X-ray absorption near edge structure and Mössbauer spectroscopy in study of iron valence states in tissues

X-ray absorption near edge structure Fe K-edge spectra and $\text{}^{57}$Fe Mössbauer spectra of selected standard compounds were recorded at room temperature. Valence and spin states of Fe in these samples known from Mössbauer spectroscopy were correlated with the shapes of X-ray absorption near edge structure spectra in search of possible application of X-ray absorption near edge structure spectroscopy as analytical tool determining local electronic states of iron in tissues. As an example, the X-ray absorption near edge structure spectra of healthy and cancerous tissues of prostate are shown, suggesting Fe$\text{}^{3+}$ in cancerous tissues

Applications of the Cracow X-ray microprobe in tomography

A nuclear microprobe at the IFJ PAN in Cracow has found numerous applications in different fields of research, mostly in biophysics, medical sciences, geology, and material research. In order to extend the research possibilities, a new X-ray microprobe was constructed. This new microprobe consists of three experimental lines dedicated to: (i) X-ray irradiation of biological specimens, (ii) elemental analysis of samples by micro X-ray fluorescence or total reflection X-ray fluorescence methods and (iii) computer microtomography. In this paper the computer microtomography line was described. The line consists of an open type Hamamatsu L9191 X-ray tube with microfocusing to about 2 μm, a high resolution X-ray sensitive CCD camera, and a precise goniometer composed of six piezoelectric motors. Depending on the required X-ray energy, the Hamamatsu tube is used with Ti, Mo, Ag, or W targets. A small focus size and short focus-to-object distance enable to obtain images of samples with a magnification of more than 1000× and resolution of the order of 2 μm. The computer microtomography measurements are carried out using home developed codes combined with commercial software. Details of the microprobe construction and preliminary results of the computer microtomography experiments are presented

EXAFS studies of prostate cancer cell lines

Sulphur plays a vital role in every human organism. It is known, that sulphur-bearing compounds, such as for example cysteine and glutathione, play critical roles in development and progression of many diseases. Any alteration in sulphur's biochemistry could become a precursor of serious pathological conditions. One of such condition is prostate cancer, the most frequently diagnosed malignancy in the western world and the second leading cause of cancer related death in men. The purpose of presented studies was to examine what changes occur in the nearest chemical environment of sulphur in prostate cancer cell lines in comparison to healthy cells. The Extended X-ray Absorption Fine Structure (EXAFS) spectroscopy was used, followed by theoretical calculations. The results of preliminary analysis is presented

Preliminary studies of sediments from the Dobczyce drinking water reservoir

The analysis of river and lake sediments indicates that the physical, chemical, biochemical and geochemical processes that influence the fate of toxic compounds and elements in sediments are numerous and complex (for example: sorption - desorption, oxidation - reduction, ion-exchange, biological activity). Due to the above-mentioned general statement, only a long term and complex research programme can lead to satisfactory answers to the questions relating to possible changes of water and environmental quality in the future. The aim of our study consisted in physical and chemical characterisation of sediments in in-depth profiles taken from the Dobczyce reservoir in southern Poland that is a main source of drinking water for the city of Kraków. Due to morphological reasons, 7 layers of sediment samples were distinguished from the ground level to about 90 cm below (total thickness of the sediments in the sampling site). Analysis of grain size distribution and application of x-ray diffraction method, enabled mineralogical description of sediments. The use of proton-induced x-ray emission (PIXE) and atomic absorption spectrometry (AAS) revealed elemental composition of the samples (Al, P, K, Ca, Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn). Concentrations of natural 40K and artificial 137Cs radionuclides were determined by the use of gamma spectrometry. The following facts were established: 1) the oldest (deepest) and newest, recently deposited layers of sediments are similar in their physical and chemical properties. It means that the inflow of contaminants and biogenic compounds to the reservoir has changed little since it was constructed and filled with water; 2) the severe flood in 1997 changed significantly sediment composition and, in fact, led to purification of sediments in the Dobczyce reservoir

Chemical composition of atherosclerotic plaques of apoE/LDLR-double knockout mice by synchrotron radiation FTIR microspectroscopy

Atherosclerosis is a multietiological inflammatory disease of large and medium-sized arteries of increasing incidence in westernized countries. The aim of this study was to identify the biochemical changes during the progression of atherosclerosis by synchrotron radiation Fourier transform infrared microspectroscopy in atheromas of apoE/$LDLR^{-//-}$ mice fed egg-rich diet supplemented or not with angiotensin converting enzyme inhibitor perindopril. Synchrotron radiation Fourier transform infrared microspectroscopy technique was used to obtain information at high spatial resolution about the distribution of proteins (C-N, N-H, CO for amide I and amide II bands), lipids ($CH_2$, $CH_3$ bands) as well as mineral deposits (calcium carbonates and phosphates). Total contents of lipids and proteins were found to be significantly lower in animals treated with the diet and perindopril. An increase in saturation level of lipids was observed in animals fed with egg-rich diet when compared to the normal diet and perindopril treatment, which did not inhibit this effect. Moreover, a significant change in the secondary structure of proteins (ratio between absorption bands 1634 $cm^{-1}$/1656 $cm^{-1}$ attributed to β-type and α-type, respectively) was observed in both experimental groups in comparison with the control. Principal component analysis was used to analyse the recorded spectra. It has revealed that higher content of phosphates (wavenumber range 950-1020 $cm^{-1}$) was observed between egg-rich diet fed animals and the control group

Preliminary investigations of elemental content, microporosity, and specific surface area of porous rocks using PIXE and X-ray microtomography techniques

Determination of physical properties of porous geological materials is of great importance for oil industry. The knowledge of rocks properties is usually obtained from porosity studies such as pore size distribution, specific surface area determination, and hydrodynamic permeability calculations. This study describes determination of elemental composition and measurements of the particular physical properties of geological samples (porous sandstone rocks) by means of the nuclear and X-ray microprobes at the Institute of Nuclear Physics, Polish Academy of Sciences in Kraków, Poland. The special emphasis has been put on the computed microtomography method. Measurements have been carried out in close cooperation with Department of Geophysics, FGGEP AGH in Kraków, Poland. Chemical composition of the Rotliegend sandstone rock samples (few millimeters diameter), extracted from a borehole at 2679.6 m, 2741.4 m and 2742.4 m depth have been investigated using the 2.2 MeV proton beam (proton induced X-ray emission technique). Next, measurements of the porosity and the specific surface area of the pore space have been carried out using the X-ray microtomography technique. Basing on microtomographic data obtained with the high spatial resolution, simulations of the fluid dynamic in the void space of porous media have been carried out. Lattice Boltzmann method in the 3DQ19 geometrical model has been used in order to predict the hydraulic permeability of the media. In order to avoid viscosity-permeability dependence the multiple-relaxation-time model with half-way bounce back boundary conditions has been used. Computing power-consuming processing has been performed with the use of modern grid infrastructure

High-Throughput In Vitro, Ex Vivo, and In Vivo Screen of Adeno-Associated Virus Vectors Based on Physical and Functional Transduction

Adeno-associated virus (AAV) vectors are quickly becoming the vectors of choice for therapeutic gene delivery. To date, hundreds of natural isolates and bioengineered variants have been reported. While factors such as high production titer and low immunoreactivity are important to consider, the ability to deliver the genetic payload (physical transduction) and to drive high transgene expression (functional transduction) remains the most important feature when selecting AAV variants for clinical applications. Reporter expression assays are the most commonly used methods for determining vector fitness. However, such approaches are time consuming and become impractical when evaluating a large number of variants. Limited access to primary human tissues or challenging model systems further complicates vector testing. To address this problem, convenient high-throughput methods based on next-generation sequencing (NGS) are being developed. To this end, we built an AAV Testing Kit that allows inherent flexibility in regard to number and type of AAV variants included, and is compatible with in vitro, ex vivo, and in vivo applications. The Testing Kit presented here consists of a mix of 30 known AAVs where each variant encodes a CMV-eGFP cassette and a unique barcode in the 3′-untranslated region of the eGFP gene, allowing NGS-barcode analysis at both the DNA and RNA/cDNA levels. To validate the AAV Testing Kit, individually packaged barcoded variants were mixed at an equal ratio and used to transduce cells/tissues of interest. DNA and RNA/cDNA were extracted and subsequently analyzed by NGS to determine the physical/functional transduction efficiencies. We were able to assess the transduction efficiencies of immortalized cells, primary cells, and induced pluripotent stem cells in vitro, as well as in vivo transduction in naïve mice and a xenograft liver model. Importantly, while our data validated previously reported transduction characteristics of individual capsids, we also identified novel previously unknown tropisms for some AAV variants

X-ray microscopy using collimated and focussed synchrotron radiation

X-ray microscopy is a field that has developed rapidly in recent years. Two different approaches have been used. Zone plates have been employed to produce focused beams with sizes as low as 0.07 ..mu..m for x-ray energies below 1 keV. Images of biological materials and elemental maps for major and minor low Z have been produced using above and below absorption edge differences. At higher energies collimators and focusing mirrors have been used to make small diameter beams for excitation of characteristic K- or L-x rays of all elements in the periodic table. The practicality of a single instrument combining all the features of these two approaches is unclear. The use of high-energy x rays for x-ray microscopy has intrinsic value for characterization of thick samples and determination of trace amounts of most elements. A summary of work done on the X-26 beam line at the National Synchrotron Light Source (NSLS) with collimated and focused x rays with energies above 4 keV is given here. 6 refs., 5 figs., 1 tab

Updating the Secondary Transition Research Base: Evidence- and Research-Based Practices in Functional Skills

Transition education should be grounded in quality research. To do so, educators need information on which practices are effective for teaching students with disabilities transition-related skills. The purpose of this systematic literature review was to identify evidence-based and research-based practices in secondary special education and transition for students with disabilities. This systematic review resulted in the identification of nine secondary transition evidence-based practices and 22 research-based practices across more than 45 different transition-related skills. The range of effects for each of the secondary transition evidence-based and research-based practices identified are also included. Limitations and implications for future research, policy, and practice are discussed

The Perfect Number Theorem and Wilson's Theorem

This article formalizes proofs of some elementary theorems of number theory (see [1, 26]): Wilson's theorem (that n is prime iff n > 1 and (n - 1)! ≅ -1 (mod n)), that all primes (1 mod 4) equal the sum of two squares, and two basic theorems of Euclid and Euler about perfect numbers. The article also formally defines Euler's sum of divisors function Φ, proves that Φ is multiplicative and that Σ k|n Φ(k) = n.Casella Postale 49, 54038 Montignoso, ItalyM. Aigner and G. M. Ziegler. Proofs from THE BOOK. Springer-Verlag, Berlin Heidelberg New York, 2004.Grzegorz Bancerek. Cardinal numbers. Formalized Mathematics, 1(2):377-382, 1990.Grzegorz Bancerek. The fundamental properties of natural numbers. Formalized Mathematics, 1(1):41-46, 1990.Grzegorz Bancerek. König's theorem. Formalized Mathematics, 1(3):589-593, 1990.Grzegorz Bancerek. The ordinal numbers. Formalized Mathematics, 1(1):91-96, 1990.Grzegorz Bancerek and Krzysztof Hryniewiecki. Segments of natural numbers and finite sequences. Formalized Mathematics, 1(1):107-114, 1990.Józef Białas. Infimum and supremum of the set of real numbers. Measure theory. Formalized Mathematics, 2(1):163-171, 1991.Czesław Byliński. Basic functions and operations on functions. Formalized Mathematics, 1(1):245-254, 1990.Czesław Byliński. The complex numbers. Formalized Mathematics, 1(3):507-513, 1990.Czesław Byliński. Finite sequences and tuples of elements of a non-empty sets. Formalized Mathematics, 1(3):529-536, 1990.Czesław Byliński. Functions and their basic properties. Formalized Mathematics, 1(1):55-65, 1990.Czesław Byliński. Functions from a set to a set. Formalized Mathematics, 1(1):153-164, 1990.Czesław Byliński. Partial functions. Formalized Mathematics, 1(2):357-367, 1990.Czesław Byliński. Some basic properties of sets. Formalized Mathematics, 1(1):47-53, 1990.Czesław Byliński. The sum and product of finite sequences of real numbers. Formalized Mathematics, 1(4):661-668, 1990.Agata Darmochwał. Finite sets. Formalized Mathematics, 1(1):165-167, 1990.Yoshinori Fujisawa and Yasushi Fuwa. The Euler's function. Formalized Mathematics, 6(4):549-551, 1997.Yoshinori Fujisawa, Yasushi Fuwa, and Hidetaka Shimizu. Public-key cryptography and Pepin's test for the primality of Fermat numbers. Formalized Mathematics, 7(2):317-321, 1998.Krzysztof Hryniewiecki. Basic properties of real numbers. Formalized Mathematics, 1(1):35-40, 1990.Krzysztof Hryniewiecki. Recursive definitions. Formalized Mathematics, 1(2):321-328, 1990.Magdalena Jastrzebska and Adam Grabowski. On the properties of the Möbius function. Formalized Mathematics, 14(1):29-36, 2006, doi:10.2478/v10037-006-0005-0.Artur Korniłowicz and Piotr Rudnicki. Fundamental Theorem of Arithmetic. Formalized Mathematics, 12(2):179-186, 2004.Jarosław Kotowicz and Yuji Sakai. Properties of partial functions from a domain to the set of real numbers. Formalized Mathematics, 3(2):279-288, 1992.Rafał Kwiatek. Factorial and Newton coefficients. Formalized Mathematics, 1(5):887-890, 1990.Rafał Kwiatek and Grzegorz Zwara. The divisibility of integers and integer relative primes. Formalized Mathematics, 1(5):829-832, 1990.W. J. LeVeque. Fundamentals of Number Theory. Dover Publication, New York, 1996.Takaya Nishiyama and Yasuho Mizuhara. Binary arithmetics. Formalized Mathematics, 4(1):83-86, 1993.Beata Padlewska. Families of sets. Formalized Mathematics, 1(1):147-152, 1990.Piotr Rudnicki. Little Bezout theorem (factor theorem). Formalized Mathematics, 12(1):49-58, 2004.Piotr Rudnicki and Andrzej Trybulec. Abian's fixed point theorem. Formalized Mathematics, 6(3):335-338, 1997.Piotr Rudnicki and Andrzej Trybulec. Multivariate polynomials with arbitrary number of variables. Formalized Mathematics, 9(1):95-110, 2001.Andrzej Trybulec. Binary operations applied to functions. Formalized Mathematics, 1(2):329-334, 1990.Andrzej Trybulec. Tuples, projections and Cartesian products. Formalized Mathematics, 1(1):97-105, 1990.Andrzej Trybulec. On the sets inhabited by numbers. Formalized Mathematics, 11(4):341-347, 2003.Andrzej Trybulec and Czesław Byliński. Some properties of real numbers. Formalized Mathematics, 1(3):445-449, 1990.Michał J. Trybulec. Integers. Formalized Mathematics, 1(3):501-505, 1990.Wojciech A. Trybulec. Non-contiguous substrings and one-to-one finite sequences. Formalized Mathematics, 1(3):569-573, 1990.Zinaida Trybulec. Properties of subsets. Formalized Mathematics, 1(1):67-71, 1990.Edmund Woronowicz. Relations and their basic properties. Formalized Mathematics, 1(1):73-83, 1990.Edmund Woronowicz. Relations defined on sets. Formalized Mathematics, 1(1):181-186, 1990.Hiroshi Yamazaki, Yasunari Shidama, and Yatsuka Nakamura. Bessel's inequality. Formalized Mathematics, 11(2):169-173, 2003