety of experiments will be discussed ranging from plasma experiments using the cavity technique or ionization threshold mass spectrometry as well as a new class of experiments using quantified radical beams to quantify surface reactions in terms of sticking coefficients directly. It is shown that the reactivity of the hydrocarbon radicals depends strongly on the state of hybridization of the hydrocarbon growth precursor, and that the sticking coefficients for various hydrocarbon radicals are strongly influenced by the simultaneous interaction of several reactive species with the film surface. With the knowledge of these interaction mechanisms and the quantification of the corresponding cross sections, a better understanding of growth processes has become possible, ranging from the deposition of polycrystalline diamond in microwave discharges to the formation of re-deposited layers in fusion experiments.

Ensemble-based uncertainty quantification for coordination and control of thermostatically controlled loads

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

Li, Weixuan; Lian, Jianming; Engel, Dave

2017-07-27

This paper presents a general uncertainty quantification (UQ) framework that provides a systematic analysis of the uncertainty involved in the modeling of a control system, and helps to improve the performance of a control strategy.

Quantification of anti-Leishmania antibodies in saliva of dogs.

PubMed

Cantos-Barreda, Ana; Escribano, Damián; Bernal, Luis J; Cerón, José J; Martínez-Subiela, Silvia

2017-08-15

Detection of serum anti-Leishmania antibodies by quantitative or qualitative techniques has been the most used method to diagnose Canine Leishmaniosis (CanL). Nevertheless, saliva may represent an alternative to blood because it is easy to collect, painless and non-invasive in comparison with serum. In this study, two time-resolved immunofluorometric assays (TR-IFMAs) for quantification of anti-Leishmania IgG2 and IgA antibodies in saliva were developed and validated and their ability to distinguish Leishmania-seronegative from seropositive dogs was evaluated. The analytical study was performed by evaluation of assay precision, sensitivity and accuracy. In addition, serum from 48 dogs (21 Leishmania-seropositive and 27 Leishmania-seronegative) were analyzed by TR-IFMAs. The assays were precise, with an intra- and inter-assay coefficients of variation lower than 11%, and showed high level of accuracy, as determined by linearity under dilution (R 2 =0.99) and recovery tests (>88.60%). Anti-Leishmania IgG2 antibodies in saliva were significantly higher in the seropositive group compared with the seronegative (p<0.0001), whereas no significant differences for anti-Leishmania IgA antibodies between both groups were observed. Furthermore, TR-IFMA for quantification of anti-Leishmania IgG2 antibodies in saliva showed higher differences between seropositive and seronegative dogs than the commercial assay used in serum. In conclusion, TR-IFMAs developed may be used to quantify anti-Leishmania IgG2 and IgA antibodies in canine saliva with an adequate precision, analytical sensitivity and accuracy. Quantification of anti-Leishmania IgG2 antibodies in saliva could be potentially used to evaluate the humoral response in CanL. However, IgA in saliva seemed not to have diagnostic value for this disease. For future studies, it would be desirable to evaluate the ability of the IgG2 assay to detect dogs with subclinical disease or with low antibody titers in serum and also to study

Two-stream Convolutional Neural Network for Methane Emissions Quantification

NASA Astrophysics Data System (ADS)

Wang, J.; Ravikumar, A. P.; McGuire, M.; Bell, C.; Tchapmi, L. P.; Brandt, A. R.

2017-12-01

Methane, a key component of natural gas, has a 25x higher global warming potential than carbon dioxide on a 100-year basis. Accurately monitoring and mitigating methane emissions require cost-effective detection and quantification technologies. Optical gas imaging, one of the most commonly used leak detection technology, adopted by Environmental Protection Agency, cannot estimate leak-sizes. In this work, we harness advances in computer science to allow for rapid and automatic leak quantification. Particularly, we utilize two-stream deep Convolutional Networks (ConvNets) to estimate leak-size by capturing complementary spatial information from still plume frames, and temporal information from plume motion between frames. We build large leak datasets for training and evaluating purposes by collecting about 20 videos (i.e. 397,400 frames) of leaks. The videos were recorded at six distances from the source, covering 10 -60 ft. Leak sources included natural gas well-heads, separators, and tanks. All frames were labeled with a true leak size, which has eight levels ranging from 0 to 140 MCFH. Preliminary analysis shows that two-stream ConvNets provides significant accuracy advantage over single steam ConvNets. Spatial stream ConvNet can achieve an accuracy of 65.2%, by extracting important features, including texture, plume area, and pattern. Temporal stream, fed by the results of optical flow analysis, results in an accuracy of 58.3%. The integration of the two-stream ConvNets gives a combined accuracy of 77.6%. For future work, we will split the training and testing datasets in distinct ways in order to test the generalization of the algorithm for different leak sources. Several analytic metrics, including confusion matrix and visualization of key features, will be used to understand accuracy rates and occurrences of false positives. The quantification algorithm can help to find and fix super-emitters, and improve the cost-effectiveness of leak detection and repair

Quantification of Histidine-Rich Protein 3 of Plasmodium falciparum.

PubMed

Palani, Balraj

2018-04-01

Malaria is a life-threatening infectious disease and continues to be a major public health crisis in many parts of the tropical world. Plasmodium falciparum is responsible for the majority of mortality and morbidity associated with malaria. During the intraerythrocytic cycle, P. falciparum releases three proteins with high histidine content as follows: histidine-rich protein 1 (HRP1), histidine-rich protein 2 (HRP2), and histidine-rich protein 3 (HRP3). Currently, most of the diagnostic tests of P. falciparum infection target HRP2, and a number of monoclonal antibodies (mAbs) against HRP2 have been developed for use in HRP2 detection and quantification. When parasites have HRP2 deletions, the detection of HRP3 could augment the sensitivity of the detection system. The combination of both HRP2 and HRP3 mAbs in the detection system will enhance the test sensitivity. In the HRP quantitative enzyme-linked immunosorbent assay (ELISA), both HRP2 and HRP3 contribute to the result, but the relative contribution of HRP2 and HRP3 was unable to investigate, because of the nonavailability of HRP3 specific antibody ELISA. Hence an ELISA test system based on HRP3 is also essential for detection and quantification. There is not much documented in the literature on HRP3 antigen and HRP3 specific mAbs and polyclonal antibodies (pAbs). In the present study, recombinant HRP3 was expressed in Escherichia coli and purified with Ni-NTA agarose column. The purified rHRP3 was used for the generation and characterization of monoclonal and pAbs. The purification of monoclonal and pAbs was done using a mixed-mode chromatography sorbent, phenylpropylamine HyperCel™. With the purified antibodies, a sandwich ELISA was developed. The sandwich ELISA method was explored to detect and quantify HRP3 of P. falciparum in the spent medium. The generated mAbs could be potentially used for the detection and quantification of P. falciparum HRP3.

Intramyocellular lipid quantification: repeatability with 1H MR spectroscopy.

PubMed

Torriani, Martin; Thomas, Bijoy J; Halpern, Elkan F; Jensen, Megan E; Rosenthal, Daniel I; Palmer, William E

2005-08-01

To prospectively determine the repeatability and variability of tibialis anterior intramyocellular lipid (IMCL) quantifications performed by using 1.5-T hydrogen 1 (1H) magnetic resonance (MR) spectroscopy in healthy subjects. Institutional review board approval and written informed consent were obtained for this Health Insurance Portability and Accountability Act-compliant study. The authors examined the anterior tibial muscles of 27 healthy subjects aged 19-48 years (12 men, 15 women; mean age, 25 years) by using single-voxel short-echo-time point-resolved 1H MR spectroscopy. During a first visit, the subjects underwent 1H MR spectroscopy before and after being repositioned in the magnet bore, with voxels carefully placed on the basis of osseous landmarks. Measurements were repeated after a mean interval of 12 days. All spectra were fitted by using Java-based MR user interface (jMRUI) and LCModel software, and lipid peaks were scaled to the unsuppressed water peak (at 4.7 ppm) and the total creatine peak (at approximately 3.0 ppm). A one-way random-effects variance components model was used to determine intraday and intervisit coefficients of variation (CVs). A power analysis was performed to determine the detectable percentage change in lipid measurements for two subject sample sizes. Measurements of the IMCL methylene protons peak at a resonance of 1.3 ppm scaled to the unsuppressed water peak (IMCL(W)) that were obtained by using jMRUI software yielded the lowest CVs overall (intraday and intervisit CVs, 13.4% and 14.4%, respectively). The random-effects variance components model revealed that nonbiologic factors (equipment and repositioning) accounted for 50% of the total variability in IMCL quantifications. Power analysis for a sample size of 20 subjects revealed that changes in IMCL(W) of greater than 15% could be confidently detected between 1H MR spectroscopic measurements obtained on different days. 1H MR spectroscopy is feasible for repeatable

Final Report: Quantification of Uncertainty in Extreme Scale Computations (QUEST)

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

Marzouk, Youssef; Conrad, Patrick; Bigoni, Daniele

QUEST (\\url{www.quest-scidac.org}) is a SciDAC Institute that is focused on uncertainty quantification (UQ) in large-scale scientific computations. Our goals are to (1) advance the state of the art in UQ mathematics, algorithms, and software; and (2) provide modeling, algorithmic, and general UQ expertise, together with software tools, to other SciDAC projects, thereby enabling and guiding a broad range of UQ activities in their respective contexts. QUEST is a collaboration among six institutions (Sandia National Laboratories, Los Alamos National Laboratory, the University of Southern California, Massachusetts Institute of Technology, the University of Texas at Austin, and Duke University) with a historymore » of joint UQ research. Our vision encompasses all aspects of UQ in leadership-class computing. This includes the well-founded setup of UQ problems; characterization of the input space given available data/information; local and global sensitivity analysis; adaptive dimensionality and order reduction; forward and inverse propagation of uncertainty; handling of application code failures, missing data, and hardware/software fault tolerance; and model inadequacy, comparison, validation, selection, and averaging. The nature of the UQ problem requires the seamless combination of data, models, and information across this landscape in a manner that provides a self-consistent quantification of requisite uncertainties in predictions from computational models. Accordingly, our UQ methods and tools span an interdisciplinary space across applied math, information theory, and statistics. The MIT QUEST effort centers on statistical inference and methods for surrogate or reduced-order modeling. MIT personnel have been responsible for the development of adaptive sampling methods, methods for approximating computationally intensive models, and software for both forward uncertainty propagation and statistical inverse problems. A key software product of the MIT QUEST effort is

Motion-aware stroke volume quantification in 4D PC-MRI data of the human aorta.

PubMed

Köhler, Benjamin; Preim, Uta; Grothoff, Matthias; Gutberlet, Matthias; Fischbach, Katharina; Preim, Bernhard

2016-02-01

4D PC-MRI enables the noninvasive measurement of time-resolved, three-dimensional blood flow data that allow quantification of the hemodynamics. Stroke volumes are essential to assess the cardiac function and evolution of different cardiovascular diseases. The calculation depends on the wall position and vessel orientation, which both change during the cardiac cycle due to the heart muscle contraction and the pumped blood. However, current systems for the quantitative 4D PC-MRI data analysis neglect the dynamic character and instead employ a static 3D vessel approximation. We quantify differences between stroke volumes in the aorta obtained with and without consideration of its dynamics. We describe a method that uses the approximating 3D segmentation to automatically initialize segmentation algorithms that require regions inside and outside the vessel for each temporal position. This enables the use of graph cuts to obtain 4D segmentations, extract vessel surfaces including centerlines for each temporal position and derive motion information. The stroke volume quantification is compared using measuring planes in static (3D) vessels, planes with fixed angulation inside dynamic vessels (this corresponds to the common 2D PC-MRI) and moving planes inside dynamic vessels. Seven datasets with different pathologies such as aneurysms and coarctations were evaluated in close collaboration with radiologists. Compared to the experts' manual stroke volume estimations, motion-aware quantification performs, on average, 1.57% better than calculations without motion consideration. The mean difference between stroke volumes obtained with the different methods is 7.82%. Automatically obtained 4D segmentations overlap by 85.75% with manually generated ones. Incorporating motion information in the stroke volume quantification yields slight but not statistically significant improvements. The presented method is feasible for the clinical routine, since computation times are low and

Targeted quantification of low ng/mL level proteins in human serum without immunoaffinity depletion

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

Shi, Tujin; Sun, Xuefei; Gao, Yuqian

2013-07-05

We recently reported an antibody-free targeted protein quantification strategy, termed high-pressure, high-resolution separations with intelligent selection and multiplexing (PRISM) for achieving significantly enhanced sensitivity using selected reaction monitoring (SRM) mass spectrometry. Integrating PRISM with front-end IgY14 immunoaffinity depletion, sensitive detection of targeted proteins at 50-100 pg/mL levels in human blood plasma/serum was demonstrated. However, immunoaffinity depletion is often associated with undesired losses of target proteins of interest. Herein we report further evaluation of PRISM-SRM quantification of low-abundance serum proteins without immunoaffinity depletion and the multiplexing potential of this technique. Limits of quantification (LOQs) at low ng/mL levels with a medianmore » CV of ~12% were achieved for proteins spiked into human female serum using as little as 2 µL serum. PRISM-SRM provided up to ~1000-fold improvement in the LOQ when compared to conventional SRM measurements. Multiplexing capability of PRISM-SRM was also evaluated by two sets of serum samples with 6 and 21 target peptides spiked at the low attomole/µL levels. The results from SRM measurements for pooled or post-concatenated samples were comparable to those obtained from individual peptide fractions in terms of signal-to-noise ratios and SRM peak area ratios of light to heavy peptides. PRISM-SRM was applied to measure several ng/mL-level endogenous plasma proteins, including prostate-specific antigen, in clinical patient sera where correlation coefficients > 0.99 were observed between the results from PRISM-SRM and ELISA assays. Our results demonstrate that PRISM-SRM can be successfully used for quantification of low-abundance endogenous proteins in highly complex samples. Moderate throughput (50 samples/week) can be achieved by applying the post-concatenation or fraction multiplexing strategies. We anticipate broad applications for targeted PRISM

Ariadne's Thread: A Robust Software Solution Leading to Automated Absolute and Relative Quantification of SRM Data.

PubMed

Nasso, Sara; Goetze, Sandra; Martens, Lennart

2015-09-04

Selected reaction monitoring (SRM) MS is a highly selective and sensitive technique to quantify protein abundances in complex biological samples. To enhance the pace of SRM large studies, a validated, robust method to fully automate absolute quantification and to substitute for interactive evaluation would be valuable. To address this demand, we present Ariadne, a Matlab software. To quantify monitored targets, Ariadne exploits metadata imported from the transition lists, and targets can be filtered according to mProphet output. Signal processing and statistical learning approaches are combined to compute peptide quantifications. To robustly estimate absolute abundances, the external calibration curve method is applied, ensuring linearity over the measured dynamic range. Ariadne was benchmarked against mProphet and Skyline by comparing its quantification performance on three different dilution series, featuring either noisy/smooth traces without background or smooth traces with complex background. Results, evaluated as efficiency, linearity, accuracy, and precision of quantification, showed that Ariadne's performance is independent of data smoothness and complex background presence and that Ariadne outperforms mProphet on the noisier data set and improved 2-fold Skyline's accuracy and precision for the lowest abundant dilution with complex background. Remarkably, Ariadne could statistically distinguish from each other all different abundances, discriminating dilutions as low as 0.1 and 0.2 fmol. These results suggest that Ariadne offers reliable and automated analysis of large-scale SRM differential expression studies.

A universal real-time PCR assay for the quantification of group-M HIV-1 proviral load.

PubMed

Malnati, Mauro S; Scarlatti, Gabriella; Gatto, Francesca; Salvatori, Francesca; Cassina, Giulia; Rutigliano, Teresa; Volpi, Rosy; Lusso, Paolo

2008-01-01

Quantification of human immunodeficiency virus type-1 (HIV-1) proviral DNA is increasingly used to measure the HIV-1 cellular reservoirs, a helpful marker to evaluate the efficacy of antiretroviral therapeutic regimens in HIV-1-infected individuals. Furthermore, the proviral DNA load represents a specific marker for the early diagnosis of perinatal HIV-1 infection and might be predictive of HIV-1 disease progression independently of plasma HIV-1 RNA levels and CD4(+) T-cell counts. The high degree of genetic variability of HIV-1 poses a serious challenge for the design of a universal quantitative assay capable of detecting all the genetic subtypes within the main (M) HIV-1 group with similar efficiency. Here, we describe a highly sensitive real-time PCR protocol that allows for the correct quantification of virtually all group-M HIV-1 strains with a higher degree of accuracy compared with other methods. The protocol involves three stages, namely DNA extraction/lysis, cellular DNA quantification and HIV-1 proviral load assessment. Owing to the robustness of the PCR design, this assay can be performed on crude cellular extracts, and therefore it may be suitable for the routine analysis of clinical samples even in developing countries. An accurate quantification of the HIV-1 proviral load can be achieved within 1 d from blood withdrawal.

Kinetic quantification of plyometric exercise intensity.

PubMed

Ebben, William P; Fauth, McKenzie L; Garceau, Luke R; Petushek, Erich J

2011-12-01

Ebben, WP, Fauth, ML, Garceau, LR, and Petushek, EJ. Kinetic quantification of plyometric exercise intensity. J Strength Cond Res 25(12): 3288-3298, 2011-Quantification of plyometric exercise intensity is necessary to understand the characteristics of these exercises and the proper progression of this mode of exercise. The purpose of this study was to assess the kinetic characteristics of a variety of plyometric exercises. This study also sought to assess gender differences in these variables. Twenty-six men and 23 women with previous experience in performing plyometric training served as subjects. The subjects performed a variety of plyometric exercises including line hops, 15.24-cm cone hops, squat jumps, tuck jumps, countermovement jumps (CMJs), loaded CMJs equal to 30% of 1 repetition maximum squat, depth jumps normalized to the subject's jump height (JH), and single leg jumps. All plyometric exercises were assessed with a force platform. Outcome variables associated with the takeoff, airborne, and landing phase of each plyometric exercise were evaluated. These variables included the peak vertical ground reaction force (GRF) during takeoff, the time to takeoff, flight time, JH, peak power, landing rate of force development, and peak vertical GRF during landing. A 2-way mixed analysis of variance with repeated measures for plyometric exercise type demonstrated main effects for exercise type and all outcome variables (p ≤ 0.05) and for the interaction between gender and peak vertical GRF during takeoff (p ≤ 0.05). Bonferroni-adjusted pairwise comparisons identified a number of differences between the plyometric exercises for the outcome variables assessed (p ≤ 0.05). These findings can be used to guide the progression of plyometric training by incorporating exercises of increasing intensity over the course of a program.

quantGenius: implementation of a decision support system for qPCR-based gene quantification.

PubMed

Baebler, Špela; Svalina, Miha; Petek, Marko; Stare, Katja; Rotter, Ana; Pompe-Novak, Maruša; Gruden, Kristina

2017-05-25

Quantitative molecular biology remains a challenge for researchers due to inconsistent approaches for control of errors in the final results. Due to several factors that can influence the final result, quantitative analysis and interpretation of qPCR data are still not trivial. Together with the development of high-throughput qPCR platforms, there is a need for a tool allowing for robust, reliable and fast nucleic acid quantification. We have developed "quantGenius" ( http://quantgenius.nib.si ), an open-access web application for a reliable qPCR-based quantification of nucleic acids. The quantGenius workflow interactively guides the user through data import, quality control (QC) and calculation steps. The input is machine- and chemistry-independent. Quantification is performed using the standard curve approach, with normalization to one or several reference genes. The special feature of the application is the implementation of user-guided QC-based decision support system, based on qPCR standards, that takes into account pipetting errors, assay amplification efficiencies, limits of detection and quantification of the assays as well as the control of PCR inhibition in individual samples. The intermediate calculations and final results are exportable in a data matrix suitable for further statistical analysis or visualization. We additionally compare the most important features of quantGenius with similar advanced software tools and illustrate the importance of proper QC system in the analysis of qPCR data in two use cases. To our knowledge, quantGenius is the only qPCR data analysis tool that integrates QC-based decision support and will help scientists to obtain reliable results which are the basis for biologically meaningful data interpretation.

StakeMeter: value-based stakeholder identification and quantification framework for value-based software systems.

PubMed

Babar, Muhammad Imran; Ghazali, Masitah; Jawawi, Dayang N A; Bin Zaheer, Kashif

2015-01-01

Value-based requirements engineering plays a vital role in the development of value-based software (VBS). Stakeholders are the key players in the requirements engineering process, and the selection of critical stakeholders for the VBS systems is highly desirable. Based on the stakeholder requirements, the innovative or value-based idea is realized. The quality of the VBS system is associated with the concrete set of valuable requirements, and the valuable requirements can only be obtained if all the relevant valuable stakeholders participate in the requirements elicitation phase. The existing value-based approaches focus on the design of the VBS systems. However, the focus on the valuable stakeholders and requirements is inadequate. The current stakeholder identification and quantification (SIQ) approaches are neither state-of-the-art nor systematic for the VBS systems. The existing approaches are time-consuming, complex and inconsistent which makes the initiation process difficult. Moreover, the main motivation of this research is that the existing SIQ approaches do not provide the low level implementation details for SIQ initiation and stakeholder metrics for quantification. Hence, keeping in view the existing SIQ problems, this research contributes in the form of a new SIQ framework called 'StakeMeter'. The StakeMeter framework is verified and validated through case studies. The proposed framework provides low-level implementation guidelines, attributes, metrics, quantification criteria and application procedure as compared to the other methods. The proposed framework solves the issues of stakeholder quantification or prioritization, higher time consumption, complexity, and process initiation. The framework helps in the selection of highly critical stakeholders for the VBS systems with less judgmental error.

StakeMeter: Value-Based Stakeholder Identification and Quantification Framework for Value-Based Software Systems

PubMed Central

Babar, Muhammad Imran; Ghazali, Masitah; Jawawi, Dayang N. A.; Zaheer, Kashif Bin

2015-01-01

Value-based requirements engineering plays a vital role in the development of value-based software (VBS). Stakeholders are the key players in the requirements engineering process, and the selection of critical stakeholders for the VBS systems is highly desirable. Based on the stakeholder requirements, the innovative or value-based idea is realized. The quality of the VBS system is associated with the concrete set of valuable requirements, and the valuable requirements can only be obtained if all the relevant valuable stakeholders participate in the requirements elicitation phase. The existing value-based approaches focus on the design of the VBS systems. However, the focus on the valuable stakeholders and requirements is inadequate. The current stakeholder identification and quantification (SIQ) approaches are neither state-of-the-art nor systematic for the VBS systems. The existing approaches are time-consuming, complex and inconsistent which makes the initiation process difficult. Moreover, the main motivation of this research is that the existing SIQ approaches do not provide the low level implementation details for SIQ initiation and stakeholder metrics for quantification. Hence, keeping in view the existing SIQ problems, this research contributes in the form of a new SIQ framework called ‘StakeMeter’. The StakeMeter framework is verified and validated through case studies. The proposed framework provides low-level implementation guidelines, attributes, metrics, quantification criteria and application procedure as compared to the other methods. The proposed framework solves the issues of stakeholder quantification or prioritization, higher time consumption, complexity, and process initiation. The framework helps in the selection of highly critical stakeholders for the VBS systems with less judgmental error. PMID:25799490

Automatic Segmentation and Quantification of Filamentous Structures in Electron Tomography

PubMed Central

Loss, Leandro A.; Bebis, George; Chang, Hang; Auer, Manfred; Sarkar, Purbasha; Parvin, Bahram

2016-01-01

Electron tomography is a promising technology for imaging ultrastructures at nanoscale resolutions. However, image and quantitative analyses are often hindered by high levels of noise, staining heterogeneity, and material damage either as a result of the electron beam or sample preparation. We have developed and built a framework that allows for automatic segmentation and quantification of filamentous objects in 3D electron tomography. Our approach consists of three steps: (i) local enhancement of filaments by Hessian filtering; (ii) detection and completion (e.g., gap filling) of filamentous structures through tensor voting; and (iii) delineation of the filamentous networks. Our approach allows for quantification of filamentous networks in terms of their compositional and morphological features. We first validate our approach using a set of specifically designed synthetic data. We then apply our segmentation framework to tomograms of plant cell walls that have undergone different chemical treatments for polysaccharide extraction. The subsequent compositional and morphological analyses of the plant cell walls reveal their organizational characteristics and the effects of the different chemical protocols on specific polysaccharides. PMID:28090597

Automatic Segmentation and Quantification of Filamentous Structures in Electron Tomography.

PubMed

Loss, Leandro A; Bebis, George; Chang, Hang; Auer, Manfred; Sarkar, Purbasha; Parvin, Bahram

2012-10-01

Electron tomography is a promising technology for imaging ultrastructures at nanoscale resolutions. However, image and quantitative analyses are often hindered by high levels of noise, staining heterogeneity, and material damage either as a result of the electron beam or sample preparation. We have developed and built a framework that allows for automatic segmentation and quantification of filamentous objects in 3D electron tomography. Our approach consists of three steps: (i) local enhancement of filaments by Hessian filtering; (ii) detection and completion (e.g., gap filling) of filamentous structures through tensor voting; and (iii) delineation of the filamentous networks. Our approach allows for quantification of filamentous networks in terms of their compositional and morphological features. We first validate our approach using a set of specifically designed synthetic data. We then apply our segmentation framework to tomograms of plant cell walls that have undergone different chemical treatments for polysaccharide extraction. The subsequent compositional and morphological analyses of the plant cell walls reveal their organizational characteristics and the effects of the different chemical protocols on specific polysaccharides.

A Spanish model for quantification and management of construction waste.

PubMed

Solís-Guzmán, Jaime; Marrero, Madelyn; Montes-Delgado, Maria Victoria; Ramírez-de-Arellano, Antonio

2009-09-01

Currently, construction and demolition waste (C&D waste) is a worldwide issue that concerns not only governments but also the building actors involved in construction activity. In Spain, a new national decree has been regulating the production and management of C&D waste since February 2008. The present work describes the waste management model that has inspired this decree: the Alcores model implemented with good results in Los Alcores Community (Seville, Spain). A detailed model is also provided to estimate the volume of waste that is expected to be generated on the building site. The quantification of C&D waste volume, from the project stage, is essential for the building actors to properly plan and control its disposal. This quantification model has been developed by studying 100 dwelling projects, especially their bill of quantities, and defining three coefficients to estimate the demolished volume (CT), the wreckage volume (CR) and the packaging volume (CE). Finally, two case studies are included to illustrate the usefulness of the model to estimate C&D waste volume in both new construction and demolition projects.

Simultaneous quantification of amoxicillin and potassium clavulanate in different commercial drugs using PIXE technique

NASA Astrophysics Data System (ADS)

Bejjani, A.; Roumié, M.; Akkad, S.; El-Yazbi, F.; Nsouli, B.

2016-03-01

We have demonstrated, in previous studies that Particle Induced X-ray Emission (PIXE) is one of the most rapid and accurate choices for quantification of an active ingredient, in a solid drug, from the reactions induced on its specific heteroatom using pellets made from original tablets. In this work, PIXE is used, for the first time, for simultaneous quantification of two active ingredients, amoxicillin trihydrate and potassium clavulanate, in six different commercial antibiotic type of drugs. Since the quality control process of a drug covers a large number of samples, the scope of this study was also to found the most rapid and low cost sample preparation needed to analyze these drugs with a good precision. The chosen drugs were analyzed in their tablets' "as received" form, in pellets made from the powder of the tablets and also in pellets made from the powder of the tablets after being heated up to 70 °C to avoid any molecular destruction until constant weight and removal of humidity. The quantification validity related to the aspects of each sample preparation (homogeneity of the drug components and humidity) are presented and discussed.

Quantification of video-taped images in microcirculation research using inexpensive imaging software (Adobe Photoshop).

PubMed

Brunner, J; Krummenauer, F; Lehr, H A

2000-04-01

Study end-points in microcirculation research are usually video-taped images rather than numeric computer print-outs. Analysis of these video-taped images for the quantification of microcirculatory parameters usually requires computer-based image analysis systems. Most software programs for image analysis are custom-made, expensive, and limited in their applicability to selected parameters and study end-points. We demonstrate herein that an inexpensive, commercially available computer software (Adobe Photoshop), run on a Macintosh G3 computer with inbuilt graphic capture board provides versatile, easy to use tools for the quantification of digitized video images. Using images obtained by intravital fluorescence microscopy from the pre- and postischemic muscle microcirculation in the skinfold chamber model in hamsters, Photoshop allows simple and rapid quantification (i) of microvessel diameters, (ii) of the functional capillary density and (iii) of postischemic leakage of FITC-labeled high molecular weight dextran from postcapillary venules. We present evidence of the technical accuracy of the software tools and of a high degree of interobserver reliability. Inexpensive commercially available imaging programs (i.e., Adobe Photoshop) provide versatile tools for image analysis with a wide range of potential applications in microcirculation research.

Spatially resolved quantification of agrochemicals on plant surfaces using energy dispersive X-ray microanalysis.

PubMed

Hunsche, Mauricio; Noga, Georg

2009-12-01

In the present study the principle of energy dispersive X-ray microanalysis (EDX), i.e. the detection of elements based on their characteristic X-rays, was used to localise and quantify organic and inorganic pesticides on enzymatically isolated fruit cuticles. Pesticides could be discriminated from the plant surface because of their distinctive elemental composition. Findings confirm the close relation between net intensity (NI) and area covered by the active ingredient (AI area). Using wide and narrow concentration ranges of glyphosate and glufosinate, respectively, results showed that quantification of AI requires the selection of appropriate regression equations while considering NI, peak-to-background (P/B) ratio, and AI area. The use of selected internal standards (ISs) such as Ca(NO(3))(2) improved the accuracy of the quantification slightly but led to the formation of particular, non-typical microstructured deposits. The suitability of SEM-EDX as a general technique to quantify pesticides was evaluated additionally on 14 agrochemicals applied at diluted or regular concentration. Among the pesticides tested, spatial localisation and quantification of AI amount could be done for inorganic copper and sulfur as well for the organic agrochemicals glyphosate, glufosinate, bromoxynil and mancozeb. (c) 2009 Society of Chemical Industry.

Adjoint-Based Uncertainty Quantification with MCNP

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

Seifried, Jeffrey E.

2011-09-01

This work serves to quantify the instantaneous uncertainties in neutron transport simulations born from nuclear data and statistical counting uncertainties. Perturbation and adjoint theories are used to derive implicit sensitivity expressions. These expressions are transformed into forms that are convenient for construction with MCNP6, creating the ability to perform adjoint-based uncertainty quantification with MCNP6. These new tools are exercised on the depleted-uranium hybrid LIFE blanket, quantifying its sensitivities and uncertainties to important figures of merit. Overall, these uncertainty estimates are small (< 2%). Having quantified the sensitivities and uncertainties, physical understanding of the system is gained and some confidence inmore » the simulation is acquired.« less

Quantification and characterization of leakage errors

NASA Astrophysics Data System (ADS)

Wood, Christopher J.; Gambetta, Jay M.

2018-03-01

We present a general framework for the quantification and characterization of leakage errors that result when a quantum system is encoded in the subspace of a larger system. To do this we introduce metrics for quantifying the coherent and incoherent properties of the resulting errors and we illustrate this framework with several examples relevant to superconducting qubits. In particular, we propose two quantities, the leakage and seepage rates, which together with average gate fidelity allow for characterizing the average performance of quantum gates in the presence of leakage and show how the randomized benchmarking protocol can be modified to enable the robust estimation of all three quantities for a Clifford gate set.

Quantification of abdominal aortic deformation after EVAR

NASA Astrophysics Data System (ADS)

Demirci, Stefanie; Manstad-Hulaas, Frode; Navab, Nassir

2009-02-01

Quantification of abdominal aortic deformation is an important requirement for the evaluation of endovascular stenting procedures and the further refinement of stent graft design. During endovascular aortic repair (EVAR) treatment, the aortic shape is subject to severe deformation that is imposed by medical instruments such as guide wires, catheters, and, the stent graft. This deformation can affect the flow characteristics and morphology of the aorta which have been shown to be elicitors for stent graft failures and be reason for reappearance of aneurysms. We present a method for quantifying the deformation of an aneurysmatic aorta imposed by an inserted stent graft device. The outline of the procedure includes initial rigid alignment of the two abdominal scans, segmentation of abdominal vessel trees, and automatic reduction of their centerline structures to one specified region of interest around the aorta. This is accomplished by preprocessing and remodeling of the pre- and postoperative aortic shapes before performing a non-rigid registration. We further narrow the resulting displacement fields to only include local non-rigid deformation and therefore, eliminate all remaining global rigid transformations. Finally, deformations for specified locations can be calculated from the resulting displacement fields. In order to evaluate our method, experiments for the extraction of aortic deformation fields are conducted on 15 patient datasets from endovascular aortic repair (EVAR) treatment. A visual assessment of the registration results and evaluation of the usage of deformation quantification were performed by two vascular surgeons and one interventional radiologist who are all experts in EVAR procedures.

Quantification of heterogeneity observed in medical images.

PubMed

Brooks, Frank J; Grigsby, Perry W

2013-03-02

There has been much recent interest in the quantification of visually evident heterogeneity within functional grayscale medical images, such as those obtained via magnetic resonance or positron emission tomography. In the case of images of cancerous tumors, variations in grayscale intensity imply variations in crucial tumor biology. Despite these considerable clinical implications, there is as yet no standardized method for measuring the heterogeneity observed via these imaging modalities. In this work, we motivate and derive a statistical measure of image heterogeneity. This statistic measures the distance-dependent average deviation from the smoothest intensity gradation feasible. We show how this statistic may be used to automatically rank images of in vivo human tumors in order of increasing heterogeneity. We test this method against the current practice of ranking images via expert visual inspection. We find that this statistic provides a means of heterogeneity quantification beyond that given by other statistics traditionally used for the same purpose. We demonstrate the effect of tumor shape upon our ranking method and find the method applicable to a wide variety of clinically relevant tumor images. We find that the automated heterogeneity rankings agree very closely with those performed visually by experts. These results indicate that our automated method may be used reliably to rank, in order of increasing heterogeneity, tumor images whether or not object shape is considered to contribute to that heterogeneity. Automated heterogeneity ranking yields objective results which are more consistent than visual rankings. Reducing variability in image interpretation will enable more researchers to better study potential clinical implications of observed tumor heterogeneity.

Use of a medication quantification scale for comparison of pain medication usage in patients with complex regional pain syndrome (CRPS).

PubMed

Gallizzi, Michael A; Khazai, Ravand S; Gagnon, Christine M; Bruehl, Stephen; Harden, R Norman

2015-03-01

To correlate the amount and types of pain medications prescribed to CRPS patients, using the Medication Quantification Scale, and patients' subjective pain levels. An international, multisite, retrospective review. University medical centers in the United States, Israel, Germany, and the Netherlands. A total of 89 subjects were enrolled from four different countries: 27 from the United States, 20 Germany, 18 Netherlands, and 24 Israel. The main outcome measures used were the Medication Quantification Scale III and numerical analog pain scale. There was no statistically significant correlation noted between the medication quantification scale and the visual analog scale for any site except for a moderate positive correlation at German sites. The medication quantification scale mean differences between the United States and Germany, the Netherlands, and Israel were 9.793 (P < 0.002), 10.389 (P < 0.001), and 4.984 (P = 0.303), respectively. There appears to be only a weak correlation between amount of pain medication prescribed and patients' reported subjective pain intensity within this limited patient population. The Medication Quantification Scale is a viable tool for the analysis of pharmaceutical treatment of CRPS patients and would be useful in further prospective studies of pain medication prescription practices in the CRPS population worldwide. Wiley Periodicals, Inc.

Real-time polymerase chain reaction-based approach for quantification of the pat gene in the T25 Zea mays event.

PubMed

Weighardt, Florian; Barbati, Cristina; Paoletti, Claudia; Querci, Maddalena; Kay, Simon; De Beuckeleer, Marc; Van den Eede, Guy

2004-01-01

In Europe, a growing interest for reliable techniques for the quantification of genetically modified component(s) of food matrixes is arising from the need to comply with the European legislative framework on novel food products. Real-time polymerase chain reaction (PCR) is currently the most powerful technique for the quantification of specific nucleic acid sequences. Several real-time PCR methodologies based on different molecular principles have been developed for this purpose. The most frequently used approach in the field of genetically modified organism (GMO) quantification in food or feed samples is based on the 5'-3'-exonuclease activity of Taq DNA polymerase on specific degradation probes (TaqMan principle). A novel approach was developed for the establishment of a TaqMan quantification system assessing GMO contents around the 1% threshold stipulated under European Union (EU) legislation for the labeling of food products. The Zea mays T25 elite event was chosen as a model for the development of the novel GMO quantification approach. The most innovative aspect of the system is represented by the use of sequences cloned in plasmids as reference standards. In the field of GMO quantification, plasmids are an easy to use, cheap, and reliable alternative to Certified Reference Materials (CRMs), which are only available for a few of the GMOs authorized in Europe, have a relatively high production cost, and require further processing to be suitable for analysis. Strengths and weaknesses of the use of novel plasmid-based standards are addressed in detail. In addition, the quantification system was designed to avoid the use of a reference gene (e.g., a single copy, species-specific gene) as normalizer, i.e., to perform a GMO quantification based on an absolute instead of a relative measurement. In fact, experimental evidences show that the use of reference genes adds variability to the measurement system because a second independent real-time PCR-based measurement

Deep-Dive Targeted Quantification for Ultrasensitive Analysis of Proteins in Nondepleted Human Blood Plasma/Serum and Tissues

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

Nie, Song; Shi, Tujin; Fillmore, Thomas L.

Mass spectrometry-based targeted proteomics (e.g., selected reaction monitoring, SRM) is emerging as an attractive alternative to immunoassays for protein quantification. Recently we have made significant progress in SRM sensitivity for enabling quantification of low ng/mL to sub-ng/mL level proteins in nondepleted human blood plasma/serum without affinity enrichment. However, precise quantification of extremely low abundant but biologically important proteins (e.g., ≤100 pg/mL in blood plasma/serum) using targeted proteomics approaches still remains challenging. To address this need, we have developed an antibody-independent Deep-Dive SRM (DD-SRM) approach that capitalizes on multidimensional high-resolution reversed-phase liquid chromatography (LC) separation for target peptide enrichment combined withmore » precise selection of target peptide fractions of interest, significantly improving SRM sensitivity by ~5 orders of magnitude when compared to conventional LC-SRM. Application of DD-SRM to human serum and tissue has been demonstrated to enable precise quantification of endogenous proteins at ~10 pg/mL level in nondepleted serum and at <10 copies per cell level in tissue. Thus, DD-SRM holds great promise for precisely measuring extremely low abundance proteins or protein modifications, especially when high-quality antibody is not available.« less

Protein Quantification by Elemental Mass Spectrometry: An Experiment for Graduate Students

ERIC Educational Resources Information Center

Schwarz, Gunnar; Ickert, Stefanie; Wegner, Nina; Nehring, Andreas; Beck, Sebastian; Tiemann, Ruediger; Linscheid, Michael W.

2014-01-01

A multiday laboratory experiment was designed to integrate inductively coupled plasma-mass spectrometry (ICP-MS) in the context of protein quantification into an advanced practical course in analytical and environmental chemistry. Graduate students were familiar with the analytical methods employed, whereas the combination of bioanalytical assays…

Interpretation of biological and mechanical variations between the Lowry versus Bradford method for protein quantification.

PubMed

Lu, Tzong-Shi; Yiao, Szu-Yu; Lim, Kenneth; Jensen, Roderick V; Hsiao, Li-Li

2010-07-01

The identification of differences in protein expression resulting from methodical variations is an essential component to the interpretation of true, biologically significant results. We used the Lowry and Bradford methods- two most commonly used methods for protein quantification, to assess whether differential protein expressions are a result of true biological or methodical variations. MATERIAL #ENTITYSTARTX00026; Differential protein expression patterns was assessed by western blot following protein quantification by the Lowry and Bradford methods. We have observed significant variations in protein concentrations following assessment with the Lowry versus Bradford methods, using identical samples. Greater variations in protein concentration readings were observed over time and in samples with higher concentrations, with the Bradford method. Identical samples quantified using both methods yielded significantly different expression patterns on Western blot. We show for the first time that methodical variations observed in these protein assay techniques, can potentially translate into differential protein expression patterns, that can be falsely taken to be biologically significant. Our study therefore highlights the pivotal need to carefully consider methodical approaches to protein quantification in techniques that report quantitative differences.

Quantification of allantoin in various Zea mays L. hybrids by RP-HPLC with UV detection.

PubMed

Maksimović, Z; Malenović, A; Jancić, B; Kovacević, N

2004-07-01

A RP-HPLC method for quantification of allantoin in silk of fifteen maize hybrids (Zea mays L., Poaceae) was described. Following extraction of the plant material with an acetone-water (7:3, VN) mixture, filtration and dilution, the extracts were analyzed without previous chemical derivatization. Separation and quantification were achieved using an Alltech Econosil C18 column under isocratic conditions at 40 degrees C. The mobile phase flow (20% methanol--80% water with 5 mM sodium laurylsulfate added at pH 2.5, adjusted with 85% orthophosphoric acid; pH of water phase was finally adjusted at 6.0 by addition of triethylamine) was maintained at 1.0 mL/min. Column effluent was monitored at 235 nm. This simple procedure afforded efficient separation and quantification of allantoin in plant material, without interference of polyphenols or other plant constituents of medium to high polarity, or similar UV absorption. Our study revealed that the silk of all investigated maize hybrids could be considered relatively rich in allantoin, covering the concentration range between 215 and 289 mg per 100 g of dry plant material.

Simple and rapid quantification of brominated vegetable oil in commercial soft drinks by LC–MS

PubMed Central

Chitranshi, Priyanka; da Costa, Gonçalo Gamboa

2016-01-01

We report here a simple and rapid method for the quantification of brominated vegetable oil (BVO) in soft drinks based upon liquid chromatography–electrospray ionization mass spectrometry. Unlike previously reported methods, this novel method does not require hydrolysis, extraction or derivatization steps, but rather a simple “dilute and shoot” sample preparation. The quantification is conducted by mass spectrometry in selected ion recording mode and a single point standard addition procedure. The method was validated in the range of 5–25 μg/mL BVO, encompassing the legal limit of 15 μg/mL established by the US FDA for fruit-flavored beverages in the US market. The method was characterized by excellent intra- and inter-assay accuracy (97.3–103.4%) and very low imprecision [0.5–3.6% (RSD)]. The direct nature of the quantification, simplicity, and excellent statistical performance of this methodology constitute clear advantages in relation to previously published methods for the analysis of BVO in soft drinks. PMID:27451219

Three-Dimensional Echocardiographic Assessment of Left Heart Chamber Size and Function with Fully Automated Quantification Software in Patients with Atrial Fibrillation.

PubMed

Otani, Kyoko; Nakazono, Akemi; Salgo, Ivan S; Lang, Roberto M; Takeuchi, Masaaki

2016-10-01

Echocardiographic determination of left heart chamber volumetric parameters by using manual tracings during multiple beats is tedious in atrial fibrillation (AF). The aim of this study was to determine the usefulness of fully automated left chamber quantification software with single-beat three-dimensional transthoracic echocardiographic data sets in patients with AF. Single-beat full-volume three-dimensional transthoracic echocardiographic data sets were prospectively acquired during consecutive multiple cardiac beats (≥10 beats) in 88 patients with AF. In protocol 1, left ventricular volumes, left ventricular ejection fraction, and maximal left atrial volume were validated using automated quantification against the manual tracing method in identical beats in 10 patients. In protocol 2, automated quantification-derived averaged values from multiple beats were compared with the corresponding values obtained from the indexed beat in all patients. Excellent correlations of left chamber parameters between automated quantification and the manual method were observed (r = 0.88-0.98) in protocol 1. The time required for the analysis with the automated quantification method (5 min) was significantly less compared with the manual method (27 min) (P < .0001). In protocol 2, there were excellent linear correlations between the averaged left chamber parameters and the corresponding values obtained from the indexed beat (r = 0.94-0.99), and test-retest variability of left chamber parameters was low (3.5%-4.8%). Three-dimensional transthoracic echocardiography with fully automated quantification software is a rapid and reliable way to measure averaged values of left heart chamber parameters during multiple consecutive beats. Thus, it is a potential new approach for left chamber quantification in patients with AF in daily routine practice. Copyright © 2016 American Society of Echocardiography. Published by Elsevier Inc. All rights reserved.

Round robin test on quantification of amyloid-β 1-42 in cerebrospinal fluid by mass spectrometry.

PubMed

Pannee, Josef; Gobom, Johan; Shaw, Leslie M; Korecka, Magdalena; Chambers, Erin E; Lame, Mary; Jenkins, Rand; Mylott, William; Carrillo, Maria C; Zegers, Ingrid; Zetterberg, Henrik; Blennow, Kaj; Portelius, Erik

2016-01-01

Cerebrospinal fluid (CSF) amyloid-β 1-42 (Aβ42) is an important biomarker for Alzheimer's disease, both in diagnostics and to monitor disease-modifying therapies. However, there is a great need for standardization of methods used for quantification. To overcome problems associated with immunoassays, liquid chromatography-tandem mass spectrometry (LC-MS/MS) has emerged as a critical orthogonal alternative. We compared results for CSF Aβ42 quantification in a round robin study performed in four laboratories using similar sample preparation methods and LC-MS instrumentation. The LC-MS results showed excellent correlation between laboratories (r(2) >0.98), high analytical precision, and good correlation with enzyme-linked immunosorbent assay (r(2) >0.85). The use of a common reference sample further decreased interlaboratory variation. Our results indicate that LC-MS is suitable for absolute quantification of Aβ42 in CSF and highlight the importance of developing a certified reference material. Copyright © 2016 The Alzheimer's Association. Published by Elsevier Inc. All rights reserved.

MEERCAT: Multiplexed Efficient Cell Free Expression of Recombinant QconCATs For Large Scale Absolute Proteome Quantification*

PubMed Central

Takemori, Nobuaki; Takemori, Ayako; Tanaka, Yuki; Endo, Yaeta; Hurst, Jane L.; Gómez-Baena, Guadalupe; Harman, Victoria M.; Beynon, Robert J.

2017-01-01

A major challenge in proteomics is the absolute accurate quantification of large numbers of proteins. QconCATs, artificial proteins that are concatenations of multiple standard peptides, are well established as an efficient means to generate standards for proteome quantification. Previously, QconCATs have been expressed in bacteria, but we now describe QconCAT expression in a robust, cell-free system. The new expression approach rescues QconCATs that previously were unable to be expressed in bacteria and can reduce the incidence of proteolytic damage to QconCATs. Moreover, it is possible to cosynthesize QconCATs in a highly-multiplexed translation reaction, coexpressing tens or hundreds of QconCATs simultaneously. By obviating bacterial culture and through the gain of high level multiplexing, it is now possible to generate tens of thousands of standard peptides in a matter of weeks, rendering absolute quantification of a complex proteome highly achievable in a reproducible, broadly deployable system. PMID:29055021

Electrochemical quantification of the antioxidant capacity of medicinal plants using biosensors.

PubMed

Rodríguez-Sevilla, Erika; Ramírez-Silva, María-Teresa; Romero-Romo, Mario; Ibarra-Escutia, Pedro; Palomar-Pardavé, Manuel

2014-08-08

The working area of a screen-printed electrode, SPE, was modified with the enzyme tyrosinase (Tyr) using different immobilization methods, namely entrapment with water-soluble polyvinyl alcohol (PVA), cross-linking using glutaraldehyde (GA), and cross-linking using GA and human serum albumin (HSA); the resulting electrodes were termed SPE/Tyr/PVA, SPE/Tyr/GA and SPE/Tyr/HSA/GA, respectively. These biosensors were characterized by means of amperometry and EIS techniques. From amperometric evaluations, the apparent Michaelis-Menten constant, Km', of each biosensor was evaluated while the respective charge transfer resistance, Rct, was assessed from impedance measurements. It was found that the SPE/Tyr/GA had the smallest Km' (57 ± 7) µM and Rct values. This electrode also displayed both the lowest detection and quantification limits for catechol quantification. Using the SPE/Tyr/GA, the Trolox Equivalent Antioxidant Capacity (TEAC) was determined from infusions prepared with "mirto" (Salvia microphylla), "hHierba dulce" (Lippia dulcis) and "salve real" (Lippia alba), medicinal plants commonly used in Mexico.

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.

Illite polytype quantification using Wildfire© calculated x-ray diffraction patterns

USGS Publications Warehouse

Grathoff, Georg H.; Moore, D.M.

1996-01-01

Illite polytype quantification allows the differentiation of diagenetic and detrital illite components. In Paleozoic shales from the Illinois Basin, we observe 3 polytypes: 1Md, 1M and 2M1. 1Md and 1M are of diagenetic origin and 2M1 is of detrital origin. In this paper, we compare experimental X-ray diffraction (XRD) traces with traces calculated using WILDFIRE© and quantify mixtures of all 3 polytypes, adjusting the effects of preferred orientation and overlapping peaks. The broad intensity (“illite hump”) around the illite 003, which is very common in illite from shales, is caused by the presence of 1Md illite and mixing of illite polytypes and is not an artifact of sample preparation or other impurities in the sample. Illite polytype quantification provides a tool to extrapolate the K/Ar age and chemistry of the detrital and diagenetic end-members by analysis of different size fractions containing different proportions of diagenetic and detrital illite polytypes.

QUANTIFICATION OF NUCLEOLAR CHANNEL SYSTEMS: UNIFORM PRESENCE THROUGHOUT THE UPPER ENDOMETRIAL CAVITY

PubMed Central

Szmyga, Michael J.; Rybak, Eli A.; Nejat, Edward J.; Banks, Erika H.; Whitney, Kathleen D.; Polotsky, Alex J.; Heller, Debra S.; Meier, U. Thomas

2014-01-01

Objective To determine the prevalence of nucleolar channel systems (NCSs) by uterine region applying continuous quantification. Design Prospective clinical study. Setting Tertiary care academic medical center. Patients 42 naturally cycling women who underwent hysterectomy for benign indications. Intervention NCS presence was quantified by a novel method in six uterine regions, fundus, left cornu, right cornu, anterior body, posterior body, and lower uterine segment (LUS), using indirect immunofluorescence. Main Outcome Measures Percent of endometrial epithelial cells (EECs) with NCSs per uterine region. Results NCS quantification was observer-independent (intraclass correlation coefficient [ICC] = 0.96) and its intra-sample variability low (coefficient of variability [CV] = 0.06). 11/42 hysterectomy specimens were midluteal, 10 of which were analyzable with 9 containing over 5% EECs with NCSs in at least one region. The percent of EECs with NCSs varied significantly between the lower uterine segment (6.1%; IQR = 3.0-9.9) and the upper five regions (16.9%; IQR = 12.7-23.4) with fewer NCSs in the basal layer of the endometrium (17% +/−6%) versus the middle (46% +/−9%) and luminal layers (38% +/−9%) of all six regions). Conclusions NCS quantification during the midluteal phase demonstrates uniform presence throughout the endometrial cavity, excluding the LUS, with a preference for the functional, luminal layers. Our quantitative NCS evaluation provides a benchmark for future studies and further supports NCS presence as a potential marker for the window of implantation. PMID:23137760

Quantification of birefringence readily measures the level of muscle damage in zebrafish

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

Berger, Joachim, E-mail: Joachim.Berger@Monash.edu; Sztal, Tamar; Currie, Peter D.

2012-07-13

Highlights: Black-Right-Pointing-Pointer Report of an unbiased quantification of the birefringence of muscle of fish larvae. Black-Right-Pointing-Pointer Quantification method readily identifies level of overall muscle damage. Black-Right-Pointing-Pointer Compare zebrafish muscle mutants for level of phenotype severity. Black-Right-Pointing-Pointer Proposed tool to survey treatments that aim to ameliorate muscular dystrophy. -- Abstract: Muscular dystrophies are a group of genetic disorders that progressively weaken and degenerate muscle. Many zebrafish models for human muscular dystrophies have been generated and analysed, including dystrophin-deficient zebrafish mutants dmd that model Duchenne Muscular Dystrophy. Under polarised light the zebrafish muscle can be detected as a bright area in anmore » otherwise dark background. This light effect, called birefringence, results from the diffraction of polarised light through the pseudo-crystalline array of the muscle sarcomeres. Muscle damage, as seen in zebrafish models for muscular dystrophies, can readily be detected by a reduction in the birefringence. Therefore, birefringence is a very sensitive indicator of overall muscle integrity within larval zebrafish. Unbiased documentation of the birefringence followed by densitometric measurement enables the quantification of the birefringence of zebrafish larvae. Thereby, the overall level of muscle integrity can be detected, allowing the identification and categorisation of zebrafish muscle mutants. In addition, we propose that the establish protocol can be used to analyse treatments aimed at ameliorating dystrophic zebrafish models.« less

The Challenges of Credible Thermal Protection System Reliability Quantification

NASA Technical Reports Server (NTRS)

Green, Lawrence L.

2013-01-01

The paper discusses several of the challenges associated with developing a credible reliability estimate for a human-rated crew capsule thermal protection system. The process of developing such a credible estimate is subject to the quantification, modeling and propagation of numerous uncertainties within a probabilistic analysis. The development of specific investment recommendations, to improve the reliability prediction, among various potential testing and programmatic options is then accomplished through Bayesian analysis.

Group refractive index quantification using a Fourier domain short coherence Sagnac interferometer.

PubMed

Montonen, Risto; Kassamakov, Ivan; Lehmann, Peter; Österberg, Kenneth; Hæggström, Edward

2018-02-15

The group refractive index is important in length calibration of Fourier domain interferometers by transparent transfer standards. We demonstrate accurate group refractive index quantification using a Fourier domain short coherence Sagnac interferometer. Because of a justified linear length calibration function, the calibration constants cancel out in the evaluation of the group refractive index, which is then obtained accurately from two uncalibrated lengths. Measurements of two standard thickness coverslips revealed group indices of 1.5426±0.0042 and 1.5434±0.0046, with accuracies quoted at the 95% confidence level. This agreed with the dispersion data of the coverslip manufacturer and therefore validates our method. Our method provides a sample specific and accurate group refractive index quantification using the same Fourier domain interferometer that is to be calibrated for the length. This reduces significantly the requirements of the calibration transfer standard.

A simple and fast method for extraction and quantification of cryptophyte phycoerythrin.

PubMed

Thoisen, Christina; Hansen, Benni Winding; Nielsen, Søren Laurentius

2017-01-01

The microalgal pigment phycoerythrin (PE) is of commercial interest as natural colorant in food and cosmetics, as well as fluoroprobes for laboratory analysis. Several methods for extraction and quantification of PE are available but they comprise typically various extraction buffers, repetitive freeze-thaw cycles and liquid nitrogen, making extraction procedures more complicated. A simple method for extraction of PE from cryptophytes is described using standard laboratory materials and equipment. The cryptophyte cells on the filters were disrupted at -80 °C and added phosphate buffer for extraction at 4 °C followed by absorbance measurement. The cryptophyte Rhodomonas salina was used as a model organism. •Simple method for extraction and quantification of phycoerythrin from cryptophytes.•Minimal usage of equipment and chemicals, and low labor costs.•Applicable for industrial and biological purposes.

Perfusion quantification in contrast-enhanced ultrasound (CEUS)--ready for research projects and routine clinical use.

PubMed

Tranquart, F; Mercier, L; Frinking, P; Gaud, E; Arditi, M

2012-07-01

With contrast-enhanced ultrasound (CEUS) now established as a valuable imaging modality for many applications, a more specific demand has recently emerged for quantifying perfusion and using measured parameters as objective indicators for various disease states. However, CEUS perfusion quantification remains challenging and is not well integrated in daily clinical practice. The development of VueBox™ alleviates existing limitations and enables quantification in a standardized way. VueBox™ operates as an off-line software application, after dynamic contrast-enhanced ultrasound (DCE-US) is performed. It enables linearization of DICOM clips, assessment of perfusion using patented curve-fitting models, and generation of parametric images by synthesizing perfusion information at the pixel level using color coding. VueBox™ is compatible with most of the available ultrasound platforms (nonlinear contrast-enabled), has the ability to process both bolus and disruption-replenishment kinetics loops, allows analysis results and their context to be saved, and generates analysis reports automatically. Specific features have been added to VueBox™, such as fully automatic in-plane motion compensation and an easy-to-use clip editor. Processing time has been reduced as a result of parallel programming optimized for multi-core processors. A long list of perfusion parameters is available for each of the two administration modes to address all possible demands currently reported in the literature for diagnosis or treatment monitoring. In conclusion, VueBox™ is a valid and robust quantification tool to be used for standardizing perfusion quantification and to improve the reproducibility of results across centers. © Georg Thieme Verlag KG Stuttgart · New York.

Characterization and Quantification of Intact 26S Proteasome Proteins by Real-Time Measurement of Intrinsic Fluorescence Prior to Top-down Mass Spectrometry

PubMed Central

Russell, Jason D.; Scalf, Mark; Book, Adam J.; Ladror, Daniel T.; Vierstra, Richard D.; Smith, Lloyd M.; Coon, Joshua J.

2013-01-01

Quantification of gas-phase intact protein ions by mass spectrometry (MS) is impeded by highly-variable ionization, ion transmission, and ion detection efficiencies. Therefore, quantification of proteins using MS-associated techniques is almost exclusively done after proteolysis where peptides serve as proxies for estimating protein abundance. Advances in instrumentation, protein separations, and informatics have made large-scale sequencing of intact proteins using top-down proteomics accessible to the proteomics community; yet quantification of proteins using a top-down workflow has largely been unaddressed. Here we describe a label-free approach to determine the abundance of intact proteins separated by nanoflow liquid chromatography prior to MS analysis by using solution-phase measurements of ultraviolet light-induced intrinsic fluorescence (UV-IF). UV-IF is measured directly at the electrospray interface just prior to the capillary exit where proteins containing at least one tryptophan residue are readily detected. UV-IF quantification was demonstrated using commercially available protein standards and provided more accurate and precise protein quantification than MS ion current. We evaluated the parallel use of UV-IF and top-down tandem MS for quantification and identification of protein subunits and associated proteins from an affinity-purified 26S proteasome sample from Arabidopsis thaliana. We identified 26 unique proteins and quantified 13 tryptophan-containing species. Our analyses discovered previously unidentified N-terminal processing of the β6 (PBF1) and β7 (PBG1) subunit - such processing of PBG1 may generate a heretofore unknown additional protease active site upon cleavage. In addition, our approach permitted the unambiguous identification and quantification both isoforms of the proteasome-associated protein DSS1. PMID:23536786

Characterization and quantification of intact 26S proteasome proteins by real-time measurement of intrinsic fluorescence prior to top-down mass spectrometry.

PubMed

Russell, Jason D; Scalf, Mark; Book, Adam J; Ladror, Daniel T; Vierstra, Richard D; Smith, Lloyd M; Coon, Joshua J

2013-01-01

Quantification of gas-phase intact protein ions by mass spectrometry (MS) is impeded by highly-variable ionization, ion transmission, and ion detection efficiencies. Therefore, quantification of proteins using MS-associated techniques is almost exclusively done after proteolysis where peptides serve as proxies for estimating protein abundance. Advances in instrumentation, protein separations, and informatics have made large-scale sequencing of intact proteins using top-down proteomics accessible to the proteomics community; yet quantification of proteins using a top-down workflow has largely been unaddressed. Here we describe a label-free approach to determine the abundance of intact proteins separated by nanoflow liquid chromatography prior to MS analysis by using solution-phase measurements of ultraviolet light-induced intrinsic fluorescence (UV-IF). UV-IF is measured directly at the electrospray interface just prior to the capillary exit where proteins containing at least one tryptophan residue are readily detected. UV-IF quantification was demonstrated using commercially available protein standards and provided more accurate and precise protein quantification than MS ion current. We evaluated the parallel use of UV-IF and top-down tandem MS for quantification and identification of protein subunits and associated proteins from an affinity-purified 26S proteasome sample from Arabidopsis thaliana. We identified 26 unique proteins and quantified 13 tryptophan-containing species. Our analyses discovered previously unidentified N-terminal processing of the β6 (PBF1) and β7 (PBG1) subunit - such processing of PBG1 may generate a heretofore unknown additional protease active site upon cleavage. In addition, our approach permitted the unambiguous identification and quantification both isoforms of the proteasome-associated protein DSS1.

Novel isotopic N, N-Dimethyl Leucine (iDiLeu) Reagents Enable Absolute Quantification of Peptides and Proteins Using a Standard Curve Approach

NASA Astrophysics Data System (ADS)

Greer, Tyler; Lietz, Christopher B.; Xiang, Feng; Li, Lingjun

2015-01-01

Absolute quantification of protein targets using liquid chromatography-mass spectrometry (LC-MS) is a key component of candidate biomarker validation. One popular method combines multiple reaction monitoring (MRM) using a triple quadrupole instrument with stable isotope-labeled standards (SIS) for absolute quantification (AQUA). LC-MRM AQUA assays are sensitive and specific, but they are also expensive because of the cost of synthesizing stable isotope peptide standards. While the chemical modification approach using mass differential tags for relative and absolute quantification (mTRAQ) represents a more economical approach when quantifying large numbers of peptides, these reagents are costly and still suffer from lower throughput because only two concentration values per peptide can be obtained in a single LC-MS run. Here, we have developed and applied a set of five novel mass difference reagents, isotopic N, N-dimethyl leucine (iDiLeu). These labels contain an amine reactive group, triazine ester, are cost effective because of their synthetic simplicity, and have increased throughput compared with previous LC-MS quantification methods by allowing construction of a four-point standard curve in one run. iDiLeu-labeled peptides show remarkably similar retention time shifts, slightly lower energy thresholds for higher-energy collisional dissociation (HCD) fragmentation, and high quantification accuracy for trypsin-digested protein samples (median errors <15%). By spiking in an iDiLeu-labeled neuropeptide, allatostatin, into mouse urine matrix, two quantification methods are validated. The first uses one labeled peptide as an internal standard to normalize labeled peptide peak areas across runs (<19% error), whereas the second enables standard curve creation and analyte quantification in one run (<8% error).

Induced nanoparticle aggregation for short nucleic acid quantification by depletion isotachophoresis.

PubMed

Marczak, Steven; Senapati, Satyajyoti; Slouka, Zdenek; Chang, Hsueh-Chia

2016-12-15

A rapid (<20min) gel-membrane biochip platform for the detection and quantification of short nucleic acids is presented based on a sandwich assay with probe-functionalized gold nanoparticles and their separation into concentrated bands by depletion-generated gel isotachophoresis. The platform sequentially exploits the enrichment and depletion phenomena of an ion-selective cation-exchange membrane created under an applied electric field. Enrichment is used to concentrate the nanoparticles and targets at a localized position at the gel-membrane interface for rapid hybridization. The depletion generates an isotachophoretic zone without the need for different conductivity buffers, and is used to separate linked nanoparticles from isolated ones in the gel medium and then by field-enhanced aggregation of only the linked particles at the depletion front. The selective field-induced aggregation of the linked nanoparticles during the subsequent depletion step produces two lateral-flow like bands within 1cm for easy visualization and quantification as the aggregates have negligible electrophoretic mobility in the gel and the isolated nanoparticles are isotachophoretically packed against the migrating depletion front. The detection limit for 69-base single-stranded DNA targets is 10 pM (about 10 million copies for our sample volume) with high selectivity against nontargets and a three decade linear range for quantification. The selectivity and signal intensity are maintained in heterogeneous mixtures where the nontargets outnumber the targets 10,000 to 1. The selective field-induced aggregation of DNA-linked nanoparticles at the ion depletion front is attributed to their trailing position at the isotachophoretic front with a large field gradient. Copyright © 2016 Elsevier B.V. All rights reserved.

VAVUQ, Python and Matlab freeware for Verification and Validation, Uncertainty Quantification

NASA Astrophysics Data System (ADS)

Courtney, J. E.; Zamani, K.; Bombardelli, F. A.; Fleenor, W. E.

2015-12-01

A package of scripts is presented for automated Verification and Validation (V&V) and Uncertainty Quantification (UQ) for engineering codes that approximate Partial Differential Equations (PDFs). The code post-processes model results to produce V&V and UQ information. This information can be used to assess model performance. Automated information on code performance can allow for a systematic methodology to assess the quality of model approximations. The software implements common and accepted code verification schemes. The software uses the Method of Manufactured Solutions (MMS), the Method of Exact Solution (MES), Cross-Code Verification, and Richardson Extrapolation (RE) for solution (calculation) verification. It also includes common statistical measures that can be used for model skill assessment. Complete RE can be conducted for complex geometries by implementing high-order non-oscillating numerical interpolation schemes within the software. Model approximation uncertainty is quantified by calculating lower and upper bounds of numerical error from the RE results. The software is also able to calculate the Grid Convergence Index (GCI), and to handle adaptive meshes and models that implement mixed order schemes. Four examples are provided to demonstrate the use of the software for code and solution verification, model validation and uncertainty quantification. The software is used for code verification of a mixed-order compact difference heat transport solver; the solution verification of a 2D shallow-water-wave solver for tidal flow modeling in estuaries; the model validation of a two-phase flow computation in a hydraulic jump compared to experimental data; and numerical uncertainty quantification for 3D CFD modeling of the flow patterns in a Gust erosion chamber.

Absolute quantification of Dehalococcoides proteins: enzyme bioindicators of chlorinated ethene dehalorespiration.

PubMed

Werner, Jeffrey J; Ptak, A Celeste; Rahm, Brian G; Zhang, Sheng; Richardson, Ruth E

2009-10-01

The quantification of trace proteins in complex environmental samples and mixed microbial communities would be a valuable monitoring tool in countless applications, including the bioremediation of groundwater contaminated with chlorinated solvents. Measuring the concentrations of specific proteins provides unique information about the activity and physiological state of organisms in a sample. We developed sensitive (< 5 fmol), selective bioindicator assays for the absolute quantification of select proteins used by Dehalococcoides spp. when reducing carbon atoms in the common pollutants trichloroethene (TCE) and tetrachloroethene (PCE). From complex whole-sample digests of two different dechlorinating mixed communities, we monitored the chromatographic peaks of selected tryptic peptides chosen to represent 19 specific Dehalococcoides proteins. This was accomplished using multiple-reaction monitoring (MRM) assays using nano-liquid chromatography-tandem mass spectrometry (nLC-MS/MS), which provided the selectivity, sensitivity and reproducibility required to quantify Dehalococcoides proteins in complex samples. We observed reproducible peak areas (average CV = 0.14 over 4 days, n = 3) and linear responses in standard curves (n = 5, R(2) > 0.98) using synthetic peptide standards spiked into a background matrix of sediment peptides. We detected and quantified TCE reductive dehalogenase (TceA) at 7.6 +/- 1.7 x 10(3) proteins cell(-1) in the KB1 bioaugmentation culture, previously thought to be lacking TceA. Fragmentation data from MS/MS shotgun proteomics experiments were helpful in developing the MRM targets. Similar shotgun proteomics data are emerging in labs around the world for many environmentally relevant microbial proteins, and these data are a valuable resource for the future development of MRM assays. We expect targeted peptide quantification in environmental samples to be a useful tool in environmental monitoring.

MPQ-cytometry: a magnetism-based method for quantification of nanoparticle-cell interactions

NASA Astrophysics Data System (ADS)

Shipunova, V. O.; Nikitin, M. P.; Nikitin, P. I.; Deyev, S. M.

2016-06-01

Precise quantification of interactions between nanoparticles and living cells is among the imperative tasks for research in nanobiotechnology, nanotoxicology and biomedicine. To meet the challenge, a rapid method called MPQ-cytometry is developed, which measures the integral non-linear response produced by magnetically labeled nanoparticles in a cell sample with an original magnetic particle quantification (MPQ) technique. MPQ-cytometry provides a sensitivity limit 0.33 ng of nanoparticles and is devoid of a background signal present in many label-based assays. Each measurement takes only a few seconds, and no complicated sample preparation or data processing is required. The capabilities of the method have been demonstrated by quantification of interactions of iron oxide nanoparticles with eukaryotic cells. The total amount of targeted nanoparticles that specifically recognized the HER2/neu oncomarker on the human cancer cell surface was successfully measured, the specificity of interaction permitting the detection of HER2/neu positive cells in a cell mixture. Moreover, it has been shown that MPQ-cytometry analysis of a HER2/neu-specific iron oxide nanoparticle interaction with six cell lines of different tissue origins quantitatively reflects the HER2/neu status of the cells. High correlation of MPQ-cytometry data with those obtained by three other commonly used in molecular and cell biology methods supports consideration of this method as a prospective alternative for both quantifying cell-bound nanoparticles and estimating the expression level of cell surface antigens. The proposed method does not require expensive sophisticated equipment or highly skilled personnel and it can be easily applied for rapid diagnostics, especially under field conditions.Precise quantification of interactions between nanoparticles and living cells is among the imperative tasks for research in nanobiotechnology, nanotoxicology and biomedicine. To meet the challenge, a rapid method

Quantification of Global DNA Methylation Levels by Mass Spectrometry.

PubMed

Fernandez, Agustin F; Valledor, Luis; Vallejo, Fernando; Cañal, Maria Jesús; Fraga, Mario F

2018-01-01

Global DNA methylation was classically considered the relative percentage of 5-methylcysine (5mC) with respect to total cytosine (C). Early approaches were based on the use of high-performance separation technologies and UV detection. However, the recent development of protocols using mass spectrometry for the detection has increased sensibility and permitted the precise identification of peak compounds based on their molecular masses. This allows work to be conducted with much less genomic DNA starting material and also to quantify 5-hydroxymethyl-cytosine (5hmC), a recently identified form of methylated cytosine that could play an important role in active DNA demethylation. Here, we describe the protocol that we currently use in our laboratory to analyze 5mC and 5hmC by mass spectrometry. The protocol, which is based on the method originally developed by Le and colleagues using Ultra Performance Liquid Chromatography (UPLC) and mass spectrometry (triple Quadrupole (QqQ)) detection, allows for the rapid and accurate quantification of relative global 5mC and 5hmC levels starting from just 1 μg of genomic DNA, which allows for the rapid and accurate quantification of relative global 5mC and 5hmC levels.

Immunoblotting Quantification Approach for Identifying Potential Hypoallergenic Citrus Cultivars.

PubMed

Wu, Jinlong; Deng, Wenjun; Lin, Dingbo; Deng, Xiuxin; Ma, Zhaocheng

2018-02-28

The inherent allergens of citrus fruits, such as Cit s 1, Cit s 2, Cit s 3 can cause allergic reactions. A better understanding of the genetic factors (cultivar to cultivar) affecting the allergenic potential of citrus fruits would be beneficial for further identification of hypoallergenic genotypes. In the present study, an immunoblotting quantification approach was adopted to assess the potential allergenicity of 21 citrus cultivars, including nine subgroups (tangerine, satsuma, orange, pummelo, grapefruit, lemon, kumquat, tangor, and tangelo). To prepare highly sensitive and specific rabbit polyclonal antibodies, antigenicity of purified rCit s 1.01, rCit s 2.01, and rCit s 3.01 peptides were enhanced with high epitope density in a single protein molecule. The data integration of three citrus allergen quantifications demonstrated that the four pummelo cultivars (Kao Phuang Pummelo, Wanbai Pummelo, Shatian Pummelo, and Guanxi Pummelo) were potential hypoallergenic, compared with other 8 subgroups. Moreover, the immunological analyses with sera of allergic subjects revealed that Shatian Pummelo and Guanxi Pummelo showed the lowest immunoreactivity in 8 representative citrus cultivars. These potential hypoallergenic genotypes are of great significance to not only allergic consumers but also citrus breeders in the genetic improvement of hypoallergenic citrus as breeding resources.

Reproducibility of Lobar Perfusion and Ventilation Quantification Using SPECT/CT Segmentation Software in Lung Cancer Patients.

PubMed

Provost, Karine; Leblond, Antoine; Gauthier-Lemire, Annie; Filion, Édith; Bahig, Houda; Lord, Martin

2017-09-01

Planar perfusion scintigraphy with 99m Tc-labeled macroaggregated albumin is often used for pretherapy quantification of regional lung perfusion in lung cancer patients, particularly those with poor respiratory function. However, subdividing lung parenchyma into rectangular regions of interest, as done on planar images, is a poor reflection of true lobar anatomy. New tridimensional methods using SPECT and SPECT/CT have been introduced, including semiautomatic lung segmentation software. The present study evaluated inter- and intraobserver agreement on quantification using SPECT/CT software and compared the results for regional lung contribution obtained with SPECT/CT and planar scintigraphy. Methods: Thirty lung cancer patients underwent ventilation-perfusion scintigraphy with 99m Tc-macroaggregated albumin and 99m Tc-Technegas. The regional lung contribution to perfusion and ventilation was measured on both planar scintigraphy and SPECT/CT using semiautomatic lung segmentation software by 2 observers. Interobserver and intraobserver agreement for the SPECT/CT software was assessed using the intraclass correlation coefficient, Bland-Altman plots, and absolute differences in measurements. Measurements from planar and tridimensional methods were compared using the paired-sample t test and mean absolute differences. Results: Intraclass correlation coefficients were in the excellent range (above 0.9) for both interobserver and intraobserver agreement using the SPECT/CT software. Bland-Altman analyses showed very narrow limits of agreement. Absolute differences were below 2.0% in 96% of both interobserver and intraobserver measurements. There was a statistically significant difference between planar and SPECT/CT methods ( P < 0.001) for quantification of perfusion and ventilation for all right lung lobes, with a maximal mean absolute difference of 20.7% for the right middle lobe. There was no statistically significant difference in quantification of perfusion and

Sensitivity of Chemical Shift-Encoded Fat Quantification to Calibration of Fat MR Spectrum

PubMed Central

Wang, Xiaoke; Hernando, Diego; Reeder, Scott B.

2015-01-01

Purpose To evaluate the impact of different fat spectral models on proton density fat-fraction (PDFF) quantification using chemical shift-encoded (CSE) MRI. Material and Methods Simulations and in vivo imaging were performed. In a simulation study, spectral models of fat were compared pairwise. Comparison of magnitude fitting and mixed fitting was performed over a range of echo times and fat fractions. In vivo acquisitions from 41 patients were reconstructed using 7 published spectral models of fat. T2-corrected STEAM-MRS was used as reference. Results Simulations demonstrate that imperfectly calibrated spectral models of fat result in biases that depend on echo times and fat fraction. Mixed fitting is more robust against this bias than magnitude fitting. Multi-peak spectral models showed much smaller differences among themselves than when compared to the single-peak spectral model. In vivo studies show all multi-peak models agree better (for mixed fitting, slope ranged from 0.967–1.045 using linear regression) with reference standard than the single-peak model (for mixed fitting, slope=0.76). Conclusion It is essential to use a multi-peak fat model for accurate quantification of fat with CSE-MRI. Further, fat quantification techniques using multi-peak fat models are comparable and no specific choice of spectral model is shown to be superior to the rest. PMID:25845713

Quantification of skin wrinkles using low coherence interferometry

NASA Astrophysics Data System (ADS)

Oh, Jung-Taek; Kim, Beop-Min; Son, Sang-Ryoon; Lee, Sang-Won; Kim, Dong-Yoon; Kim, Youn-Soo

2004-07-01

We measure the skin wrinkle topology by means of low coherence interferometry (LCI), which forms the basis of the optical coherence tomography (OCT). The skin topology obtained using LCI and corresponding 2-D fast Fourier transform allow quantification of skin wrinkles. It took approximately 2 minutes to obtain 2.1 mm x 2.1 mm topological image with 4 um and 16 um resolutions in axial and transverse directions, respectively. Measurement examples show the particular case of skin contour change after-wrinkle cosmeceutical treatments and atopic dermatitis

SU-D-218-05: Material Quantification in Spectral X-Ray Imaging: Optimization and Validation.

PubMed

Nik, S J; Thing, R S; Watts, R; Meyer, J

2012-06-01

To develop and validate a multivariate statistical method to optimize scanning parameters for material quantification in spectral x-rayimaging. An optimization metric was constructed by extensively sampling the thickness space for the expected number of counts for m (two or three) materials. This resulted in an m-dimensional confidence region ofmaterial quantities, e.g. thicknesses. Minimization of the ellipsoidal confidence region leads to the optimization of energy bins. For the given spectrum, the minimum counts required for effective material separation can be determined by predicting the signal-to-noise ratio (SNR) of the quantification. A Monte Carlo (MC) simulation framework using BEAM was developed to validate the metric. Projection data of the m-materials was generated and material decomposition was performed for combinations of iodine, calcium and water by minimizing the z-score between the expected spectrum and binned measurements. The mean square error (MSE) and variance were calculated to measure the accuracy and precision of this approach, respectively. The minimum MSE corresponds to the optimal energy bins in the BEAM simulations. In the optimization metric, this is equivalent to the smallest confidence region. The SNR of the simulated images was also compared to the predictions from the metric. TheMSE was dominated by the variance for the given material combinations,which demonstrates accurate material quantifications. The BEAMsimulations revealed that the optimization of energy bins was accurate to within 1keV. The SNRs predicted by the optimization metric yielded satisfactory agreement but were expectedly higher for the BEAM simulations due to the inclusion of scattered radiation. The validation showed that the multivariate statistical method provides accurate material quantification, correct location of optimal energy bins and adequateprediction of image SNR. The BEAM code system is suitable for generating spectral x- ray imaging simulations. �

Quantification of cytokine mRNA in peripheral blood mononuclear cells using branched DNA (bDNA) technology.

PubMed

Shen, L P; Sheridan, P; Cao, W W; Dailey, P J; Salazar-Gonzalez, J F; Breen, E C; Fahey, J L; Urdea, M S; Kolberg, J A

1998-06-01

Changes in the patterns of cytokine expression are thought to be of central importance in human infectious and inflammatory diseases. As such, there is a need for precise, reproducible assays for quantification of cytokine mRNA that are amenable to routine use in a clinical setting. In this report, we describe the design and performance of a branched DNA (bDNA) assay for the direct quantification of multiple cytokine mRNA levels in peripheral blood mononuclear cells (PBMCs). Oligonucleotide target probe sets were designed for several human cytokines, including TNFalpha, IL-2, IL-4, IL-6, IL-10, and IFNgamma. The bDNA assay yielded highly reproducible quantification of cytokine mRNAs, exhibited a broad linear dynamic range of over 3-log10, and showed a sensitivity sufficient to measure at least 3000 molecules. The potential clinical utility of the bDNA assay was explored by measuring cytokine mRNA levels in PBMCs from healthy and immunocompromised individuals. Cytokine expression levels in PBMCs from healthy blood donors were found to remain relatively stable over a one-month period of time. Elevated levels of IFNgamma mRNA were detected in PBMCs from HIV-1 seropositive individuals, but no differences in mean levels of TNFalpha or IL-6 mRNA were detected between seropositive and seronegative individuals. By providing a reproducible method for quantification of low abundance transcripts in clinical specimens, the bDNA assay may be useful for studies addressing the role of cytokine expression in disease.

Feasibility and accuracy of dual-layer spectral detector computed tomography for quantification of gadolinium: a phantom study.

PubMed

van Hamersvelt, Robbert W; Willemink, Martin J; de Jong, Pim A; Milles, Julien; Vlassenbroek, Alain; Schilham, Arnold M R; Leiner, Tim

2017-09-01

The aim of this study was to evaluate the feasibility and accuracy of dual-layer spectral detector CT (SDCT) for the quantification of clinically encountered gadolinium concentrations. The cardiac chamber of an anthropomorphic thoracic phantom was equipped with 14 tubular inserts containing different gadolinium concentrations, ranging from 0 to 26.3 mg/mL (0.0, 0.1, 0.2, 0.4, 0.5, 1.0, 2.0, 3.0, 4.0, 5.1, 10.6, 15.7, 20.7 and 26.3 mg/mL). Images were acquired using a novel 64-detector row SDCT system at 120 and 140 kVp. Acquisitions were repeated five times to assess reproducibility. Regions of interest (ROIs) were drawn on three slices per insert. A spectral plot was extracted for every ROI and mean attenuation profiles were fitted to known attenuation profiles of water and pure gadolinium using in-house-developed software to calculate gadolinium concentrations. At both 120 and 140 kVp, excellent correlations between scan repetitions and true and measured gadolinium concentrations were found (R > 0.99, P < 0.001; ICCs > 0.99, CI 0.99-1.00). Relative mean measurement errors stayed below 10% down to 2.0 mg/mL true gadolinium concentration at 120 kVp and below 5% down to 1.0 mg/mL true gadolinium concentration at 140 kVp. SDCT allows for accurate quantification of gadolinium at both 120 and 140 kVp. Lowest measurement errors were found for 140 kVp acquisitions. • Gadolinium quantification may be useful in patients with contraindication to iodine. • Dual-layer spectral detector CT allows for overall accurate quantification of gadolinium. • Interscan variability of gadolinium quantification using SDCT material decomposition is excellent.

Quantification of Kryptofix 2.2.2 in [18F]fluorine-labelled radiopharmaceuticals by rapid-resolution liquid chromatography.

PubMed

Lao, Yexing; Yang, Cuiping; Zou, Wei; Gan, Manquan; Chen, Ping; Su, Weiwei

2012-05-01

The cryptand Kryptofix 2.2.2 is used extensively as a phase-transfer reagent in the preparation of [18F]fluoride-labelled radiopharmaceuticals. However, it has considerable acute toxicity. The aim of this study was to develop and validate a method for rapid (within 1 min), specific and sensitive quantification of Kryptofix 2.2.2 at trace levels. Chromatographic separations were carried out by rapid-resolution liquid chromatography (Agilent ZORBAX SB-C18 rapid-resolution column, 2.1 × 30 mm, 3.5 μm). Tandem mass spectra were acquired using a triple quadrupole mass spectrometer equipped with an electrospray ionization interface. Quantitative mass spectrometric analysis was conducted in positive ion mode and multiple reaction monitoring mode for the m/z 377.3 → 114.1 transition for Kryptofix 2.2.2. The external standard method was used for quantification. The method met the precision and efficiency requirements for PET radiopharmaceuticals, providing satisfactory results for specificity, matrix effect, stability, linearity (0.5-100 ng/ml, r(2)=0.9975), precision (coefficient of variation < 5%), accuracy (relative error < ± 3%), sensitivity (lower limit of quantification=0.5 ng) and detection time (<1 min). Fluorodeoxyglucose (n=6) was analysed, and the Kryptofix 2.2.2 content was found to be well below the maximum permissible levels approved by the US Food and Drug Administration. The developed method has a short analysis time (<1 min) and high sensitivity (lower limit of quantification=0.5 ng/ml) and can be successfully applied to rapid quantification of Kryptofix 2.2.2 at trace levels in fluorodeoxyglucose. This method could also be applied to other [18F]fluorine-labelled radiopharmaceuticals that use Kryptofix 2.2.2 as a phase-transfer reagent.

Quantification of Spatial Heterogeneity in Old Growth Forst of Korean Pine

Treesearch

Wang Zhengquan; Wang Qingcheng; Zhang Yandong

1997-01-01

Spatial hetergeneity is a very important issue in studying functions and processes of ecological systems at various scales. Semivariogram analysis is an effective technique to summarize spatial data, and quantification of sptail heterogeneity. In this paper, we propose some principles to use semivariograms to characterize and compare spatial heterogeneity of...

Easy, Fast, and Reproducible Quantification of Cholesterol and Other Lipids in Human Plasma by Combined High Resolution MSX and FTMS Analysis

NASA Astrophysics Data System (ADS)

Gallego, Sandra F.; Højlund, Kurt; Ejsing, Christer S.

2018-01-01

Reliable, cost-effective, and gold-standard absolute quantification of non-esterified cholesterol in human plasma is of paramount importance in clinical lipidomics and for the monitoring of metabolic health. Here, we compared the performance of three mass spectrometric approaches available for direct detection and quantification of cholesterol in extracts of human plasma. These approaches are high resolution full scan Fourier transform mass spectrometry (FTMS) analysis, parallel reaction monitoring (PRM), and novel multiplexed MS/MS (MSX) technology, where fragments from selected precursor ions are detected simultaneously. Evaluating the performance of these approaches in terms of dynamic quantification range, linearity, and analytical precision showed that the MSX-based approach is superior to that of the FTMS and PRM-based approaches. To further show the efficacy of this approach, we devised a simple routine for extensive plasma lipidome characterization using only 8 μL of plasma, using a new commercially available ready-to-spike-in mixture with 14 synthetic lipid standards, and executing a single 6 min sample injection with combined MSX analysis for cholesterol quantification and FTMS analysis for quantification of sterol esters, glycerolipids, glycerophospholipids, and sphingolipids. Using this simple routine afforded reproducible and absolute quantification of 200 lipid species encompassing 13 lipid classes in human plasma samples. Notably, the analysis time of this procedure can be shortened for high throughput-oriented clinical lipidomics studies or extended with more advanced MSALL technology (Almeida R. et al., J. Am. Soc. Mass Spectrom. 26, 133-148 [1]) to support in-depth structural elucidation of lipid molecules. [Figure not available: see fulltext.

Easy, Fast, and Reproducible Quantification of Cholesterol and Other Lipids in Human Plasma by Combined High Resolution MSX and FTMS Analysis.

PubMed

Gallego, Sandra F; Højlund, Kurt; Ejsing, Christer S

2018-01-01

Reliable, cost-effective, and gold-standard absolute quantification of non-esterified cholesterol in human plasma is of paramount importance in clinical lipidomics and for the monitoring of metabolic health. Here, we compared the performance of three mass spectrometric approaches available for direct detection and quantification of cholesterol in extracts of human plasma. These approaches are high resolution full scan Fourier transform mass spectrometry (FTMS) analysis, parallel reaction monitoring (PRM), and novel multiplexed MS/MS (MSX) technology, where fragments from selected precursor ions are detected simultaneously. Evaluating the performance of these approaches in terms of dynamic quantification range, linearity, and analytical precision showed that the MSX-based approach is superior to that of the FTMS and PRM-based approaches. To further show the efficacy of this approach, we devised a simple routine for extensive plasma lipidome characterization using only 8 μL of plasma, using a new commercially available ready-to-spike-in mixture with 14 synthetic lipid standards, and executing a single 6 min sample injection with combined MSX analysis for cholesterol quantification and FTMS analysis for quantification of sterol esters, glycerolipids, glycerophospholipids, and sphingolipids. Using this simple routine afforded reproducible and absolute quantification of 200 lipid species encompassing 13 lipid classes in human plasma samples. Notably, the analysis time of this procedure can be shortened for high throughput-oriented clinical lipidomics studies or extended with more advanced MS ALL technology (Almeida R. et al., J. Am. Soc. Mass Spectrom. 26, 133-148 [1]) to support in-depth structural elucidation of lipid molecules. Graphical Abstract ᅟ.

Installation Restoration Program. Phase II--Confirmation/Quantification. Stage 1.

DTIC Science & Technology

1985-03-01

four phases. Phase I, Initial Assessment/ Records Search, is designed to identify possible hazardous waste contami- nated sites and potential...7 71 -. - - IL’ -, 1% 33 AihlIII Is 33 n~iL t iiC UII! ii CL C LU 1-3, Phase II, Confirmation and Quantification, is designed to confirm the...additional monitoring data upon which design of mitigative actions are based. In Phase III, Technology Base Development, appropriate technology is selected and

Quantification of free fatty acids in human stratum corneum using tandem mass spectrometry and surrogate analyte approach.

PubMed

Dapic, Irena; Kobetic, Renata; Brkljacic, Lidija; Kezic, Sanja; Jakasa, Ivone

2018-02-01

The free fatty acids (FFAs) are one of the major components of the lipids in the stratum corneum (SC), the uppermost layer of the skin. Relative composition of FFAs has been proposed as a biomarker of the skin barrier status in patients with atopic dermatitis (AD). Here, we developed an LC-ESI-MS/MS method for simultaneous quantification of a range of FFAs with long and very long chain length in the SC collected by adhesive tape (D-Squame). The method, based on derivatization with 2-bromo-1-methylpyridinium iodide and 3-carbinol-1-methylpyridinium iodide, allowed highly sensitive detection and quantification of FFAs using multiple reaction monitoring. For the quantification, we applied a surrogate analyte approach and internal standardization using isotope labeled derivatives of FFAs. Adhesive tapes showed the presence of several FFAs, which are also present in the SC, a problem encountered in previous studies. Therefore, the levels of FFAs in the SC were corrected using C12:0, which was present on the adhesive tape, but not detected in the SC. The method was applied to SC samples from patients with atopic dermatitis and healthy subjects. Quantification using multiple reaction monitoring allowed sufficient sensitivity to analyze FFAs of chain lengths C16-C28 in the SC collected on only one tape strip. Copyright © 2017 John Wiley & Sons, Ltd.

Biofilm Quantification on Nasolacrimal Silastic Stents After Dacryocystorhinostomy.

PubMed

Murphy, Jae; Ali, Mohammed Javed; Psaltis, Alkis James

2015-01-01

Biofilms are now recognized as potential factors in the pathogenesis of chronic inflammatory and infective diseases. The aim of this study was to examine the presence of biofilms and quantify their biomass on silastic nasolacrimal duct stents inserted after dacryocystorhinostomy (DCR). A prospective study was performed on a series of patients undergoing DCR with O'Donoghue stent insertion. After removal, the stents were subjected to biofilm analysis using standard protocols of confocal laser scanning microscopy (CLSM) and scanning electron microscopy. These stents were compared against negative controls and positive in vitro ones established using Staphylococcus aureus strain ATCC 25923. Biofilm quantification was performed using the COMSTAT2 software and the total biofilm biomass was calculated. A total of nine consecutive patient samples were included in this prospective study. None of the patients had any evidence of postoperative infection. All the stents demonstrated evidence of biofilm formation using both imaging modalities. The presence of various different sized organisms within a common exopolysaccharide matrix on CLSM suggested the existence of polymicrobial communities. The mean biomass of patient samples was 0.9385 μm³/μm² (range: 0.3901-1.9511 μm³/μm²). This is the first study to report the quantification of biomass on lacrimal stents. The presence of biofilms on lacrimal stents after DCR is a common finding but this need not necessarily translate to postoperative clinical infection.

Quantification of neutral human milk oligosaccharides by graphitic carbon HPLC with tandem mass spectrometry

PubMed Central

Bao, Yuanwu; Chen, Ceng; Newburg, David S.

2012-01-01

Defining the biologic roles of human milk oligosaccharides (HMOS) requires an efficient, simple, reliable, and robust analytical method for simultaneous quantification of oligosaccharide profiles from multiple samples. The HMOS fraction of milk is a complex mixture of polar, highly branched, isomeric structures that contain no intrinsic facile chromophore, making their resolution and quantification challenging. A liquid chromatography-mass spectrometry (LC-MS) method was devised to resolve and quantify 11 major neutral oligosaccharides of human milk simultaneously. Crude HMOS fractions are reduced, resolved by porous graphitic carbon HPLC with a water/acetonitrile gradient, detected by mass spectrometric specific ion monitoring, and quantified. The HPLC separates isomers of identical molecular weights allowing 11 peaks to be fully resolved and quantified by monitoring mass to charge (m/z) ratios of the deprotonated negative ions. The standard curves for each of the 11 oligosaccharides is linear from 0.078 or 0.156 to 20 μg/mL (R2 > 0.998). Precision (CV) ranges from 1% to 9%. Accuracy is from 86% to 104%. This analytical technique provides sensitive, precise, accurate quantification for each of the 11 milk oligosaccharides and allows measurement of differences in milk oligosaccharide patterns between individuals and at different stages of lactation. PMID:23068043

Nondestructive Detection and Quantification of Blueberry Bruising using Near-infrared (NIR) Hyperspectral Reflectance Imaging

NASA Astrophysics Data System (ADS)

Jiang, Yu; Li, Changying; Takeda, Fumiomi

2016-10-01

Currently, blueberry bruising is evaluated by either human visual/tactile inspection or firmness measurement instruments. These methods are destructive, time-consuming, and subjective. The goal of this paper was to develop a non-destructive approach for blueberry bruising detection and quantification. Experiments were conducted on 300 samples of southern highbush blueberry (Camellia, Rebel, and Star) and on 1500 samples of northern highbush blueberry (Bluecrop, Jersey, and Liberty) for hyperspectral imaging analysis, firmness measurement, and human evaluation. An algorithm was developed to automatically calculate a bruise ratio index (ratio of bruised to whole fruit area) for bruise quantification. The spectra of bruised and healthy tissues were statistically separated and the separation was independent of cultivars. Support vector machine (SVM) classification of the spectra from the regions of interest (ROIs) achieved over 94%, 92%, and 96% accuracy on the training set, independent testing set, and combined set, respectively. The statistical results showed that the bruise ratio index was equivalent to the measured firmness but better than the predicted firmness in regard to effectiveness of bruise quantification, and the bruise ratio index had a strong correlation with human assessment (R2 = 0.78 - 0.83). Therefore, the proposed approach and the bruise ratio index are effective to non-destructively detect and quantify blueberry bruising.

Nondestructive Detection and Quantification of Blueberry Bruising using Near-infrared (NIR) Hyperspectral Reflectance Imaging.

PubMed

Jiang, Yu; Li, Changying; Takeda, Fumiomi

2016-10-21

Currently, blueberry bruising is evaluated by either human visual/tactile inspection or firmness measurement instruments. These methods are destructive, time-consuming, and subjective. The goal of this paper was to develop a non-destructive approach for blueberry bruising detection and quantification. Experiments were conducted on 300 samples of southern highbush blueberry (Camellia, Rebel, and Star) and on 1500 samples of northern highbush blueberry (Bluecrop, Jersey, and Liberty) for hyperspectral imaging analysis, firmness measurement, and human evaluation. An algorithm was developed to automatically calculate a bruise ratio index (ratio of bruised to whole fruit area) for bruise quantification. The spectra of bruised and healthy tissues were statistically separated and the separation was independent of cultivars. Support vector machine (SVM) classification of the spectra from the regions of interest (ROIs) achieved over 94%, 92%, and 96% accuracy on the training set, independent testing set, and combined set, respectively. The statistical results showed that the bruise ratio index was equivalent to the measured firmness but better than the predicted firmness in regard to effectiveness of bruise quantification, and the bruise ratio index had a strong correlation with human assessment (R2 = 0.78 - 0.83). Therefore, the proposed approach and the bruise ratio index are effective to non-destructively detect and quantify blueberry bruising.

An alternative method for irones quantification in iris rhizomes using headspace solid-phase microextraction.

PubMed

Roger, B; Fernandez, X; Jeannot, V; Chahboun, J

2010-01-01

The essential oil obtained from iris rhizomes is one of the most precious raw materials for the perfume industry. Its fragrance is due to irones that are gradually formed by oxidative degradation of iridals during rhizome ageing. The development of an alternative method allowing irone quantification in iris rhizomes using HS-SPME-GC. The development of the method using HS-SPME-GC was achieved using the results obtained from a conventional method, i.e. a solid-liquid extraction (SLE) followed by irone quantification by CG. Among several calibration methods tested, internal calibration gave the best results and was the least sensitive to the matrix effect. The proposed method using HS-SPME-GC is as accurate and reproducible as the conventional one using SLE. These two methods were used to monitor and compare irone concentrations in iris rhizomes that had been stored for 6 months to 9 years. Irone quantification in iris rhizome can be achieved using HS-SPME-GC. This method can thus be used for the quality control of the iris rhizomes. It offers the advantage of combining extraction and analysis with an automated device and thus allows a large number of rhizome batches to be analysed and compared in a limited amount of time. Copyright © 2010 John Wiley & Sons, Ltd.

Adaptive polynomial chaos techniques for uncertainty quantification of a gas cooled fast reactor transient

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

Perko, Z.; Gilli, L.; Lathouwers, D.

2013-07-01

Uncertainty quantification plays an increasingly important role in the nuclear community, especially with the rise of Best Estimate Plus Uncertainty methodologies. Sensitivity analysis, surrogate models, Monte Carlo sampling and several other techniques can be used to propagate input uncertainties. In recent years however polynomial chaos expansion has become a popular alternative providing high accuracy at affordable computational cost. This paper presents such polynomial chaos (PC) methods using adaptive sparse grids and adaptive basis set construction, together with an application to a Gas Cooled Fast Reactor transient. Comparison is made between a new sparse grid algorithm and the traditionally used techniquemore » proposed by Gerstner. An adaptive basis construction method is also introduced and is proved to be advantageous both from an accuracy and a computational point of view. As a demonstration the uncertainty quantification of a 50% loss of flow transient in the GFR2400 Gas Cooled Fast Reactor design was performed using the CATHARE code system. The results are compared to direct Monte Carlo sampling and show the superior convergence and high accuracy of the polynomial chaos expansion. Since PC techniques are easy to implement, they can offer an attractive alternative to traditional techniques for the uncertainty quantification of large scale problems. (authors)« less

A Probabilistic Framework for Peptide and Protein Quantification from Data-Dependent and Data-Independent LC-MS Proteomics Experiments

PubMed Central

Richardson, Keith; Denny, Richard; Hughes, Chris; Skilling, John; Sikora, Jacek; Dadlez, Michał; Manteca, Angel; Jung, Hye Ryung; Jensen, Ole Nørregaard; Redeker, Virginie; Melki, Ronald; Langridge, James I.; Vissers, Johannes P.C.

2013-01-01

A probability-based quantification framework is presented for the calculation of relative peptide and protein abundance in label-free and label-dependent LC-MS proteomics data. The results are accompanied by credible intervals and regulation probabilities. The algorithm takes into account data uncertainties via Poisson statistics modified by a noise contribution that is determined automatically during an initial normalization stage. Protein quantification relies on assignments of component peptides to the acquired data. These assignments are generally of variable reliability and may not be present across all of the experiments comprising an analysis. It is also possible for a peptide to be identified to more than one protein in a given mixture. For these reasons the algorithm accepts a prior probability of peptide assignment for each intensity measurement. The model is constructed in such a way that outliers of any type can be automatically reweighted. Two discrete normalization methods can be employed. The first method is based on a user-defined subset of peptides, while the second method relies on the presence of a dominant background of endogenous peptides for which the concentration is assumed to be unaffected. Normalization is performed using the same computational and statistical procedures employed by the main quantification algorithm. The performance of the algorithm will be illustrated on example data sets, and its utility demonstrated for typical proteomics applications. The quantification algorithm supports relative protein quantification based on precursor and product ion intensities acquired by means of data-dependent methods, originating from all common isotopically-labeled approaches, as well as label-free ion intensity-based data-independent methods. PMID:22871168

Quantification of polyhydroxyalkanoates in mixed and pure cultures biomass by Fourier transform infrared spectroscopy: comparison of different approaches.

PubMed

Isak, I; Patel, M; Riddell, M; West, M; Bowers, T; Wijeyekoon, S; Lloyd, J

2016-08-01

Fourier transform infrared (FTIR) spectroscopy was used in this study for the rapid quantification of polyhydroxyalkanoates (PHA) in mixed and pure culture bacterial biomass. Three different statistical analysis methods (regression, partial least squares (PLS) and nonlinear) were applied to the FTIR data and the results were plotted against the PHA values measured with the reference gas chromatography technique. All methods predicted PHA content in mixed culture biomass with comparable efficiency, indicated by similar residuals values. The PHA in these cultures ranged from low to medium concentration (0-44 wt% of dried biomass content). However, for the analysis of the combined mixed and pure culture biomass with PHA concentration ranging from low to high (0-93% of dried biomass content), the PLS method was most efficient. This paper reports, for the first time, the use of a single calibration model constructed with a combination of mixed and pure cultures covering a wide PHA range, for predicting PHA content in biomass. Currently no one universal method exists for processing FTIR data for polyhydroxyalkanoates (PHA) quantification. This study compares three different methods of analysing FTIR data for quantification of PHAs in biomass. A new data-processing approach was proposed and the results were compared against existing literature methods. Most publications report PHA quantification of medium range in pure culture. However, in our study we encompassed both mixed and pure culture biomass containing a broader range of PHA in the calibration curve. The resulting prediction model is useful for rapid quantification of a wider range of PHA content in biomass. © 2016 The Society for Applied Microbiology.

Being Something: Prospects for a Property-Based Approach to Predicative Quantification

ERIC Educational Resources Information Center

Rieppel, Michael Olivier

2013-01-01

Few questions concerning the character of our talk about the world are more basic than how predicates combine with names to form truth-evaluable sentences. One particularly intriguing fact that any account of predication needs to make room for is that natural language allows for quantification into predicate position, through constructions like…

Quantification of triglyceride content in oleaginous materials using thermo-gravimetry

DOE PAGES

Maddi, Balakrishna; Vadlamani, Agasteswar; Viamajala, Sridhar; ...

2017-10-16

Laboratory analytical methods for quantification of triglyceride content in oleaginous biomass samples, especially microalgae, require toxic chemicals and/or organic solvents and involve multiple steps. We describe a simple triglyceride quantification method that uses thermo-gravimetry. This method is based on the observation that triglycerides undergo near-complete volatilization/degradation over a narrow temperature interval with a derivative weight loss peak at 420 °C when heated in an inert atmosphere. Degradation of the other constituents of oleaginous biomass (protein and carbohydrates) is largely complete after prolonged exposure of samples at 320 °C. Based on these observations, the triglyceride content of oleaginous biomass was estimatedmore » by using the following two-step process. In Step 1, samples were heated to 320 °C and kept isothermal at this temperature for 15 min. In Step 2, samples were heated from 320 °C to 420 °C and then kept isothermal at 420 °C for 15 min. The results show that mass loss in step 2 correlated well with triglyceride content estimates obtained from conventional techniques for diverse microalgae and oilseed samples.« less

Quantification of triglyceride content in oleaginous materials using thermo-gravimetry

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

Maddi, Balakrishna; Vadlamani, Agasteswar; Viamajala, Sridhar

Laboratory analytical methods for quantification of triglyceride content in oleaginous biomass samples, especially microalgae, require toxic chemicals and/or organic solvents and involve multiple steps. We describe a simple triglyceride quantification method that uses thermo-gravimetry. This method is based on the observation that triglycerides undergo near-complete volatilization/degradation over a narrow temperature interval with a derivative weight loss peak at 420 °C when heated in an inert atmosphere. Degradation of the other constituents of oleaginous biomass (protein and carbohydrates) is largely complete after prolonged exposure of samples at 320 °C. Based on these observations, the triglyceride content of oleaginous biomass was estimatedmore » by using the following two-step process. In Step 1, samples were heated to 320 °C and kept isothermal at this temperature for 15 min. In Step 2, samples were heated from 320 °C to 420 °C and then kept isothermal at 420 °C for 15 min. The results show that mass loss in step 2 correlated well with triglyceride content estimates obtained from conventional techniques for diverse microalgae and oilseed samples.« less

Fingerprinting and quantification of GMOs in the agro-food sector.

PubMed

Taverniers, I; Van Bockstaele, E; De Loose, M

2003-01-01

Most strategies for analyzing GMOs in plants and derived food and feed products, are based on the polymerase chain reaction (PCR) technique. In conventional PCR methods, a 'known' sequence between two specific primers is amplified. To the contrary, with the 'anchor PCR' technique, unknown sequences adjacent to a known sequence, can be amplified. Because T-DNA/plant border sequences are being amplified, anchor PCR is the perfect tool for unique identification of transgenes, including non-authorized GMOs. In this work, anchor PCR was applied to characterize the 'transgene locus' and to clarify the complete molecular structure of at least six different commercial transgenic plants. Based on sequences of T-DNA/plant border junctions, obtained by anchor PCR, event specific primers were developed. The junction fragments, together with endogeneous reference gene targets, were cloned in plasmids. The latter were then used as event specific calibrators in real-time PCR, a new technique for the accurate relative quantification of GMOs. We demonstrate here the importance of anchor PCR for identification and the usefulness of plasmid DNA calibrators in quantification strategies for GMOs, throughout the agro-food sector.

Antibiotic Resistome: Improving Detection and Quantification Accuracy for Comparative Metagenomics.

PubMed

Elbehery, Ali H A; Aziz, Ramy K; Siam, Rania

2016-04-01

The unprecedented rise of life-threatening antibiotic resistance (AR), combined with the unparalleled advances in DNA sequencing of genomes and metagenomes, has pushed the need for in silico detection of the resistance potential of clinical and environmental metagenomic samples through the quantification of AR genes (i.e., genes conferring antibiotic resistance). Therefore, determining an optimal methodology to quantitatively and accurately assess AR genes in a given environment is pivotal. Here, we optimized and improved existing AR detection methodologies from metagenomic datasets to properly consider AR-generating mutations in antibiotic target genes. Through comparative metagenomic analysis of previously published AR gene abundance in three publicly available metagenomes, we illustrate how mutation-generated resistance genes are either falsely assigned or neglected, which alters the detection and quantitation of the antibiotic resistome. In addition, we inspected factors influencing the outcome of AR gene quantification using metagenome simulation experiments, and identified that genome size, AR gene length, total number of metagenomics reads and selected sequencing platforms had pronounced effects on the level of detected AR. In conclusion, our proposed improvements in the current methodologies for accurate AR detection and resistome assessment show reliable results when tested on real and simulated metagenomic datasets.

TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics

PubMed Central

Röst, Hannes L.; Liu, Yansheng; D’Agostino, Giuseppe; Zanella, Matteo; Navarro, Pedro; Rosenberger, George; Collins, Ben C.; Gillet, Ludovic; Testa, Giuseppe; Malmström, Lars; Aebersold, Ruedi

2016-01-01

Large scale, quantitative proteomic studies have become essential for the analysis of clinical cohorts, large perturbation experiments and systems biology studies. While next-generation mass spectrometric techniques such as SWATH-MS have substantially increased throughput and reproducibility, ensuring consistent quantification of thousands of peptide analytes across multiple LC-MS/MS runs remains a challenging and laborious manual process. To produce highly consistent and quantitatively accurate proteomics data matrices in an automated fashion, we have developed the TRIC software which utilizes fragment ion data to perform cross-run alignment, consistent peak-picking and quantification for high throughput targeted proteomics. TRIC uses a graph-based alignment strategy based on non-linear retention time correction to integrate peak elution information from all LC-MS/MS runs acquired in a study. When compared to state-of-the-art SWATH-MS data analysis, the algorithm was able to reduce the identification error by more than 3-fold at constant recall, while correcting for highly non-linear chromatographic effects. On a pulsed-SILAC experiment performed on human induced pluripotent stem (iPS) cells, TRIC was able to automatically align and quantify thousands of light and heavy isotopic peak groups and substantially increased the quantitative completeness and biological information in the data, providing insights into protein dynamics of iPS cells. Overall, this study demonstrates the importance of consistent quantification in highly challenging experimental setups, and proposes an algorithm to automate this task, constituting the last missing piece in a pipeline for automated analysis of massively parallel targeted proteomics datasets. PMID:27479329

Quantification of susceptibility change at high-concentrated SPIO-labeled target by characteristic phase gradient recognition.

PubMed

Zhu, Haitao; Nie, Binbin; Liu, Hua; Guo, Hua; Demachi, Kazuyuki; Sekino, Masaki; Shan, Baoci

2016-05-01

Phase map cross-correlation detection and quantification may produce highlighted signal at superparamagnetic iron oxide nanoparticles, and distinguish them from other hypointensities. The method may quantify susceptibility change by performing least squares analysis between a theoretically generated magnetic field template and an experimentally scanned phase image. Because characteristic phase recognition requires the removal of phase wrap and phase background, additional steps of phase unwrapping and filtering may increase the chance of computing error and enlarge the inconsistence among algorithms. To solve problem, phase gradient cross-correlation and quantification method is developed by recognizing characteristic phase gradient pattern instead of phase image because phase gradient operation inherently includes unwrapping and filtering functions. However, few studies have mentioned the detectable limit of currently used phase gradient calculation algorithms. The limit may lead to an underestimation of large magnetic susceptibility change caused by high-concentrated iron accumulation. In this study, mathematical derivation points out the value of maximum detectable phase gradient calculated by differential chain algorithm in both spatial and Fourier domain. To break through the limit, a modified quantification method is proposed by using unwrapped forward differentiation for phase gradient generation. The method enlarges the detectable range of phase gradient measurement and avoids the underestimation of magnetic susceptibility. Simulation and phantom experiments were used to quantitatively compare different methods. In vivo application performs MRI scanning on nude mice implanted by iron-labeled human cancer cells. Results validate the limit of detectable phase gradient and the consequent susceptibility underestimation. Results also demonstrate the advantage of unwrapped forward differentiation compared with differential chain algorithms for susceptibility

Simultaneous quantification of adalimumab and infliximab in human plasma by liquid chromatography-tandem mass spectrometry.

PubMed

Jourdil, Jean-François; Némoz, Benjamin; Gautier-Veyret, Elodie; Romero, Charlotte; Stanke-Labesque, Françoise

2018-03-30

Adalimumab (ADA) and infliximab (IFX) are therapeutic monoclonal antibodies (TMabs) targeting tumor necrosis factor-alpha (TNFα). They are used to treat inflammatory diseases. Clinical trials have suggested that therapeutic drug monitoring for ADA or IFX could improve treatment response and cost-effectiveness. However, ADA and IFX were quantified by ELISA in all these studies, and the discrepancies between the results obtained raise questions about their reliability.We describe here the validation of a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for the simultaneous quantification of ADA and IFX in human samples. Full-length antibodies labeled with stable isotopes were added to plasma samples as an internal standard. Samples were then prepared using Mass Spectrometry Immuno Assay (MSIA) followed by trypsin digestion prior ADA and IFX quantification by LC-MS/MS.ADA and IFX were quantified in serum from patients treated with ADA (n=21) or IFX (n=22), and the concentrations obtained were compared with those obtained with a commercial ELISA kit. The chromatography run lasted 8.6 minutes and the quantification range was 1 to 26 mg/L. The method was reproducible, repeatable and accurate. For both levels of internal quality control, for ADA and IFX inter and intra-day coefficients of variation and accuracies were all within 15%, in accordance with FDA recommendations. No significant cross-contamination effect was noted.Good agreement was found between LC-MS/MS and ELISA results, for both ADA and IFX. This LC-MS/MS method can be used for the quantification of ADA and IFX in a single analytical run and for the optimization of LC-MS/MS resource use in clinical pharmacology laboratories.

Quantification of immobilized Candida antarctica lipase B (CALB) using ICP-AES combined with Bradford method.

PubMed

Nicolás, Paula; Lassalle, Verónica L; Ferreira, María L

2017-02-01

The aim of this manuscript was to study the application of a new method of protein quantification in Candida antarctica lipase B commercial solutions. Error sources associated to the traditional Bradford technique were demonstrated. Eight biocatalysts based on C. antarctica lipase B (CALB) immobilized onto magnetite nanoparticles were used. Magnetite nanoparticles were coated with chitosan (CHIT) and modified with glutaraldehyde (GLUT) and aminopropyltriethoxysilane (APTS). Later, CALB was adsorbed on the modified support. The proposed novel protein quantification method included the determination of sulfur (from protein in CALB solution) by means of Atomic Emission by Inductive Coupling Plasma (AE-ICP). Four different protocols were applied combining AE-ICP and classical Bradford assays, besides Carbon, Hydrogen and Nitrogen (CHN) analysis. The calculated error in protein content using the "classic" Bradford method with bovine serum albumin as standard ranged from 400 to 1200% when protein in CALB solution was quantified. These errors were calculated considering as "true protein content values" the results of the amount of immobilized protein obtained with the improved method. The optimum quantification procedure involved the combination of Bradford method, ICP and CHN analysis. Copyright © 2016 Elsevier Inc. All rights reserved.

Evaluation of Direct Infusion-Multiple Reaction Monitoring Mass Spectrometry for Quantification of Heat Shock Proteins

PubMed Central

Xiang, Yun; Koomen, John M.

2012-01-01

Protein quantification with liquid chromatography-multiple reaction monitoring mass spectrometry (LC-MRM) has emerged as a powerful platform for assessing panels of biomarkers. In this study, direct infusion, using automated, chip-based nanoelectrospray ionization, coupled with MRM (DI-MRM) is used for protein quantification. Removal of the LC separation step increases the importance of evaluating the ratios between the transitions. Therefore, the effects of solvent composition, analyte concentration, spray voltage, and quadrupole resolution settings on fragmentation patterns have been studied using peptide and protein standards. After DI-MRM quantification was evaluated for standards, quantitative assays for the expression of heat shock proteins (HSPs) were translated from LC-MRM to DI-MRM for implementation in cell line models of multiple myeloma. Requirements for DI-MRM assay development are described. Then, the two methods are compared; criteria for effective DI-MRM analysis are reported based on the analysis of HSP expression in digests of whole cell lysates. The increased throughput of DI-MRM analysis is useful for rapid analysis of large batches of similar samples, such as time course measurements of cellular responses to therapy. PMID:22293045

Application of Targeted Mass Spectrometry for the Quantification of Sirtuins in the Central Nervous System

NASA Astrophysics Data System (ADS)

Jayasena, T.; Poljak, A.; Braidy, N.; Zhong, L.; Rowlands, B.; Muenchhoff, J.; Grant, R.; Smythe, G.; Teo, C.; Raftery, M.; Sachdev, P.

2016-10-01

Sirtuin proteins have a variety of intracellular targets, thereby regulating multiple biological pathways including neurodegeneration. However, relatively little is currently known about the role or expression of the 7 mammalian sirtuins in the central nervous system. Western blotting, PCR and ELISA are the main techniques currently used to measure sirtuin levels. To achieve sufficient sensitivity and selectivity in a multiplex-format, a targeted mass spectrometric assay was developed and validated for the quantification of all seven mammalian sirtuins (SIRT1-7). Quantification of all peptides was by multiple reaction monitoring (MRM) using three mass transitions per protein-specific peptide, two specific peptides for each sirtuin and a stable isotope labelled internal standard. The assay was applied to a variety of samples including cultured brain cells, mammalian brain tissue, CSF and plasma. All sirtuin peptides were detected in the human brain, with SIRT2 being the most abundant. Sirtuins were also detected in human CSF and plasma, and guinea pig and mouse tissues. In conclusion, we have successfully applied MRM mass spectrometry for the detection and quantification of sirtuin proteins in the central nervous system, paving the way for more quantitative and functional studies.

Design and characterization of a direct ELISA for the detection and quantification of leucomalachite green

PubMed Central

Singh, Gurmit; Koerner, Terence; Gelinas, Jean-Marc; Abbott, Michael; Brady, Beth; Huet, Anne-Catherine; Charlier, Caroline; Delahaut, Philippe; Godefroy, Samuel Benrejeb

2011-01-01

Malachite green (MG), a member of the N-methylated triphenylmethane class of dyes, has long been used to control fungal and protozoan infections in fish. MG is easily absorbed by fish during waterborne exposure and is rapidly metabolized into leucomalachite green (LMG), which is known for its long residence time in edible fish tissue. This paper describes the development of an enzyme-linked immunosorbent assay (ELISA) for the detection and quantification of LMG in fish tissue. This development includes a simple and versatile method for the conversion of LMG to monodesmethyl-LMG, which is then conjugated to bovine serum albumin (BSA) to produce an immunogenic material. Rabbit polyclonal antibodies are generated against this immunogen, purified and used to develop a direct competitive enzyme-linked immunosorbent assay (ELISA) for the screening and quantification of LMG in fish tissue. The assay performed well, with a limit of detection (LOD) and limit of quantification (LOQ) of 0.1 and 0.3 ng g−1 of fish tissue, respectively. The average extraction efficiency from a matrix of tilapia fillets was approximately 73% and the day-to-day reproducibility for these extractions in the assay was between 5 and 10%. PMID:21623496

Quantum non-Gaussianity and quantification of nonclassicality

NASA Astrophysics Data System (ADS)

Kühn, B.; Vogel, W.

2018-05-01

The algebraic quantification of nonclassicality, which naturally arises from the quantum superposition principle, is related to properties of regular nonclassicality quasiprobabilities. The latter are obtained by non-Gaussian filtering of the Glauber-Sudarshan P function. They yield lower bounds for the degree of nonclassicality. We also derive bounds for convex combinations of Gaussian states for certifying quantum non-Gaussianity directly from the experimentally accessible nonclassicality quasiprobabilities. Other quantum-state representations, such as s -parametrized quasiprobabilities, insufficiently indicate or even fail to directly uncover detailed information on the properties of quantum states. As an example, our approach is applied to multi-photon-added squeezed vacuum states.

Multiplex quantification of protein toxins in human biofluids and food matrices using immunoextraction and high-resolution targeted mass spectrometry.

PubMed

Dupré, Mathieu; Gilquin, Benoit; Fenaille, François; Feraudet-Tarisse, Cécile; Dano, Julie; Ferro, Myriam; Simon, Stéphanie; Junot, Christophe; Brun, Virginie; Becher, François

2015-08-18

The development of rapid methods for unambiguous identification and precise quantification of protein toxins in various matrices is essential for public health surveillance. Nowadays, analytical strategies classically rely on sensitive immunological assays, but mass spectrometry constitutes an attractive complementary approach thanks to direct measurement and protein characterization ability. We developed here an innovative multiplex immuno-LC-MS/MS method for the simultaneous and specific quantification of the three potential biological warfare agents, ricin, staphylococcal enterotoxin B, and epsilon toxin, in complex human biofluids and food matrices. At least 7 peptides were targeted for each toxin (43 peptides in total) with a quadrupole-Orbitrap high-resolution instrument for exquisite detection specificity. Quantification was performed using stable isotope-labeled toxin standards spiked early in the sample. Lower limits of quantification were determined at or close to 1 ng·mL(-1). The whole process was successfully applied to the quantitative analysis of toxins in complex samples such as milk, human urine, and plasma. Finally, we report new data on toxin stability with no evidence of toxin degradation in milk in a 48 h time frame, allowing relevant quantitative toxin analysis for samples collected in this time range.

Quantification of excess water loss in plant canopies warmed with infrared heating

USDA-ARS?s Scientific Manuscript database

Here we investigate the extent to which infrared heating used to warm plant canopies in climate manipulation experiments increases transpiration. Concerns regarding the impact of the infrared heater technique on the water balance have been raised before, but a quantification is lacking. We calculate...

PCR technology for screening and quantification of genetically modified organisms (GMOs).

PubMed

Holst-Jensen, Arne; Rønning, Sissel B; Løvseth, Astrid; Berdal, Knut G

2003-04-01

Although PCR technology has obvious limitations, the potentially high degree of sensitivity and specificity explains why it has been the first choice of most analytical laboratories interested in detection of genetically modified (GM) organisms (GMOs) and derived materials. Because the products that laboratories receive for analysis are often processed and refined, the quality and quantity of target analyte (e.g. protein or DNA) frequently challenges the sensitivity of any detection method. Among the currently available methods, PCR methods are generally accepted as the most sensitive and reliable methods for detection of GM-derived material in routine applications. The choice of target sequence motif is the single most important factor controlling the specificity of the PCR method. The target sequence is normally a part of the modified gene construct, for example a promoter, a terminator, a gene, or a junction between two of these elements. However, the elements may originate from wildtype organisms, they may be present in more than one GMO, and their copy number may also vary from one GMO to another. They may even be combined in a similar way in more than one GMO. Thus, the choice of method should fit the purpose. Recent developments include event-specific methods, particularly useful for identification and quantification of GM content. Thresholds for labelling are now in place in many countries including those in the European Union. The success of the labelling schemes is dependent upon the efficiency with which GM-derived material can be detected. We will present an overview of currently available PCR methods for screening and quantification of GM-derived DNA, and discuss their applicability and limitations. In addition, we will discuss some of the major challenges related to determination of the limits of detection (LOD) and quantification (LOQ), and to validation of methods.

Quantification of penicillin G during labor and delivery by capillary electrophoresis.

PubMed

Thomas, Andrea; Ukpoma, Omon K; Inman, Jennifer A; Kaul, Anil K; Beeson, James H; Roberts, Kenneth P

2008-04-24

In this study, a capillary electrophoresis (CE) method was developed as a means to measure levels of penicillin G (PCN G) in Group B Streptococcus (GBS) positive pregnant women during labor and delivery. Volunteers for this developmental study were administered five million units of PCN G at the onset of labor. Urine, blood, and amniotic fluid samples were collected during labor and post delivery. Samples were semi-purified by solid-phase extraction (SPE) using Waters tC18 SepPak 3cc cartridges with a sodium phosphate/methanol step gradient for elution. Capillary electrophoresis or reversed-phase high-performance liquid chromatography (RP-HPLC) with diode-array absorbance detection were used to separate the samples in less than 30 min. Quantification was accomplished by establishing a calibration curve with a linear dynamic range. The tC18 SPE methodology provided substantial sample clean-up with high recovery yields of PCN G ( approximately 90%). It was found that SPE was critical for maintaining the integrity of the separation column when using RP-HPLC, but was not necessary for sample analysis by CE where no stationary phase is present. Quantification results ranged from millimolar concentrations of PCN G in maternal urine to micromolar concentrations in amniotic fluid. Serum and cord blood levels of PCN G were below quantification limits, which is likely due to the prolonged delay in sample collection after antibiotic administration. These results show that CE can serve as a simple and effective means to characterize the pharmacokinetic distribution of PCN G from mother to unborn fetus during labor and delivery. It is anticipated that similar methodologies have the potential to provide a quick, simple, and cost-effective means of monitoring the clinical efficacy of PCN G and other drugs during pregnancy.

On the complex quantification of risk: systems-based perspective on terrorism.

PubMed

Haimes, Yacov Y

2011-08-01

This article highlights the complexity of the quantification of the multidimensional risk function, develops five systems-based premises on quantifying the risk of terrorism to a threatened system, and advocates the quantification of vulnerability and resilience through the states of the system. The five premises are: (i) There exists interdependence between a specific threat to a system by terrorist networks and the states of the targeted system, as represented through the system's vulnerability, resilience, and criticality-impact. (ii) A specific threat, its probability, its timing, the states of the targeted system, and the probability of consequences can be interdependent. (iii) The two questions in the risk assessment process: "What is the likelihood?" and "What are the consequences?" can be interdependent. (iv) Risk management policy options can reduce both the likelihood of a threat to a targeted system and the associated likelihood of consequences by changing the states (including both vulnerability and resilience) of the system. (v) The quantification of risk to a vulnerable system from a specific threat must be built on a systemic and repeatable modeling process, by recognizing that the states of the system constitute an essential step to construct quantitative metrics of the consequences based on intelligence gathering, expert evidence, and other qualitative information. The fact that the states of all systems are functions of time (among other variables) makes the time frame pivotal in each component of the process of risk assessment, management, and communication. Thus, risk to a system, caused by an initiating event (e.g., a threat) is a multidimensional function of the specific threat, its probability and time frame, the states of the system (representing vulnerability and resilience), and the probabilistic multidimensional consequences. © 2011 Society for Risk Analysis.

Quantification of RNA Content in Reconstituted Ebola Virus Nucleocapsids by Immunoprecipitation.

PubMed

Banadyga, Logan; Ebihara, Hideki

2017-01-01

Immunoprecipitations are commonly used to isolate proteins or protein complexes and assess protein-protein interactions; however, they can also be used to assess protein-RNA complexes. Here we describe an adapted RNA immunoprecipitation technique that permits the quantification of RNA content in Ebola virus nucleocapsids that have been reconstituted in vitro by transient transfection.

Spot quantification in two dimensional gel electrophoresis image analysis: comparison of different approaches and presentation of a novel compound fitting algorithm

PubMed Central

2014-01-01

Background Various computer-based methods exist for the detection and quantification of protein spots in two dimensional gel electrophoresis images. Area-based methods are commonly used for spot quantification: an area is assigned to each spot and the sum of the pixel intensities in that area, the so-called volume, is used a measure for spot signal. Other methods use the optical density, i.e. the intensity of the most intense pixel of a spot, or calculate the volume from the parameters of a fitted function. Results In this study we compare the performance of different spot quantification methods using synthetic and real data. We propose a ready-to-use algorithm for spot detection and quantification that uses fitting of two dimensional Gaussian function curves for the extraction of data from two dimensional gel electrophoresis (2-DE) images. The algorithm implements fitting using logical compounds and is computationally efficient. The applicability of the compound fitting algorithm was evaluated for various simulated data and compared with other quantification approaches. We provide evidence that even if an incorrect bell-shaped function is used, the fitting method is superior to other approaches, especially when spots overlap. Finally, we validated the method with experimental data of urea-based 2-DE of Aβ peptides andre-analyzed published data sets. Our methods showed higher precision and accuracy than other approaches when applied to exposure time series and standard gels. Conclusion Compound fitting as a quantification method for 2-DE spots shows several advantages over other approaches and could be combined with various spot detection methods. The algorithm was scripted in MATLAB (Mathworks) and is available as a supplemental file. PMID:24915860

Electrochemical Quantification of the Antioxidant Capacity of Medicinal Plants Using Biosensors

PubMed Central

Rodríguez-Sevilla, Erika; Ramírez-Silva, María-Teresa; Romero-Romo, Mario; Ibarra-Escutia, Pedro; Palomar-Pardavé, Manuel

2014-01-01

The working area of a screen-printed electrode, SPE, was modified with the enzyme tyrosinase (Tyr) using different immobilization methods, namely entrapment with water-soluble polyvinyl alcohol (PVA), cross-linking using glutaraldehyde (GA), and cross-linking using GA and human serum albumin (HSA); the resulting electrodes were termed SPE/Tyr/PVA, SPE/Tyr/GA and SPE/Tyr/HSA/GA, respectively. These biosensors were characterized by means of amperometry and EIS techniques. From amperometric evaluations, the apparent Michaelis-Menten constant, Km′, of each biosensor was evaluated while the respective charge transfer resistance, Rct, was assessed from impedance measurements. It was found that the SPE/Tyr/GA had the smallest Km′ (57 ± 7) μM and Rct values. This electrode also displayed both the lowest detection and quantification limits for catechol quantification. Using the SPE/Tyr/GA, the Trolox Equivalent Antioxidant Capacity (TEAC) was determined from infusions prepared with “mirto” (Salvia microphylla), “hHierba dulce” (Lippia dulcis) and “salve real” (Lippia alba), medicinal plants commonly used in Mexico. PMID:25111237

Droplet Digital Enzyme-Linked Oligonucleotide Hybridization Assay for Absolute RNA Quantification.

PubMed

Guan, Weihua; Chen, Liben; Rane, Tushar D; Wang, Tza-Huei

2015-09-03

We present a continuous-flow droplet-based digital Enzyme-Linked Oligonucleotide Hybridization Assay (droplet digital ELOHA) for sensitive detection and absolute quantification of RNA molecules. Droplet digital ELOHA incorporates direct hybridization and single enzyme reaction via the formation of single probe-RNA-probe (enzyme) complex on magnetic beads. It enables RNA detection without reverse transcription and PCR amplification processes. The magnetic beads are subsequently encapsulated into a large number of picoliter-sized droplets with enzyme substrates in a continuous-flow device. This device is capable of generating droplets at high-throughput. It also integrates in-line enzymatic incubation and detection of fluorescent products. Our droplet digital ELOHA is able to accurately quantify (differentiate 40% difference) as few as ~600 RNA molecules in a 1 mL sample (equivalent to 1 aM or lower) without molecular replication. The absolute quantification ability of droplet digital ELOHA is demonstrated with the analysis of clinical Neisseria gonorrhoeae 16S rRNA to show its potential value in real complex samples.

Droplet Digital Enzyme-Linked Oligonucleotide Hybridization Assay for Absolute RNA Quantification

PubMed Central

Guan, Weihua; Chen, Liben; Rane, Tushar D.; Wang, Tza-Huei

2015-01-01

We present a continuous-flow droplet-based digital Enzyme-Linked Oligonucleotide Hybridization Assay (droplet digital ELOHA) for sensitive detection and absolute quantification of RNA molecules. Droplet digital ELOHA incorporates direct hybridization and single enzyme reaction via the formation of single probe-RNA-probe (enzyme) complex on magnetic beads. It enables RNA detection without reverse transcription and PCR amplification processes. The magnetic beads are subsequently encapsulated into a large number of picoliter-sized droplets with enzyme substrates in a continuous-flow device. This device is capable of generating droplets at high-throughput. It also integrates in-line enzymatic incubation and detection of fluorescent products. Our droplet digital ELOHA is able to accurately quantify (differentiate 40% difference) as few as ~600 RNA molecules in a 1 mL sample (equivalent to 1 aM or lower) without molecular replication. The absolute quantification ability of droplet digital ELOHA is demonstrated with the analysis of clinical Neisseria gonorrhoeae 16S rRNA to show its potential value in real complex samples. PMID:26333806

Microfluidic electrochemical assay for rapid detection and quantification of Escherichia coli.

PubMed

Safavieh, Mohammadali; Ahmed, Minhaz Uddin; Tolba, Mona; Zourob, Mohammed

2012-01-15

Microfluidic electrochemical biosensor for performing Loop-mediated isothermal amplification (LAMP) was developed for the detection and quantification of Escherichia coli. The electrochemical detection for detecting the DNA amplification was achieved using Hoechst 33258 redox molecule and linear sweep voltametry (LSV). The DNA aggregation and minor groove binding with redox molecule cause a significant drop in the anodic oxidation of LSV. Unlike other electrochemical techniques, this method does not require the probe immobilization and the detection of the bacteria can be accomplished in a single chamber without DNA extraction and purification steps. The isothermal amplification time has a major role in the quantification of the bacteria. We have shown that we could detect and quantify 24 CFU/ml of bacteria and 8.6 fg/μl DNA in 60 min and 48 CFU/ml of bacteria in 35 min in LB media and urine samples. We believe that this microfluidic chip has great potential to be used as a point of care diagnostic (POC) device in the clinical/hospital application. Copyright © 2011 Elsevier B.V. All rights reserved.

Droplet Digital Enzyme-Linked Oligonucleotide Hybridization Assay for Absolute RNA Quantification

NASA Astrophysics Data System (ADS)

Guan, Weihua; Chen, Liben; Rane, Tushar D.; Wang, Tza-Huei

2015-09-01

We present a continuous-flow droplet-based digital Enzyme-Linked Oligonucleotide Hybridization Assay (droplet digital ELOHA) for sensitive detection and absolute quantification of RNA molecules. Droplet digital ELOHA incorporates direct hybridization and single enzyme reaction via the formation of single probe-RNA-probe (enzyme) complex on magnetic beads. It enables RNA detection without reverse transcription and PCR amplification processes. The magnetic beads are subsequently encapsulated into a large number of picoliter-sized droplets with enzyme substrates in a continuous-flow device. This device is capable of generating droplets at high-throughput. It also integrates in-line enzymatic incubation and detection of fluorescent products. Our droplet digital ELOHA is able to accurately quantify (differentiate 40% difference) as few as ~600 RNA molecules in a 1 mL sample (equivalent to 1 aM or lower) without molecular replication. The absolute quantification ability of droplet digital ELOHA is demonstrated with the analysis of clinical Neisseria gonorrhoeae 16S rRNA to show its potential value in real complex samples.

Establishing Ion Ratio Thresholds Based on Absolute Peak Area for Absolute Protein Quantification using Protein Cleavage Isotope Dilution Mass Spectrometry

PubMed Central

Loziuk, Philip L.; Sederoff, Ronald R.; Chiang, Vincent L.; Muddiman, David C.

2014-01-01

Quantitative mass spectrometry has become central to the field of proteomics and metabolomics. Selected reaction monitoring is a widely used method for the absolute quantification of proteins and metabolites. This method renders high specificity using several product ions measured simultaneously. With growing interest in quantification of molecular species in complex biological samples, confident identification and quantitation has been of particular concern. A method to confirm purity or contamination of product ion spectra has become necessary for achieving accurate and precise quantification. Ion abundance ratio assessments were introduced to alleviate some of these issues. Ion abundance ratios are based on the consistent relative abundance (RA) of specific product ions with respect to the total abundance of all product ions. To date, no standardized method of implementing ion abundance ratios has been established. Thresholds by which product ion contamination is confirmed vary widely and are often arbitrary. This study sought to establish criteria by which the relative abundance of product ions can be evaluated in an absolute quantification experiment. These findings suggest that evaluation of the absolute ion abundance for any given transition is necessary in order to effectively implement RA thresholds. Overall, the variation of the RA value was observed to be relatively constant beyond an absolute threshold ion abundance. Finally, these RA values were observed to fluctuate significantly over a 3 year period, suggesting that these values should be assessed as close as possible to the time at which data is collected for quantification. PMID:25154770

Rapid quantification of plant-powdery mildew interactions by qPCR and conidiospore counts.

PubMed

Weßling, Ralf; Panstruga, Ralph

2012-08-31

The powdery mildew disease represents a valuable patho-system to study the interaction between plant hosts and obligate biotrophic fungal pathogens. Numerous discoveries have been made on the basis of the quantitative evaluation of plant-powdery mildew interactions, especially in the context of hyper-susceptible and/or resistant plant mutants. However, the presently available methods to score the pathogenic success of powdery mildew fungi are laborious and thus not well suited for medium- to high-throughput analysis. Here we present two new protocols that allow the rapid quantitative assessment of powdery mildew disease development. One procedure depends on quantitative polymerase chain reaction (qPCR)-based evaluation of fungal biomass, while the other relies on the quantification of fungal conidiospores. We validated both techniques using the powdery mildew pathogen Golovinomyces orontii on a set of hyper-susceptible and resistant Arabidopsis thaliana mutants and found that both cover a wide dynamic range of one to two (qPCR) and four to five (quantification of conidia) orders of magnitude, respectively. The two approaches yield reproducible results and are easy to perform without specialized equipment. The qPCR and spore count assays rapidly and reproducibly quantify powdery mildew pathogenesis. Our methods are performed at later stages of infection and discern mutant phenotypes accurately. The assays therefore complement currently used procedures of powdery mildew quantification and can overcome some of their limitations. In addition, they can easily be adapted to other plant-powdery mildew patho-systems.

Comparative quantification of human intestinal bacteria based on cPCR and LDR/LCR

PubMed Central

Tang, Zhou-Rui; Li, Kai; Zhou, Yu-Xun; Xiao, Zhen-Xian; Xiao, Jun-Hua; Huang, Rui; Gu, Guo-Hao

2012-01-01

AIM: To establish a multiple detection method based on comparative polymerase chain reaction (cPCR) and ligase detection reaction (LDR)/ligase chain reaction (LCR) to quantify the intestinal bacterial components. METHODS: Comparative quantification of 16S rDNAs from different intestinal bacterial components was used to quantify multiple intestinal bacteria. The 16S rDNAs of different bacteria were amplified simultaneously by cPCR. The LDR/LCR was examined to actualize the genotyping and quantification. Two beneficial (Bifidobacterium, Lactobacillus) and three conditionally pathogenic bacteria (Enterococcus, Enterobacterium and Eubacterium) were used in this detection. With cloned standard bacterial 16S rDNAs, standard curves were prepared to validate the quantitative relations between the ratio of original concentrations of two templates and the ratio of the fluorescence signals of their final ligation products. The internal controls were added to monitor the whole detection flow. The quantity ratio between two bacteria was tested. RESULTS: cPCR and LDR revealed obvious linear correlations with standard DNAs, but cPCR and LCR did not. In the sample test, the distributions of the quantity ratio between each two bacterial species were obtained. There were significant differences among these distributions in the total samples. But these distributions of quantity ratio of each two bacteria remained stable among groups divided by age or sex. CONCLUSION: The detection method in this study can be used to conduct multiple intestinal bacteria genotyping and quantification, and to monitor the human intestinal health status as well. PMID:22294830

Comparative quantification of human intestinal bacteria based on cPCR and LDR/LCR.

PubMed

Tang, Zhou-Rui; Li, Kai; Zhou, Yu-Xun; Xiao, Zhen-Xian; Xiao, Jun-Hua; Huang, Rui; Gu, Guo-Hao

2012-01-21

To establish a multiple detection method based on comparative polymerase chain reaction (cPCR) and ligase detection reaction (LDR)/ligase chain reaction (LCR) to quantify the intestinal bacterial components. Comparative quantification of 16S rDNAs from different intestinal bacterial components was used to quantify multiple intestinal bacteria. The 16S rDNAs of different bacteria were amplified simultaneously by cPCR. The LDR/LCR was examined to actualize the genotyping and quantification. Two beneficial (Bifidobacterium, Lactobacillus) and three conditionally pathogenic bacteria (Enterococcus, Enterobacterium and Eubacterium) were used in this detection. With cloned standard bacterial 16S rDNAs, standard curves were prepared to validate the quantitative relations between the ratio of original concentrations of two templates and the ratio of the fluorescence signals of their final ligation products. The internal controls were added to monitor the whole detection flow. The quantity ratio between two bacteria was tested. cPCR and LDR revealed obvious linear correlations with standard DNAs, but cPCR and LCR did not. In the sample test, the distributions of the quantity ratio between each two bacterial species were obtained. There were significant differences among these distributions in the total samples. But these distributions of quantity ratio of each two bacteria remained stable among groups divided by age or sex. The detection method in this study can be used to conduct multiple intestinal bacteria genotyping and quantification, and to monitor the human intestinal health status as well.

Impacts of the ENSO Modoki and other Tropical Indo-Pacific Climate-Drivers on African Rainfall

PubMed Central

Preethi, B.; Sabin, T. P.; Adedoyin, J. A.; Ashok, K.

2015-01-01

The study diagnoses the relative impacts of the four known tropical Indo-Pacific drivers, namely, El Niño Southern Oscillation (ENSO), ENSO Modoki, Indian Ocean Dipole (IOD), and Indian Ocean Basin-wide mode (IOBM) on African seasonal rainfall variability. The canonical El Niño and El Niño Modoki are in general associated with anomalous reduction (enhancement) of rainfall in southern (northern) hemispheric regions during March-May season. However, both the El Niño flavours anomalously reduce the northern hemispheric rainfall during June-September. Interestingly, during boreal spring and summer, in many regions, the Indian Ocean drivers have influences opposite to those from tropical Pacific drivers. On the other hand, during the October-December season, the canonical El Niño and/or positive IOD are associated with an anomalous enhancement of rainfall in the Eastern Africa, while the El Niño Modoki events are associated with an opposite impact. In addition to the Walker circulation changes, the Indo-Pacific drivers influence the African rainfall through modulating jet streams. During boreal summer, the El Niño Modoki and canonical El Niño (positive IOD) tend to weaken (strengthen) the tropical easterly jet, and result in strengthening (weakening) and southward shift of African easterly jet. This anomalously reduces (enhances) rainfall in the tropical north, including Sahelian Africa. PMID:26567458

Impacts of the ENSO Modoki and other Tropical Indo-Pacific Climate-Drivers on African Rainfall.

PubMed

Preethi, B; Sabin, T P; Adedoyin, J A; Ashok, K

2015-11-16

The study diagnoses the relative impacts of the four known tropical Indo-Pacific drivers, namely, El Niño Southern Oscillation (ENSO), ENSO Modoki, Indian Ocean Dipole (IOD), and Indian Ocean Basin-wide mode (IOBM) on African seasonal rainfall variability. The canonical El Niño and El Niño Modoki are in general associated with anomalous reduction (enhancement) of rainfall in southern (northern) hemispheric regions during March-May season. However, both the El Niño flavours anomalously reduce the northern hemispheric rainfall during June-September. Interestingly, during boreal spring and summer, in many regions, the Indian Ocean drivers have influences opposite to those from tropical Pacific drivers. On the other hand, during the October-December season, the canonical El Niño and/or positive IOD are associated with an anomalous enhancement of rainfall in the Eastern Africa, while the El Niño Modoki events are associated with an opposite impact. In addition to the Walker circulation changes, the Indo-Pacific drivers influence the African rainfall through modulating jet streams. During boreal summer, the El Niño Modoki and canonical El Niño (positive IOD) tend to weaken (strengthen) the tropical easterly jet, and result in strengthening (weakening) and southward shift of African easterly jet. This anomalously reduces (enhances) rainfall in the tropical north, including Sahelian Africa.

Screening, confirmation and quantification of boldenone sulfate in equine urine after administration of boldenone undecylenate (Equipoise).

PubMed

Weidolf, L O; Chichila, T M; Henion, J D

1988-12-09

Methods for screening by thin-layer chromatography, quantification by high-performance liquid chromatography with ultraviolet detection and confirmation by gas chromatography-mass spectrometry of boldenone sulfate in equine urine after administration of boldenone undecylenate (Equipoise) are presented. Sample work-up was done with C18 liquid-solid extraction followed by solvolytic cleavage of the sulfate ester. Confirmatory evidence of boldenone sulfate in equine urine was obtained from 2 h to 42 days following a therapeutic intramuscular dose of Equipoise. The use of 19-nortestosterone sulfate as the internal standard for quantification of boldenone sulfate is discussed.

Review of the quantification techniques for polycyclic aromatic hydrocarbons (PAHs) in food products.

PubMed

Bansal, Vasudha; Kumar, Pawan; Kwon, Eilhann E; Kim, Ki-Hyun

2017-10-13

There is a growing need for accurate detection of trace-level PAHs in food products due to the numerous detrimental effects caused by their contamination (e.g., toxicity, carcinogenicity, and teratogenicity). This review aims to discuss the up-to-date knowledge on the measurement techniques available for PAHs contained in food or its related products. This article aims to provide a comprehensive outline on the measurement techniques of PAHs in food to help reduce their deleterious impacts on human health based on the accurate quantification. The main part of this review is dedicated to the opportunities and practical options for the treatment of various food samples and for accurate quantification of PAHs contained in those samples. Basic information regarding all available analytical measurement techniques for PAHs in food samples is also evaluated with respect to their performance in terms of quality assurance.

Quantification by SEM-EDS in uncoated non-conducting samples

NASA Astrophysics Data System (ADS)

Galván Josa, V.; Castellano, G.; Bertolino, S. R.

2013-07-01

An approach to perform elemental quantitative analysis in a conventional scanning electron microscope with an energy dispersive spectrometer has been developed for non-conductive samples in which the conductive coating should be avoided. Charge accumulation effects, which basically decrease the energy of the primary beam, were taken into account by means of the Duane-Hunt limit. This value represents the maximum energy of the continuum X-ray spectrum, and is related to the effective energy of the incident electron beam. To validate the results obtained by this procedure, a non-conductive sample of known composition was quantified without conductive coating. Complementarily, changes in the X-ray spectrum due to charge accumulation effects were studied by Monte Carlo simulations, comparing relative characteristic intensities as a function of the incident energy. This methodology is exemplified here to obtain the chemical composition of white and reddish archaeological pigments belonging to the Ambato style of "Aguada" culture (Catamarca, Argentina 500-1100 AD). The results obtained in this work show that the quantification procedure taking into account the Duane-Hunt limit is suitable for this kind of samples. This approach may be recommended for the quantification of samples for which coating is not desirable, such as ancient artwork, forensic or archaeological samples, or when the coating element is also present in the sample.

Update on Controls for Isolation and Quantification Methodology of Extracellular Vesicles Derived from Adipose Tissue Mesenchymal Stem Cells

PubMed Central

Franquesa, Marcella; Hoogduijn, Martin J.; Ripoll, Elia; Luk, Franka; Salih, Mahdi; Betjes, Michiel G. H.; Torras, Juan; Baan, Carla C.; Grinyó, Josep M.; Merino, Ana Maria

2014-01-01

The research field on extracellular vesicles (EV) has rapidly expanded in recent years due to the therapeutic potential of EV. Adipose tissue human mesenchymal stem cells (ASC) may be a suitable source for therapeutic EV. A major limitation in the field is the lack of standardization of the challenging techniques to isolate and characterize EV. The aim of our study was to incorporate new controls for the detection and quantification of EV derived from ASC and to analyze the applicability and limitations of the available techniques. ASC were cultured in medium supplemented with 5% of vesicles-free fetal bovine serum. The EV were isolated from conditioned medium by differential centrifugation with size filtration (0.2 μm). As a control, non-conditioned culture medium was used (control medium). To detect EV, electron microscopy, conventional flow cytometry, and western blot were used. The quantification of the EV was by total protein quantification, ExoELISA immunoassay, and Nanosight. Cytokines and growth factors in the EV samples were measured by multiplex bead array kit. The EV were detected by electron microscope. Total protein measurement was not useful to quantify EV as the control medium showed similar protein contents as the EV samples. The ExoELISA kits had technical troubles and it was not possible to quantify the concentration of exosomes in the samples. The use of Nanosight enabled quantification and size determination of the EV. It is, however, not possible to distinguish protein aggregates from EV with this method. The technologies for quantification and characterization of the EV need to be improved. In addition, we detected protein contaminants in the EV samples, which make it difficult to determine the real effect of EV in experimental models. It will be crucial in the future to optimize design novel methods for purification and characterization of EV. PMID:25374572

[Performance evaluation of Abbott RealTime HBV Quantification Kit for HBV viral load by real-time PCR].

PubMed

Kim, Myeong Hee; Cha, Choong Hwan; An, Dongheui; Choi, Sung Eun; Oh, Heung Bum

2008-04-01

Hepatitis B virus (HBV) DNA quantification is necessary for starting and monitoring of antiviral therapy in patients with chronic hepatitis B. This study was intended to assess the clinical performance of Abbott RealTime HBV Quantification kit (Abbott Laboratories, USA). The performance was evaluated in terms of precision, linearity, detection sensitivity, cross-reactivity, and carry-over. A correlation with the Real-Q HBV Quantification kit (BioSewoom Inc., Korea) was also examined using serum samples from 64 patients diagnosed with chronic hepatitis B and underwent lamivudine therapy in Asan Medical Center. We verified the trueness of the system by comparing the outputs with the assigned values of the BBI panel (BBI Diagnostics, USA). Within-run and between-run coefficients of variation (CV) were 3.56-4.71% and 3.03-4.98%, respectively. Linearity was manifested ranging from 53 to 10(9)copies/mL and the detection sensitivity was verified to be 51 copies/mL. None of hepatitis C virus showed cross-reactivity. No cross-contamination occurred when negative and positive samples were alternatively placed in a row. It showed a good correlation with the Real-Q HBV (r(2)=0.9609) and the test results for the BBI panel were also well agreed to the assigned values (r(2)=0.9933). The performance of Abbott RealTime HBV Quantification kit was excellent; thus, it should be widely used in starting and monitoring of antiviral therapy in Korean patients with chronic hepatitis B.

Simultaneous quantification of 21 water soluble vitamin circulating forms in human plasma by liquid chromatography-mass spectrometry.

PubMed

Meisser Redeuil, Karine; Longet, Karin; Bénet, Sylvie; Munari, Caroline; Campos-Giménez, Esther

2015-11-27

This manuscript reports a validated analytical approach for the quantification of 21 water soluble vitamins and their main circulating forms in human plasma. Isotope dilution-based sample preparation consisted of protein precipitation using acidic methanol enriched with stable isotope labelled internal standards. Separation was achieved by reversed-phase liquid chromatography and detection performed by tandem mass spectrometry in positive electrospray ionization mode. Instrumental lower limits of detection and quantification reached <0.1-10nM and 0.2-25nM, respectively. Commercially available pooled human plasma was used to build matrix-matched calibration curves ranging 2-500, 5-1250, 20-5000 or 150-37500nM depending on the analyte. The overall performance of the method was considered adequate, with 2.8-20.9% and 5.2-20.0% intra and inter-day precision, respectively and averaged accuracy reaching 91-108%. Recovery experiments were also performed and reached in average 82%. This analytical approach was then applied for the quantification of circulating water soluble vitamins in human plasma single donor samples. The present report provides a sensitive and reliable approach for the quantification of water soluble vitamins and main circulating forms in human plasma. In the future, the application of this analytical approach will give more confidence to provide a comprehensive assessment of water soluble vitamins nutritional status and bioavailability studies in humans. Copyright © 2015 Elsevier B.V. All rights reserved.

Quantification of integrated HIV DNA by repetitive-sampling Alu-HIV PCR on the basis of poisson statistics.

PubMed

De Spiegelaere, Ward; Malatinkova, Eva; Lynch, Lindsay; Van Nieuwerburgh, Filip; Messiaen, Peter; O'Doherty, Una; Vandekerckhove, Linos

2014-06-01

Quantification of integrated proviral HIV DNA by repetitive-sampling Alu-HIV PCR is a candidate virological tool to monitor the HIV reservoir in patients. However, the experimental procedures and data analysis of the assay are complex and hinder its widespread use. Here, we provide an improved and simplified data analysis method by adopting binomial and Poisson statistics. A modified analysis method on the basis of Poisson statistics was used to analyze the binomial data of positive and negative reactions from a 42-replicate Alu-HIV PCR by use of dilutions of an integration standard and on samples of 57 HIV-infected patients. Results were compared with the quantitative output of the previously described Alu-HIV PCR method. Poisson-based quantification of the Alu-HIV PCR was linearly correlated with the standard dilution series, indicating that absolute quantification with the Poisson method is a valid alternative for data analysis of repetitive-sampling Alu-HIV PCR data. Quantitative outputs of patient samples assessed by the Poisson method correlated with the previously described Alu-HIV PCR analysis, indicating that this method is a valid alternative for quantifying integrated HIV DNA. Poisson-based analysis of the Alu-HIV PCR data enables absolute quantification without the need of a standard dilution curve. Implementation of the CI estimation permits improved qualitative analysis of the data and provides a statistical basis for the required minimal number of technical replicates. © 2014 The American Association for Clinical Chemistry.

Uncertainty quantification and optimal decisions

PubMed Central

2017-01-01

A mathematical model can be analysed to construct policies for action that are close to optimal for the model. If the model is accurate, such policies will be close to optimal when implemented in the real world. In this paper, the different aspects of an ideal workflow are reviewed: modelling, forecasting, evaluating forecasts, data assimilation and constructing control policies for decision-making. The example of the oil industry is used to motivate the discussion, and other examples, such as weather forecasting and precision agriculture, are used to argue that the same mathematical ideas apply in different contexts. Particular emphasis is placed on (i) uncertainty quantification in forecasting and (ii) how decisions are optimized and made robust to uncertainty in models and judgements. This necessitates full use of the relevant data and by balancing costs and benefits into the long term may suggest policies quite different from those relevant to the short term. PMID:28484343

Ultra-high Performance Liquid Chromatography Tandem Mass-Spectrometry for Simple and Simultaneous Quantification of Cannabinoids

PubMed Central

Jamwal, Rohitash; Topletz, Ariel R.; Ramratnam, Bharat; Akhlaghi, Fatemeh

2017-01-01

Cannabis is used widely in the United States, both recreationally and for medical purposes. Current methods for analysis of cannabinoids in human biological specimens rely on complex extraction process and lengthy analysis time. We established a rapid and simple assay for quantification of Δ9-tetrahydrocannabinol (THC), cannabidiol (CBD), 11-hydroxy Δ9-tetrahydrocannabinol (11-OH THC) and 11-nor-9-carboxy-Δ9-tetrahydrocannbinol (THC-COOH) in human plasma by U-HPLC-MS/MS using Δ9-tetrahydrocannabinol-D3 as the internal standard. Chromatographic separation was achieved on an Acquity BEH C18 column using a gradient comprising of water (0.1% formic acid) and methanol (0.1% formic acid) over a 6 min run-time. Analytes from 200 µL plasma were extracted using acetonitrile (containing 1% formic acid and THC-D3). Mass spectrometry was performed in positive ionization mode, and total ion chromatogram was used for quantification of analytes. The assay was validated according to guidelines set forth by Food and Drug Administration of United States. An eight-point calibration curve was fitted with quadratic regression (r2>0.99) from 1.56 to 100 ng mL−1 and a lower limit of quantification (LLOQ) of 1.56 ng mL−1 was achieved. Accuracy and precision calculated from six calibration curves was between 85 to 115% while the mean extraction recovery was >90% for all the analytes. Several plasma phospholipids eluted after the analytes thus did not interfere with the assay. Bench-top, freeze-thaw, auto-sampler and short-term stability ranged from 92.7 to 106.8% of nominal values. Application of the method was evaluated by quantification of analytes in human plasma from six subjects. PMID:28192758

Simultaneous quantification of the viral antigens hemagglutinin and neuraminidase in influenza vaccines by LC-MSE.

PubMed

Creskey, Marybeth C; Li, Changgui; Wang, Junzhi; Girard, Michel; Lorbetskie, Barry; Gravel, Caroline; Farnsworth, Aaron; Li, Xuguang; Smith, Daryl G S; Cyr, Terry D

2012-07-06

Current methods for quality control of inactivated influenza vaccines prior to regulatory approval include determining the hemagglutinin (HA) content by single radial immunodiffusion (SRID), verifying neuraminidase (NA) enzymatic activity, and demonstrating that the levels of the contaminant protein ovalbumin are below a set threshold of 1 μg/dose. The SRID assays require the availability of strain-specific reference HA antigens and antibodies, the production of which is a potential rate-limiting step in vaccine development and release, particularly during a pandemic. Immune responses induced by neuraminidase also contribute to protection from infection; however, the amounts of NA antigen in influenza vaccines are currently not quantified or standardized. Here, we report a method for vaccine analysis that yields simultaneous quantification of HA and NA levels much more rapidly than conventional HA quantification techniques, while providing additional valuable information on the total protein content. Enzymatically digested vaccine proteins were analyzed by LC-MS(E), a mass spectrometric technology that allows absolute quantification of analytes, including the HA and NA antigens, other structural influenza proteins and chicken egg proteins associated with the manufacturing process. This method has potential application for increasing the accuracy of reference antigen standards and for validating label claims for HA content in formulated vaccines. It can also be used to monitor NA and chicken egg protein content in order to monitor manufacturing consistency. While this is a useful methodology with potential for broad application, we also discuss herein some of the inherent limitations of this approach and the care and caution that must be taken in its use as a tool for absolute protein quantification. The variations in HA, NA and chicken egg protein concentrations in the vaccines analyzed in this study are indicative of the challenges associated with the current

Quantification of trans-1,4-polyisoprene in Eucommia ulmoides by fourier transform infrared spectroscopy and pyrolysis-gas chromatography/mass spectrometry.

PubMed

Takeno, Shinya; Bamba, Takeshi; Nakazawa, Yoshihisa; Fukusaki, Eiichiro; Okazawa, Atsushi; Kobayashi, Akio

2008-04-01

Commercial development of trans-1,4-polyisoprene from Eucommia ulmoides Oliver (EU-rubber) requires specific knowledge on selection of high-rubber-content lines and establishment of agronomic cultivation methods for achieving maximum EU-rubber yield. The development can be facilitated by high-throughput and highly sensitive analytical techniques for EU-rubber extraction and quantification. In this paper, we described an efficient EU-rubber extraction method, and validated that the accuracy was equivalent to that of the conventional Soxhlet extraction method. We also described a highly sensitive quantification method for EU-rubber by Fourier transform infrared spectroscopy (FT-IR) and pyrolysis-gas chromatography/mass spectrometry (PyGC/MS). We successfully applied the extraction/quantification method for study of seasonal changes in EU-rubber content and molecular weight distribution.

Microfluidic platform for detection and quantification of magnetic markers

NASA Astrophysics Data System (ADS)

Kokkinis, Georgios; Cardoso, Susana; Giouroudi, Ioanna

2017-05-01

This paper reports on a microfluidic platform with an integrated spin valve giant magneto-resistance (GMR) sensor used for the detection and quantification of single magnetic micromarkers. A microfluidic channel containing the magnetic fluid, microconductors (MCs) for collection of the magnetic markers and a spin valve GMR sensor for detecting the presence of their magnetic stray field were integrated on a single chip. The results show that the sensor is capable of detecting a single magnetic marker with 2.8 μm diameter.

Nondestructive Detection and Quantification of Blueberry Bruising using Near-infrared (NIR) Hyperspectral Reflectance Imaging

PubMed Central

Jiang, Yu; Li, Changying; Takeda, Fumiomi

2016-01-01

Currently, blueberry bruising is evaluated by either human visual/tactile inspection or firmness measurement instruments. These methods are destructive, time-consuming, and subjective. The goal of this paper was to develop a non-destructive approach for blueberry bruising detection and quantification. Experiments were conducted on 300 samples of southern highbush blueberry (Camellia, Rebel, and Star) and on 1500 samples of northern highbush blueberry (Bluecrop, Jersey, and Liberty) for hyperspectral imaging analysis, firmness measurement, and human evaluation. An algorithm was developed to automatically calculate a bruise ratio index (ratio of bruised to whole fruit area) for bruise quantification. The spectra of bruised and healthy tissues were statistically separated and the separation was independent of cultivars. Support vector machine (SVM) classification of the spectra from the regions of interest (ROIs) achieved over 94%, 92%, and 96% accuracy on the training set, independent testing set, and combined set, respectively. The statistical results showed that the bruise ratio index was equivalent to the measured firmness but better than the predicted firmness in regard to effectiveness of bruise quantification, and the bruise ratio index had a strong correlation with human assessment (R2 = 0.78 − 0.83). Therefore, the proposed approach and the bruise ratio index are effective to non-destructively detect and quantify blueberry bruising. PMID:27767050

Sensitive and selective quantification of free and total malondialdehyde in plasma using UHPLC-HRMS.

PubMed

Mendonça, Rute; Gning, Ophélie; Di Cesaré, Claudia; Lachat, Laurence; Bennett, Nigel C; Helfenstein, Fabrice; Glauser, Gaétan

2017-09-01

Quantification of malondialdehyde (MDA) as a marker of lipid peroxidation is relevant for many research fields. We describe a new sensitive and selective method to measure free and total plasmatic MDA using derivatization with 2,4-dinitrophenylhydrazine (DNPH) and ultra-HPLC-high-resolution MS. Free and total MDA were extracted from minute sample amounts (10 μl) using acidic precipitation and alkaline hydrolysis followed by acidic precipitation, respectively. Derivatization was completed within 10 min at room temperature, and the excess DNPH discarded by liquid-liquid extraction. Quantification was achieved by internal standardization using dideuterated MDA as internal standard. The method's lowest limit of quantification was 100 nM and linearity spanned greater than three orders of magnitude. Intra- and inter-day precisions for total MDA were 2.9% and 3.0%, respectively, and those for free MDA were 12.8% and 24.9%, respectively. Accuracy was 101% and 107% at low and high concentrations, respectively. In human plasma, free MDA levels were 120 nM (SD 36.26) and total MDA levels were 6.7 μM (SD 0.46). In addition, we show the applicability of this method to measure MDA plasma levels from a variety of animal species, making it invaluable to scientists in various fields. Copyright © 2017 by the American Society for Biochemistry and Molecular Biology, Inc.

Near-infrared spectroscopy for the detection and quantification of bacterial contaminations in pharmaceutical products.

PubMed

Quintelas, Cristina; Mesquita, Daniela P; Lopes, João A; Ferreira, Eugénio C; Sousa, Clara

2015-08-15

Accurate detection and quantification of microbiological contaminations remains an issue mainly due the lack of rapid and precise analytical techniques. Standard methods are expensive and time-consuming being associated to high economic losses and public health threats. In the context of pharmaceutical industry, the development of fast analytical techniques able to overcome these limitations is crucial and spectroscopic techniques might constitute a reliable alternative. In this work we proved the ability of Fourier transform near infrared spectroscopy (FT-NIRS) to detect and quantify bacteria (Bacillus subtilis, Escherichia coli, Pseudomonas fluorescens, Salmonella enterica, Staphylococcus epidermidis) from 10 to 10(8) CFUs/mL in sterile saline solutions (NaCl 0.9%). Partial least squares discriminant analysis (PLSDA) models showed that FT-NIRS was able to discriminate between sterile and contaminated solutions for all bacteria as well as to identify the contaminant bacteria. Partial least squares (PLS) models allowed bacterial quantification with limits of detection ranging from 5.1 to 9 CFU/mL for E. coli and B. subtilis, respectively. This methodology was successfully validated in three pharmaceutical preparations (contact lens solution, cough syrup and topic anti-inflammatory solution) proving that this technique possess a high potential to be routinely used for the detection and quantification of bacterial contaminations. Copyright © 2015 Elsevier B.V. All rights reserved.

A SIMPLE METHOD FOR THE EXTRACTION AND QUANTIFICATION OF PHOTOPIGMENTS FROM SYMBIODINIUM SPP.

EPA Science Inventory

John E. Rogers and Dragoslav Marcovich. Submitted. Simple Method for the Extraction and Quantification of Photopigments from Symbiodinium spp.. Limnol. Oceanogr. Methods. 19 p. (ERL,GB 1192).

We have developed a simple, mild extraction procedure using methanol which, when...

Quantification of Dynamic 11C-Phenytoin PET Studies.

PubMed

Mansor, Syahir; Boellaard, Ronald; Froklage, Femke E; Bakker, Esther D M; Yaqub, Maqsood; Voskuyl, Rob A; Schwarte, Lothar A; Verbeek, Joost; Windhorst, Albert D; Lammertsma, Adriaan

2015-09-01

The overexpression of P-glycoprotein (Pgp) is thought to be an important mechanism of pharmacoresistance in epilepsy. Recently, (11)C-phenytoin has been evaluated preclinically as a tracer for Pgp. The aim of the present study was to assess the optimal plasma kinetic model for quantification of (11)C-phenytoin studies in humans. Dynamic (11)C-phenytoin PET scans of 6 healthy volunteers with arterial sampling were acquired twice on the same day and analyzed using single- and 2-tissue-compartment models with and without a blood volume parameter. Global and regional test-retest (TRT) variability was determined for both plasma to tissue rate constant (K1) and volume of distribution (VT). According to the Akaike information criterion, the reversible single-tissue-compartment model with blood volume parameter was the preferred plasma input model. Mean TRT variability ranged from 1.5% to 16.9% for K1 and from 0.5% to 5.8% for VT. Larger volumes of interest showed better repeatabilities than smaller regions. A 45-min scan provided essentially the same K1 and VT values as a 60-min scan. A reversible single-tissue-compartment model with blood volume seems to be a good candidate model for quantification of dynamic (11)C-phenytoin studies. Scan duration may be reduced to 45 min without notable loss of accuracy and precision of both K1 and VT, although this still needs to be confirmed under pathologic conditions. © 2015 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

AQuA: An Automated Quantification Algorithm for High-Throughput NMR-Based Metabolomics and Its Application in Human Plasma.

PubMed

Röhnisch, Hanna E; Eriksson, Jan; Müllner, Elisabeth; Agback, Peter; Sandström, Corine; Moazzami, Ali A

2018-02-06

A key limiting step for high-throughput NMR-based metabolomics is the lack of rapid and accurate tools for absolute quantification of many metabolites. We developed, implemented, and evaluated an algorithm, AQuA (Automated Quantification Algorithm), for targeted metabolite quantification from complex 1 H NMR spectra. AQuA operates based on spectral data extracted from a library consisting of one standard calibration spectrum for each metabolite. It uses one preselected NMR signal per metabolite for determining absolute concentrations and does so by effectively accounting for interferences caused by other metabolites. AQuA was implemented and evaluated using experimental NMR spectra from human plasma. The accuracy of AQuA was tested and confirmed in comparison with a manual spectral fitting approach using the ChenomX software, in which 61 out of 67 metabolites quantified in 30 human plasma spectra showed a goodness-of-fit (r 2 ) close to or exceeding 0.9 between the two approaches. In addition, three quality indicators generated by AQuA, namely, occurrence, interference, and positional deviation, were studied. These quality indicators permit evaluation of the results each time the algorithm is operated. The efficiency was tested and confirmed by implementing AQuA for quantification of 67 metabolites in a large data set comprising 1342 experimental spectra from human plasma, in which the whole computation took less than 1 s.

Simultaneous quantification of hepatic MRI-PDFF and R2* in a rabbit model with nonalcoholic fatty liver disease.

PubMed

Wang, Xiaomin; Zhang, Xiaojing; Ma, Lin; Li, Shengli

2018-06-20

Quantification of hepatic fat and iron content is important for early detection and monitoring of nonalcoholic fatty liver disease (NAFLD) patients. This study evaluated quantification efficiency of hepatic proton density fat fraction (PDFF) by MRI using NAFLD rabbits. R2* was also measured to investigate whether it correlates with fat levels in NAFLD. NAFLD rabbit model was successfully established by high fat and cholesterol diet. Rabbits underwent MRI examination for fat and iron analyses, compared with liver histological findings. MR examinations were performed on a 3.0T MR system using multi-echo 3D gradient recalled echo (GRE) sequence. MRI-PDFF showed significant differences between different steatosis grades with medians of 3.72% (normal), 5.43% (mild), 9.11% (moderate) and 11.17% (severe), whereas this was not observed in R2*. Close correlation between MRI-PDFF and histological steatosis was observed (r=0.78, P=0.000). Hepatic iron deposit was not found in any rabbits. There was no correlation between R2* and either liver MRI-PDFF or histological steatosis. MR measuring MRI-PDFF and R2* simultaneously provides promising quantification of steatosis and iron. Rabbit NAFLD model confirmed accuracy of MRI-PDFF for liver fat quantification. R2* measurement and relationship between fat and iron of NAFLD liver need further experimental investigation.

Asian Monsoon Variability from the Monsoon Asia Drought Atlas (MADA) and Links to Indo-Pacific Climate

NASA Astrophysics Data System (ADS)

Ummenhofer, Caroline; D'Arrigo, Rosanne; Anchukaitis, Kevin; Hernandez, Manuel; Buckley, Brendan; Cook, Edward

2014-05-01

Drought patterns across monsoon and temperate Asia over the period 1877-2005 are linked to Indo-Pacific climate variability associated with the El Niño-Southern Oscillation (ENSO) and the Indian Ocean Dipole (IOD). Using the Monsoon Asia Drought Atlas (MADA) composed of a high-resolution network of hydroclimatically sensitive tree-ring records with a focus on the June-August months, spatial drought patterns during El Niño and IOD events are assessed as to their agreement with an instrumental drought index and consistency in the drought response amongst ENSO/IOD events. Spatial characteristics in drought patterns are related to regional climate anomalies over the Indo-Pacific basin, using reanalysis products, including changes in the Asian monsoon systems, zonal Walker circulation, moisture fluxes, and precipitation. A weakening of the monsoon circulation over the Indian subcontinent and Southeast Asia during El Niño events, along with anomalous subsidence over monsoon Asia and reduced moisture flux, is reflected in anomalous drought conditions over India, Southeast Asia and Indonesia. When an IOD event co-occurs with an El Niño, severe drought conditions identified in the MADA for Southeast Asia, Indonesia, eastern China and central Asia are associated with a weakened South Asian monsoon, reduced moisture flux over China, and anomalous divergent flow and subsidence over Indonesia. Variations in the strength of the South Asian monsoon can also be linked to the Strange Parallels Drought (1756-1768) affecting much of Southeast Asia and the Indian subcontinent in the mid-18th Century. Large-scale climate anomalies across the wider region during years with an anomalously strengthened/weakened South Asian monsoon are discussed with implications for severe droughts prior to the instrumental period. Insights into the relative influences of Pacific and Indian Ocean variability for Asian monsoon climate on interannual to decadal and longer timescales, as recorded in the

Effects of local and regional climatic fluctuations on dengue outbreaks in southern Taiwan

PubMed Central

Chaves, Luis Fernando; Chen, Po-Jiang

2017-01-01

Background Southern Taiwan has been a hotspot for dengue fever transmission since 1998. During 2014 and 2015, Taiwan experienced unprecedented dengue outbreaks and the causes are poorly understood. This study aims to investigate the influence of regional and local climate conditions on the incidence of dengue fever in Taiwan, as well as to develop a climate-based model for future forecasting. Methodology/Principle findings Historical time-series data on dengue outbreaks in southern Taiwan from 1998 to 2015 were investigated. Local climate variables were analyzed using a distributed lag non-linear model (DLNM), and the model of best fit was used to predict dengue incidence between 2013 and 2015. The cross-wavelet coherence approach was used to evaluate the regional El Niño Southern Oscillation (ENSO) and Indian Ocean Dipole (IOD) effects on dengue incidence and local climate variables. The DLNM results highlighted the important non-linear and lag effects of minimum temperature and precipitation. Minimum temperature above 23°C or below 17°C can increase dengue incidence rate with lag effects of 10 to 15 weeks. Moderate to high precipitation can increase dengue incidence rates with a lag of 10 or 20 weeks. The model of best fit successfully predicted dengue transmission between 2013 and 2015. The prediction accuracy ranged from 0.7 to 0.9, depending on the number of weeks ahead of the prediction. ENSO and IOD were associated with nonstationary inter-annual patterns of dengue transmission. IOD had a greater impact on the seasonality of local climate conditions. Conclusions/Significance Our findings suggest that dengue transmission can be affected by regional and local climatic fluctuations in southern Taiwan. The climate-based model developed in this study can provide important information for dengue early warning systems in Taiwan. Local climate conditions might be influenced by ENSO and IOD, to result in unusual dengue outbreaks. PMID:28575035

Targeted Quantification of Phosphorylation Dynamics in the Context of EGFR-MAPK Pathway.

PubMed

Yi, Lian; Shi, Tujin; Gritsenko, Marina A; X'avia Chan, Chi-Yuet; Fillmore, Thomas L; Hess, Becky M; Swensen, Adam C; Liu, Tao; Smith, Richard D; Wiley, H Steven; Qian, Wei-Jun

2018-04-17

Large-scale phosphoproteomics with coverage of over 10,000 sites of phosphorylation have now been routinely achieved with advanced mass spectrometry (MS)-based workflows. However, accurate targeted MS-based quantification of phosphorylation dynamics, an important direction for gaining quantitative understanding of signaling pathways or networks, has been much less investigated. Herein, we report an assessment of the targeted workflow in the context of signal transduction pathways, using the epidermal growth factor receptor (EGFR)-mitogen-activated protein kinase (MAPK) pathway as our model. A total of 43 phosphopeptides from the EGFR-MAPK pathway were selected for the study. The recovery and sensitivity of two commonly used enrichment methods, immobilized metal affinity chromatography (IMAC) and titanium oxide (TiO 2 ), combined with selected reaction monitoring (SRM)-MS were evaluated. The recovery of phosphopeptides by IMAC and TiO 2 enrichment was quantified to be 38 ± 5% and 58 ± 20%, respectively, based on internal standards. Moreover, both enrichment methods provided comparable sensitivity from 1 to 100 μg starting peptides. Robust quantification was consistently achieved for most targeted phosphopeptides when starting with 25-100 μg peptides. However, the numbers of quantified targets significantly dropped when peptide samples were in the 1-25 μg range. Finally, IMAC-SRM was applied to quantify signaling dynamics of EGFR-MAPK pathway in Hs578T cells following 10 ng/mL EGF treatment. The kinetics of phosphorylation clearly revealed early and late phases of phosphorylation, even for very low abundance proteins. These results demonstrate the feasibility of robust targeted quantification of phosphorylation dynamics for specific pathways, even starting with relatively small amounts of protein.

Targeted Quantification of Phosphorylation Dynamics in the Context of EGFR-MAPK Pathway

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

Yi, Lian; Shi, Tujin; Gritsenko, Marina A.

2018-03-27

Large-scale phosphoproteomics with coverage of over 10,000 sites of phosphorylation have now been routinely achieved with advanced mass spectrometry (MS)-based workflows. However, accurate targeted MS-based quantification of phosphorylation dynamics, an important direction for gaining quantitative understanding of signaling pathways or networks, has been much less investigated. Herein, we report an assessment of the targeted workflow in the context of signal transduction pathways, using the epidermal growth factor receptor (EGFR)–mitogen-activated protein kinase (MAPK) pathway as our model. 43 phosphopeptides from the EGFR–MAPK pathway were selected for the study. The recovery and sensitivity of a workflow consisted of two commonly used enrichmentmore » methods, immobilized metal affinity chromatography (IMAC) and titanium oxide (TiO2), combined with selected reaction monitoring (SRM)-MS, were evaluated. The recovery of phosphopeptides by IMAC and TiO2 enrichment was quantified to be 38 ± 5% and 58 ± 20%, respectively, based on internal standards. Moreover, both enrichment methods provided comparable sensitivity from 1-100 g starting peptides. Robust quantification was consistently achieved for most targeted phosphopeptides when starting with 25-100 g peptides. However, the numbers of quantified targets significantly dropped when peptide samples were in the 1-25g range. Finally, IMAC-SRM was applied to quantify signaling dynamics of EGFR-MAPK pathway in Hs578T cells following 3 ng/mL EGF treatment. The kinetics of phosphorylation clearly revealed early and late phases of phosphorylation, even for very low abundance proteins. These results demonstrate the feasibility of robust targeted quantification of phosphorylation dynamics for specific pathways, even starting with relatively small amounts of protein.« less

Accuracy of Rhenium-188 SPECT/CT activity quantification for applications in radionuclide therapy using clinical reconstruction methods.

PubMed

Esquinas, Pedro L; Uribe, Carlos F; Gonzalez, M; Rodríguez-Rodríguez, Cristina; Häfeli, Urs O; Celler, Anna

2017-07-20

The main applications of 188 Re in radionuclide therapies include trans-arterial liver radioembolization and palliation of painful bone-metastases. In order to optimize 188 Re therapies, the accurate determination of radiation dose delivered to tumors and organs at risk is required. Single photon emission computed tomography (SPECT) can be used to perform such dosimetry calculations. However, the accuracy of dosimetry estimates strongly depends on the accuracy of activity quantification in 188 Re images. In this study, we performed a series of phantom experiments aiming to investigate the accuracy of activity quantification for 188 Re SPECT using high-energy and medium-energy collimators. Objects of different shapes and sizes were scanned in Air, non-radioactive water (Cold-water) and water with activity (Hot-water). The ordered subset expectation maximization algorithm with clinically available corrections (CT-based attenuation, triple-energy window (TEW) scatter and resolution recovery was used). For high activities, the dead-time corrections were applied. The accuracy of activity quantification was evaluated using the ratio of the reconstructed activity in each object to this object's true activity. Each object's activity was determined with three segmentation methods: a 1% fixed threshold (for cold background), a 40% fixed threshold and a CT-based segmentation. Additionally, the activity recovered in the entire phantom, as well as the average activity concentration of the phantom background were compared to their true values. Finally, Monte-Carlo simulations of a commercial [Formula: see text]-camera were performed to investigate the accuracy of the TEW method. Good quantification accuracy (errors  <10%) was achieved for the entire phantom, the hot-background activity concentration and for objects in cold background segmented with a 1% threshold. However, the accuracy of activity quantification for objects segmented with 40% threshold or CT-based methods

Carotenoid Extraction and Quantification from Capsicum annuum.

PubMed

Richins, Richard D; Kilcrease, James; Rodgriguez-Uribe, Laura; O'Connell, Mary A

2014-10-05

Carotenoids are ubiquitous pigments that play key roles in photosynthesis and also accumulate to high levels in fruit and flowers. Specific carotenoids play essential roles in human health as these compounds are precursors for Vitamin A; other specific carotenoids are important sources of macular pigments and all carotenoids are important anti-oxidants. Accurate determination of the composition and concentration of this complex set of natural products is therefore important in many different scientific areas. One of the richest sources of these compounds is the fruit of Capsicum ; these red, yellow and orange fruit accumulate multiple carotenes and xanthophylls. This report describes the detailed method for the extraction and quantification of specific carotenes and xanthophylls.

Ranking Fragment Ions Based on Outlier Detection for Improved Label-Free Quantification in Data-Independent Acquisition LC-MS/MS

PubMed Central

Bilbao, Aivett; Zhang, Ying; Varesio, Emmanuel; Luban, Jeremy; Strambio-De-Castillia, Caterina; Lisacek, Frédérique; Hopfgartner, Gérard

2016-01-01

Data-independent acquisition LC-MS/MS techniques complement supervised methods for peptide quantification. However, due to the wide precursor isolation windows, these techniques are prone to interference at the fragment ion level, which in turn is detrimental for accurate quantification. The “non-outlier fragment ion” (NOFI) ranking algorithm has been developed to assign low priority to fragment ions affected by interference. By using the optimal subset of high priority fragment ions these interfered fragment ions are effectively excluded from quantification. NOFI represents each fragment ion as a vector of four dimensions related to chromatographic and MS fragmentation attributes and applies multivariate outlier detection techniques. Benchmarking conducted on a well-defined quantitative dataset (i.e. the SWATH Gold Standard), indicates that NOFI on average is able to accurately quantify 11-25% more peptides than the commonly used Top-N library intensity ranking method. The sum of the area of the Top3-5 NOFIs produces similar coefficients of variation as compared to the library intensity method but with more accurate quantification results. On a biologically relevant human dendritic cell digest dataset, NOFI properly assigns low priority ranks to 85% of annotated interferences, resulting in sensitivity values between 0.92 and 0.80 against 0.76 for the Spectronaut interference detection algorithm. PMID:26412574

Analytical validation of a flow cytometric protocol for quantification of platelet microparticles in dogs.

PubMed

Cremer, Signe E; Krogh, Anne K H; Hedström, Matilda E K; Christiansen, Liselotte B; Tarnow, Inge; Kristensen, Annemarie T

2018-06-01

Platelet microparticles (PMPs) are subcellular procoagulant vesicles released upon platelet activation. In people with clinical diseases, alterations in PMP concentrations have been extensively investigated, but few canine studies exist. This study aims to validate a canine flow cytometric protocol for PMP quantification and to assess the influence of calcium on PMP concentrations. Microparticles (MP) were quantified in citrated whole blood (WB) and platelet-poor plasma (PPP) using flow cytometry. Anti-CD61 antibody and Annexin V (AnV) were used to detect platelets and phosphatidylserine, respectively. In 13 healthy dogs, CD61 + /AnV - concentrations were analyzed with/without a calcium buffer. CD61 + /AnV - , CD61 + /AnV + , and CD61 - /AnV + MP quantification were validated in 10 healthy dogs. The coefficient of variation (CV) for duplicate (intra-assay) and parallel (inter-assay) analyses and detection limits (DLs) were calculated. CD61 + /AnV - concentrations were higher in calcium buffer; 841,800 MP/μL (526,000-1,666,200) vs without; 474,200 MP/μL (278,800-997,500), P < .05. In WB, PMP were above DLs and demonstrated acceptable (<20%) intra-assay and inter-assay CVs in 9/10 dogs: 1.7% (0.5-8.9) and 9.0% (0.9-11.9), respectively, for CD61 + /AnV - and 2.4% (0.2-8.7) and 7.8% (0.0-12.8), respectively, for CD61 + /AnV + . Acceptable CVs were not seen for the CD61 - /AnV + MP. In PPP, quantifications were challenged by high inter-assay CV, overlapping DLs and hemolysis and lipemia interfered with quantification in 5/10 dogs. Calcium induced higher in vitro PMP concentrations, likely due to platelet activation. PMP concentrations were reliably quantified in WB, indicating the potential for clinical applications. PPP analyses were unreliable due to high inter-CV and DL overlap, and not obtainable due to hemolysis and lipemia interference. © 2018 American Society for Veterinary Clinical Pathology.

Generation of monoclonal pan-hemagglutinin antibodies for the quantification of multiple strains of influenza

PubMed Central

Zou, Wei; Marcil, Anne; Paquet, Eric; Gadoury, Christine; Jaentschke, Bozena; Li, Xuguang; Petiot, Emma; Durocher, Yves; Baardsnes, Jason; Rosa-Calatrava, Manuel; Ansorge, Sven; Kamen, Amine A.

2017-01-01

Vaccination is the most effective course of action to prevent influenza. About 150 million doses of influenza vaccines were distributed for the 2015–2016 season in the USA alone according to the Centers for Disease Control and Prevention. Vaccine dosage is calculated based on the concentration of hemagglutinin (HA), the main surface glycoprotein expressed by influenza which varies from strain to strain. Therefore yearly-updated strain-specific antibodies and calibrating antigens are required. Preparing these quantification reagents can take up to three months and significantly slows down the release of new vaccine lots. Therefore, to circumvent the need for strain-specific sera, two anti-HA monoclonal antibodies (mAbs) against a highly conserved sequence have been produced by immunizing mice with a novel peptide-conjugate. Immunoblots demonstrate that 40 strains of influenza encompassing HA subtypes H1 to H13, as well as B strains from the Yamagata and Victoria lineage were detected when the two mAbs are combined to from a pan-HA mAb cocktail. Quantification using this pan-HA mAbs cocktail was achieved in a dot blot assay and results correlated with concentrations measured in a hemagglutination assay with a coefficient of correlation of 0.80. A competitive ELISA was also optimised with purified viral-like particles. Regardless of the quantification method used, pan-HA antibodies can be employed to accelerate process development when strain-specific antibodies are not available, and represent a valuable tool in case of pandemics. These antibodies were also expressed in CHO cells to facilitate large-scale production using bioreactor technologies which might be required to meet industrial needs for quantification reagents. Finally, a simulation model was created to predict the binding affinity of the two anti-HA antibodies to the amino acids composing the highly conserved epitope; different probabilities of interaction between a given amino acid and the antibodies

Combination of elastography and tissue quantification using the acoustic radiation force impulse (ARFI) technology for differential diagnosis of breast masses.

PubMed

Tozaki, Mitsuhiro; Isobe, Sachiko; Sakamoto, Masaaki

2012-10-01

We evaluated the diagnostic performance of elastography and tissue quantification using acoustic radiation force impulse (ARFI) technology for differential diagnosis of breast masses. There were 161 mass lesions. First, lesion correspondence on ARFI elastographic images to those on the B-mode images was evaluated: no findings on ARFI images (pattern 1), lesions that were bright inside (pattern 2), lesions that were dark inside (pattern 4), lesions that contained both bright and dark areas (pattern 3). In addition, pattern 4 was subdivided into 4a (dark area same as B-mode lesion) and 4b (dark area larger than lesion). Next, shear wave velocity (SWV) was measured using virtual touch tissue quantification. There were 13 pattern 1 lesions and five pattern 2 lesions; all of these lesions were benign, whereas all pattern 4b lesions (n = 43) were malignant. When the value of 3.59 m/s was chosen as the cutoff value, the combination of elastography and tissue quantification showed 91 % (83-91) sensitivity, 93 % (65-70) specificity, and 92 % (148-161) accuracy. The combination of elastography and tissue quantification is thought to be a promising ultrasound technique for differential diagnosis of breast-mass lesions.

Robustness of Fat Quantification using Chemical Shift Imaging

PubMed Central

Hansen, Katie H; Schroeder, Michael E; Hamilton, Gavin; Sirlin, Claude B; Bydder, Mark

2011-01-01

This purpose of this study was to investigate the effect of parameter changes that can potentially lead to unreliable measurements in fat quantification. Chemical shift imaging was performed using spoiled gradient echo sequences with systematic variations in the following: 2D/3D sequence, number of echoes, delta echo time, fractional echo factor, slice thickness, repetition time, flip angle, bandwidth, matrix size, flow compensation and field strength. Results indicated no significant (or significant but small) changes in fat fraction with parameter. The significant changes can be attributed to known effects of T1 bias and the two forms of noise bias. PMID:22055856

Molecular nonlinear dynamics and protein thermal uncertainty quantification

PubMed Central

Xia, Kelin; Wei, Guo-Wei

2014-01-01

This work introduces molecular nonlinear dynamics (MND) as a new approach for describing protein folding and aggregation. By using a mode system, we show that the MND of disordered proteins is chaotic while that of folded proteins exhibits intrinsically low dimensional manifolds (ILDMs). The stability of ILDMs is found to strongly correlate with protein energies. We propose a novel method for protein thermal uncertainty quantification based on persistently invariant ILDMs. Extensive comparison with experimental data and the state-of-the-art methods in the field validate the proposed new method for protein B-factor prediction. PMID:24697365

Universal absolute quantification of biomolecules using element mass spectrometry and generic standards.

PubMed

Calderón-Celis, Francisco; Sanz-Medel, Alfredo; Encinar, Jorge Ruiz

2018-01-23

We present a novel and highly sensitive ICP-MS approach for absolute quantification of all important target biomolecule containing P, S, Se, As, Br, and/or I (e.g., proteins and phosphoproteins, metabolites, pesticides, drugs), under the same simple instrumental conditions and without requiring any specific and/or isotopically enriched standard.

Instantaneous Wavenumber Estimation for Damage Quantification in Layered Plate Structures

NASA Technical Reports Server (NTRS)

Mesnil, Olivier; Leckey, Cara A. C.; Ruzzene, Massimo

2014-01-01

This paper illustrates the application of instantaneous and local wavenumber damage quantification techniques for high frequency guided wave interrogation. The proposed methodologies can be considered as first steps towards a hybrid structural health monitoring/ nondestructive evaluation (SHM/NDE) approach for damage assessment in composites. The challenges and opportunities related to the considered type of interrogation and signal processing are explored through the analysis of numerical data obtained via EFIT simulations of damage in CRFP plates. Realistic damage configurations are modeled from x-ray CT scan data of plates subjected to actual impacts, in order to accurately predict wave-damage interactions in terms of scattering and mode conversions. Simulation data is utilized to enhance the information provided by instantaneous and local wavenumbers and mitigate the complexity related to the multi-modal content of the plate response. Signal processing strategies considered for this purpose include modal decoupling through filtering in the frequency/wavenumber domain, the combination of displacement components, and the exploitation of polarization information for the various modes as evaluated through the dispersion analysis of the considered laminate lay-up sequence. The results presented assess the effectiveness of the proposed wavefield processing techniques as a hybrid SHM/NDE technique for damage detection and quantification in composite, plate-like structures.

Quantification of Lignin and Its Structural Features in Plant Biomass Using 13C Lignin as Internal Standard for Pyrolysis-GC-SIM-MS.

PubMed

van Erven, Gijs; de Visser, Ries; Merkx, Donny W H; Strolenberg, Willem; de Gijsel, Peter; Gruppen, Harry; Kabel, Mirjam A

2017-10-17

Understanding the mechanisms underlying plant biomass recalcitrance at the molecular level can only be achieved by accurate analyses of both the content and structural features of the molecules involved. Current quantification of lignin is, however, majorly based on unspecific gravimetric analysis after sulfuric acid hydrolysis. Hence, our research aimed at specific lignin quantification with concurrent characterization of its structural features. Hereto, for the first time, a polymeric 13 C lignin was used as internal standard (IS) for lignin quantification via analytical pyrolysis coupled to gas chromatography with mass-spectrometric detection in selected ion monitoring mode (py-GC-SIM-MS). In addition, relative response factors (RRFs) for the various pyrolysis products obtained were determined and applied. First, 12 C and 13 C lignin were isolated from nonlabeled and uniformly 13 C labeled wheat straw, respectively, and characterized by heteronuclear single quantum coherence (HSQC), nuclear magnetic resonance (NMR), and py-GC/MS. The two lignin isolates were found to have identical structures. Second, 13 C-IS based lignin quantification by py-GC-SIM-MS was validated in reconstituted biomass model systems with known contents of the 12 C lignin analogue and was shown to be extremely accurate (>99.9%, R 2 > 0.999) and precise (RSD < 1.5%). Third, 13 C-IS based lignin quantification was applied to four common poaceous biomass sources (wheat straw, barley straw, corn stover, and sugar cane bagasse), and lignin contents were in good agreement with the total gravimetrically determined lignin contents. Our robust method proves to be a promising alternative for the high-throughput quantification of lignin in milled biomass samples directly and simultaneously provides a direct insight into the structural features of lignin.

Direct quantification of lipopeptide biosurfactants in biological samples via HPLC and UPLC-MS requires sample modification with an organic solvent.

PubMed

Biniarz, Piotr; Łukaszewicz, Marcin

2017-06-01

The rapid and accurate quantification of biosurfactants in biological samples is challenging. In contrast to the orcinol method for rhamnolipids, no simple biochemical method is available for the rapid quantification of lipopeptides. Various liquid chromatography (LC) methods are promising tools for relatively fast and exact quantification of lipopeptides. Here, we report strategies for the quantification of the lipopeptides pseudofactin and surfactin in bacterial cultures using different high- (HPLC) and ultra-performance liquid chromatography (UPLC) systems. We tested three strategies for sample pretreatment prior to LC analysis. In direct analysis (DA), bacterial cultures were injected directly and analyzed via LC. As a modification, we diluted the samples with methanol and detected an increase in lipopeptide recovery in the presence of methanol. Therefore, we suggest this simple modification as a tool for increasing the accuracy of LC methods. We also tested freeze-drying followed by solvent extraction (FDSE) as an alternative for the analysis of "heavy" samples. In FDSE, the bacterial cultures were freeze-dried, and the resulting powder was extracted with different solvents. Then, the organic extracts were analyzed via LC. Here, we determined the influence of the extracting solvent on lipopeptide recovery. HPLC methods allowed us to quantify pseudofactin and surfactin with run times of 15 and 20 min per sample, respectively, whereas UPLC quantification was as fast as 4 and 5.5 min per sample, respectively. Our methods provide highly accurate measurements and high recovery levels for lipopeptides. At the same time, UPLC-MS provides the possibility to identify lipopeptides and their structural isoforms.

A rapid Fourier-transform infrared (FTIR) spectroscopic method for direct quantification of paracetamol content in solid pharmaceutical formulations

NASA Astrophysics Data System (ADS)

Mallah, Muhammad Ali; Sherazi, Syed Tufail Hussain; Bhanger, Muhammad Iqbal; Mahesar, Sarfaraz Ahmed; Bajeer, Muhammad Ashraf

2015-04-01

A transmission FTIR spectroscopic method was developed for direct, inexpensive and fast quantification of paracetamol content in solid pharmaceutical formulations. In this method paracetamol content is directly analyzed without solvent extraction. KBr pellets were formulated for the acquisition of FTIR spectra in transmission mode. Two chemometric models: simple Beer's law and partial least squares employed over the spectral region of 1800-1000 cm-1 for quantification of paracetamol content had a regression coefficient of (R2) of 0.999. The limits of detection and quantification using FTIR spectroscopy were 0.005 mg g-1 and 0.018 mg g-1, respectively. Study for interference was also done to check effect of the excipients. There was no significant interference from the sample matrix. The results obviously showed the sensitivity of transmission FTIR spectroscopic method for pharmaceutical analysis. This method is green in the sense that it does not require large volumes of hazardous solvents or long run times and avoids prior sample preparation.

Quantification of biofilm in microtiter plates: overview of testing conditions and practical recommendations for assessment of biofilm production by staphylococci.

PubMed

Stepanović, Srdjan; Vuković, Dragana; Hola, Veronika; Di Bonaventura, Giovanni; Djukić, Slobodanka; Cirković, Ivana; Ruzicka, Filip

2007-08-01

The details of all steps involved in the quantification of biofilm formation in microtiter plates are described. The presented protocol incorporates information on assessment of biofilm production by staphylococci, gained both by direct experience as well as by analysis of methods for assaying biofilm production. The obtained results should simplify quantification of biofilm formation in microtiter plates, and make it more reliable and comparable among different laboratories.

Precision and accuracy of clinical quantification of myocardial blood flow by dynamic PET: A technical perspective.

PubMed

Moody, Jonathan B; Lee, Benjamin C; Corbett, James R; Ficaro, Edward P; Murthy, Venkatesh L

2015-10-01

A number of exciting advances in PET/CT technology and improvements in methodology have recently converged to enhance the feasibility of routine clinical quantification of myocardial blood flow and flow reserve. Recent promising clinical results are pointing toward an important role for myocardial blood flow in the care of patients. Absolute blood flow quantification can be a powerful clinical tool, but its utility will depend on maintaining precision and accuracy in the face of numerous potential sources of methodological errors. Here we review recent data and highlight the impact of PET instrumentation, image reconstruction, and quantification methods, and we emphasize (82)Rb cardiac PET which currently has the widest clinical application. It will be apparent that more data are needed, particularly in relation to newer PET technologies, as well as clinical standardization of PET protocols and methods. We provide recommendations for the methodological factors considered here. At present, myocardial flow reserve appears to be remarkably robust to various methodological errors; however, with greater attention to and more detailed understanding of these sources of error, the clinical benefits of stress-only blood flow measurement may eventually be more fully realized.

Quantification of genetically modified soya using strong anion exchange chromatography and time-of-flight mass spectrometry.

PubMed

Chang, Po-Chih; Reddy, P Muralidhar; Ho, Yen-Peng

2014-09-01

Stable-isotope dimethyl labeling was applied to the quantification of genetically modified (GM) soya. The herbicide-resistant gene-related protein 5-enolpyruvylshikimate-3-phosphate synthase (CP4 EPSPS) was labeled using a dimethyl labeling reagent, formaldehyde-H2 or -D2. The identification and quantification of CP4 EPSPS was performed using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The CP4 EPSPS protein was separated from high abundance proteins using strong anion exchange chromatography and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Then, the tryptic peptides from the samples and reference were labeled with formaldehyde-H2 and formaldehyde-D2, respectively. The two labeled pools were mixed and analyzed using MALDI-MS. The data showed a good correlation between the peak ratio of the H- and D-labeled peptides and the GM soya percentages at 0.5, 1, 3, and 5 %, with R (2) of 0.99. The labeling reagents are readily available. The labeling experiments and the detection procedures are simple. The approach is useful for the quantification of GM soya at a level as low as 0.5 %.

New class of radioenzymatic assay for the quantification of p-tyramine and phenylethylamine

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

Henry, D.P.; Van Huysse, J.W.; Bowsher, R.R.

Radioenzymatic assays are widely used for the quantification of a number of biogenic amines. All previous procedures have utilized methyltransferases derived from mammalian tissues. In this assay for the quantification of the trace aralkylamines, p-tyramine (p-tym) and phenylethylamine (PEA), an enzyme, tyramine N-methyltransferase isolated from sprouted barley roots was used. The enzyme was specific for phenylethylamines. Of 26 structurally-related compounds, only p-tym, PEA, m-tym and amphetamine were substrates in vitro. Theoretic maximal methylation of substrates occurred at 10-20/sup 0/C. When TLC was used to separate the radiolabeled reaction products, a specific method was developed for p-tym and PEA. The assaymore » had a sensitivity of 0.8 and 2.8 pg/tube with a C.V. < 5% and was applicable to human plasma and urine. Assay throughput is similar to that of other TLC based radioenzymatic assays.« less

Microwave-assisted extraction of green coffee oil and quantification of diterpenes by HPLC.

PubMed

Tsukui, A; Santos Júnior, H M; Oigman, S S; de Souza, R O M A; Bizzo, H R; Rezende, C M

2014-12-01

The microwave-assisted extraction (MAE) of 13 different green coffee beans (Coffea arabica L.) was compared to Soxhlet extraction for oil obtention. The full factorial design applied to the microwave-assisted extraction (MAE), related to time and temperature parameters, allowed to develop a powerful fast and smooth methodology (10 min at 45°C) compared to a 4h Soxhlet extraction. The quantification of cafestol and kahweol diterpenes present in the coffee oil was monitored by HPLC/UV and showed satisfactory linearity (R(2)=0.9979), precision (CV 3.7%), recovery (<93%), limit of detection (0.0130 mg/mL), and limit of quantification (0.0406 mg/mL). The space-time yield calculated on the diterpenes content for sample AT1 (Arabica green coffee) showed a six times higher value compared to the traditional Soxhlet method. Copyright © 2014 Elsevier Ltd. All rights reserved.

Ferromagnetic resonance for the quantification of superparamagnetic iron oxide nanoparticles in biological materials

PubMed Central

Gamarra, Lionel F; daCosta-Filho, Antonio J; Mamani, Javier B; de Cassia Ruiz, Rita; Pavon, Lorena F; Sibov, Tatiana T; Vieira, Ernanni D; Silva, André C; Pontuschka, Walter M; Amaro, Edson

2010-01-01

The aim of the present work is the presentation of a quantification methodology for the control of the amount of superparamagnetic iron oxide nanoparticles (SPIONs) administered in biological materials by means of the ferromagnetic resonance technique (FMR) applied to studies both in vivo and in vitro. The in vivo study consisted in the analysis of the elimination and biodistribution kinetics of SPIONs after intravenous administration in Wistar rats. The results were corroborated by X-ray fluorescence. For the in vitro study, a quantitative analysis of the concentration of SPIONs bound to the specific AC133 monoclonal antibodies was carried out in order to detect the expression of the antigenic epitopes (CD133) in stem cells from human umbilical cord blood. In both studies FMR has proven to be an efficient technique for the SPIONs quantification per volume unit (in vivo) or per labeled cell (in vitro). PMID:20463936

Elemental labelling combined with liquid chromatography inductively coupled plasma mass spectrometry for quantification of biomolecules: A review

PubMed Central

Kretschy, Daniela; Koellensperger, Gunda; Hann, Stephan

2012-01-01

This article reviews novel quantification concepts where elemental labelling is combined with flow injection inductively coupled plasma mass spectrometry (FI-ICP-MS) or liquid chromatography inductively coupled plasma mass spectrometry (LC–ICP-MS), and employed for quantification of biomolecules such as proteins, peptides and related molecules in challenging sample matrices. In the first sections an overview on general aspects of biomolecule quantification, as well as of labelling will be presented emphasizing the potential, which lies in such methodological approaches. In this context, ICP-MS as detector provides high sensitivity, selectivity and robustness in biological samples and offers the capability for multiplexing and isotope dilution mass spectrometry (IDMS). Fundamental methodology of elemental labelling will be highlighted and analytical, as well as biomedical applications will be presented. A special focus will lie on established applications underlining benefits and bottlenecks of such approaches for the implementation in real life analysis. Key research made in this field will be summarized and a perspective for future developments including sophisticated and innovative applications will given. PMID:23062431

Uncertainty Quantification and Statistical Engineering for Hypersonic Entry Applications

NASA Technical Reports Server (NTRS)

Cozmuta, Ioana

2011-01-01

NASA has invested significant resources in developing and validating a mathematical construct for TPS margin management: a) Tailorable for low/high reliability missions; b) Tailorable for ablative/reusable TPS; c) Uncertainty Quantification and Statistical Engineering are valuable tools not exploited enough; and d) Need to define strategies combining both Theoretical Tools and Experimental Methods. The main reason for this lecture is to give a flavor of where UQ and SE could contribute and hope that the broader community will work with us to improve in these areas.

Methods for the physical characterization and quantification of extracellular vesicles in biological samples.

PubMed

Rupert, Déborah L M; Claudio, Virginia; Lässer, Cecilia; Bally, Marta

2017-01-01

Our body fluids contain a multitude of cell-derived vesicles, secreted by most cell types, commonly referred to as extracellular vesicles. They have attracted considerable attention for their function as intercellular communication vehicles in a broad range of physiological processes and pathological conditions. Extracellular vesicles and especially the smallest type, exosomes, have also generated a lot of excitement in view of their potential as disease biomarkers or as carriers for drug delivery. In this context, state-of-the-art techniques capable of comprehensively characterizing vesicles in biological fluids are urgently needed. This review presents the arsenal of techniques available for quantification and characterization of physical properties of extracellular vesicles, summarizes their working principles, discusses their advantages and limitations and further illustrates their implementation in extracellular vesicle research. The small size and physicochemical heterogeneity of extracellular vesicles make their physical characterization and quantification an extremely challenging task. Currently, structure, size, buoyant density, optical properties and zeta potential have most commonly been studied. The concentration of vesicles in suspension can be expressed in terms of biomolecular or particle content depending on the method at hand. In addition, common quantification methods may either provide a direct quantitative measurement of vesicle concentration or solely allow for relative comparison between samples. The combination of complementary methods capable of detecting, characterizing and quantifying extracellular vesicles at a single particle level promises to provide new exciting insights into their modes of action and to reveal the existence of vesicle subpopulations fulfilling key biological tasks. Copyright © 2016 Elsevier B.V. All rights reserved.

Clarity™ digital PCR system: a novel platform for absolute quantification of nucleic acids.

PubMed

Low, Huiyu; Chan, Shun-Jie; Soo, Guo-Hao; Ling, Belinda; Tan, Eng-Lee

2017-03-01

In recent years, digital polymerase chain reaction (dPCR) has gained recognition in biomedical research as it provides a platform for precise and accurate quantification of nucleic acids without the need for a standard curve. However, this technology has not yet been widely adopted as compared to real-time quantitative PCR due to its more cumbersome workflow arising from the need to sub-divide a PCR sample into a large number of smaller partitions prior to thermal cycling to achieve zero or at least one copy of the target RNA/DNA per partition. A recently launched platform, the Clarity™ system from JN Medsys, simplifies dPCR workflow through the use of a novel chip-in-a-tube technology for sample partitioning. In this study, the performance of Clarity™ was evaluated through quantification of the single-copy human RNase P gene. The system demonstrated high precision and accuracy and also excellent linearity across a range of over 4 orders of magnitude for the absolute quantification of the target gene. Moreover, consistent DNA copy measurements were also attained using a panel of different probe- and dye-based master mixes, demonstrating the system's compatibility with commercial master mixes. The Clarity™ was then compared to the QX100™ droplet dPCR system from Bio-Rad using a set of DNA reference materials, and the copy number concentrations derived from both systems were found to be closely associated. Collectively, the results showed that Clarity™ is a reliable, robust and flexible platform for next-generation genetic analysis.

Detecting transitions in protein dynamics using a recurrence quantification analysis based bootstrap method.

PubMed

Karain, Wael I

2017-11-28

Proteins undergo conformational transitions over different time scales. These transitions are closely intertwined with the protein's function. Numerous standard techniques such as principal component analysis are used to detect these transitions in molecular dynamics simulations. In this work, we add a new method that has the ability to detect transitions in dynamics based on the recurrences in the dynamical system. It combines bootstrapping and recurrence quantification analysis. We start from the assumption that a protein has a "baseline" recurrence structure over a given period of time. Any statistically significant deviation from this recurrence structure, as inferred from complexity measures provided by recurrence quantification analysis, is considered a transition in the dynamics of the protein. We apply this technique to a 132 ns long molecular dynamics simulation of the β-Lactamase Inhibitory Protein BLIP. We are able to detect conformational transitions in the nanosecond range in the recurrence dynamics of the BLIP protein during the simulation. The results compare favorably to those extracted using the principal component analysis technique. The recurrence quantification analysis based bootstrap technique is able to detect transitions between different dynamics states for a protein over different time scales. It is not limited to linear dynamics regimes, and can be generalized to any time scale. It also has the potential to be used to cluster frames in molecular dynamics trajectories according to the nature of their recurrence dynamics. One shortcoming for this method is the need to have large enough time windows to insure good statistical quality for the recurrence complexity measures needed to detect the transitions.

How to Improve Your Impact Factor: Questioning the Quantification of Academic Quality

ERIC Educational Resources Information Center

Smeyers, Paul; Burbules, Nicholas C.

2011-01-01

A broad-scale quantification of the measure of quality for scholarship is under way. This trend has fundamental implications for the future of academic publishing and employment. In this essay we want to raise questions about these burgeoning practices, particularly how they affect philosophy of education and similar sub-disciplines. First,…

Determination of statin drugs in hospital effluent with dispersive liquid-liquid microextraction and quantification by liquid chromatography.

PubMed

Martins, Ayrton F; Frank, Carla da S; Altissimo, Joseline; de Oliveira, Júlia A; da Silva, Daiane S; Reichert, Jaqueline F; Souza, Darliana M

2017-08-24

Statins are classified as being amongst the most prescribed agents for treating hypercholesterolaemia and preventing vascular diseases. In this study, a rapid and effective liquid chromatography method, assisted by diode array detection, was designed and validated for the simultaneous quantification of atorvastatin (ATO) and simvastatin (SIM) in hospital effluent samples. The solid phase extraction (SPE) of the analytes was optimized regarding sorbent material and pH, and the dispersive liquid-liquid microextraction (DLLME), in terms of pH, ionic strength, type and volume of extractor/dispersor solvents. The performance of both extraction procedures was evaluated in terms of linearity, quantification limits, accuracy (recovery %), precision and matrix effects for each analyte. The methods proved to be linear in the concentration range considered; the quantification limits were 0.45 µg L -1 for ATO and 0.75 µg L -1 for SIM; the matrix effect was almost absent in both methods and the average recoveries remained between 81.5-90.0%; and the RSD values were <20%. The validated methods were applied to the quantification of the statins in real samples of hospital effluent; the concentrations ranged from 18.8 µg L -1 to 35.3 µg L -1 for ATO, and from 30.3 µg L -1 to 38.5 µg L -1 for SIM. Since the calculated risk quotient was ≤192, the occurrence of ATO and SIM in hospital effluent poses a potential serious risk to human health and the aquatic ecosystem.

Quantification of in vivo short echo-time proton magnetic resonance spectra at 14.1 T using two different approaches of modelling the macromolecule spectrum

NASA Astrophysics Data System (ADS)

Cudalbu, C.; Mlynárik, V.; Xin, L.; Gruetter, Rolf

2009-10-01

Reliable quantification of the macromolecule signals in short echo-time 1H MRS spectra is particularly important at high magnetic fields for an accurate quantification of metabolite concentrations (the neurochemical profile) due to effectively increased spectral resolution of the macromolecule components. The purpose of the present study was to assess two approaches of quantification, which take the contribution of macromolecules into account in the quantification step. 1H spectra were acquired on a 14.1 T/26 cm horizontal scanner on five rats using the ultra-short echo-time SPECIAL (spin echo full intensity acquired localization) spectroscopy sequence. Metabolite concentrations were estimated using LCModel, combined with a simulated basis set of metabolites using published spectral parameters and either the spectrum of macromolecules measured in vivo, using an inversion recovery technique, or baseline simulated by the built-in spline function. The fitted spline function resulted in a smooth approximation of the in vivo macromolecules, but in accordance with previous studies using Subtract-QUEST could not reproduce completely all features of the in vivo spectrum of macromolecules at 14.1 T. As a consequence, the measured macromolecular 'baseline' led to a more accurate and reliable quantification at higher field strengths.

Rapid quantification of soilborne pathogen communities in wheat-based long-term field experiments

USDA-ARS?s Scientific Manuscript database

Traditional isolation and quantification of inoculum density is difficult for most soilborne pathogens. Quantitative PCR methods have been developed to rapidly identify and quantify many of these pathogens using a single DNA extract from soil. Rainfed experiments operated continuously for up to 84 y...

Uncertainty Quantification and Certification Prediction of Low-Boom Supersonic Aircraft Configurations

NASA Technical Reports Server (NTRS)

West, Thomas K., IV; Reuter, Bryan W.; Walker, Eric L.; Kleb, Bil; Park, Michael A.

2014-01-01

The primary objective of this work was to develop and demonstrate a process for accurate and efficient uncertainty quantification and certification prediction of low-boom, supersonic, transport aircraft. High-fidelity computational fluid dynamics models of multiple low-boom configurations were investigated including the Lockheed Martin SEEB-ALR body of revolution, the NASA 69 Delta Wing, and the Lockheed Martin 1021-01 configuration. A nonintrusive polynomial chaos surrogate modeling approach was used for reduced computational cost of propagating mixed, inherent (aleatory) and model-form (epistemic) uncertainty from both the computation fluid dynamics model and the near-field to ground level propagation model. A methodology has also been introduced to quantify the plausibility of a design to pass a certification under uncertainty. Results of this study include the analysis of each of the three configurations of interest under inviscid and fully turbulent flow assumptions. A comparison of the uncertainty outputs and sensitivity analyses between the configurations is also given. The results of this study illustrate the flexibility and robustness of the developed framework as a tool for uncertainty quantification and certification prediction of low-boom, supersonic aircraft.

Quantification of concentrated Chinese medicine granules by quantitative polymerase chain reaction.

PubMed

Lo, Yat-Tung; Shaw, Pang-Chui

2017-10-25

Determination of the amount of constituent in a multi-herb product is important for quality control. In concentrated Chinese medicine granules (CCMG), no dregs are left after dissolution of the CCMG. This study is the first to examine the feasibility of using quantitative polymerase chain reaction (qPCR) to find the amount of CCMG in solution form. DNA was extracted from Hirudo and Zaocys CCMG mixed at different ratios and amplified in qPCR using species-specific primers. The threshold cycle (C T ) obtained was compared with the respective standard curves. Results showed that reproducible quantification results could be obtained (1) for 5-50mg CCMG using a modified DNA extraction protocol, (2) amongst DNA extracted from the same batch of CCMG and (3) amongst different batches of CCMG from the same company. This study demonstrated the constitute amount of CCMG in a mixture could be determined using qPCR. This work has extended the application of DNA techniques for the quantification of herbal products and this approach may be developed for quality assurance in the CCMG industry. Copyright © 2017 Elsevier B.V. All rights reserved.

Empirical quantification of lacustrine groundwater discharge - different methods and their limitations

NASA Astrophysics Data System (ADS)

Meinikmann, K.; Nützmann, G.; Lewandowski, J.

2015-03-01

Groundwater discharge into lakes (lacustrine groundwater discharge, LGD) can be an important driver of lake eutrophication. Its quantification is difficult for several reasons, and thus often neglected in water and nutrient budgets of lakes. In the present case several methods were applied to determine the expansion of the subsurface catchment, to reveal areas of main LGD and to identify the variability of LGD intensity. Size and shape of the subsurface catchment served as a prerequisite in order to calculate long-term groundwater recharge and thus the overall amount of LGD. Isotopic composition of near-shore groundwater was investigated to validate the quality of catchment delineation in near-shore areas. Heat as a natural tracer for groundwater-surface water interactions was used to find spatial variations of LGD intensity. Via an analytical solution of the heat transport equation, LGD rates were calculated from temperature profiles of the lake bed. The method has some uncertainties, as can be found from the results of two measurement campaigns in different years. The present study reveals that a combination of several different methods is required for a reliable identification and quantification of LGD and groundwater-borne nutrient loads.

Volatile organic silicon compounds in biogases: development of sampling and analytical methods for total silicon quantification by ICP-OES.

PubMed

Chottier, Claire; Chatain, Vincent; Julien, Jennifer; Dumont, Nathalie; Lebouil, David; Germain, Patrick

2014-01-01

Current waste management policies favor biogases (digester gases (DGs) and landfill gases (LFGs)) valorization as it becomes a way for energy politics. However, volatile organic silicon compounds (VOSiCs) contained into DGs/LFGs severely damage combustion engines and endanger the conversion into electricity by power plants, resulting in a high purification level requirement. Assessing treatment efficiency is still difficult. No consensus has been reached to provide a standardized sampling and quantification of VOSiCs into gases because of their diversity, their physicochemical properties, and the omnipresence of silicon in analytical chains. Usually, samplings are done by adsorption or absorption and quantification made by gas chromatography-mass spectrometry (GC-MS) or inductively coupled plasma-optical emission spectrometry (ICP-OES). In this objective, this paper presents and discusses the optimization of a patented method consisting in VOSiCs sampling by absorption of 100% ethanol and quantification of total Si by ICP-OES.

A critical view on microplastic quantification in aquatic organisms.

PubMed

Vandermeersch, Griet; Van Cauwenberghe, Lisbeth; Janssen, Colin R; Marques, Antonio; Granby, Kit; Fait, Gabriella; Kotterman, Michiel J J; Diogène, Jorge; Bekaert, Karen; Robbens, Johan; Devriese, Lisa

2015-11-01

Microplastics, plastic particles and fragments smaller than 5mm, are ubiquitous in the marine environment. Ingestion and accumulation of microplastics have previously been demonstrated for diverse marine species ranging from zooplankton to bivalves and fish, implying the potential for microplastics to accumulate in the marine food web. In this way, microplastics can potentially impact food safety and human health. Although a few methods to quantify microplastics in biota have been described, no comparison and/or intercalibration of these techniques have been performed. Here we conducted a literature review on all available extraction and quantification methods. Two of these methods, involving wet acid destruction, were used to evaluate the presence of microplastics in field-collected mussels (Mytilus galloprovincialis) from three different "hotspot" locations in Europe (Po estuary, Italy; Tagus estuary, Portugal; Ebro estuary, Spain). An average of 0.18±0.14 total microplastics g(-1) w.w. for the Acid mix Method and 0.12±0.04 total microplastics g(-1) w.w. for the Nitric acid Method was established. Additionally, in a pilot study an average load of 0.13±0.14 total microplastics g(-1) w.w. was recorded in commercial mussels (Mytilus edulis and M. galloprovincialis) from five European countries (France, Italy, Denmark, Spain and The Netherlands). A detailed analysis and comparison of methods indicated the need for further research to develop a standardised operating protocol for microplastic quantification and monitoring. Copyright © 2015 Elsevier Inc. All rights reserved.