Assessing blood flow control through a bootstrap method

In order to assess blood flow control, the relationship between blood pressure and blood flow can be modeled by linear filters. We present a bootstrap method, which allows the statistical analysis of an index of blood flow control that is obtained from constrained system identification using an established set of pre-defined filters.     

A microcontroller-based portable electrocardiograph recorder

We describe a low cost portable Holter design that can be implemented with off-the-shelf components. The recorder is battery powered and includes a graphical display and keyboard. The recorder is capable of acquiring up to 48 hours of continuous electrocardiogram data at a sample rate of up to 250 Hz.     

Liquid chromatography with mass spectrometry in tandem mode applied for the identification of wine markers in residues from ancient Egyptian vessels

Presented in this paper is a new method for the identification of tartaric acid as a wine marker in archaeological residues from Egyptian vessels using liquid chromatography with mass spectrometry in tandem mode (LC/MS/MS). Owing to the special characteristics of these samples, such as the dryness and the small quantity available for analysis, it was necessary to have a very sensitive and highly specific analytical method to detect tartaric acid at trace levels in the residues. Furthermore, an alkaline fusion was carried out to identify syringic acid derived from malvidin as a red wine marker, in a deposit residue from a wine jar found at the tomb of king Tutankhamun. Malvidin-3-glucoside, the main anthocyanin that gives young wines their red color, polymerizes with aging into more stable pigments. However, the presence of malvidin in ancient residues can be proved by alkaline fusion of the residue to release syringic acid from the pigment, which has been identified, here for the first time, by using the LC/MS/MS method revealing the red grape origin of an ancient Egyptian wine residue.     

Isotopic variations of Zn in biological materials

Variations in the isotopic composition of Zn present in various biological materials were determined using high-resolution multicollector inductively coupled plasma mass spectrometry (MC-ICPMS), following digestion and purification by anion exchange chromatography. To correct for differences in instrumental mass discrimination effects between samples and standards, Cu was employed as an elemental spike. Complementary analyses of Zn separates by sector field ICPMS instruments revealed that the concentrations of the majority of potentially interfering elements were reduced to negligible levels. Residual spectral interferences resulting from (35)Cl(16)O(2)(+), (40)Ar(14)N(2)(+), and (40)Ar(14)N(16)O(+) could be instrumentally resolved from the (67)Zn, (68)Zn, and (70)Zn ion beams, respectively, during measurement by MC-ICPMS. The only other observed interference in the Cu and Zn mass range that could not be effectively eliminated by high-resolution multicollection resulted from (35)Cl(2)(+), necessitating modification of the sample preparation procedure to allow accurate (70)Zn detection. Complete duplication of the entire analytical procedure for human whole blood and hair, as well as bovine liver and muscle, provided an external reproducibility of 0.05-0.12 per thousand (2sigma) for measured delta(66/64)Zn, delta(67/64)Zn, and delta(68/64)Zn values, demonstrating the utility of the method for the precise isotopic analysis of Zn in biological materials. Relative to the selected Zn isotopic standard, delta(66/64)Zn values for biological samples varied from -0.60 per thousand in human hair to +0.56 per thousand in human whole blood, identifying the former material as the isotopically lightest Zn source found in nature to date.     

Statistical model for large-scale peptide identification in databases from tandem mass spectra using SEQUEST

Recent technological advances have made multidimensional peptide separation techniques coupled with tandem mass spectrometry the method of choice for high-throughput identification of proteins. Due to these advances, the development of software tools for large-scale, fully automated, unambiguous peptide identification is highly necessary. In this work, we have used as a model the nuclear proteome from Jurkat cells and present a processing algorithm that allows accurate predictions of random matching distributions, based on the two SEQUEST scores Xcorr and DeltaCn. Our method permits a very simple and precise calculation of the probabilities associated with individual peptide assignments, as well as of the false discovery rate among the peptides identified in any experiment. A further mathematical analysis demonstrates that the score distributions are highly dependent on database size and precursor mass window and suggests that the probability associated with SEQUEST scores depends on the number of candidate peptide sequences available for the search. Our results highlight the importance of adjusting the filtering criteria to discriminate between correct and incorrect peptide sequences according to the circumstances of each particular experiment.     

Isotopic fractionation during diffusion of transition metal ions in solution

Isotope ratios and elemental concentrations were measured in aqueous solutions sampled at varying distances from sources of Fe or Zn ions. The measurements reveal fractionation of isotopes resulting from pure diffusion in solution. Our data demonstrate that diffusion alone can cause changes in (56)Fe/(54)Fe and (66)Zn/(64)Zn isotope ratios in excess of -0.3 per thousand. These findings thus confirm previous suspicions that transport processes contribute to observed variations in isotopic compositions. Diffusion must therefore be considered when attempting to make inferences from isotope measurements on samples originating from aqueous systems where concentration gradients may develop.     

Microcontact printing of DNA molecules

The controlled placement of DNA molecules onto solid surfaces is the first step in the fabrication of DNA arrays. The sequential deposition of tiny drops containing the probe DNA fragments using arrays of spotting needles or ink jet nozzles has become a standard. However, a caveat of liquid spotting is the drying of the deposited drop because this creates the typical inhomogeneities, i.e., rims around the spot. Another drawback is that each DNA array is an original and has to be fabricated individually. Microcontact printing is a versatile technique to place proteins onto different target surfaces in uniformly patterned monolayers with high lateral resolution. Here, we show for the first time that DNA can also be printed with equally high resolution in the submicrometer range using an elastomeric stamp with chemically tailored surface. Two regimes for the transfer of the molecules were observed. Finally, microcontact printing of an array of DNA probes onto a solid support and its use in a subsequent hybridization assay was demonstrated.     

General strategy for biosensor design and construction employing multifunctional surface-tethered components

Biosensors function by reversibly linking bioreceptor-target analyte binding with closely integrated signal generation and can either continuously monitor analyte concentrations or be returned to baseline readout values by removal of analyte. We present an approach for producing fully reversible, reagentless, self-assembling biosensors on surfaces. In the prototype biosensor, quencher-dye-labeled biotin-linked E. coli maltose binding protein (MBP) bound in a specific orientation to a NeutrAvidin-coated surface is employed as a bioreceptor. To complete sensor formation, a modular tether arm consisting of a flexible biotinylated DNA oligonucleotide, a fluorescence resonance energy-transfer (FRET) donor dye, and a distal beta-cyclodextrin (beta-CD) analyte analogue is bound in an equimolar amount to the same surface by means of DNA-directed immobilization. After self-assembly, a baseline level of FRET quenching is observed due to specific interaction between the beta-CD of the flexible tether arm and the sugar binding site of MBP, which brings the two dyes into proximity. Addition of the target analyte, the nutrient maltose, displaces the linked beta-CD-dye of the DNA-based tether arm, and a concentration-dependent change in FRET results. Biosensor sensitivity and dynamic range can be controlled by either using MBP variants having different binding constants or by binding of modulator DNA oligonucleotides that are complementary to the flexible DNA tether. The sensor can be regenerated and returned to baseline quenching levels by washing away analyte. A complex set of interactions apparently exists on the sensing surface that may contribute to sensor behavior and range. This approach may represent a general way to assemble a wide range of useful biosensors.     

Multiplexed toxin analysis using four colors of quantum dot fluororeagents

Quantum dots (QDs) have the potential to simplify the performance of multiplexed analysis. In this work, we prepared bioinorganic conjugates made with highly luminescent semiconductor nanocrystals (CdSe-ZnS core-shell QDs) and antibodies to perform multiplexed fluoroimmunoassays. Sandwich immunoassays for the detection of cholera toxin, ricin, shiga-like toxin 1, and staphylococcal enterotoxin B were performed simultaneously in single wells of a microtiter plate. Initially the assay performance for the detection of each toxin was examined. We then demonstrated the simultaneous detection of the four toxins from a single sample probed with a mixture of all four QD-antibody reagents. Using a simple linear equation-based algorithm, it was possible to deconvolute the signal from mixed toxin samples, which allowed quantitation of all four toxins simultaneously.     

Optical properties of scandium films in the far and the extreme ultraviolet

The optical properties of thin Sc films deposited in ultrahigh-vacuum conditions have been investigated in the 6.7-174.4-nm spectral range. We measured transmittance and multiangle reflectance in situ in the 53.6-174.4 nm spectral range and used these measurements to obtain the complex refractive index of a Sc film at every individual wavelength investigated. Transmittance measurements were made of Sc samples that were deposited over grids coated with a support C film. The transmittance and the extinction coefficient of Sc films at wavelengths shorter than 30 nm were measured ex situ. The ex situ samples were protected with an additional top C film before their removal from vacuum. To our knowledge, these are the first optical measurements of Sc films reported in the spectral ranges cited.