Quantitative and qualitative analysis of flavonoids in leaves of Adinandra nitida by high performance liquid chromatography with UV and electrospray ionization tandem mass spectrometry detection

The extract of Adinandra nitida leaves, named as Shiyacha in China, was studied by high performance liquid chromatography (HPLC)-ultraviolet detection-electrospray ionisation (ESI) tandem mass spectrometry (MS). Under the optimized condition, the analysis could be finished in 45 min on a Hypersil C18 column combined with negative ion detection using information-dependent acquisition (IDA) mode of a Q TRAP (TM) instrument. Six flavonoids were identified as epicatechin, rhoifolin, apigenin, quercitrin, camellianin A, and camellianin B among which rhoifolin was for the first time found in Shiyacha. And the fragment pathways of these flavonoids were elucidated. Furthermore, with epicatechin, rhoifolin, and apigenin as markers, the quality control method for Shiyacha and its relevant product was firstly established. Calibration linearity was good (R-2 > 0.9992) over a three to four orders of magnitude concentration range with an S/N = 3 detection limit of 2.5 ng. (c) 2004 Elsevier B.V. All rights reserved.

Quantitative determination of compounds in tobacco essential oils by comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry

A quantitative analysis of the individual compounds in tobacco essential oils is performed by comprehensive two-dimensional gas chromatography (GC x GC) combined with flame ionization detector (FID). A time-of-flight mass spectrometer (TOF/MS) was coupled to GC x GC for the identification of the resolved peaks. The response of a flame ionization detector to different compound classes was calibrated using multiple internal standards. In total, 172 compounds were identified with good match and 61 compounds with high probability value were reliably quantified. For comparative purposes, the essential oil sample was also quantified by one-dimensional gas chromatography-mass spectrometry (GC/MS) with multiple internal standards method. The results showed that there was close agreement between the two analysis methods when the peak purity and match quality in one-dimensional GC/MS are high enough. (c) 2005 Elsevier B.V. All rights reserved.

Reference genes for quantitative RT-PCR data in gastric tissues and cell lines

AIM: To evaluate the suitability of reference genes in gastric tissue samples and cell lines.METHODS: the suitability of genes ACTB, B2M, GAPDH, RPL29, and 18S rRNA was assessed in 21 matched pairs of neoplastic and adjacent nonneoplastic gastric tissues from patients with gastric adenocarcinoma, 27 normal gastric tissues from patients without cancer, and 4 cell lines using reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR). the ranking of the best single and combination of reference genes was determined by NormFinder, geNorm (TM), BestKeeper, and DataAssist (TM). in addition, GenEx software was used to determine the optimal number of reference genes. To validate the results, the mRNA expression of a target gene, DNMT1, was quantified using the different reference gene combinations suggested by the various software packages for normalization.RESULTS: ACTB was the best reference gene for all gastric tissues, cell lines and all gastric tissues plus cell lines. GAPDH + B2M or ACTB + B2M was the best combination of reference genes for all the gastric tissues. On the other hand, ACTB + B2M was the best combination for all the cell lines tested and was also the best combination for analyses involving all the gastric tissues plus cell lines. According to the GenEx software, 2 or 3 genes were the optimal number of references genes for all the gastric tissues. the relative quantification of DNMT1 showed similar patterns when normalized by each combination of reference genes. the level of expression of DNMT1 in neoplastic, adjacent non-neoplastic and normal gastric tissues did not differ when these samples were normalized using GAPDH + B2M (P = 0.32), ACTB + B2M (P = 0.61), or GAPDH + B2M + ACTB (P = 0.44).CONCLUSION: GAPDH + B2M or ACTB + B2M is the best combination of reference gene for all the gastric tissues, and ACTB + B2M is the best combination for the cell lines tested. (C) 2013 Baishideng Publishing Group Co., Limited. All rights reserved.

The Development of a Holistic and Quantitative Tool for the Assessment and Improvement of Survey Quality.

There are a variety of guidelines and methods available to measure and assess survey quality. Most of these are based on qualitative descriptions. In practice, they are not easy to implement and it is very difficult to make comparisons between surveys. Hence there is a theoretical and pragmatic demand to develop a mainly quantitative based survey assessment tool. This research aimed to meet this need and make contributions to the evaluation and improvement of survey quality. Acknowledging the critical importance of measurement issues in survey research, this thesis starts with a comprehensive introduction to measurement theory and identifies the types of measurement errors associated with measurement procedures through three experiments. Then it moves on to describe concepts, guidelines and methods available for measuring and assessing survey quality. Combining these with measurement principles leads to the development of a quantitative based statistical holistic tool to measure and assess survey quality. The criteria, weights and subweights for the assessment tool are determined using Multi-Criteria Decision-Making (MCDM) and a survey questionnaire based on the Delphi method. Finally the model is applied to a database of surveys which was constructed to develop methods of classification, assessment and improvement of survey quality. The model developed in this thesis enables survey researchers and/or commissioners to make a holistic assessment of the value of the particular survey(s). This model is an Excel based audit which takes a holistic approach, following all stages of the survey from inception, to design, construction, execution, analysis and dissemination. At each stage a set of criteria are applied to assess quality. Scores attained against these assessments are weighted by the importance of the criteria and summed to give an overall assessment of the stage. The total score for a survey can be obtained by a combination of the scores for every stage weighted again by the importance of each stage. The advantage of this is to construct a means of survey assessment which can be used in a diagnostic manner to assess and improve survey quality.

Rapid and quantitative detection of the microbial spoilage of meat by Fourier Transform Infrared Spectroscopy and machine learning

Ellis, D. I., Broadhurst, D., Kell, D. B., Rowland, J. J., Goodacre, R. (2002). Rapid and quantitative detection of the microbial spoilage of meat by Fourier Transform Infrared Spectroscopy and machine learning. ? Applied and Environmental Microbiology, 68, (6), 2822-2828 Sponsorship: BBSRC

Evaluation of the KA24 (Knowledge Access 24) service for health and social care staff in London and the South-East of England. Part 1: Quantitative

Cumbers, B., Urquhart, C. & Durbin, J. (2006). Evaluation of the KA24 (Knowledge Access 24) service for health and social care staff in London and the South-East of England. Part 1: Quantitative. Health Information and Libraries Journal, 23(2), 133-139 Sponsorship: KA24 - NHS Trusts, London

The validity of ultrasound estimation of muscle volumes

Infantolino, B., Gales, D., Winter, S., Challis, J., The validity of ultrasound estimation of muscle volumes, Journal of applied biomechanics, ISSN 1065-8483, Vol. 23, N?. 3, 2007 , pags. 213-217 RAE2008

Quantitative evaluation of electron beam writing in passivated gold nanoclusters

Jenkins, Tudor; Hayton, D.J.; Bedson, T.R.; Palmer, R.E., (2001) 'Quantitative evaluation of electron beam writing in passivated gold nanoclusters', Applied Physics Letters (78) pp.1921-1923 RAE2008

Quantitative Analysis of Single Nucleotide Polymorphisms within Copy Number Variation

Background Single nucleotide polymorphisms (SNPs) have been used extensively in genetics and epidemiology studies. Traditionally, SNPs that did not pass the Hardy-Weinberg equilibrium (HWE) test were excluded from these analyses. Many investigators have addressed possible causes for departure from HWE, including genotyping errors, population admixture and segmental duplication. Recent large-scale surveys have revealed abundant structural variations in the human genome, including copy number variations (CNVs). This suggests that a significant number of SNPs must be within these regions, which may cause deviation from HWE. Results We performed a Bayesian analysis on the potential effect of copy number variation, segmental duplication and genotyping errors on the behavior of SNPs. Our results suggest that copy number variation is a major factor of HWE violation for SNPs with a small minor allele frequency, when the sample size is large and the genotyping error rate is 0~1%. Conclusions Our study provides the posterior probability that a SNP falls in a CNV or a segmental duplication, given the observed allele frequency of the SNP, sample size and the significance level of HWE testing.

Genome-wide association with bone mass and geometry in the Framingham Heart Study

BACKGROUND:Osteoporosis is characterized by low bone mass and compromised bone structure, heritable traits that contribute to fracture risk. There have been no genome-wide association and linkage studies for these traits using high-density genotyping platforms.METHODS:We used the Affymetrix 100K SNP GeneChip marker set in the Framingham Heart Study (FHS) to examine genetic associations with ten primary quantitative traits: bone mineral density (BMD), calcaneal ultrasound, and geometric indices of the hip. To test associations with multivariable-adjusted residual trait values, we used additive generalized estimating equation (GEE) and family-based association tests (FBAT) models within each sex as well as sexes combined. We evaluated 70,987 autosomal SNPs with genotypic call rates [greater than or equal to]80%, HWE p [greater than or equal to] 0.001, and MAF [greater than or equal to]10% in up to 1141 phenotyped individuals (495 men and 646 women, mean age 62.5 yrs). Variance component linkage analysis was performed using 11,200 markers.RESULTS:Heritability estimates for all bone phenotypes were 30-66%. LOD scores [greater than or equal to]3.0 were found on chromosomes 15 (1.5 LOD confidence interval: 51,336,679-58,934,236 bp) and 22 (35,890,398-48,603,847 bp) for femoral shaft section modulus. The ten primary phenotypes had 12 associations with 100K SNPs in GEE models at p < 0.000001 and 2 associations in FBAT models at p < 0.000001. The 25 most significant p-values for GEE and FBAT were all less than 3.5 x 10-6 and 2.5 x 10-5, respectively. Of the 40 top SNPs with the greatest numbers of significantly associated BMD traits (including femoral neck, trochanter, and lumbar spine), one half to two-thirds were in or near genes that have not previously been studied for osteoporosis. Notably, pleiotropic associations between BMD and bone geometric traits were uncommon. Evidence for association (FBAT or GEE p < 0.05) was observed for several SNPs in candidate genes for osteoporosis, such as rs1801133 in MTHFR; rs1884052 and rs3778099 in ESR1; rs4988300 in LRP5; rs2189480 in VDR; rs2075555 in COLIA1; rs10519297 and rs2008691 in CYP19, as well as SNPs in PPARG (rs10510418 and rs2938392) and ANKH (rs2454873 and rs379016). All GEE, FBAT and linkage results are provided as an open-access results resource at http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?id=phs000007.CONCLUSION:The FHS 100K SNP project offers an unbiased genome-wide strategy to identify new candidate loci and to replicate previously suggested candidate genes for osteoporosis.

INVESTIGATION OF BUBBLE DYNAMICS AND HEATING DURING FOCUSED ULTRASOUND INSONATION IN TISSUE-MIMICKING MATERIALS

The deposition of ultrasonic energy in tissue can cause tissue damage due to local heating. For pressures above a critical threshold, cavitation will occur in tissue and bubbles will be created. These oscillating bubbles can induce a much larger thermal energy deposition in the local region. Traditionally, clinicians and researchers have not exploited this bubble-enhanced heating since cavitation behavior is erratic and very difficult to control. The present work is an attempt to control and utilize this bubble-enhanced heating. First, by applying appropriate bubble dynamic models, limits on the asymptotic bubble size distribution are obtained for different driving pressures at 1 MHz. The size distributions are bounded by two thresholds: the bubble shape instability threshold and the rectified diffusion threshold. The growth rate of bubbles in this region is also given, and the resulting time evolution of the heating in a given insonation scenario is modeled. In addition, some experimental results have been obtained to investigate the bubble-enhanced heating in an agar and graphite based tissue- mimicking material. Heating as a function of dissolved gas concentrations in the tissue phantom is investigated. Bubble-based contrast agents are introduced to investigate the effect on the bubble-enhanced heating, and to control the initial bubble size distribution. The mechanisms of cavitation-related bubble heating are investigated, and a heating model is established using our understanding of the bubble dynamics. By fitting appropriate bubble densities in the ultrasound field, the peak temperature changes are simulated. The results for required bubble density are given. Finally, a simple bubbly liquid model is presented to estimate the shielding effects which may be important even for low void fraction during high intensity focused ultrasound (HIFU) treatment.

THE ROLE OF ACOUSTIC CAVITATION IN ENHANCED ULTRASOUND-INDUCED HEATING IN A TISSUE-MIMICKING PHANTOM

A complete understanding of high-intensity focused ultrasound-induced temperature changes in tissue requires insight into all potential mechanisms for heat deposition. Applications of therapeutic ultrasound often utilize acoustic pressures capable of producing cavitation activity. Recognizing the ability of bubbles to transfer acoustic energy into heat generation, a study of the role bubbles play in tissue hyperthermia becomes necessary. These bubbles are typically less than 50μm. This dissertation examines the contribution of bubbles and their motion to an enhanced heating effect observed in a tissue-mimicking phantom. A series of experiments established a relationship between bubble activity and an enhanced temperature rise in the phantom by simultaneously measuring both the temperature change and acoustic emissions from bubbles. It was found that a strong correlation exists between the onset of the enhanced heating effect and observable cavitation activity. In addition, the likelihood of observing the enhanced heating effect was largely unaffected by the insonation duration for all but the shortest of insonation times, 0.1 seconds. Numerical simulations were used investigate the relative importance of two candidate mechanisms for heat deposition from bubbles as a means to quantify the number of bubbles required to produce the enhanced temperature rise. The energy deposition from viscous dissipation and the absorption of radiated sound from bubbles were considered as a function of the bubble size and the viscosity of the surrounding medium. Although both mechanisms were capable of producing the level of energy required for the enhanced heating effect, it was found that inertial cavitation, associated with high acoustic radiation and low viscous dissipation, coincided with the the nature of the cavitation best detected by the experimental system. The number of bubbles required to account for the enhanced heating effect was determined through the numerical study to be on the order of 150 or less.

APPLICATION OF THE KHOKHLOV-ZABOLOTSKAYA-KUZNETSOV EQUATION TO MODELING HIGH-INTENSITY FOCUSED ULTRASOUND BEAMS

High-intensity focused ultrasound is a form of therapeutic ultrasound which uses high amplitude acoustic waves to heat and ablate tissue. HIFU employs acoustic amplitudes that are high enough that nonlinear propagation effects are important in the evolution of the sound field. A common model for HIFU beams is the Khokhlov-Zabolotskaya-Kuznetsov (KZK) equation which accounts for nonlinearity, diffraction, and absorption. The KZK equation models diffraction using the parabolic or paraxial approximation. Many HIFU sources have an aperture diameter similar to the focal length and the paraxial approximation may not be appropriate. Here, results obtained using the “Texas code,” a time-domain numerical solution to the KZK equation, were used to assess when the KZK equation can be employed. In a linear water case comparison with the O’Neil solution, the KZK equation accurately predicts the pressure field in the focal region. The KZK equation was also compared to simulations of the exact fluid dynamics equations (no paraxial approximation). The exact equations were solved using the Fourier-Continuation (FC) method to approximate derivatives in the equations. Results have been obtained for a focused HIFU source in tissue. For a low focusing gain transducer (focal length 50λ and radius 10λ), the KZK and FC models showed excellent agreement, however, as the source radius was increased to 30λ, discrepancies started to appear. Modeling was extended to the case of tissue with the appropriate power law using a relaxation model. The relaxation model resulted in a higher peak pressure and a shift in the location of the peak pressure, highlighting the importance of employing the correct attenuation model. Simulations from the code that were compared to experimental data in water showed good agreement through the focal plane.

ACOUSTO-OPTIC IMAGING IN DIFFUSE MEDIA USING PULSED ULTRASOUND AND THE PHOTOREFRACTIVE EFFECT

Acousto-optic imaging (AOI) in optically diffuse media is a hybrid imaging modality in which a focused ultrasound beam is used to locally phase modulate light inside of turbid media. The modulated optical field carries with it information about the optical properties in the region where the light and sound interact. The motivation for the development of AOI systems is to measure optical properties at large depths within biological tissue with high spatial resolution. A photorefractive crystal (PRC) based interferometry system is developed for the detection of phase modulated light in AOI applications. Two-wave mixing in the PRC creates a reference beam that is wavefront matched to the modulated optical field collected from the specimen. The phase modulation is converted to an intensity modulation at the optical detector when these two fields interfere. The interferometer has a high optical etendue, making it well suited for AOI where the scattered light levels are typically low. A theoretical model for the detection of acoustically induced phase modulation in turbid media using PRC based interferometry is detailed. An AOI system, using a single element focused ultrasound transducer to pump the AO interaction and the PRC based detection system, is fabricated and tested on tissue mimicking phantoms. It is found that the system has sufficient sensitivity to detect broadband AO signals generated using pulsed ultrasound, allowing for AOI at low time averaged ultrasound output levels. The spatial resolution of the AO imaging system is studied as a function of the ultrasound pulse parameters. A theoretical model of light propagation in turbid media is used to explore the dependence of the AO response on the experimental geometry, light collection aperture, and target optical properties. Finally, a multimodal imaging system combining pulsed AOI and conventional B- mode ultrasound imaging is developed. B-mode ultrasound and AO images of targets embedded in both highly diffuse phantoms and biological tissue ex vivo are obtained, and millimeter resolution is demonstrated in three dimensions. The AO images are intrinsically co-registered with the B-mode ultrasound images. The results suggest that AOI can be used to supplement conventional B-mode ultrasound imaging with optical information.

HEATING IN VASCULAR TISSUE AND FLOW-THROUGH TISSUE PHANTOMS INDUCED BY FOCUSED ULTRASOUND

High intensity focused ultrasound (HIFU) can be used to control bleeding, both from individual blood vessels as well as from gross damage to the capillary bed. This process, called acoustic hemostasis, is being studied in the hope that such a method would ultimately provide a lifesaving treatment during the so-called "golden hour", a brief grace period after a severe trauma in which prompt therapy can save the life of an injured person. Thermal effects play a major role in occlusion of small vessels and also appear to contribute to the sealing of punctures in major blood vessels. However, aggressive ultrasound-induced tissue heating can also impact healthy tissue and can lead to deleterious mechanical bioeffects. Moreover, the presence of vascularity can limit one’s ability to elevate the temperature of blood vessel walls owing to convective heat transport. In an effort to better understand the heating process in tissues with vascular structure we have developed a numerical simulation that couples models for ultrasound propagation, acoustic streaming, ultrasound heating and blood cooling in Newtonian viscous media. The 3-D simulation allows for the study of complicated biological structures and insonation geometries. We have also undertaken a series of in vitro experiments, in non-uniform flow-through tissue phantoms, designed to provide a ground truth verification of the model predictions. The calculated and measured results were compared over a range of values for insonation pressure, insonation time, and flow rate; we show good agreement between predictions and measurements. We then conducted a series of simulations that address two limiting problems of interest: hemostasis in small and large vessels. We employed realistic human tissue properties and considered more complex geometries. Results show that the heating pattern in and around a blood vessel is different for different vessel sizes, flow rates and for varying beam orientations relative to the flow axis. Complete occlusion and wall- puncture sealing are both possible depending on the exposure conditions. These results concur with prior clinical observations and may prove useful for planning of a more effective procedure in HIFU treatments.