Flow cytometry and FISH to measure the average length of telomeres (flow FISH)

Telomeres have emerged as crucial cellular elements in aging and various diseases including cancer. To measure the average length of telomere repeats in cells, we describe our protocols that use fluorescent in situ hybridization (FISH) with labeled peptide nucleic acid (PNA) probes specific for telomere repeats in combination with fluorescence measurements by flow cytometry (flow FISH). Flow FISH analysis can be performed using commercially available flow cytometers, and has the unique advantage over other methods for measuring telomere length of providing multi-parameter information on the length of telomere repeats in thousands of individual cells. The accuracy and reproducibility of the measurements is augmented by the automation of most pipetting (aspiration and dispensing) steps, and by including an internal standard (control cells) with a known telomere length in every tube. The basic protocol for the analysis of nucleated blood cells from 22 different individuals takes about 12 h spread over 2-3 days.

Thermodilution and esophageal Doppler ultrasound in the assessment of blood flow changes induced by endotoxin and dobutamine

BACKGROUND: Intermittent (IT) and continuous (CT) thermodilution and esophageal Doppler (ED), are all used for hemodynamic monitoring. The aim of this study was to test the agreement between these methods during endotoxin (ET) and dobutamine infusion. METHODS: Twenty-two pigs (39 +/- 1.8 kg body weight) were randomized to general anesthesia and either continuous ET (n = 9) or placebo (PL, n = 13) infusion. After 18 hours of ET or PL infusion, the animals were further randomized to receive dobutamine (n = 3 in ET, n = 5 in PL) or PL. A set of measurements using the three methods were obtained every hour, and the relative blood flow changes between two subsequent measurements were calculated. RESULTS: Bias or limits of agreement for flows were 0.73 L/min or 1.80 L/min for IT and CT, -0.33 L/min or 4.29 L/min for IT and ED, and -1.06 or 3.94 for CT and ED (n = 515, each). For flow changes they were 1% or 44%, 2% or 59%, and 3% or 45%, respectively. Bias and limits of agreement did not differ in ET- and PL-treated animals or in animals with or without dobutamine. Despite significant correlation between any two methods, the respective correlation coefficients (r) were small (IT vs. CT: 0.452; IT vs. ED: 0.042; CT vs. ED: 0.069; all p < 0.001). The same directional changes were measured by any two methods in 49%, 40%, and 50%. When IT flows >5 L/min were compared with IT flows of agreement than the former (p = 0.012). CONCLUSION: IT and CT cardiac output agree only to a moderate level, and agreement between the respective relative blood flow changes is even worse. ED has poor agreement with both thermodilution methods, especially when cardiac output is >5 L/min.

Theoretical estimation of optical absorption and photoluminescence in nanostructured silicon; an approach to improve efficiency in nanostructured solar cells

Renewable energy is growing in demand, and thus the the manufacture of solar cells and photovoltaic arrays has advanced dramatically in recent years. This is proved by the fact that the photovoltaic production has doubled every 2 years, increasing by an average of 48% each year since 2002. Covering the general overview of solar cell working, and its model, this thesis will start with the three generations of photovoltaic solar cell technology, and move to the motivation of dedicating research to nanostructured solar cell. For the current generation solar cells, among several factors, like photon capture, photon reflection, carrier generation by photons, carrier transport and collection, the efficiency also depends on the absorption of photons. The absorption coefficient,α, and its dependence on the wavelength, λ, is of major concern to improve the efficiency. Nano-silicon structures (quantum wells and quantum dots) have a unique advantage compared to bulk and thin film crystalline silicon that multiple direct and indirect band gaps can be realized by appropriate size control of the quantum wells. This enables multiple wavelength photons of the solar spectrum to be absorbed efficiently. There is limited research on the calculation of absorption coefficient in nano structures of silicon. We present a theoretical approach to calculate the absorption coefficient using quantum mechanical calculations on the interaction of photons with the electrons of the valence band. One model is that the oscillator strength of the direct optical transitions is enhanced by the quantumconfinement effect in Si nanocrystallites. These kinds of quantum wells can be realized in practice in porous silicon. The absorption coefficient shows a peak of 64638.2 cm-1 at = 343 nm at photon energy of ξ = 3.49 eV ( = 355.532 nm). I have shown that a large value of absorption coefficient α comparable to that of bulk silicon is possible in silicon QDs because of carrier confinement. Our results have shown that we can enhance the absorption coefficient by an order of 10, and at the same time a nearly constant absorption coefficient curve over the visible spectrum. The validity of plots is verified by the correlation with experimental photoluminescence plots. A very generic comparison for the efficiency of p-i-n junction solar cell is given for a cell incorporating QDs and sans QDs. The design and fabrication technique is discussed in brief. I have shown that by using QDs in the intrinsic region of a cell, we can improve the efficiency by a factor of 1.865 times. Thus for a solar cell of efficiency of 26% for first generation solar cell, we can improve the efficiency to nearly 48.5% on using QDs.

Two dimensional Lattice Boltzmann simulation of fluid flow through an idealized micro-structure of disordered media

This technical report discusses the application of Lattice Boltzmann Method (LBM) in the fluid flow simulation through porous filter-wall of disordered media. The diesel particulate filter (DPF) is an example of disordered media. DPF is developed as a cutting edge technology to reduce harmful particulate matter in the engine exhaust. Porous filter-wall of DPF traps these soot particles in the after-treatment of the exhaust gas. To examine the phenomena inside the DPF, researchers are looking forward to use the Lattice Boltzmann Method as a promising alternative simulation tool. The lattice Boltzmann method is comparatively a newer numerical scheme and can be used to simulate fluid flow for single-component single-phase, single-component multi-phase. It is also an excellent method for modelling flow through disordered media. The current work focuses on a single-phase fluid flow simulation inside the porous micro-structure using LBM. Firstly, the theory concerning the development of LBM is discussed. LBM evolution is always related to Lattice gas Cellular Automata (LGCA), but it is also shown that this method is a special discretized form of the continuous Boltzmann equation. Since all the simulations are conducted in two-dimensions, the equations developed are in reference with D2Q9 (two-dimensional 9-velocity) model. The artificially created porous micro-structure is used in this study. The flow simulations are conducted by considering air and CO2 gas as fluids. The numerical model used in this study is explained with a flowchart and the coding steps. The numerical code is constructed in MATLAB. Different types of boundary conditions and their importance is discussed separately. Also the equations specific to boundary conditions are derived. The pressure and velocity contours over the porous domain are studied and recorded. The results are compared with the published work. The permeability values obtained in this study can be fitted to the relation proposed by Nabovati [8], and the results are in excellent agreement within porosity range of 0.4 to 0.8.

Impact of optic media opacities and image compression on quantitative analysis of optical coherence tomography

To analyze the impact of opacities in the optical pathway and image compression of 32-bit raw data to 8-bit jpg images on quantified optical coherence tomography (OCT) image analysis.

Performance Evaluation of Material Flow Systems in Discrete Time

Im folgenden Beitrag werden zeitdiskrete analytische Methoden vorgestellt, mit Hilfe derer Informations- und Materialflüsse in logistischen Systemen analysiert und bewertet werden können. Bestehende zeitdiskrete Verfahren sind jedoch auf die Bearbeitung und Weitergabe in immer gleichen Mengen („One Piece Flow“) beschränkt. Vor allem in Materialflusssystemen kommt es, bedingt durch die Zusammenfassung von Aufträgen, durch Transporte und durch Sortiervorgänge, zur Bildung von Batches. Daher wurden analytische Methoden entwickelt, die es ermöglichen, verschiedene Sammelprozesse, Batchankünfte an Ressourcen, Batchbearbeitung und Sortieren von Batches analytisch abzubilden und Leistungskenngrößen zu deren Bewertung zu bestimmen. Die im Rahmen der Entwicklungsarbeiten entstandene Software-Lösung „Logistic Analyzer“ ermöglicht eine einfache Modellierung und Analyse von praktischen Problemen. Der Beitrag schließt mit einem numerischen Beispiel.

Technical throughput of material flow systems required to achieve design flow – determined by simulation with aniteration algorithm

This article deals with complex material flow systems and series connections of conveyor and op-erating elements. These can be characterised by a specific availability. The thus resultant overall availabil-ity of necessary “technical throughput” of the individual elements for the achievement of a specified throughput. When the conveyor and operating elements are subjected to a stochastic distribution, the interposition of buffers is necessary but these can also lead to a reduction of the necessary throughput due faults. The system behaviour of complex installations can only be investigated by simulation. The parame-ter changes required in order to achieve specific target values can also be determined by simulation runs in iteration loops.

Setting Inventory Levels of CONWIP Flow Lines via Linear Programming

This paper treats the problem of setting the inventory level and optimizing the buffer allocation of closed-loop flow lines operating under the constant-work-in-process (CONWIP) protocol. We solve a very large but simple linear program that models an entire simulation run of a closed-loop flow line in discrete time to determine a production rate estimate of the system. This approach introduced in Helber, Schimmelpfeng, Stolletz, and Lagershausen (2011) for open flow lines with limited buffer capacities is extended to closed-loop CONWIP flow lines. Via this method, both the CONWIP level and the buffer allocation can be optimized simultaneously. The first part of a numerical study deals with the accuracy of the method. In the second part, we focus on the relationship between the CONWIP inventory level and the short-term profit. The accuracy of the method turns out to be best for such configurations that maximize production rate and/or short-term profit.

Importance of vegetation, topography and flow paths for water transit times of base flow in alpine headwater catchments

The mean transit time (MTT) of water in a catchment gives information about storage, flow paths, sources of water and thus also about retention and release of solutes in a catchment. To our knowledge there are only a few catchment studies on the influence of vegetation cover changes on base flow MTTs. The main changes in vegetation cover in the Swiss Alps are massive shrub encroachment and forest expansion into formerly open habitats. Four small and relatively steep headwater catchments in the Swiss Alps (Ursern Valley) were investigated to relate different vegetation cover to water transit times. Time series of water stable isotopes were used to calculate MTTs. The high temporal variation of the stable isotope signals in precipitation was strongly dampened in stream base flow samples. MTTs of the four catchments were 70 to 102 weeks. The strong dampening of the stable isotope input signal as well as stream water geochemistry points to deeper flow paths and mixing of waters of different ages at the catchments' outlets. MTTs were neither related to topographic indices nor vegetation cover. The major part of the quickly infiltrating precipitation likely percolates through fractured and partially karstified deeper rock zones, which increases the control of bedrock flow paths on MTT. Snow accumulation and the timing of its melt play an important role for stable isotope dynamics during spring and early summer. We conclude that, in mountainous headwater catchments with relatively shallow soil layers, the hydrogeological and geochemical patterns (i.e. geochemistry, porosity and hydraulic conductivity of rocks) and snow dynamics influence storage, mixing and release of water in a stronger way than vegetation cover or topography do.

Modeling of ore-forming and geoenvironmental systems: Roles of fluid flow and chemical reaction processes

Ore-forming and geoenviromental systems commonly involve coupled fluid flowand chemical reaction processes. The advanced numerical methods and computational modeling have become indispensable tools for simulating such processes in recent years. This enables many hitherto unsolvable geoscience problems to be addressed using numerical methods and computational modeling approaches. For example, computational modeling has been successfully used to solve ore-forming and mine site contamination/remediation problems, in which fluid flow and geochemical processes play important roles in the controlling dynamic mechanisms. The main purpose of this paper is to present a generalized overview of: (1) the various classes and models associated with fluid flow/chemically reacting systems in order to highlight possible opportunities and developments for the future; (2) some more general issues that need attention in the development of computational models and codes for simulating ore-forming and geoenviromental systems; (3) the related progresses achieved on the geochemical modeling over the past 50 years or so; (4) the general methodology for modeling of oreforming and geoenvironmental systems; and (5) the future development directions associated with modeling of ore-forming and geoenviromental systems.

Assessment of low-flow, low-gradient, severe aortic stenosis: an invasive evaluation is required for decision making.

Low-flow, low-gradient severe aortic stenosis (AS) is characterised by a small aortic valve area (AVA) and low mean gradient (MG) secondary to a low cardiac output and may occur in patients with either a preserved or reduced left ventricular ejection fraction (LVEF). Symptomatic patients presenting with low-flow, low-gradient severe AS have a dismal prognosis independent of baseline LVEF if managed conservatively and should therefore undergo aortic valve replacement if feasible. Transthoracic echocardiography (TTE) is the first-line investigation for the assessment of AS haemodynamic severity. However, when confronted with guideline-discordant AVA (small) and MG (low) values, there are several reasons other than severe AS combined with a low cardiac output which may lead to such a situation, including erroneous measurements, small body size, inherent inconsistencies in the guidelines' criteria, prolonged ejection time and aortic pseudostenosis. The distinction between these various entities poses a diagnostic challenge. However, it is important to make a distinction because each has very different implications in terms of risk stratification and therapeutic management. In such instances, cardiac catheterisation forms an integral part of the work-up of these patients in order to confirm or refute the echocardiographic findings to guide management decisions appropriately.