Search Results
corr2D: Implementation of Two-Dimensional Correlation Analysis in R
In the package corr2D two-dimensional correlation analysis is implemented in R. This paper describes how two-dimensional correlation analysis is done in the package and how the mathematical equations are translated into R code. The paper features a simple tutorial with executable code for beginners, insight into the calculations done before the correlation analysis, a detailed look at the parallelization of the fast Fourier transformation based correlation analysis and a speed test of the calculation. The package corr2D offers the possibility to preprocess, correlate and postprocess spectroscopic data using exclusively the R language. Thus, corr2D is a welcome addition to the toolbox of spectroscopists and makes two-dimensional correlation analysis more accessible and transparent.
Surface deep profile synchrotron studies of mechanically modified top-down silicon nanowires array using ultrasoft X-ray absorption near edge structure spectroscopy
Atomic, electronic structure and composition of top-down metal-assisted wet-chemically etched silicon nanowires were studied by synchrotron radiation based X-ray absorption near edge structure technique. Local surrounding of the silicon and oxygen atoms in silicon nanowires array was studied on as-prepared nanostructured surfaces (atop part of nanowires) and their bulk part after, first time applied, in-situ mechanical removal atop part of the formed silicon nanowires. Silicon suboxides together with disturbed silicon dioxide were found in the composition of the formed arrays that affects the electronic structure of silicon nanowires. The results obtained by us convincingly testify to the homogeneity of the phase composition of the side walls of silicon nanowires and the electronic structure in the entire length of the nanowire. The controlled formation of the silicon nanowires array may lead to smart engineering of its atomic and electronic structure that influences the exploiting strategy of metal-assisted wet-chemically etched silicon nanowires as universal matrices for different applications.
Raman and infrared spectroscopy reveal that proliferating and quiescent human fibroblast cells age by biochemically similar but not identical processes
Dermal fibroblast cells can adopt different cell states such as proliferation, quiescence, apoptosis or senescence, in order to ensure tissue homeostasis. Proliferating (dividing) cells pass through the phases of the cell cycle, while quiescent and senescent cells exist in a non-proliferating cell cycle-arrested state. However, the reversible quiescence state is in contrast to the irreversible senescence state. Long-term quiescent cells transit into senescence indicating that cells age also when not passing through the cell cycle. Here, by label-free in vitro vibrational spectroscopy, we studied the biomolecular composition of quiescent dermal fibroblast cells and compared them with those of proliferating and senescent cells. Spectra were examined by multivariate statistical analysis using a PLS-LDA classification model, revealing differences in the biomolecular composition between the cell states mainly associated with protein alterations (variations in the side chain residues of amino acids and protein secondary structure), but also within nucleic acids and lipids. We observed spectral changes in quiescent compared to proliferating cells, which increased with quiescence cultivation time. Raman and infrared spectroscopy, which yield complementary biochemical information, clearly distinguished contact-inhibited from serum-starved quiescent cells. Furthermore, the spectra displayed spectral differences between quiescent cells and proliferating cells, which had recovered from quiescence. This became more distinct with increasing quiescence cultivation time. When comparing proliferating, (in particular long-term) quiescent and senescent cells, we found that Raman as well as infrared spectroscopy can separate these three cellular states from each other due to differences in their biomolecular composition. Our spectroscopic analysis shows that proliferating and quiescent fibroblast cells age by similar but biochemically not identical processes. Despite their aging induced changes, over long time periods quiescent cells can return into the cell cycle. Finally however, the cell cycle arrest becomes irreversible indicating senescence.Dermal fibroblast cells can adopt different cell states such as proliferation, quiescence, apoptosis or senescence, in order to ensure tissue homeostasis. Proliferating (dividing) cells pass through the phases of the cell cycle, while quiescent and senescent cells exist in a non-proliferating cell cycle-arrested state. However, the reversible quiescence state is in contrast to the irreversible senescence state. Long-term quiescent cells transit into senescence indicating that cells age also when not passing through the cell cycle. Here, by label-free in vitro vibrational spectroscopy, we studied the biomolecular composition of quiescent dermal fibroblast cells and compared them with those of proliferating and senescent cells. Spectra were examined by multivariate statistical analysis using a PLS-LDA classification model, revealing differences in the biomolecular composition between the cell states mainly associated with protein alterations (variations in the side chain residues of amino acids and protein secondary structure), but also within nucleic acids and lipids. We observed spectral changes in quiescent compared to proliferating cells, which increased with quiescence cultivation time. Raman and infrared spectroscopy, which yield complementary biochemical information, clearly distinguished contact-inhibited from serum-starved quiescent cells. Furthermore, the spectra displayed spectral differences between quiescent cells and proliferating cells, which had recovered from quiescence. This became more distinct with increasing quiescence cultivation time. When comparing proliferating, (in particular long-term) quiescent and senescent cells, we found that Raman as well as infrared spectroscopy can separate these three cellular states from each other due to differences in their biomolecular composition. Our spectroscopic analysis shows that proliferating and quiescent fibroblast cells age by similar but biochemically not identical processes. Despite their aging induced changes, over long time periods quiescent cells can return into the cell cycle. Finally however, the cell cycle arrest becomes irreversible indicating senescence.
Multi-watt, multi-octave, mid-infrared femtosecond source
Spectroscopy in the wavelength range from 2 to 11 μm (900 to 5000 cm−1) implies a multitude of applications in fundamental physics, chemistry, as well as environmental and life sciences. The related vibrational transitions, which all infrared-active small molecules, the most common functional groups, as well as biomolecules like proteins, lipids, nucleic acids, and carbohydrates exhibit, reveal information about molecular structure and composition. However, light sources and detectors in the mid-infrared have been inferior to those in the visible or near-infrared, in terms of power, bandwidth, and sensitivity, severely limiting the performance of infrared experimental techniques. This article demonstrates the generation of femtosecond radiation with up to 5 W at 4.1 μm and 1.3 W at 8.5 μm, corresponding to an order-of-magnitude average power increase for ultrafast light sources operating at wavelengths longer than 5 μm. The presented concept is based on power-scalable near-infrared lasers emitting at a wavelength near 1 μm, which pump optical parametric amplifiers. In addition, both wavelength tunability and supercontinuum generation are reported, resulting in spectral coverage from 1.6 to 10.2 μm with power densities exceeding state-of-the-art synchrotron sources over the entire range. The flexible frequency conversion scheme is highly attractive for both up-conversion and frequency comb spectroscopy, as well as for a variety of time-domain applications.Spectroscopy in the wavelength range from 2 to 11 μm (900 to 5000 cm−1) implies a multitude of applications in fundamental physics, chemistry, as well as environmental and life sciences. The related vibrational transitions, which all infrared-active small molecules, the most common functional groups, as well as biomolecules like proteins, lipids, nucleic acids, and carbohydrates exhibit, reveal information about molecular structure and composition. However, light sources and detectors in the mid-infrared have been inferior to those in the visible or near-infrared, in terms of power, bandwidth, and sensitivity, severely limiting the performance of infrared experimental techniques. This article demonstrates the generation of femtosecond radiation with up to 5 W at 4.1 μm and 1.3 W at 8.5 μm, corresponding to an order-of-magnitude average power increase for ultrafast light sources operating at wavelengths longer than 5 μm. The presented concept is based on power-scalable near-infrared lasers emitting at a wavelength near 1 μm, which pump optical parametric amplifiers. In addition, both wavelength tunability and supercontinuum generation are reported, resulting in spectral coverage from 1.6 to 10.2 μm with power densities exceeding state-of-the-art synchrotron sources over the entire range. The flexible frequency conversion scheme is highly attractive for both up-conversion and frequency comb spectroscopy, as well as for a variety of time-domain applications.