Sensitivity of the NMR density matrix to pulse sequence parameters : a simplified analytic approach

We present a formalism for the analysis of sensitivity of nuclear magnetic resonance pulse sequences to variations of pulse sequence parameters, such as radiofrequency pulses, gradient pulses or evolution delays. The formalism enables the calculation of compact, analytic expressions for the derivatives of the density matrix and the observed signal with respect to the parameters varied. The analysis is based on two constructs computed in the course of modified density-matrix simulations: the error interrogation operators and error commutators. The approach presented is consequently named the Error Commutator Formalism (ECF). It is used to evaluate the sensitivity of the density matrix to parameter variation based on the simulations carried out for the ideal parameters, obviating the need for finite-difference calculations of signal errors. The ECF analysis therefore carries a computational cost comparable to a single density-matrix or product-operator simulation. Its application is illustrated using a number of examples from basic NMR spectroscopy. We show that the strength of the ECF is its ability to provide analytic insights into the propagation of errors through pulse sequences and the behaviour of signal errors under phase cycling. Furthermore, the approach is algorithmic and easily amenable to implementation in the form of a programming code. It is envisaged that it could be incorporated into standard NMR product-operator simulation packages.

Regulation of ROCK1 via Notch1 during breast cancer cell migration into dense matrices

Background The behaviour of tumour cells depends on factors such as genetics and the tumour microenvironment. The latter plays a crucial role in normal mammary gland development and also in breast cancer initiation and progression. Breast cancer tissues tend to be highly desmoplastic and dense matrix as a pre-existing condition poses one of the highest risk factors for cancer development. However, matrix influence on tumour cell gene expression and behaviour such as cell migration is not fully elucidated. Results We generated high-density (HD) matrices that mimicked tumour collagen content of 20 mg/cm3 that were ~14-fold stiffer than low-density (LD) matrix of 1 mg/cm3. Live-cell imaging showed breast cancer cells utilizing cytoplasmic streaming and cell body contractility for migration within HD matrix. Cell migration was blocked in the presence of both the ROCK inhibitor, Y-27632, and the MMP inhibitor, GM6001, but not by the drugs individually. This suggests roles for ROCK1 and MMP in cell migration are complicated by compensatory mechanisms. ROCK1 expression and protein activity, were significantly upregulated in HD matrix but these were blocked by treatment with a histone deacetylase (HDAC) inhibitor, MS-275. In HD matrix, the inhibition of ROCK1 by MS-275 was indirect and relied upon protein synthesis and Notch1. Inhibition of Notch1 using pooled siRNA or DAPT abrogated the inhibition of ROCK1 by MS-275. Conclusion Increased matrix density elevates ROCK1 activity, which aids in cell migration via cell contractility. The upregulation of ROCK1 is epigenetically regulated in an indirect manner involving the repression of Notch1. This is demonstrated from inhibition of HDACs by MS-275, which caused an upregulation of Notch1 levels leading to blockade of ROCK1 expression.

Cell density alters matrix accumulation in two distinct fractions and the mechanical integrity of alginate-chondrocyte constructs

Chondrocyte density in articular cartilage is known to change with the development and growth of the tissue and may play an important role in the formation of a functional extracellular matrix (ECM). The objective of this study was to determine how initial chondrocyte density in an alginate hydrogel affects the matrix composition, its distribution between the cell-associated (CM) and further removed matrix (FRM) fractions, and the tensile mechanical properties of the developing engineered cartilage. Alginate constructs containing primary bovine chondrocytes at densities of 0, 4, 16, and 64 million cells/ml were fabricated and cultured for 1 or 2 weeks, at which time structural, biochemical, and mechanical properties were analyzed. Both matrix content and distribution varied with the initial cell density. Increasing cell density resulted in an increasing content of collagen and sulfated-glycosaminoglycan (GAG) and an increasing proportion of these molecules localized in the CM. While the equilibrium tensile modulus of cell-free alginate did not change with time in culture, the constructs with highest cell density were 116% stiffer than cell-free controls after 2 weeks of culture. The equilibrium tensile modulus was positively correlated with total collagen (r2 = 0.47, p < 0.001) and GAG content (r2 = 0.68, p < 0.001), and these relationships were enhanced when analyzing only those matrix molecules in the CM fraction (r2 = 0.60 and 0.72 for collagen and GAG, respectively, each p < 0.001). Overall, the results of this study indicate that initial cell density has a considerable effect on the developing composition, structure, and function of alginate–chondrocyte constructs.

Single-step, rapid low-temperature synthesis of Si quantum dots embedded in an amorphous SiC matrix in high-density reactive plasmas

A simple, effective and innovative approach based on low-pressure, thermally nonequilibrium, high-density inductively coupled plasmas is proposed to rapidly synthesize Si quantum dots (QDs) embedded in an amorphous SiC (a-SiC) matrix at a low substrate temperature and without any commonly used hydrogen dilution. The experimental results clearly demonstrate that uniform crystalline Si QDs with a size of 3-4 nm embedded in the silicon-rich (carbon content up to 10.7at.%) a-SiC matrix can be formed from the reactive mixture of silane and methane gases, with high growth rates of ∼1.27-2.34 nm s-1 and at a low substrate temperature of 200 °C. The achievement of the high-rate growth of Si QDs embedded in the a-SiC without any commonly used hydrogen dilution is discussed based on the unique properties of the inductively coupled plasma-based process. This work is particularly important for the development of the all-Si tandem cell-based third generation photovoltaic solar cells.

Studies of granulosa cell maturation in dominant and subordinate bovine follicles : novel extracellular matrix focimatrix is co-ordinately regulated with cholesterol side-chain cleavage CYP11A1

During growth of antral ovarian follicles granulosa cells first become associated with a novel type of extracellular matrix, focimatrix, and at larger sizes follicles become either subordinate or dominant. To examine this, bovine subordinate (9.0±s.e.m. 0.4 mm; n=16), partially dominant (12.0±0.6 mm; n=18) and fully dominant (15.0±0.4 mm; n=14) follicles were examined by real time RT-PCR analyses of granulosa cells and by immunohistochemistry of focimatrix. Changes in the expression of FSH receptor, LH receptor, cholesterol side-chain cleavage (CYP11A1), 3β-hydroxysteroid dehydrogenase, aromatase (CYP19A1) and inhibin-α and β-B were observed as expected for follicle sizes examined. After adjusting for size differences, only CYP11A1 was significantly different between the groups, and elevated in dominant follicles. Also after adjusting for differences in size there were no significant differences in expression of focimatrix components collagen type IV α-1 (COL4A1), laminin β-2, nidogen 1 (NID1), and perlecan (HSPG2) or the volume density of NID1 and -2 and HSPG2. The volume density of focimatrix components in laminin 111 was significantly elevated in dominant follicles. Adjusting for analysis of more than one follicle per animal and for multiple correlations, CYP11A1 mRNA levels were highly correlated with the focimatrix genes COL4A1, NID1 and -2 and HSPG2. Thus, focimatrix may potentially regulate CYP11A1 expression, and the regulation of both could be important in follicular dominance.

An investigation into factors affecting electron density calibration for a megavoltage cone-beam CT system

There is a growing interest in the use of megavoltage cone-beam computed tomography (MV CBCT) data for radiotherapy treatment planning. To calculate accurate dose distributions, knowledge of the electron density (ED) of the tissues being irradiated is required. In the case of MV CBCT, it is necessary to determine a calibration-relating CT number to ED, utilizing the photon beam produced for MV CBCT. A number of different parameters can affect this calibration. This study was undertaken on the Siemens MV CBCT system, MVision, to evaluate the effect of the following parameters on the reconstructed CT pixel value to ED calibration: the number of monitor units (MUs) used (5, 8, 15 and 60 MUs), the image reconstruction filter (head and neck, and pelvis), reconstruction matrix size (256 by 256 and 512 by 512), and the addition of extra solid water surrounding the ED phantom. A Gammex electron density CT phantom containing EDs from 0.292 to 1.707 was imaged under each of these conditions. The linear relationship between MV CBCT pixel value and ED was demonstrated for all MU settings and over the range of EDs. Changes in MU number did not dramatically alter the MV CBCT ED calibration. The use of different reconstruction filters was found to affect the MV CBCT ED calibration, as was the addition of solid water surrounding the phantom. Dose distributions from treatment plans calculated with simulated image data from a 15 MU head and neck reconstruction filter MV CBCT image and a MV CBCT ED calibration curve from the image data parameters and a 15 MU pelvis reconstruction filter showed small and clinically insignificant differences. Thus, the use of a single MV CBCT ED calibration curve is unlikely to result in any clinical differences. However, to ensure minimal uncertainties in dose reporting, MV CBCT ED calibration measurements could be carried out using parameter-specific calibration measurements.

The rationale for using microscopic units of a donor matrix in cartilage defect repair

The efficacy of existing articular cartilage defect repair strategies are limited. Native cartilage tissue forms via a series of exquisitely orchestrated morphogenic events spanning through gestation into early childhood. However, defect repair must be achieved in a non-ideal microenvironment over an accelerated time-frame compatible with the normal life of an adult patient. Scaffolds formed from decellularized tissues are commonly utilized to enable the rapid and accurate repair of tissues such as skin, bladder and heart valves. The intact extracellular matrix remaining following the decellularization of these relatively low-matrix-density tissues is able to rapidly and accurately guide host cell repopulation. By contrast, the extraordinary density of cartilage matrix limits both the initial decellularization of donor material as well as its subsequent repopulation. Repopulation of donor cartilage matrix is generally limited to the periphery, with repopulation of lacunae deeper within the matrix mass being highly inefficient. Herein, we review the relevant literature and discuss the trend toward the use of decellularized donor cartilage matrix of microscopic dimensions. We show that 2-µm microparticles of donor matrix are rapidly integrate with articular chondrocytes, forming a robust cartilage-like composites with enhanced chondrogenic gene expression. Strategies for the clinical application of donor matrix microparticles in cartilage defect repair are discussed.

High-throughput indentational elasticity measurements of hydrogel extracellular matrix substrates

Much interest surrounds the effect of extracellular matrix (ECM) elasticity on cell behavior. Here we present a rapid method for measuring the elasticity of synthetic ECM substrates based on indentation of the substrate with a ferromagnetic sphere and optical tracking of the resulting deformation. We find that this method yields order-of-magnitude agreement with atomic force microscopy elasticity measurements, but that the degree of this agreement depends strongly on sphere density and gel elasticity. In its regime of greatest accuracy, we envision that this method may be used for high-throughput characterization of ECM substrates in cell biological studies.

Mammographic density-a review on the current understanding of its association with breast cancer

There has been considerable recent interest in the genetic, biological and epidemiological basis of mammographic density (MD), and the search for causative links between MD and breast cancer (BC) risk. This report will critically review the current literature on MD and summarize the current evidence for its association with BC. Keywords 'mammographic dens*', 'dense mammary tissue' or 'percent dens*' were used to search the existing literature in English on PubMed and Medline. All reports were critically analyzed. The data were assigned to one of the following aspects of MD: general association with BC, its relationship with the breast hormonal milieu, the cellular basis of MD, the generic variations of MD, and its significance in the clinical setting. MD adjusted for age, and BMI is associated with increased risk of BC diagnosis, advanced tumour stage at diagnosis and increased risk of both local recurrence and second primary cancers. The MD measures that predict BC risk have high heritability, and to date several genetic markers associated with BC risk have been found to also be associated with these MD risk predictors. Change in MD could be a predictor of the extent of chemoprevention with tamoxifen. Although the biological and genetic pathways that determine and perhaps modulate MD remain largely unresolved, significant inroads are being made into the understanding of MD, which may lead to benefits in clinical screening, assessment and treatment strategies. This review provides a timely update on the current understanding of MD's association with BC risk.

Polarized infrared absorption spectrum of matrix-isolated methylperoxyl radicals, CH3OO (X)over-tilde 2A ''

We have used a tandem pair of supersonic nozzles to produce clean samples of CH3OO radicals in cryogenic matrices. One hyperthermal nozzle decomposes azomethane (CH3NNCH3) to generate intense pulses of CH3 radicals, While the second nozzle alternately fires a burst Of O-2/Ar at the 20 K matrix. The CH3/O-2/20 K argon radical sandwich acts to produce target methylperoxyl radicals: CH3 + O-2 --> CH3OO. The absorption spectra of the radicals are monitored with a Fourier transform infrared spectrometer. We report 10 of the 12 fundamental infrared bands of the methylperoxyl radical CH3OO, (X) over tilde (2)A", in an argon matrix at 20 K. The experimental frequencies (cm(-1)) and polarizations follow: the a' modes are 3032, 2957, 1448, 1410, 1180, 1109, 90, 492, while the a" modes are 3024 and 1434. We cannot detect the asymmetric CH3 rocking mode, nu(11), nor the torsion, nu(12). The infrared spectra of (CH3OO)-O-18-O-18, (CH3OO)-C-13, and CD3OO have been measured as well in order to determine the isotopic shifts. The experimental frequencies, {nu}, for the methylperoxyl radicals are compared to harmonic frequencies, {omega}, resulting from a UB3LYP/6-311G(d,p) electronic structure calculation. Linear dichroism spectra were measured with photooriented radical samples in order to establish the experimental polarizations of most vibrational bands. The methylperoxyl radical matrix frequencies listed above are within +/-2% of the gas-phase vibrational frequencies. A final set of vibrational frequencies for the H radical, are recommended. See also http://ellison.colorado.edu/methylperoxyl.

Phagocytosis of cross-linked gelatin matrix by human breast carcinoma cells correlates with their invasive capacity

During invasion and metastasis, cancer cells interact closely with the extracellular matrix molecules by attachment, degradation, and migration. We demonstrated previously the local degradation of fluorescently labeled gelatin matrix by cancer cells at invasive membrane protrusions, called invadopodia. Using the newly developed quantitative fluorescence-activated cell sorting-phagocytosis assay and image analysis of localized degradation of fluorescently labeled matrix, we document here that degradation and site- specific removal of cross-linked gelatin matrix is correlated with the extent of phagocytosis in human breast cancer cells. A higher phagocytic capacity is generally associated with increasing invasiveness, documented in other invasion and motility assays as well. Gelatin phagocytosis is time and cell density dependent, and it is mediated by the actin cytoskeleton. Most of the intracellular gelatin is routed to actively acidified vesicles, as demonstrated by the fluorescent colocalization of gelatin with acidic vesicles, indicating the intracellular degradation of the phagocytosed matrix in lysosomes. We show here that normal intracellular routing is blocked after treatment with acidification inhibitors. In addition, the need for partial proteolytic degradation of the matrix prior to phagocytosis is demonstrated by the inhibition of gelatin phagocytosis with different serine and metalloproteinase inhibitors and its stimulation by conditioned medium containing the matrix metalloproteinases MMP-2 and MMP-9. Our results demonstrate that phagocytosis of extracellular matrix is an inherent feature of breast tumor cells that correlates with and may even directly contribute to their invasive capacity. This assay is useful for screening and evaluating potential anti-invasive agents because it is fast, reproducible, and versatile.

The pathobiology of mammographic density

High mammographic density confers a significantly increased risk of breast cancer. As it is relatively common in the normal population the risk of cancer attributable to increased mammographic density could potentially account for an important percentage of total BCa cases. The underlying cause for high mammographic density and its association with increased BCa risk and progression is unknown. In this review we describe the work that has been done to define the histopathological characteristics of mammographic density. Mammograms define breast tissues with areas of high density due to an increased amount of radio-opaque tissue (stromal and epithelial cells) and also less areas of radiolucent fat. Histological work however can define the roles played by each cell type. We review the work that has been performed assessing changes in epithelial cells, stromal cells, the extracellular matrix, and immune infiltrate. To determine how these changes may be increasing breast cancer risk we also discuss the roles of each of the cell types in breast cancer initiation and progression.

Si quantum dots embedded in an amorphous SiC matrix : nanophase control by non-equilibrium plasma hydrogenation

Nanophase nc-Si/a-SiC films that contain Si quantum dots (QDs) embedded in an amorphous SiC matrix were deposited on single-crystal silicon substrates using inductively coupled plasma-assisted chemical vapor deposition from the reactive silane and methane precursor gases diluted with hydrogen at a substrate temperature of 200 °C. The effect of the hydrogen dilution ratio X (X is defined as the flow rate ratio of hydrogen-to-silane plus methane gases), ranging from 0 to 10.0, on the morphological, structural, and compositional properties of the deposited films, is extensively and systematically studied by scanning electron microscopy, high-resolution transmission electron microscopy, X-ray diffraction, Raman spectroscopy, Fourier-transform infrared absorption spectroscopy, and X-ray photoelectron spectroscopy. Effective nanophase segregation at a low hydrogen dilution ratio of 4.0 leads to the formation of highly uniform Si QDs embedded in the amorphous SiC matrix. It is also shown that with the increase of X, the crystallinity degree and the crystallite size increase while the carbon content and the growth rate decrease. The obtained experimental results are explained in terms of the effect of hydrogen dilution on the nucleation and growth processes of the Si QDs in the high-density plasmas. These results are highly relevant to the development of next-generation photovoltaic solar cells, light-emitting diodes, thin-film transistors, and other applications.

Accounting for management costs in sensitivity analyses of matrix population models

Traditional sensitivity and elasticity analyses of matrix population models have been used to inform management decisions, but they ignore the economic costs of manipulating vital rates. For example, the growth rate of a population is often most sensitive to changes in adult survival rate, but this does not mean that increasing that rate is the best option for managing the population because it may be much more expensive than other options. To explore how managers should optimize their manipulation of vital rates, we incorporated the cost of changing those rates into matrix population models. We derived analytic expressions for locations in parameter space where managers should shift between management of fecundity and survival, for the balance between fecundity and survival management at those boundaries, and for the allocation of management resources to sustain that optimal balance. For simple matrices, the optimal budget allocation can often be expressed as simple functions of vital rates and the relative costs of changing them. We applied our method to management of the Helmeted Honeyeater (Lichenostomus melanops cassidix; an endangered Australian bird) and the koala (Phascolarctos cinereus) as examples. Our method showed that cost-efficient management of the Helmeted Honeyeater should focus on increasing fecundity via nest protection, whereas optimal koala management should focus on manipulating both fecundity and survival simultaneously. These findings are contrary to the cost-negligent recommendations of elasticity analysis, which would suggest focusing on managing survival in both cases. A further investigation of Helmeted Honeyeater management options, based on an individual-based model incorporating density dependence, spatial structure, and environmental stochasticity, confirmed that fecundity management was the most cost-effective strategy. Our results demonstrate that decisions that ignore economic factors will reduce management efficiency. ©2006 Society for Conservation Biology.

Influence of kaolinite particle size on cross-link density, microstructure and mechanical properties of latex blending styrene butadiene rubber composites

Cross-link density, microstructure and mechanical properties of styrene butadiene rubber (SBR) composites filled with different particle sized kaolinites are investigated. With the increase of kaolinite particle size, the cross-link density of the filled SBR composites, the dispersibility and orientation degree of kaolinite particles gradually decrease. Some big cracks in filled rubber composites are distributed along the fringe of kaolinite aggregates, and the absorbance of all the absorption bands of kaolinites gradually increase with the increase of kaolinite particle size. All mechanical property indexes of kaolinite filled SBR composites decrease due to the decrease of cross-linking and reduction of interface interaction between filler and rubber matrix.