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At least 595 records · Page 33Linked to original sources
PubMed2006

Joint transform correlator with spatial code division multiplexing.

A joint transform correlator may suffer from overlapping of the zero diffraction order of the output, which does not contain relevant information, and the correlation peaks that appear in the first diffraction orders if objects are not sufficiently separated. Such overlapping significantly reduces the signal-to-noise ratio of the identification process. We propose a novel approach based on code division multiplexing technique in which the contrast of the identification peaks is significantly enhanced. The approach does not include placing the two objects side by side but rather includes code multiplexing them. Moreover, the code division multiplexing technique allows the space-bandwidth product to be improved. Optical implementation results are given.

Journal Article↗
PubMed2006

Optimization of a thick polyvinyl alcohol-acrylamide photopolymer for data storage using a combination of angular and peristrophic holographic multiplexing.

The capability of polyvinyl alcohol-acrylamide photopolymer materials to obtain angularly multiplexed holographic gratings has been demonstrated [Appl. Phys. B 76, 851 (2003)]. A combination of two multiplexing methods--peristrophic and angular multiplexing--is used to record 60 holograms. An exposure schedule method is used to optimize the capability of the photopolymerizable holographic material and obtain holograms with a higher, more uniform diffraction efficiency. In addition, because of this exposure schedule method, the entire dynamic range (M#) of the material will be exploited, obtaining values of approximately M# approximately 9 in layers approximately 800 microm thick.

Journal Article↗
PubMed2007

Dispersion multiplexing with broadband filtering for miniature spectrometers.

We replace the traditional grating used in a dispersive spectrometer with a multiplex holographic grating to increase the spectral range sensed by the instrument. The multiplexed grating allows us to measure three different, overlapping spectral bands on a color digital focal plane. The detector's broadband color filters, along with a computational inversion algorithm, let us disambiguate measurements made from the three bands. The overlapping spectral bands allow us to measure a greater spectral bandwidth than a traditional spectrometer with the same sized detector. Additionally, our spectrometer uses a static coded aperture mask in the place of a slit. The aperture mask allows increased light throughput, offsetting the photon loss at the broadband filters. We present our proof-of-concept dispersion multiplexing spectrometer design with experimental measurements to verify its operation.

Algorithms↗
PubMed2005

Two-loop-based low-coherence multiplexing fiber-optic sensor network with a Michelson optical path demodulator.

A two-loop-based low-coherence multiplexing fiber-optic sensor network is proposed and demonstrated. It greatly extends the multiplexing capacity of this kind of sensor. A practical implementation of this scheme uses a popular amplified spontaneous emission light source and standard single-mode fiber, which are commonly used in the communications industry. The sensor's two-loop topology is completely passive. Absolute length measurements can be obtained for each sensing fiber segment for use in measuring the quasi-distribution strain or temperature. For large-scale smart structures this technique not only extends the multiplexing potential but also provides a redundancy for the sensing system. This means that the two-loop sensor network can break down at several points and the sensing system will still work even if some of the embedded two-loop sensors have been destroyed. The robustness of the nine-sensor two-loop sensing network is investigated and discussed.

Journal Article↗
PubMed2005

Multiple-image encryption by wavelength multiplexing.

We introduce the technique of wavelength multiplexing into a double random-phase encoding system to achieve multiple-image encryption. Each primary image is first encrypted by the double phase encoding method and then superposed to yield the final enciphered image. We analyze the minimum separation between two adjacent multiplexing wavelengths through cross talk and the multiplexing capacity through the correlation coefficient. Computer simulations are performed to demonstrate the concept. This technique can be used for hiding multiple images as well.

Journal Article↗
PubMed2005

Interchannel nonlinear transmission penalties in polarization-multiplexed 2 x 10 Gbit/s differential phase-shift keying transmission.

We discuss the performance of a multichannel 2 x 10 Gbit/s polarization-multiplexed differential phase-shift keying transmission system. Through simulations and transmission experiments we find that, despite the constant power envelope of non-return-to-zero phase-shift keying modulation formats, polarization multiplexing strongly reduces the nonlinear tolerance and transmission performance at a 2 x 10 Gbit/s line rate with multichannel transmission. This results in a 10 dB power penalty when comparing single- and nine-channel transmission. Additionally, multichannel impairments in differential phase-shift keying and on-off keying are compared for 2 x 10 Gbit/s polarization-multiplexed transmission.

Journal Article↗
PubMed2005

Multiplex single strand conformation polymorphism analysis by capillary electrophoresis with on-the-fly fluorescence lifetime detection.

This paper describes the use of on-the-fly fluorescence lifetime detection (OFLD) for multiplex single strand conformation polymorphism (SSCP) analysis by capillary electrophoresis (CE). The dye labels studied for multiplex SSCP-OFLD-CE analyses included RG, NBD, and BODIPY-FL. The dyes were first investigated for a model system of "Wild Type" and "Mutant" 43-base fragments designed to vary by a single A/T substitution. Two dye pairs, BODIPY-FL/ RG and BODIPY-FL/NBD, were then used to detect the G20210A mutation in the human prothrombin gene. Mobility correction was required for the BODIPY-FL/RG system. Three "blind" analyses were performed of three mixtures that combined a control fragment (wild type-BODIPY-FL) with two "unknown" fragments selected among four possibilities (wild type or mutant labeled with NBD or RG). In each multiplex analysis, the "origin" of the unknown fragments was correctly identified on the basis of fluorescence lifetime of the dye label and the presence or absence of the mutation was correctly determined on the basis of conformation-induced differences in migration time.

Amino Acid Substitution↗
PubMed2003

Multiplex minisequencing screen for common Southeast Asian and Indian beta-thalassemia mutations.

BACKGROUND: Beta-thalassemia is endemic to many regions in Southeast Asia and India, and <20 beta-globin gene mutations account for > or =90% of beta-thalassemia alleles in these places. We describe a multiplex minisequencing assay to detect these common mutations. METHODS: Gap-PCR was used to simultaneously amplify the beta-globin gene from genomic DNA and to detect the Delta619bp deletion mutation. Multiplex minisequencing was then performed on the amplified beta-globin fragment to detect an additional 15 common Southeast Asian and Indian beta-thalassemia mutations. Site-specific primers of different lengths were subjected to multiple rounds of annealing and single-nucleotide extension in the presence of thermostable DNA polymerase and the four dideoxynucleotides, each labeled with a different fluorophore. Minisequencing products were separated and detected by capillary electrophoresis, followed by automated genotyping. The optimized assay was subjected to a double-blind validation analysis of 89 beta-thalassemia and wild-type DNA samples of known genotype. RESULTS: Homozygous wild-type or mutant DNA samples produced electropherograms containing only a single colored peak for each mutation site, whereas samples heterozygous for a specific mutation displayed two different-colored peaks for that mutation site. Samples were automatically genotyped based on color and position of primer peaks in the electropherogram. In the double-blind validation analysis, all 89 DNA samples were genotyped correctly (100% assay specificity). CONCLUSIONS: The described semiautomated multiplex minisequencing assay can detect the most common Southeast Asian and Indian beta-thalassemia mutations, is amenable to high-throughput scale up, and may bring population-based screening of beta-thalassemia in endemic regions a step closer to implementation.

Asia, Southeastern↗
PubMed2004

Reverse transcription-multiplex PCR assay for simultaneous detection of Escherichia coli O157:H7, Vibrio cholerae O1, and Salmonella Typhi.

BACKGROUND: Escherichia coli O157:H7, Vibrio cholerae O1, and Salmonella Typhi are pathogenic bacteria that can be found in contaminated water supplies throughout the world. No currently available assays can simultaneously detect and identify all three pathogens. Our aim was to develop a rapid and reliable technique for simultaneous detection of these pathogens. METHODS: Four unique genes were chosen as the targets of detection. Forward and reverse primers were designed to specifically amplify different sizes of these target genes: a 239-bp region of the E. coli O157 lipopolysaccharide (LPS) gene (rfbE); a 179-bp region of the H7 flagellin gene (fliC); a 419-bp region of the V. cholerae O1 LPS gene (rfbE); and a 329-bp region of Salmonella Typhi LPS gene (tyv). To ensure the detection of only viable replicating bacteria, RNA was extracted for analysis. After reverse transcription, cDNAs were simultaneously amplified in a single tube by multiplex PCR. The multiplex PCR products were analyzed by gel electrophoresis. To characterize the assay we analyzed, in a blinded fashion, seven unknown RNA samples containing various combinations of total RNA from these bacteria as well as clinical isolates. RESULTS: All seven unknown RNA samples were correctly identified. The assay was able to detect and identify as few as 30 cells of E. coli O157:H7 and Salmonella Typhi in clinical isolates, and the presence of other bacteria did not interfere with the analysis. CONCLUSION: An assay combining reverse transcription with single-tube multiplex PCR was successfully developed and validated for simultaneous detection of viable E. coli O157:H7, V. cholerae O1, and Salmonella Typhi.

Bacterial Proteins↗
PubMed2004

High-throughput mitochondrial genome screening method for nonmelanoma skin cancer using multiplexed temperature gradient capillary electrophoresis.

BACKGROUND: We explored the utility of multiplexed temperature gradient capillary electrophoresis (TGCE) as a screening tool for identifying genetic changes in the human mitochondrial genome. We examined changes in mitochondrial DNA (mtDNA) in nonmelanoma skin cancers (NMSCs), using TGCE to resolve genetic differences contained within the tumors compared with the control DNA. METHODS: The entire mtDNA from NMSC tissue samples was amplified in 17 overlapping amplicons averaging 1.1 kb in size. Fourteen of these amplicons were digested with restriction endonucleases into as many as five smaller analyzable fragments. Digested tumor mtDNA amplicons were annealed with digested amplicons from the control DNA to form heteroduplexes in regions of DNA mismatch. TGCE was performed in a 96-well parallel format to detect mtDNA changes in a high-throughput fashion. RESULTS: TGCE resolved heteroduplexes from homoduplexes in singlet reactions and in multiplexed assays. Using a single programmed temperature gradient, we detected 18 of 20 mtDNA changes contained within the specimens. This system was also able to detect a single nucleotide change in a fragment as large as 2 kb. CONCLUSION: Multiplexed TGCE is a sensitive and high-throughput screening tool for identifying mtDNA variations.

Base Sequence↗
PubMed2005

Multiplex human papillomavirus serology based on in situ-purified glutathione s-transferase fusion proteins.

BACKGROUND: More than 100 different human papillomaviruses (HPVs) can cause proliferative diseases, many of which are malignant, such as cervical cancer. HPV serology is complex because infection and disease lead to distinct type-specific antibody responses. Using bead-based technology, we have developed an assay platform that allows the simultaneous detection of antibodies against up to 100 in situ affinity-purified recombinant HPV proteins. METHODS: Twenty-seven HPV proteins were expressed as glutathione S-transferase fusion proteins and affinity-purified in one step by incubation of glutathione-displaying beads in bacterial lysate. Spectrally distinct bead sets, each carrying one particular antigen, were mixed, incubated with serum, and differentiated in a flow cytometer-like analyzer (xMAP; Luminex Corp). Antibodies bound to the antigens were detected via fluorescent secondary reagents. We studied 756 sera from 2 case-control studies of cervical cancer. RESULTS: Glutathione S-transferase fusion proteins bound with high affinity to glutathione-displaying beads (Kd = 6.9 x 10(-9) mol/L). The dynamic range of multiplex serology covered 1.5 orders of magnitude, and antibodies were detected at serum dilutions >1:1,000,000. Imprecision (median CV) was < or = 5.4%, and assay reproducibility was high (R2 = 0.97). Results on clinical samples showed high concordance with ELISA (kappa = 0.846), but multiplex serology exhibited increased detection of weak antibody responses. Antibodies to the E6 oncoproteins of the rare HPV types 52 and 58 were associated with cervical cancer (P < 0.001). CONCLUSION: Multiplex serology enables antibody analyses of large numbers of sera against up to 100 antigens in parallel and has the potential to replace ELISA technology.

Antibodies, Viral↗
PubMed2006

Multiplex tetra-primer amplification refractory mutation system PCR to detect 6 common germline mutations of the MUTYH gene associated with polyposis and colorectal cancer.

BACKGROUND: We describe a simple tetra-primer amplification refractory mutation system PCR (T-ARMS-PCR) for detecting MUTYH mutations, which are associated with colorectal adenomas and colorectal cancer. METHODS: We designed specific T-ARMS-PCR assays for 6 mutations (Y165C, G382D, 1395_7delGGA, Y90X, 1103delC, and R231H) selected on the basis of the frequency of their occurrence. We also designed a set of 3 multiplex T-ARMS PCR assays, each for detection of 2 mutations. We tested DNA samples from patients with attenuated or classic adenomatous polyposis coli and no detectable APC germline mutations. RESULTS: All mutations were easily detected with both the specific and multiplex T-ARMS-PCR assays. Results were confirmed by DNA HPLC analysis in all 54 patients, and each mutation was confirmed by direct DNA sequencing. CONCLUSIONS: T-ARMS-PCR does not require any special equipment, and it provides rapid, reproducible, and cost-effective detection of common MUTYH mutations. Multiplex T-ARMS-PCR allows the detection of 6 common MUTYH mutations with use of as few as 3 single tube PCR reactions. It could be useful to carry out large population-based epidemiologic studies.

Adenomatous Polyposis Coli↗
PubMed2006

A multiplex assay for the detection and mapping of complex glycerol kinase deficiency.

BACKGROUND: Glycerol kinase deficiency (GKD) is an X-linked recessive disorder that presents in both isolated and complex forms. The contiguous deletion that leads to GKD also commonly affects NR0B1 (DAX1), the gene associated with adrenal hypoplasia congenita, and DMD, the Duchenne muscular dystrophy gene. Molecular testing to delineate this deletion is expensive and has only limited availability. METHODS: We designed a multiplex PCR assay for the detection and mapping of a contiguous deletion potentially affecting the IL1RAPL1, NR0B1, GK, and DMD genes in a 29-month-old male patient with GKD. RESULTS: Multiplex PCR detected a contiguous deletion that involved the IL1RAPL1, NR0B1, GK, and DMD genes. Although the patient had a creatine kinase concentration within the reference interval, further mapping with PCR revealed that exon 74 was the last intact exon at the 3' end of the DMD gene. CONCLUSIONS: Multiplex PCR is an effective and inexpensive way to detect and map the contiguous deletion in cases of complex GKD. The extension of a deletion to include DMD exon 75 in a patient with a creatine kinase concentration within the reference interval suggests that this region of the gene may not be essential for protein function.

Child, Preschool↗
PubMed2005

Multiplex quantitative real-time PCR of laser microdissected tissue.

This chapter describes a method for the rapid assessment of gene copy number in laser microdissected material using multiplex real-time polymerase chain reaction (PCR). Here a putative oncogene (ZNF217) was evaluated in a series of colon tumors, but the method is applicable to any locus for which a nucleic acid sequence is available. The preparation, laser microdissection, and optimum storage of snap-frozen tumor material from freshly resected tissue is described. A set of guidelines specific for real-time PCR assays is included to assist with optimum primer and probe design. In this assay multiplex real-time PCR was performed and our experience has demonstrated that a multiplex reaction allows for a more accurate assessment of gene copy number than a "singleplex" assay because it removes the need for an external control.

Animals↗
PubMed2005

Typing of Y chromosome SNPs with multiplex PCR methods.

We describe a method for the simultaneous typing of Y-chromosome single nucleotide polymorphism (SNP) markers by means of multiplex polymerase chain reaction (PCR) strategies that allow the detection of 35 Y chromosome SNPs on 25 amplicons from 100 to 200 pg of chromosomal deoxyribonucleic acid (DNA). Multiplex PCR amplification of the DNA was performed with slight modifications of standard PCR conditions. Single-base extension (SBE) was performed using the SNaPshot kit containing fluorescently labeled ddNTPs. The extended primers were detected on an ABI 3100 sequencer. The most important factors for the creation of larger SNP typing PCR multiplexes include careful selection of primers for the primary amplification and the SBE reaction, use of DNA primers with homogenous composition, and balancing the primer concentrations for both the amplification and the SBE reactions.

Base Sequence↗
PubMed2005

Y chromosome SNP analysis using the single-base extension: a hierarchical multiplex design.

Single nucleotide polymorphisms (SNPs) are the most frequent polymorphisms described in the human genome, and their analysis is becoming an extensive routine in molecular biology, not only in the forensic field, but also in population and clinical genetics. In particular, SNPs located on the Y chromosome have a specific utility as forensic tools, and based on this fact, we have designed a strategy that allows us to identify the most frequent haplogroups in European populations. We selected 29 markers among the 245 binary polymorphisms described in the Y-Chromosome Consortium tree. The whole set was grouped into four multiplexes in a hierarchical way, allowing us to determine the final haplogroup using only one or two multiplexes. In this way, we only type in the best-case nine SNPs, and in the worst possible combination 17 SNPs, to define the haplogroup. The selected strategy to type the SNPs was a single-base extension method using the SNaPshot multiplex kit from Applied Biosystems, and detailed practical procedures are described here. With this hierarchical strategy adapted for European populations the massive typing of SNPs was avoided, and therefore the time and money involved in the study was also reduced.

Base Sequence↗
PubMed1998

Analysis of clonality in T-lymphoproliferative diseases by multiplex PCR.

Distinction between benign and malignant T-cell lymphoproliferative diseases can be difficult using morphological criteria. Using multiplex polymerase chain reaction system we have tested a series of patients with various lymphoproliferative disorders to detect clonal T-lymphocyte populations. Results show that clonal amplification products were obtained from all 10 patients with T-cell lymphoproliferative disorders while the amplification of DNA samples from B-cell neoplasms and normal individuals revealed polyclonal amplification products. By splitting the multiplex primer mix, the patient specific T-cell receptor gamma rearrangement was determined: five out of ten patients showed the exclusive presence of a single T-cell receptor gamma gene rearrangement. Three patients exhibited two rearranged T-cell receptor gamma genes, while in two patients positive reactions were obtained with three pairs of primers for variable and joining segments. Molecular analysis of rearranged T-cell receptor genes by multiplex polymerase chain reaction represents a useful and rapid tool for confirming diagnosis, to determine the extent of disease and to monitor the response to therapy.

Gene Rearrangement, T-Lymphocyte↗
PubMed2000

Multiplex in-cell reverse transcription-polymerase chain reaction for the simultaneous detection of p210 and p190 BCR-ABL mRNAs in chronic myeloid leukemia and Philadelphia-positive acute lymphoblastic leukemia cell lines.

We designed a novel multiplex in-cell reverse transcription-polymerase chain reaction method for the simultaneous detection and differentiation of p190 and p210 BCR-ABL mRNAs within single cells from the human chronic myeloid leukemia and Philadelphia positive acute lymphoblastic leukemia. Human K562 chronic myeloid leukemia and SUP B-15 Ph+ acute lymphoblastic leukemia cell lines were used as positive controls for p210 and p190 BCR-ABL mRNAs, respectively. HL60 cell line was used as a negative control. After the leukemia cells were fixed and permeabilized, without extracting nucleic acids, the mRNAs were reverse transcribed to cDNAs, and the cDNAs were amplified by multiplex polymerase chain reaction with fluorescent primers specific for p190 and p210 BCR-ABL mRNAs. After transfer onto glass slides by cytospin, the amplified cells were detected by fluorescence microscopy. Fluorescence microscopy after propidium iodide or 4',6-diamidino-2-phenylindone counterstaining showed that the positive K562 cells exhibited a yellow-green fluorescent cytoplasm around a red nucleus, and that the positive SUP B-15 cells exhibited an orange cytoplasm around a blue nucleus. Only the red or blue nucleus was visible in respective negative HL60 cells. The specificity of amplification was confirmed by the absence of a signal when control experiments were performed either with RNase digestion of mRNA or without reverse transcriptase/Taq polymerase. We conclude that the multiplex in-cell reverse transcription-polymerase chain reaction method is capable of simultaneously detecting and differentiating the p210 and p190 BCR-ABL mRNAs of chronic myeloid leukemia and Philadelphia-positive acute lymphoblastic leukemia cells, and that it may be useful in quantitatively monitoring the minimal residual disease during therapy.

DNA Primers↗