Suppression subtractive hybridization library construction and identification of epidermal bladder cell related genes in the common ice plant, Mesembryanthemum crystallinum L.

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Siranet Roeurn

2016-10-01

Full Text Available Mesembryanthemum crystallinum L., a halophytic species, displays modified trichomes, epidermal bladder cells (EBC, on the surfaces of its aerial organs. EBCs serve to sequester excessive salt from underlying metabolically active tissues. To elucidate the molecular determinants governing EBC development in the common ice plant, we constructed a cDNA-based suppression subtractive hybridization library and identified genes differentially expressed between the wild-type and the EBC-less mutant. After hybridization, 38 clones were obtained. Among them, 24 clones had homology with plant genes of known functions, whose roles might not be directly related to EBC-morphology, while 14 clones were homologous to genes of unknown functions. After confirmation by northern blot analysis, 12 out of 14 clones of unknown functions were chosen for semi-quantitative RT-PCR analysis, and the results revealed that three clones designated as MW3, MW21, and MW31 preferentially expressed in the EBC-less mutant, whereas the other two designated as WM10 and WM28 preferentially expressed in the wild type. Among these genes, the expression of a putative jasmonate-induced gene, designated as WM28 was completely suppressed in the EBC-mutant. In addition, the deletion of C-box cis-acting element was found in the promoter region of WM28 in the EBC-less mutant. Overexpression of WM28 in Arabidopsis resulted in increased trichome number due to the upregulation of key trichome-related genes GLABRA1 (GL1, and GLABRA3 (GL3. These results demonstrate that WM28 can be an important factor responsible for EBC formation, and also suggest the similarity of developmental mechanism between trichome in Arabidopsis and EBC in common ice plant.

Identification of Differentially Expressed Genes Associated with Apple Fruit Ripening and Softening by Suppression Subtractive Hybridization.

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Zhang, Zongying; Jiang, Shenghui; Wang, Nan; Li, Min; Ji, Xiaohao; Sun, Shasha; Liu, Jingxuan; Wang, Deyun; Xu, Haifeng; Qi, Sumin; Wu, Shujing; Fei, Zhangjun; Feng, Shouqian; Chen, Xuesen

2015-01-01

Apple is one of the most economically important horticultural fruit crops worldwide. It is critical to gain insights into fruit ripening and softening to improve apple fruit quality and extend shelf life. In this study, forward and reverse suppression subtractive hybridization libraries were generated from 'Taishanzaoxia' apple fruits sampled around the ethylene climacteric to isolate ripening- and softening-related genes. A set of 648 unigenes were derived from sequence alignment and cluster assembly of 918 expressed sequence tags. According to gene ontology functional classification, 390 out of 443 unigenes (88%) were assigned to the biological process category, 356 unigenes (80%) were classified in the molecular function category, and 381 unigenes (86%) were allocated to the cellular component category. A total of 26 unigenes differentially expressed during fruit development period were analyzed by quantitative RT-PCR. These genes were involved in cell wall modification, anthocyanin biosynthesis, aroma production, stress response, metabolism, transcription, or were non-annotated. Some genes associated with cell wall modification, anthocyanin biosynthesis and aroma production were up-regulated and significantly correlated with ethylene production, suggesting that fruit texture, coloration and aroma may be regulated by ethylene in 'Taishanzaoxia'. Some of the identified unigenes associated with fruit ripening and softening have not been characterized in public databases. The results contribute to an improved characterization of changes in gene expression during apple fruit ripening and softening.

Suppression subtractive hybridization identified differentially expressed genes in lung adenocarcinoma: ERGIC3 as a novel lung cancer-related gene

International Nuclear Information System (INIS)

Wu, Mingsong; Tu, Tao; Huang, Yunchao; Cao, Yi

2013-01-01

To understand the carcinogenesis caused by accumulated genetic and epigenetic alterations and seek novel biomarkers for various cancers, studying differentially expressed genes between cancerous and normal tissues is crucial. In the study, two cDNA libraries of lung cancer were constructed and screened for identification of differentially expressed genes. Two cDNA libraries of differentially expressed genes were constructed using lung adenocarcinoma tissue and adjacent nonmalignant lung tissue by suppression subtractive hybridization. The data of the cDNA libraries were then analyzed and compared using bioinformatics analysis. Levels of mRNA and protein were measured by quantitative real-time polymerase chain reaction (q-RT-PCR) and western blot respectively, as well as expression and localization of proteins were determined by immunostaining. Gene functions were investigated using proliferation and migration assays after gene silencing and gene over-expression. Two libraries of differentially expressed genes were obtained. The forward-subtracted library (FSL) and the reverse-subtracted library (RSL) contained 177 and 59 genes, respectively. Bioinformatic analysis demonstrated that these genes were involved in a wide range of cellular functions. The vast majority of these genes were newly identified to be abnormally expressed in lung cancer. In the first stage of the screening for 16 genes, we compared lung cancer tissues with their adjacent non-malignant tissues at the mRNA level, and found six genes (ERGIC3, DDR1, HSP90B1, SDC1, RPSA, and LPCAT1) from the FSL were significantly up-regulated while two genes (GPX3 and TIMP3) from the RSL were significantly down-regulated (P < 0.05). The ERGIC3 protein was also over-expressed in lung cancer tissues and cultured cells, and expression of ERGIC3 was correlated with the differentiated degree and histological type of lung cancer. The up-regulation of ERGIC3 could promote cellular migration and proliferation in vitro. The

Screening and identification of male-specific DNA fragments in common carps Cyprinus carpio using suppression subtractive hybridization.

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Chen, J J; Du, Q Y; Yue, Y Y; Dang, B J; Chang, Z J

2010-08-01

In this study, a sex subtractive genomic DNA library was constructed using suppression subtractive hybridization (SSH) between male and female Cyprinus carpio. Twenty-two clones with distinguishable hybridization signals were selected and sequenced. The specific primers were designed based on the sequence data. Those primers were then used to amplify the sex-specific fragments from the genomic DNA of male and female carp. The amplified fragments from two clones showed specificity to males but not to females, which were named as Ccmf2 [387 base pairs (bp)] and Ccmf3 (183 bp), respectively. The sex-specific pattern was analysed in a total of 40 individuals from three other different C. carpio. stocks and grass carp Ctenopharyngodon idella using Ccmf2 and Ccmf3 as dot-blotting probes. The results revealed that the molecular diversity exists on the Y chromosome of C. carpio. No hybridization signals, however, were detected from individuals of C. idella, suggesting that the two sequences are specific to C. carpio. No significant homologous sequences of Ccmf2 and Ccmf3 were found in GenBank. Therefore, it was interpreted that the results as that Ccmf2 and Ccmf3 are two novel male-specific sequences; and both fragments could be used as markers to rapidly and accurately identify the genetic sex of part of C. carpio. This may provide a very efficient selective tool for practically breeding monosex female populations in aquacultural production.

Probabilistic Model-based Background Subtraction

DEFF Research Database (Denmark)

Krüger, Volker; Anderson, Jakob; Prehn, Thomas

2005-01-01

is the correlation between pixels. In this paper we introduce a model-based background subtraction approach which facilitates prior knowledge of pixel correlations for clearer and better results. Model knowledge is being learned from good training video data, the data is stored for fast access in a hierarchical...

Identification of differentially expressed genes in the oviduct of two rabbit lines divergently selected for uterine capacity using suppression subtractive hybridization.

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Ballester, M; Castelló, A; Peiró, R; Argente, M J; Santacreu, M A; Folch, J M

2013-06-01

Suppressive subtractive hybridization libraries from oviduct at 62 h post-mating of two lines of rabbits divergently selected for uterine capacity were generated to identify differentially expressed genes. A total of 438 singletons and 126 contigs were obtained by cluster assembly and sequence alignment of 704 expressed sequence tags (ESTs), of which 54% showed homology to known proteins of the non-redundant NCBI databases. Differential screening by dot blot validated 71 ESTs, of which 47 showed similarity to known genes. Transcripts of genes were functionally annotated in the molecular function and the biological process gene ontology categories using the BLAST2GO software and were assigned to reproductive developmental process, immune response, amino acid metabolism and degradation, response to stress and apoptosis terms. Finally, three interesting genes, PGR, HSD17B4 and ERO1L, were identified as overexpressed in the low line using RT-qPCR. Our study provides a list of candidate genes that can be useful to understanding the molecular mechanisms underlying the phenotypic differences observed in early embryo survival and development traits. © 2012 The Authors, Animal Genetics © 2012 Stichting International Foundation for Animal Genetics.

Combined adaptive multiple subtraction based on optimized event tracing and extended wiener filtering

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Tan, Jun; Song, Peng; Li, Jinshan; Wang, Lei; Zhong, Mengxuan; Zhang, Xiaobo

2017-06-01

The surface-related multiple elimination (SRME) method is based on feedback formulation and has become one of the most preferred multiple suppression methods used. However, some differences are apparent between the predicted multiples and those in the source seismic records, which may result in conventional adaptive multiple subtraction methods being barely able to effectively suppress multiples in actual production. This paper introduces a combined adaptive multiple attenuation method based on the optimized event tracing technique and extended Wiener filtering. The method firstly uses multiple records predicted by SRME to generate a multiple velocity spectrum, then separates the original record to an approximate primary record and an approximate multiple record by applying the optimized event tracing method and short-time window FK filtering method. After applying the extended Wiener filtering method, residual multiples in the approximate primary record can then be eliminated and the damaged primary can be restored from the approximate multiple record. This method combines the advantages of multiple elimination based on the optimized event tracing method and the extended Wiener filtering technique. It is an ideal method for suppressing typical hyperbolic and other types of multiples, with the advantage of minimizing damage of the primary. Synthetic and field data tests show that this method produces better multiple elimination results than the traditional multi-channel Wiener filter method and is more suitable for multiple elimination in complicated geological areas.

Single base pair mutation analysis by PNA directed PCR clamping

DEFF Research Database (Denmark)

Ørum, H.; Nielsen, P.E.; Egholm, M.

1993-01-01

A novel method that allows direct analysis of single base mutation by the polymerase chain reaction (PCR) is described. The method utilizes the finding that PNAs (peptide nucleic acids) recognize and bind to their complementary nucleic acid sequences with higher thermal stability and specificity...... allows selective amplification/suppression of target sequences that differ by only one base pair. Finally we show that PNAs can be designed in such a way that blockage can be accomplished when the PNA target sequence is located between the PCR primers....

A comparison of subtracted images from dental subtraction programs

International Nuclear Information System (INIS)

Han, Won Jeong

2002-01-01

To compare the standard deviation of gray levels on digital subtracted images obtained by different dental subtraction programs. Paired periapical films were taken at the lower premolar and molar areas of the phantoms involving human mandible. The bite registration group used Rinn XCP equipment and bite registration material, based on polyvinyl siloxane, for standardization. The no bite registration group used only Rinn XCP equipment. The periapical film images were digitized at 1200 dpi resolution and 256 gray levels by a flat bed scanner with transparency unit. Dental digital subtraction programs used for this study were Subtractor (Biomedisys Co., Korea) and Emago (Oral Diagnostic Systems, The Netherlands). To measure the similarities between the subtracted images, the standard deviations of the gray levels were obtained using a histogram of subtracted images, which were then analyzed statistically. Subtracted images obtained by using the Emago program without manual selection of corresponding points showed the lowest standard deviation of gray levels (p<0.01). And the standard deviation of gray levels was lower in subtracted images in the group of a bite registration than in the group of no use of bite registration (p<0.01). Digital radiographic subtraction without manual selection of reference points was found to be a convenient and superior method.

Evaluation of sacroiliitis: contrast-enhanced MRI with subtraction technique

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Algin, Oktay; Gokalp, Gokhan; Baran, Bulent; Ocakoglu, Gokhan; Yazici, Zeynep [Uludag University, Medical Faculty, Department of Radiology, Gorukle, Bursa (Turkey)

2009-10-15

The purpose of the study was to investigate the diagnostic value of contrast-enhanced MRI using the subtraction technique in the detection of active sacroiliitis. Magnetic resonance imaging was performed in 8 asymptomatic volunteers and 50 patients with clinically suspected active sacroiliitis. On precontrast MR images, T1-weighted spin-echo images with and without fat saturation (T1WFS and T1W), STIR and 3D-FLASH images with fat saturation were obtained in the semicoronal plane using a 1.5 Tesla imager. Postcontrast MRI was performed using the same T1WFS sequence as before contrast injection for all volunteers and patients. Postcontrast images were subtracted from fat-suppressed precontrast images. Enhancement within the joint space and bone marrow was considered to demonstrate active sacroiliitis. In 50 patients (100 sacroiliac joints [SIJs]), 40 (76 SIJs) were considered to have active sacroiliitis based on MR images. Bone marrow edema was present in 33 patients (62 SIJs) on STIR images. Routine MRI allowed identification of contrast enhancement in SIJs on postcontrast T1WFS images in 31 patients (49 SIJs). Contrast enhancement was observed in 40 patients (76 SIJs) who were examined by MRI using the subtraction technique. Contrast enhancement was significantly more conspicuous on subtraction images than on non-subtracted postcontrast T1WFS images (Mann-Whitney U test, p<0.001). Contrast-enhanced MRI with subtraction technique may be useful for early detection of active sacroiliitis. (orig.)

Transcriptome responses in the rectal gland of fed and fasted spiny dogfish shark (Squalus acanthias) determined by suppression subtractive hybridization.

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Deck, Courtney A; McKay, Sheldon J; Fiedler, Tristan J; LeMoine, Christophe M R; Kajimura, Makiko; Nawata, C Michele; Wood, Chris M; Walsh, Patrick J

2013-12-01

Prior studies of the elasmobranch rectal gland have demonstrated that feeding induces profound and rapid up regulation of the gland's ability to secrete concentrated NaCl solutions and the metabolic capacity to support this highly ATP consuming process. We undertook the current study to attempt to determine the degree to which up regulation of mRNA transcription was involved in the gland's activation. cDNA libraries were created from mRNA isolated from rectal glands of fasted (7days post-feeding) and fed (6h and 22h post-feeding) spiny dogfish sharks (Squalus acanthias), and the libraries were subjected to suppression subtractive hybridization (SSH) analysis. Quantitative real time PCR (qPCR) was also used to ascertain the mRNA expression of several genes revealed by the SSH analysis. In total the treatments changed the abundance of 170 transcripts, with 103 up regulated by feeding, and 67 up regulated by fasting. While many of the changes took place in 'expected' Gene Ontology (GO) categories (e.g., metabolism, transport, structural proteins, DNA and RNA turnover, etc.), KEGG analysis revealed a number of categories which identify oxidative stress as a topic of interest for the gland. GO analysis also revealed that branched chain essential amino acids (e.g., valine, leucine, isoleucine) are potential metabolic fuels for the rectal gland. In addition, up regulation of transcripts for many genes in the anticipated GO categories did not agree (i.e., fasting down regulated in feeding treatments) with previously observed increases in their respective proteins/enzyme activities. These results suggest an 'anticipatory' storage of selected mRNAs which presumably supports the rapid translation of proteins upon feeding activation of the gland. © 2013 Elsevier Inc. All rights reserved.

Suppression subtractive hybridization reveals transcript profiling of Chlorella under heterotrophy to photoautotrophy transition.

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Jianhua Fan

Full Text Available Microalgae have been extensively investigated and exploited because of their competitive nutritive bioproducts and biofuel production ability. Chlorella are green algae that can grow well heterotrophically and photoautotrophically. Previous studies proved that shifting from heterotrophy to photoautotrophy in light-induced environments causes photooxidative damage as well as distinct physiologic features that lead to dynamic changes in Chlorella intracellular components, which have great potential in algal health food and biofuel production. However, the molecular mechanisms underlying the trophic transition remain unclear.In this study, suppression subtractive hybridization strategy was employed to screen and characterize genes that are differentially expressed in response to the light-induced shift from heterotrophy to photoautotrophy. Expressed sequence tags (ESTs were obtained from 770 and 803 randomly selected clones among the forward and reverse libraries, respectively. Sequence analysis identified 544 unique genes in the two libraries. The functional annotation of the assembled unigenes demonstrated that 164 (63.1% from the forward library and 62 (21.8% from the reverse showed significant similarities with the sequences in the NCBI non-redundant database. The time-course expression patterns of 38 selected differentially expressed genes further confirmed their responsiveness to a diverse trophic status. The majority of the genes enriched in the subtracted libraries were associated with energy metabolism, amino acid metabolism, protein synthesis, carbohydrate metabolism, and stress defense.The data presented here offer the first insights into the molecular foundation underlying the diverse microalgal trophic niche. In addition, the results can be used as a reference for unraveling candidate genes associated with the transition of Chlorella from heterotrophy to photoautotrophy, which holds great potential for further improving its lipid and

A standard curve based method for relative real time PCR data processing

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Krause Andreas

2005-03-01

Full Text Available Abstract Background Currently real time PCR is the most precise method by which to measure gene expression. The method generates a large amount of raw numerical data and processing may notably influence final results. The data processing is based either on standard curves or on PCR efficiency assessment. At the moment, the PCR efficiency approach is preferred in relative PCR whilst the standard curve is often used for absolute PCR. However, there are no barriers to employ standard curves for relative PCR. This article provides an implementation of the standard curve method and discusses its advantages and limitations in relative real time PCR. Results We designed a procedure for data processing in relative real time PCR. The procedure completely avoids PCR efficiency assessment, minimizes operator involvement and provides a statistical assessment of intra-assay variation. The procedure includes the following steps. (I Noise is filtered from raw fluorescence readings by smoothing, baseline subtraction and amplitude normalization. (II The optimal threshold is selected automatically from regression parameters of the standard curve. (III Crossing points (CPs are derived directly from coordinates of points where the threshold line crosses fluorescence plots obtained after the noise filtering. (IV The means and their variances are calculated for CPs in PCR replicas. (V The final results are derived from the CPs' means. The CPs' variances are traced to results by the law of error propagation. A detailed description and analysis of this data processing is provided. The limitations associated with the use of parametric statistical methods and amplitude normalization are specifically analyzed and found fit to the routine laboratory practice. Different options are discussed for aggregation of data obtained from multiple reference genes. Conclusion A standard curve based procedure for PCR data processing has been compiled and validated. It illustrates that

Background suppression of infrared small target image based on inter-frame registration

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Ye, Xiubo; Xue, Bindang

2018-04-01

We propose a multi-frame background suppression method for remote infrared small target detection. Inter-frame information is necessary when the heavy background clutters make it difficult to distinguish real targets and false alarms. A registration procedure based on points matching in image patches is used to compensate the local deformation of background. Then the target can be separated by background subtraction. Experiments show our method serves as an effective preliminary of target detection.

Spectral Subtraction Approach for Interference Reduction of MIMO Channel Wireless Systems

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Tomohiro Ono

2005-08-01

Full Text Available In this paper, a generalized spectral subtraction approach for reducing additive impulsive noise, narrowband signals, white Gaussian noise and DS-CDMA interferences in MIMO channel DS-CDMA wireless communication systems is investigated. The interference noise reduction or suppression is essential problem in wireless mobile communication systems to improve the quality of communication. The spectrum subtraction scheme is applied to the interference noise reduction problems for noisy MIMO channel systems. The interferences in space and time domain signals can effectively be suppressed by selecting threshold values, and the computational load with the FFT is not large. Further, the fading effects of channel are compensated by spectral modification with the spectral subtraction process. In the simulations, the effectiveness of the proposed methods for the MIMO channel DS-CDMA is shown to compare with the conventional MIMO channel DS-CDMA.

Identification of Bacillus anthracis specific chromosomal sequences by suppressive subtractive hybridization

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Redkar Rajendra

2004-02-01

Full Text Available Abstract Background Bacillus anthracis, Bacillus thuringiensis and Bacillus cereus are closely related members of the B. cereus-group of bacilli. Suppressive subtractive hybridization (SSH was used to identify specific chromosomal sequences unique to B. anthracis. Results Two SSH libraries were generated. Genomic DNA from plasmid-cured B. anthracis was used as the tester DNA in both libraries, while genomic DNA from either B. cereus or B. thuringiensis served as the driver DNA. Progressive screening of the libraries by colony filter and Southern blot analyses identified 29 different clones that were specific for the B. anthracis chromosome relative not only to the respective driver DNAs, but also to seven other different strains of B. cereus and B. thuringiensis included in the process. The nucleotide sequences of the clones were compared with those found in genomic databases, revealing that over half of the clones were located into 2 regions on the B. anthracis chromosome. Conclusions Genes encoding potential cell wall synthesis proteins dominated one region, while bacteriophage-related sequences dominated the other region. The latter supports the hypothesis that acquisition of these bacteriophage sequences occurred during or after speciation of B. anthracis relative to B. cereus and B. thuringiensis. This study provides insight into the chromosomal differences between B. anthracis and its closest phylogenetic relatives.

A Feature Subtraction Method for Image Based Kinship Verification under Uncontrolled Environments

DEFF Research Database (Denmark)

Duan, Xiaodong; Tan, Zheng-Hua

2015-01-01

The most fundamental problem of local feature based kinship verification methods is that a local feature can capture the variations of environmental conditions and the differences between two persons having a kin relation, which can significantly decrease the performance. To address this problem...... the feature distance between face image pairs with kinship and maximize the distance between non-kinship pairs. Based on the subtracted feature, the verification is realized through a simple Gaussian based distance comparison method. Experiments on two public databases show that the feature subtraction method...

Genomic suppression subtractive hybridization as a tool to identify differences in mycorrhizal fungal genomes.

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Murat, Claude; Zampieri, Elisa; Vallino, Marta; Daghino, Stefania; Perotto, Silvia; Bonfante, Paola

2011-05-01

Characterization of genomic variation among different microbial species, or different strains of the same species, is a field of significant interest with a wide range of potential applications. We have investigated the genomic variation in mycorrhizal fungal genomes through genomic suppressive subtractive hybridization. The comparison was between phylogenetically distant and close truffle species (Tuber spp.), and between isolates of the ericoid mycorrhizal fungus Oidiodendron maius featuring different degrees of metal tolerance. In the interspecies experiment, almost all the sequences that were identified in the Tuber melanosporum genome and absent in Tuber borchii and Tuber indicum corresponded to transposable elements. In the intraspecies comparison, some specific sequences corresponded to regions coding for enzymes, among them a glutathione synthetase known to be involved in metal tolerance. This approach is a quick and rather inexpensive tool to develop molecular markers for mycorrhizal fungi tracking and barcoding, to identify functional genes and to investigate the genome plasticity, adaptation and evolution. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Identification of warm day and cool night conditions induced flowering-related genes in a Phalaenopsis orchid hybrid by suppression subtractive hybridization.

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Li, D M; Lü, F B; Zhu, G F; Sun, Y B; Xu, Y C; Jiang, M D; Liu, J W; Wang, Z

2014-02-14

The influence of warm day and cool night conditions on induction of spikes in Phalaenopsis orchids has been studied with respect to photosynthetic efficiency, metabolic cycles and physiology. However, molecular events involved in spike emergence induced by warm day and cool night conditions are not clearly understood. We examined gene expression induced by warm day and cool night conditions in the Phalaenopsis hybrid Fortune Saltzman through suppression subtractive hybridization, which allowed identification of flowering-related genes in warm day and cool night conditions in spikes and leaves at vegetative phase grown under warm daily temperatures. In total, 450 presumably regulated expressed sequence tags (ESTs) were identified and classified into functional categories, including metabolism, development, transcription factor, signal transduction, transportation, cell defense, and stress. Furthermore, database comparisons revealed a notable number of Phalaenopsis hybrid Fortune Saltzman ESTs that matched genes with unknown function. The expression profiles of 24 genes (from different functional categories) have been confirmed by quantitative real-time PCR in induced spikes and juvenile apical leaves. The results of the real-time PCR showed that, compared to the vegetative apical leaves, the transcripts of genes encoding flowering locus T, AP1, AP2, KNOX1, knotted1-like homeobox protein, R2R3-like MYB, adenosine kinase 2, S-adenosylmethionine synthetase, dihydroflavonol 4-reductase, and naringenin 3-dioxygenase accumulated significantly higher levels, and genes encoding FCA, retrotransposon protein Ty3 and C3HC4-type RING finger protein accumulated remarkably lower levels in spikes of early developmental stages. These results suggested that the genes of two expression changing trends may play positive and negative roles in the early floral transition of Phalaenopsis orchids. In conclusion, spikes induced by warm day and cool night conditions were complex in

Screening differentially expressed genes in an amphipod (Hyalella azteca) exposed to fungicide vinclozolin by suppression subtractive hybridization.

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Wu, Yun H; Wu, Tsung M; Hong, Chwan Y; Wang, Yei S; Yen, Jui H

2014-01-01

Vinclozolin, a dicarboximide fungicide, is an endocrine disrupting chemical that competes with an androgenic endocrine disruptor compound. Most research has focused on the epigenetic effect of vinclozolin in humans. In terms of ecotoxicology, understanding the effect of vinclozolin on non-target organisms is important. The expression profile of a comprehensive set of genes in the amphipod Hyalella azteca exposed to vinclozolin was examined. The expressed sequence tags in low-dose vinclozolin-treated and -untreated amphipods were isolated and identified by suppression subtractive hybridization. DNA dot blotting was used to confirm the results and establish a subtracted cDNA library for comparing all differentially expressed sequences with and without vinclozolin treatment. In total, 494 differentially expressed genes, including hemocyanin, heatshock protein, cytochrome, cytochrome oxidase and NADH dehydrogenase were detected. Hemocyanin was the most abundant gene. DNA dot blotting revealed 55 genes with significant differential expression. These genes included larval serum protein 1 alpha, E3 ubiquitin-protein ligase, mitochondrial cytochrome c oxidase, mitochondrial protein, proteasome inhibitor, hemocyanin, zinc-finger-containing protein, mitochondrial NADH-ubiquinone oxidoreductase and epididymal sperm-binding protein. Vinclozolin appears to upregulate stress-related genes and hemocyanin, related to immunity. Moreover, vinclozolin downregulated NADH dehydrogenase, related to respiration. Thus, even a non-lethal concentration of vinclozolin still has an effect at the genetic level in H. azteca and presents a potential risk, especially as it would affect non-target organism hormone metabolism.

Identification of water stress genes in Pinus pinaster Ait. by controlled progressive stress and suppression-subtractive hybridization.

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Perdiguero, Pedro; Collada, Carmen; Barbero, María Del Carmen; García Casado, Gloria; Cervera, María Teresa; Soto, Alvaro

2012-01-01

Climate change is a major challenge particularly for forest tree species, which will have to face the severe alterations of environmental conditions with their current genetic pool. Thus, an understanding of their adaptive responses is of the utmost interest. In this work we have selected Pinus pinaster as a model species. This pine is one of the most important conifers (for which molecular tools and knowledge are far more scarce than for angiosperms) in the Mediterranean Basin, which is characterised in all foreseen scenarios as one of the regions most drastically affected by climate change, mainly because of increasing temperature and, particularly, by increasing drought. We have induced a controlled, increasing water stress by adding PEG to a hydroponic culture. We have generated a subtractive library, with the aim of identifying the genes induced by this stress and have searched for the most reliable expressional candidate genes, based on their overexpression during water stress, as revealed by microarray analysis and confirmed by RT-PCR. We have selected a set of 67 candidate genes belonging to different functional groups that will be useful molecular tools for further studies on drought stress responses, adaptation, and population genomics in conifers, as well as in breeding programs. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

Putative in vitro expressed gene fragments unique to Mycobacterium avium subspecies para tuberculosis

DEFF Research Database (Denmark)

Nielsen, Kirstine Klitgaard; Ahrens, Peter

2002-01-01

By a suppression subtractive hybridization based method, nine novel Mycobacterium avium subsp. para tuberculosis (M. para tuberculosis) fragments of between 318 and 596 bp have been identified and characterized. Database search revealed little or no similarity with other mycobacteria. The uniquen......By a suppression subtractive hybridization based method, nine novel Mycobacterium avium subsp. para tuberculosis (M. para tuberculosis) fragments of between 318 and 596 bp have been identified and characterized. Database search revealed little or no similarity with other mycobacteria....... The uniqueness and diagnostic potential of seven of these fragments in relation to M. paratuberculosis closest relative Mycobacterium avium subsp. avium (M. avium) was confirmed by species-specific PCR and Southern blot. Furthermore, RT-PCR indicated that eight of the nine fragments originate from areas...

A new double digestion ligation mediated suppression PCR method for simultaneous bacteria DNA-typing and confirmation of species: an Acinetobacter sp. model.

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Karolina Stojowska

Full Text Available We have designed a new ddLMS PCR (double digestion Ligation Mediated Suppression PCR method based on restriction site polymorphism upstream from the specific target sequence for the simultaneous identification and differentiation of bacterial strains. The ddLMS PCR combines a simple PCR used for species or genus identification and the LM PCR strategy for strain differentiation. The bacterial identification is confirmed in the form of the PCR product(s, while the length of the PCR product makes it possible to differentiate between bacterial strains. If there is a single copy of the target sequence within genomic DNA, one specific PCR product is created (simplex ddLMS PCR, whereas for multiple copies of the gene the fingerprinting patterns can be obtained (multiplex ddLMS PCR. The described ddLMS PCR method is designed for rapid and specific strain differentiation in medical and microbiological studies. In comparison to other LM PCR it has substantial advantages: enables specific species' DNA-typing without the need for pure bacterial culture selection, is not sensitive to contamination with other cells or genomic DNA, and gives univocal "band-based" results, which are easy to interpret. The utility of ddLMS PCR was shown for Acinetobacter calcoaceticus-baumannii (Acb complex, the genetically closely related and phenotypically similar species and also important nosocomial pathogens, for which currently, there are no recommended methods for screening, typing and identification. In this article two models are proposed: 3' recA-ddLMS PCR-MaeII/RsaI for Acb complex interspecific typing and 5' rrn-ddLMS PCR-HindIII/ApaI for Acinetobacter baumannii intraspecific typing. ddLMS PCR allows not only for DNA-typing but also for confirmation of species in one reaction. Also, practical guidelines for designing a diagnostic test based on ddLMS PCR for genotyping different species of bacteria are provided.

A new double digestion ligation mediated suppression PCR method for simultaneous bacteria DNA-typing and confirmation of species: an Acinetobacter sp. model.

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Stojowska, Karolina; Krawczyk, Beata

2014-01-01

We have designed a new ddLMS PCR (double digestion Ligation Mediated Suppression PCR) method based on restriction site polymorphism upstream from the specific target sequence for the simultaneous identification and differentiation of bacterial strains. The ddLMS PCR combines a simple PCR used for species or genus identification and the LM PCR strategy for strain differentiation. The bacterial identification is confirmed in the form of the PCR product(s), while the length of the PCR product makes it possible to differentiate between bacterial strains. If there is a single copy of the target sequence within genomic DNA, one specific PCR product is created (simplex ddLMS PCR), whereas for multiple copies of the gene the fingerprinting patterns can be obtained (multiplex ddLMS PCR). The described ddLMS PCR method is designed for rapid and specific strain differentiation in medical and microbiological studies. In comparison to other LM PCR it has substantial advantages: enables specific species' DNA-typing without the need for pure bacterial culture selection, is not sensitive to contamination with other cells or genomic DNA, and gives univocal "band-based" results, which are easy to interpret. The utility of ddLMS PCR was shown for Acinetobacter calcoaceticus-baumannii (Acb) complex, the genetically closely related and phenotypically similar species and also important nosocomial pathogens, for which currently, there are no recommended methods for screening, typing and identification. In this article two models are proposed: 3' recA-ddLMS PCR-MaeII/RsaI for Acb complex interspecific typing and 5' rrn-ddLMS PCR-HindIII/ApaI for Acinetobacter baumannii intraspecific typing. ddLMS PCR allows not only for DNA-typing but also for confirmation of species in one reaction. Also, practical guidelines for designing a diagnostic test based on ddLMS PCR for genotyping different species of bacteria are provided.

RNAi screening of subtracted transcriptomes reveals tumor suppression by taurine-activated GABAA receptors involved in volume regulation

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van Nierop, Pim; Vormer, Tinke L.; Foijer, Floris; Verheij, Joanne; Lodder, Johannes C.; Andersen, Jesper B.; Mansvelder, Huibert D.; te Riele, Hein

2018-01-01

To identify coding and non-coding suppressor genes of anchorage-independent proliferation by efficient loss-of-function screening, we have developed a method for enzymatic production of low complexity shRNA libraries from subtracted transcriptomes. We produced and screened two LEGO (Low-complexity by Enrichment for Genes shut Off) shRNA libraries that were enriched for shRNA vectors targeting coding and non-coding polyadenylated transcripts that were reduced in transformed Mouse Embryonic Fibroblasts (MEFs). The LEGO shRNA libraries included ~25 shRNA vectors per transcript which limited off-target artifacts. Our method identified 79 coding and non-coding suppressor transcripts. We found that taurine-responsive GABAA receptor subunits, including GABRA5 and GABRB3, were induced during the arrest of non-transformed anchor-deprived MEFs and prevented anchorless proliferation. We show that taurine activates chloride currents through GABAA receptors on MEFs, causing seclusion of cell volume in large membrane protrusions. Volume seclusion from cells by taurine correlated with reduced proliferation and, conversely, suppression of this pathway allowed anchorage-independent proliferation. In human cholangiocarcinomas, we found that several proteins involved in taurine signaling via GABAA receptors were repressed. Low GABRA5 expression typified hyperproliferative tumors, and loss of taurine signaling correlated with reduced patient survival, suggesting this tumor suppressive mechanism operates in vivo. PMID:29787571

Subtractive Leadership

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Larwin, K. H.; Thomas, Eugene M.; Larwin, David A.

2015-01-01

This paper introduces a new term and concept to the leadership discourse: Subtractive Leadership. As an extension of the distributive leadership model, the notion of subtractive leadership refers to a leadership style that detracts from organizational culture and productivity. Subtractive leadership fails to embrace and balance the characteristics…

Identification of Genes Associated with Morphology in Aspergillus Niger by Using Suppression Subtractive Hybridization

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Dai, Ziyu; Mao, Xingxue; Magnuson, Jon K.; Lasure, Linda L.

2004-04-01

The morphology of citric acid production strains of Aspergillus niger is sensitive to a variety of factors including the concentration of manganese (Mn2+). Upon increasing the Mn2+ concentration in A. niger (ATCC 11414) cultures to 14 ppb or higher, the morphology switches from pelleted to filamentous, accompanied by a rapid decline in citric acid production. Molecular mechanisms through which Mn2+ exerts effects on morphology and citric acid production in A. niger have not been well defined, but our use of suppression subtractive hybridization has identified 22 genes responsive to Mn2+. Fifteen genes were differentially expressed when A. niger was grown in media containing 1000 ppb Mn2+ (filamentous form) and seven genes in 10 ppb Mn2+ (pelleted form). Of the fifteen filamentous-associated genes, seven are novel and eight share 47-100% identity to genes from other organisms. Five of the pellet-associated genes are novel, and the other two genes encode a pepsin-type protease and polyubiquitin. All ten genes with deduced functions are either involved in amino acid metabolism/protein catabolism or cell regulatory processes. Northern-blot analysis showed that the transcripts of all 22 genes were rapidly enhanced or suppressed by Mn2+. Steady-state mRNA levels of six selected filamentous associated genes remained high during five days of culture in a filamentous state and low under pelleted growth conditions. The opposite behavior was observed for four selected pellet-associated genes. The full-length cDNA of the filamentous-associated clone, Brsa-25 was isolated. Antisense expression of Brsa-25 permitted pelleted growth and increased citrate production at higher concentrations of Mn2+ than could be tolerated by the parent strain. The results suggest the involvement of the newly isolated genes in regulation of A. niger morphology.

Identification of gene products suppressed by human immunodeficiency virus type 1 infection or gp120 exposure of primary human astrocytes by rapid subtraction hybridization.

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Su, Zao-Zhong; Kang, Dong-Chul; Chen, Yinming; Pekarskaya, Olga; Chao, Wei; Volsky, David J; Fisher, Paul B

2003-06-01

Neurodegeneration and human immunodeficiency virus type 1 (HIV-1)-associated dementia (HAD) are the major disease manifestations of HIV-1 colonization of the central nervous system (CNS). In the brain, HIV-1 replicates in microglial cells and infiltrating macrophages and it persists in a low-productive, noncytolytic state in astrocytes. Astrocytes play critical roles in the maintenance of the brain microenvironment, responses to injury, and in neuronal signal transmission, and disruption of these functions by HIV-1 could contribute to HAD. To better understand the potential effects of HIV-1 on astrocyte biology, the authors investigated changes in gene expression using an efficient and sensitive rapid subtraction hybridization approach, RaSH. Primary human astrocytes were isolated from abortus brain tissue, low-passage cells were infected with HIV-1 or mock infected, and total cellular RNAs were isolated at multiple time points over a period of 1 week. This approach is designed to identify gene products modulated early and late after HIV-1 infection and limits the cloning of genes displaying normal cell-cycle fluctuations in astrocytes. By subtracting temporal cDNAs derived from HIV-1-infected astrocytes from temporal cDNAs made from uninfected cells, 10 genes displaying reduced expression in infected cells, termed astrocyte suppressed genes (ASGs), were identified and their suppression was confirmed by Northern blot hybridization. Both known and novel ASGs, not reported in current DNA databases, that are down-regulated by HIV-1 infection are described. Northern blotting confirms suppression of the same panel of ASGs by treatment of astrocytes with recombinant HIV-1 envelope glycoprotein, gp120. These results extend our previous analysis of astrocyte genes induced or enhanced by HIV-1 infection and together they suggest that HIV-1 and viral proteins have profound effects on astrocyte physiology, which may influence their function in the CNS.

Identification of differential gene expression in in vitro FSH treated pig granulosa cells using suppression subtractive hybridization

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Tosser-Klopp G

2006-07-01

Full Text Available Abstract FSH, which binds to specific receptors on granulosa cells in mammals, plays a key role in folliculogenesis. Its biological activity involves stimulation of intercellular communication and upregulation of steroidogenesis, but the entire spectrum of the genes regulated by FSH has yet to be fully characterized. In order to find new regulated transcripts, however rare, we have used a Suppression Subtractive Hybridization approach (SSH on pig granulosa cells in primary culture treated or not with FSH. Two SSH libraries were generated and 76 clones were sequenced after selection by differential screening. Sixty four different sequences were identified, including 3 novel sequences. Experiments demonstrated the presence of 25 regulated transcripts. A gene ontology analysis of these 25 genes revealed (1 catalytic; (2 transport; (3 signal transducer; (4 binding; (5 anti-oxidant and (6 structural activities. These findings may deepen our understanding of FSH's effects. Particularly, they suggest that FSH is involved in the modulation of peroxidase activity and remodelling of chromatin.

Cloning the Gravity and Shear Stress Related Genes from MG-63 Cells by Subtracting Hybridization

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Zhang, Shu; Dai, Zhong-quan; Wang, Bing; Cao, Xin-sheng; Li, Ying-hui; Sun, Xi-qing

2008-06-01

Background The purpose of the present study was to clone the gravity and shear stress related genes from osteoblast-like human osteosarcoma MG-63 cells by subtractive hybridization. Method MG-63 cells were divided into two groups (1G group and simulated microgravity group). After cultured for 60 h in two different gravitational environments, two groups of MG-63 cells were treated with 1.5Pa fluid shear stress (FSS) for 60 min, respectively. The total RNA in cells was isolated. The gravity and shear stress related genes were cloned by subtractive hybridization. Result 200 clones were gained. 30 positive clones were selected using PCR method based on the primers of vector and sequenced. The obtained sequences were analyzed by blast. changes of 17 sequences were confirmed by RT-PCR and these genes are related to cell proliferation, cell differentiation, protein synthesis, signal transduction and apoptosis. 5 unknown genes related to gravity and shear stress were found. Conclusion In this part of our study, our result indicates that simulated microgravity may change the activities of MG-63 cells by inducing the functional alterations of specific genes.

A diagnostic PCR assay for the detection of an Australian epidemic strain of Pseudomonas aeruginosa

Science.gov (United States)

2010-01-01

Background Chronic lung infection with the bacterium Pseudomonas aeruginosa is one of the hallmarks of cystic fibrosis (CF) and is associated with worsening lung function, increased hospitalisation and reduced life expectancy. A virulent clonal strain of P. aeruginosa (Australian epidemic strain I; AES-I) has been found to be widespread in CF patients in eastern Australia. Methods Suppression subtractive hybridization (SSH) was employed to identify genetic sequences that are present in the AES-I strain but absent from the sequenced reference strain PAO1. We used PCR to evaluate the distribution of several of the AES-I loci amongst a collection of 188 P. aeruginosa isolates which was comprised of 35 AES-I isolates (as determined by PFGE), 78 non-AES-I CF isolates including other epidemic CF strains as well as 69 P. aeruginosa isolates from other clinical and environmental sources. Results We have identified a unique AES-I genetic locus that is present in all 35 AES-I isolates tested and not present in any of the other 153 P. aeruginosa strains examined. We have used this unique AES-I locus to develop a diagnostic PCR and a real-time PCR assay to detect the presence of P. aeruginosa and AES-I in patient sputum samples. Conclusions We have developed diagnostic PCR assays that are 100% sensitive and 100% specific for the P. aeruginosa strain AES-I. We have also shown that Whatman FTA® Elute cards may be used with PCR-based assays to rapidly detect the presence of P. aeruginosa strains in CF sputum. PMID:20637114

A diagnostic PCR assay for the detection of an Australian epidemic strain of Pseudomonas aeruginosa

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Murphy Anna

2010-07-01

Full Text Available Abstract Background Chronic lung infection with the bacterium Pseudomonas aeruginosa is one of the hallmarks of cystic fibrosis (CF and is associated with worsening lung function, increased hospitalisation and reduced life expectancy. A virulent clonal strain of P. aeruginosa (Australian epidemic strain I; AES-I has been found to be widespread in CF patients in eastern Australia. Methods Suppression subtractive hybridization (SSH was employed to identify genetic sequences that are present in the AES-I strain but absent from the sequenced reference strain PAO1. We used PCR to evaluate the distribution of several of the AES-I loci amongst a collection of 188 P. aeruginosa isolates which was comprised of 35 AES-I isolates (as determined by PFGE, 78 non-AES-I CF isolates including other epidemic CF strains as well as 69 P. aeruginosa isolates from other clinical and environmental sources. Results We have identified a unique AES-I genetic locus that is present in all 35 AES-I isolates tested and not present in any of the other 153 P. aeruginosa strains examined. We have used this unique AES-I locus to develop a diagnostic PCR and a real-time PCR assay to detect the presence of P. aeruginosa and AES-I in patient sputum samples. Conclusions We have developed diagnostic PCR assays that are 100% sensitive and 100% specific for the P. aeruginosa strain AES-I. We have also shown that Whatman FTA® Elute cards may be used with PCR-based assays to rapidly detect the presence of P. aeruginosa strains in CF sputum.

Construction and partial sequencing of a subtractive library in Calcutta 4 (Musa AA in early stage of infection with Mycosphaerella fijiensis Morelet

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Milady Mendoza-Rodríguez

2006-10-01

Full Text Available The study of genes involved in plant defense response against pathogen attack, is one of most important steps leading to the elucidation of disease resistance molecular mechanisms. The generation of subtracted deoxyribonucleic acid libraries (cDNA, by means of suppression subtractive hybridization technique (SSH, has been used for this purpose. A subtractive hybridization was made between a cDNA population obtained from ‘Calcutta 4’ inoculated leaves with M. fijiensis (CCIBP-Pf83 and a mixture of cDNA from ‘Calcutta 4’ non inoculated leaves and mycelium. Leaves samples were taken at 6, 10 and 12 days after inoculation. The subtracted library was obtained by cloning and transformation of subtracted products and as a result, 600 recombinants clones were obtained. Sequence analysis of sixty nine clones, revealed redundancy of the expressed sequence tags and most of them showed no homology with reported sequences at databases and only 13 % had a high homology with metalothioneins. The results constitute a step in advance in the molecular study of Musa-Mycosphaerella fijiensis interaction. Key words: Banana-Mycosphaerella fijiensis interaction, BlackSigatoka, Musa spp., suppression subtractive hybridization

Temporal subtraction of dual-energy chest radiographs

International Nuclear Information System (INIS)

Armato, Samuel G. III; Doshi, Devang J.; Engelmann, Roger; Caligiuri, Philip; MacMahon, Heber

2006-01-01

Temporal subtraction and dual-energy imaging are two enhanced radiography techniques that are receiving increased attention in chest radiography. Temporal subtraction is an image processing technique that facilitates the visualization of pathologic change across serial chest radiographic images acquired from the same patient; dual-energy imaging exploits the differential relative attenuation of x-ray photons exhibited by soft-tissue and bony structures at different x-ray energies to generate a pair of images that accentuate those structures. Although temporal subtraction images provide a powerful mechanism for enhancing visualization of subtle change, misregistration artifacts in these images can mimic or obscure abnormalities. The purpose of this study was to evaluate whether dual-energy imaging could improve the quality of temporal subtraction images. Temporal subtraction images were generated from 100 pairs of temporally sequential standard radiographic chest images and from the corresponding 100 pairs of dual-energy, soft-tissue radiographic images. The registration accuracy demonstrated in the resulting temporal subtraction images was evaluated subjectively by two radiologists. The registration accuracy of the soft-tissue-based temporal subtraction images was rated superior to that of the conventional temporal subtraction images. Registration accuracy also was evaluated objectively through an automated method, which achieved an area-under-the-ROC-curve value of 0.92 in the distinction between temporal subtraction images that demonstrated clinically acceptable and clinically unacceptable registration accuracy. By combining dual-energy soft-tissue images with temporal subtraction, misregistration artifacts can be reduced and superior image quality can be obtained

A study on computer-aided diagnosis based on temporal subtraction of sequential chest radiographs (in Japanese)

International Nuclear Information System (INIS)

Kano, Akiko

2001-01-01

An automated digital image subtraction technique for use with pairs of temporally sequential chest radiographs has been developed to aid radiologists in the detection of interval changes. Automated image registration based on nonlinear geometric warping is performed prior to subtraction in order to deal with complicated radiographic misregistration. Processing includes global matching, to achieve rough registration between the entire lung fields in the two images, and local matching, based on a cross-correlation method, to determine local shift values for a number of small regions. A proper warping of x,y-coordinates is determined by fitting two-dimensional polynomials to the distributions of the shift values. One image is warped and then subtracted from the other. The resultant subtraction images were able to enhance the conspicuity of various types of interval changes. Improved global matching based on a weighted template matching method achieved robust registration even with photofluorographs taken in chest mass screening programs, which had previously presented us with a relatively large number of poor-registration images. The new method was applied to 129 pairs of chest mass screening images, and offered registration accuracy as good as manual global matching. An observer test using 114 cases including 57 lung cancer cases presented better sensitivity and specificity on average compared to conventional comparison readings. In addition, newly developed image processing that eliminates the rib edge artifacts in subtraction images was applied to 26 images having pathological interval changes; results showed the potential for application to automated schemes for the detection of interval change patterns. With its capacity to improve the diagnostic accuracy of chest radiographs, the chest temporal subtraction technique promises to become an important element of computer-aided diagnosis (CAD) systems

Small lung cancers: improved detection by use of bone suppression imaging--comparison with dual-energy subtraction chest radiography.

Science.gov (United States)

Li, Feng; Engelmann, Roger; Pesce, Lorenzo L; Doi, Kunio; Metz, Charles E; Macmahon, Heber

2011-12-01

To determine whether use of bone suppression (BS) imaging, used together with a standard radiograph, could improve radiologists' performance for detection of small lung cancers compared with use of standard chest radiographs alone and whether BS imaging would provide accuracy equivalent to that of dual-energy subtraction (DES) radiography. Institutional review board approval was obtained. The requirement for informed consent was waived. The study was HIPAA compliant. Standard and DES chest radiographs of 50 patients with 55 confirmed primary nodular cancers (mean diameter, 20 mm) as well as 30 patients without cancers were included in the observer study. A new BS imaging processing system that can suppress the conspicuity of bones was applied to the standard radiographs to create corresponding BS images. Ten observers, including six experienced radiologists and four radiology residents, indicated their confidence levels regarding the presence or absence of a lung cancer for each lung, first by using a standard image, then a BS image, and finally DES soft-tissue and bone images. Receiver operating characteristic (ROC) analysis was used to evaluate observer performance. The average area under the ROC curve (AUC) for all observers was significantly improved from 0.807 to 0.867 with BS imaging and to 0.916 with DES (both P chest radiographs. Further improvements can be achieved by use of DES radiography but with the requirement for special equipment and a potential small increase in radiation dose. © RSNA, 2011.

Suppression of high-density artefacts in x-ray CT images using temporal digital subtraction with application to cryotherapy

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Baissalov, R.; Sandison, G.A.; Rewcastle, J.C. [Department of Medical Physics, Tom Baker Cancer Center, Calgary, Canada, T2N 4N2 2 Department of Physics and Astronomy, University of Calgary, Calgary T2N 2N4 (Canada); Donnelly, B.J. [Department of Surgery, Tom Baker Cancer Center, Calgary, Canada, T2N 4N2 4 Department of Surgery, Foothills Hospital, Calgary T2N 2T7 (Canada); Saliken, J.C. [Department of Surgery, Tom Baker Cancer Center, Calgary T2N 4N2 (Canada); Department of Diagnostic Imaging, Foothills Hospital, Calgary T2N 2T7 (Canada); McKinnon, J.G. [Department of Surgery, Foothills Hospital, Calgary T2N 2T7 (Canada); Muldrew, K. [Department of Surgery, Faculty of Medicine, University of Calgary, Calgary T2N 2T7 (Canada)

2000-05-01

Image guidance in cryotherapy is usually performed using ultrasound. Although not currently in routine clinical use, x-ray CT imaging is an alternative means of guidance that can display the full 3D structure of the iceball, including frozen and unfrozen regions. However, the quality of x-ray CT images is compromised by the presence of high-density streak artefacts. To suppress these artefacts we applied temporal digital subtraction (TDS). This TDS method has the added advantage of improving the grey-scale contrast between frozen and unfrozen tissue in the CT images. Two sets of CT images were taken of a phantom material, cryoprobes and a urethral warmer (UW) before and during the cryoprobe freeze cycle. The high-density artefacts persisted in both image sets. TDS was performed on these two image sets using the corresponding mask image of unfrozen material and the same geometrical configuration of the cryoprobes and the UW. The resultant difference image had a significantly reduced artefact content. Thus TDS can be used to significantly suppress or eliminate high-density CT streak artefacts without reducing the metallic content of the cryoprobes. In vivo study needs to be conducted to establish the utility of this TDS procedure for CT assisted prostate or liver cryotherapy. Applying TDS in x-ray CT guided cryotherapy will facilitate estimation of the number and location of all frozen and unfrozen regions, potentially making cryotherapy safer and less operator dependent. (author)

Suppression of high-density artefacts in x-ray CT images using temporal digital subtraction with application to cryotherapy

International Nuclear Information System (INIS)

Baissalov, R.; Sandison, G.A.; Rewcastle, J.C.; Donnelly, B.J.; Saliken, J.C.; McKinnon, J.G.; Muldrew, K.

2000-01-01

Image guidance in cryotherapy is usually performed using ultrasound. Although not currently in routine clinical use, x-ray CT imaging is an alternative means of guidance that can display the full 3D structure of the iceball, including frozen and unfrozen regions. However, the quality of x-ray CT images is compromised by the presence of high-density streak artefacts. To suppress these artefacts we applied temporal digital subtraction (TDS). This TDS method has the added advantage of improving the grey-scale contrast between frozen and unfrozen tissue in the CT images. Two sets of CT images were taken of a phantom material, cryoprobes and a urethral warmer (UW) before and during the cryoprobe freeze cycle. The high-density artefacts persisted in both image sets. TDS was performed on these two image sets using the corresponding mask image of unfrozen material and the same geometrical configuration of the cryoprobes and the UW. The resultant difference image had a significantly reduced artefact content. Thus TDS can be used to significantly suppress or eliminate high-density CT streak artefacts without reducing the metallic content of the cryoprobes. In vivo study needs to be conducted to establish the utility of this TDS procedure for CT assisted prostate or liver cryotherapy. Applying TDS in x-ray CT guided cryotherapy will facilitate estimation of the number and location of all frozen and unfrozen regions, potentially making cryotherapy safer and less operator dependent. (author)

PCA-based approach for subtracting thermal background emission in high-contrast imaging data

Science.gov (United States)

Hunziker, S.; Quanz, S. P.; Amara, A.; Meyer, M. R.

2018-03-01

Aims.Ground-based observations at thermal infrared wavelengths suffer from large background radiation due to the sky, telescope and warm surfaces in the instrument. This significantly limits the sensitivity of ground-based observations at wavelengths longer than 3 μm. The main purpose of this work is to analyse this background emission in infrared high-contrast imaging data as illustrative of the problem, show how it can be modelled and subtracted and demonstrate that it can improve the detection of faint sources, such as exoplanets. Methods: We used principal component analysis (PCA) to model and subtract the thermal background emission in three archival high-contrast angular differential imaging datasets in the M' and L' filter. We used an M' dataset of β Pic to describe in detail how the algorithm works and explain how it can be applied. The results of the background subtraction are compared to the results from a conventional mean background subtraction scheme applied to the same dataset. Finally, both methods for background subtraction are compared by performing complete data reductions. We analysed the results from the M' dataset of HD 100546 only qualitatively. For the M' band dataset of β Pic and the L' band dataset of HD 169142, which was obtained with an angular groove phase mask vortex vector coronagraph, we also calculated and analysed the achieved signal-to-noise ratio (S/N). Results: We show that applying PCA is an effective way to remove spatially and temporarily varying thermal background emission down to close to the background limit. The procedure also proves to be very successful at reconstructing the background that is hidden behind the point spread function. In the complete data reductions, we find at least qualitative improvements for HD 100546 and HD 169142, however, we fail to find a significant increase in S/N of β Pic b. We discuss these findings and argue that in particular datasets with strongly varying observing conditions or

A feasibility study of projection-based energy weighting based on a photon-counting detector in contrast-enhanced digital subtraction mammography: a simulation study

International Nuclear Information System (INIS)

Choi, Sunghoon; Lee, Seungwan; Choi, Yuna; Kim, Heejoung

2014-01-01

Contrast media, such as iodine and gadolinium, are generally used in digital subtraction mammography to enhance the contrast between target and background materials. In digital subtraction mammography, where one image (with contrast medium) is subtracted from another (anatomical background) to facilitate visualization of the tumor structure, tumors can be more easily distinguished after the injection of a contrast medium. In order to have more an effective method to increase the contrast-to-noise ratio (CNR), we applied a projection-based energy-weighting method. The purpose of this study is to demonstrate the feasibility of using the projection-based energy-weighting method in digital subtraction mammography. Unlike some other previous studies, we applied the projection-based energy-weighting method to more practical mammography conditions by using the Monte Carlo method to simulate four different iodine solutions embedded in a breast phantom comprised of 50% adipose and 50% glandular tissues. We also considered an optimal tube voltage and anode/filter combination in digital iodine contrast media mammography in order to maximize the figure-of-merit (FOM). The simulated source energy was from 20 to 45 keV to prevent electronic noise and include the k-edge energy of iodine (33.2 keV). The results showed that the projection-based energy-weighting improved the CNR by factors of 1.05 - 1.86 compared to the conventionally integrated images. Consequently, the CNR of digital subtraction mammography images can be improved by using projection-based energy-weighting with photon-counting detectors.

A feasibility study of projection-based energy weighting based on a photon-counting detector in contrast-enhanced digital subtraction mammography: a simulation study

Energy Technology Data Exchange (ETDEWEB)

Choi, Sunghoon; Lee, Seungwan; Choi, Yuna; Kim, Heejoung [Yonsei University, Wonju (Korea, Republic of)

2014-06-15

Contrast media, such as iodine and gadolinium, are generally used in digital subtraction mammography to enhance the contrast between target and background materials. In digital subtraction mammography, where one image (with contrast medium) is subtracted from another (anatomical background) to facilitate visualization of the tumor structure, tumors can be more easily distinguished after the injection of a contrast medium. In order to have more an effective method to increase the contrast-to-noise ratio (CNR), we applied a projection-based energy-weighting method. The purpose of this study is to demonstrate the feasibility of using the projection-based energy-weighting method in digital subtraction mammography. Unlike some other previous studies, we applied the projection-based energy-weighting method to more practical mammography conditions by using the Monte Carlo method to simulate four different iodine solutions embedded in a breast phantom comprised of 50% adipose and 50% glandular tissues. We also considered an optimal tube voltage and anode/filter combination in digital iodine contrast media mammography in order to maximize the figure-of-merit (FOM). The simulated source energy was from 20 to 45 keV to prevent electronic noise and include the k-edge energy of iodine (33.2 keV). The results showed that the projection-based energy-weighting improved the CNR by factors of 1.05 - 1.86 compared to the conventionally integrated images. Consequently, the CNR of digital subtraction mammography images can be improved by using projection-based energy-weighting with photon-counting detectors.

Non-contrast-enhanced MR angiography in critical limb ischemia: performance of quiescent-interval single-shot (QISS) and TSE-based subtraction techniques

International Nuclear Information System (INIS)

Altaha, Mustafa A.; Jaskolka, Jeffrey D.; Tan, Kongteng; Menezes, Ravi J.; Rick, Manuela; Schmitt, Peter; Wintersperger, Bernd J.

2017-01-01

The aim of this study was to evaluate diagnostic performance of non-contrast-enhanced 2D quiescent-interval single-shot (QISS) and 3D turbo spin-echo (TSE)-based subtraction magnetic resonance angiography (MRA) in the assessment of peripheral arteries in patients with critical limb ischemia (CLI). Nineteen consecutive patients (74 % male, 72.8 ± 9.9 years) with CLI underwent 2D QISS and 3D TSE-based subtraction MRA at 1.5 T. Axial-overlapping QISS MRA (3 mm/2 mm; 1 x 1 mm 2 ) covered from the toes to the aortic bifurcation while coronal 3D TSE-based subtraction MRA (1.3 x 1.2 x 1.3 mm 3 ) was restricted to the calf only. MRA data sets (two readers) were evaluated for stenosis (≥50 %) and image quality. Results were compared with digital subtraction angiography (DSA). Two hundred and sixty-seven (267) segments were available for MRA-DSA comparison, with a prevalence of stenosis ≥50 % of 41.9 %. QISS MRA was rated as good to excellent in 79.5-96.0 % of segments without any nondiagnostic segments; 89.8-96.1 % of segments in 3D TSE-based subtraction MRA were rated as nondiagnostic or poor. QISS MRA sensitivities and specificities (segmental) were 92 % and 95 %, respectively, for reader one and 81-97 % for reader two. Due to poor image quality of 3D TSE-based subtraction MRA, diagnostic performance measures were not calculated. QISS MRA demonstrates excellent diagnostic performance and higher robustness than 3D TSE-based subtraction MRA in the challenging patient population with CLI. (orig.)

Non-contrast-enhanced MR angiography in critical limb ischemia: performance of quiescent-interval single-shot (QISS) and TSE-based subtraction techniques

Energy Technology Data Exchange (ETDEWEB)

Altaha, Mustafa A. [University Health Network, Department of Medical Imaging, Peter Munk Cardiac Centre, Toronto, Ontario (Canada); Jaskolka, Jeffrey D.; Tan, Kongteng; Menezes, Ravi J. [University Health Network, Department of Medical Imaging, Peter Munk Cardiac Centre, Toronto, Ontario (Canada); University of Toronto, Department of Medical Imaging, Toronto, Ontario (Canada); Rick, Manuela; Schmitt, Peter [Siemens Healthcare, Erlangen (Germany); Wintersperger, Bernd J. [University Health Network, Department of Medical Imaging, Peter Munk Cardiac Centre, Toronto, Ontario (Canada); University of Toronto, Department of Medical Imaging, Toronto, Ontario (Canada); Toronto General Hospital, Department of Medical Imaging, Toronto, Ontario (Canada)

2017-03-15

The aim of this study was to evaluate diagnostic performance of non-contrast-enhanced 2D quiescent-interval single-shot (QISS) and 3D turbo spin-echo (TSE)-based subtraction magnetic resonance angiography (MRA) in the assessment of peripheral arteries in patients with critical limb ischemia (CLI). Nineteen consecutive patients (74 % male, 72.8 ± 9.9 years) with CLI underwent 2D QISS and 3D TSE-based subtraction MRA at 1.5 T. Axial-overlapping QISS MRA (3 mm/2 mm; 1 x 1 mm{sup 2}) covered from the toes to the aortic bifurcation while coronal 3D TSE-based subtraction MRA (1.3 x 1.2 x 1.3 mm{sup 3}) was restricted to the calf only. MRA data sets (two readers) were evaluated for stenosis (≥50 %) and image quality. Results were compared with digital subtraction angiography (DSA). Two hundred and sixty-seven (267) segments were available for MRA-DSA comparison, with a prevalence of stenosis ≥50 % of 41.9 %. QISS MRA was rated as good to excellent in 79.5-96.0 % of segments without any nondiagnostic segments; 89.8-96.1 % of segments in 3D TSE-based subtraction MRA were rated as nondiagnostic or poor. QISS MRA sensitivities and specificities (segmental) were 92 % and 95 %, respectively, for reader one and 81-97 % for reader two. Due to poor image quality of 3D TSE-based subtraction MRA, diagnostic performance measures were not calculated. QISS MRA demonstrates excellent diagnostic performance and higher robustness than 3D TSE-based subtraction MRA in the challenging patient population with CLI. (orig.)

Automatic dipole subtraction

International Nuclear Information System (INIS)

Hasegawa, K.

2008-01-01

The Catani-Seymour dipole subtraction is a general procedure to treat infrared divergences in real emission processes at next-to-leading order in QCD. We automatized the procedure in a computer code. The code is useful especially for the processes with many parton legs. In this talk, we first explain the algorithm of the dipole subtraction and the whole structure of our code. After that we show the results for some processes where the infrared divergences of real emission processes are subtracted. (author)

Comparison of RNA expression profiles on generations of Porphyra yezoensis (Rhodophyta, based on suppression subtractive hybridization (SSH

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Shen Songdong

2011-10-01

Full Text Available Abstract Background Porphyra yezoensis Ueda is one of the most important edible seaweed, with a dimorphic life cycle which consists of gametophyte as macroscopical blade and sporophyte as microscopic filamentous. Conspicuous differences exist in the two generations, such as morphology, cell structure, biochemistry, physiology, and so on. The developmental process of Porphyra yezoensis has been studied thoroughly, but the mechanism is still ambiguous and few studies on genetic expression have been carried out. In this study, the suppression subtractive hybridization (SSH method conducted to generate large-scale expressed sequence tags (EST is designed to identify gene candidates related to the morphological and physiological differences between the gametophytic and sporophytic generations of Porphyra yezoensis Ueda. Findings Each 300 clones of sporophyte and gametophyte cells were dipped onto the membrane for hybridization. The result of dot-blot suggested there were 222 positive clones in gametophyte library and 236 positive clones in sporophyte library. 383 positive clones of strongest signals had been sequenced, and 191 EST sequences of gametophyte and 192 of sporophyte were obtained. A total of 196 genes were obtained, within which 104 genes were identified from the gametophyte and 92 from the sporophyte. Thirty-nine genes of the gametophyte and 62 genes of the sporophyte showed sequence similarity to those genes with known or putative functions which were classified according to their putative biological roles and molecular functions. The GO annotation showed about 58% of the cellular component of sporophyte and gametophyte cells were mainly located in cytoplasm and nucleus. The special genes were located in Golgi apparatus, and high expression in plastid, ribosome and endoplasmic reticulum. The main biological functions of gametophyte cells contributed to DNA repair/replication, carbohydrate metabolism, transport and transcription

Construction and analysis of the cDNA subtraction library of yeast and mycelial phases of Sporothrix globosa isolated in China: identification of differentially expressed genes*

Science.gov (United States)

Hu, Qing-bi; He, Yu; Zhou, Xun

2015-01-01

Species included in the Sporothrix schenckii complex are temperature-dependent with dimorphic growth and cause sporotrichosis that is characterized by chronic and fatal lymphocutaneous lesions. The putative species included in the Sporothrix complex are S. brasiliensis, S. globosa, S. mexicana, S. pallida, S. schenckii, and S. lurei. S. globosa is the causal agent of sporotrichosis in China, and its pathogenicity appears to be closely related to the dimorphic transition, i.e. from the mycelial to the yeast phase, it adapts to changing environmental conditions. To determine the molecular mechanisms of the switching process that mediates the dimorphic transition of S. globosa, suppression subtractive hybridization (SSH) was used to prepare a complementary DNA (cDNA) subtraction library from the yeast and mycelial phases. Bioinformatics analysis was performed to profile the relationship between differently expressed genes and the dimorphic transition. Two genes that were expressed at higher levels by the yeast form were selected, and their differential expression levels were verified using a quantitative real-time reverse transcriptase polymerase chain reaction (qRT-PCR). It is believed that these differently expressed genes are involved in the pathogenesis of S. globosa infection in China. PMID:26642182

THE APPLICATION OF CONTINUOUS WAVELET TRANSFORM BASED FOREGROUND SUBTRACTION METHOD IN 21 cm SKY SURVEYS

International Nuclear Information System (INIS)

Gu Junhua; Xu Haiguang; Wang Jingying; Chen Wen; An Tao

2013-01-01

We propose a continuous wavelet transform based non-parametric foreground subtraction method for the detection of redshifted 21 cm signal from the epoch of reionization. This method works based on the assumption that the foreground spectra are smooth in frequency domain, while the 21 cm signal spectrum is full of saw-tooth-like structures, thus their characteristic scales are significantly different. We can distinguish them in the wavelet coefficient space easily and perform the foreground subtraction. Compared with the traditional spectral fitting based method, our method is more tolerant to complex foregrounds. Furthermore, we also find that when the instrument has uncorrected response error, our method can also work significantly better than the spectral fitting based method. Our method can obtain similar results with the Wp smoothing method, which is also a non-parametric method, but our method consumes much less computing time

N-jettiness subtractions for gg→H at subleading power

Energy Technology Data Exchange (ETDEWEB)

Moult, Ian [California Univ., Berkeley, CA (United States). Berkeley Center for Theoretical Physics; Lawrence Berkeley National Laboratory, CA (United States). Theoretical Physics Group; Rothen, Lorena; Tackmann, Frank J. [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany). Gruppe Theorie; Stewart, Iain W. [Massachusetts Institute of Technology, Cambridge, MA (United States). Center for Theoretical Physics; Zhu, Hua Xing [Massachusetts Institute of Technology, Cambridge, MA (United States). Center for Theoretical Physics; Zhejiang Univ. (China). Dept. of Physics

2017-10-15

N-jettiness subtractions provide a general approach for performing fully-differential next-to-next-to-leading order (NNLO) calculations. Since they are based on the physical resolution variable N-jettiness, T{sub N}, subleading power corrections in τ =T{sub N}/Q, with Q a hard interaction scale, can also be systematically computed. We study the structure of power corrections for 0-jettiness, T{sub 0}, for the gg→H process. Using the soft-collinear effective theory we analytically compute the leading power corrections α{sub s}τ ln τ and α{sub s}{sup 2}τ ln{sup 3}τ (finding partial agreement with a previous result in the literature), and perform a detailed numerical study of the power corrections in the gg, gq, and q anti q channels. This includes a numerical extraction of the α{sub s}τ and α{sub s}{sup 2}τ ln{sup 2}τ corrections, and a study of the dependence on the T{sub 0} definition. Including such power suppressed logarithms significantly reduces the size of missing power corrections, and hence improves the numerical efficiency of the subtraction method. Having a more detailed understanding of the power corrections for both q anti q and gg initiated processes also provides insight into their universality, and hence their behavior in more complicated processes where they have not yet been analytically calculated.

N-jettiness subtractions for gg→H at subleading power

International Nuclear Information System (INIS)

Moult, Ian; Lawrence Berkeley National Laboratory, CA; Rothen, Lorena; Tackmann, Frank J.; Stewart, Iain W.; Zhu, Hua Xing; Zhejiang Univ.

2017-10-01

N-jettiness subtractions provide a general approach for performing fully-differential next-to-next-to-leading order (NNLO) calculations. Since they are based on the physical resolution variable N-jettiness, T N , subleading power corrections in τ =T N /Q, with Q a hard interaction scale, can also be systematically computed. We study the structure of power corrections for 0-jettiness, T 0 , for the gg→H process. Using the soft-collinear effective theory we analytically compute the leading power corrections α s τ ln τ and α s 2 τ ln 3 τ (finding partial agreement with a previous result in the literature), and perform a detailed numerical study of the power corrections in the gg, gq, and q anti q channels. This includes a numerical extraction of the α s τ and α s 2 τ ln 2 τ corrections, and a study of the dependence on the T 0 definition. Including such power suppressed logarithms significantly reduces the size of missing power corrections, and hence improves the numerical efficiency of the subtraction method. Having a more detailed understanding of the power corrections for both q anti q and gg initiated processes also provides insight into their universality, and hence their behavior in more complicated processes where they have not yet been analytically calculated.

Feasibility study of 2D thick-slice MR digital subtraction angiography

International Nuclear Information System (INIS)

Ishimori, Yoshiyuki; Takeuchi, Miho; Higashimura, Kyouji; Komuro, Hiroyuki

2000-01-01

Conditions required to perform contrast MR digital subtraction angiography using a two-dimensional thick-slice high-speed gradient echo were investigated. The conditions in the phantom experiment included: slice profile, flip angle, imaging matrix, fat suppression, duration of IR pulse and frequency selectivity, flip angle of IR pulse and inversion time. Based on the results of the experiment, 2D thick-slice MRDSA was performed in volunteers. Under TR/TE=5.3-9/1.3-1.8 ms conditions, the requirements were a slice thick enough to include the target region, a flip angle of 10 degrees, and a phase matrix of 96 or more. Fat suppression was required for adipose-tissue-rich regions, such as the abdomen. The optimal conditions for applying the IR preparation pulse of the IR prepped fast gradient recalled echo as spectrally selective inversion recovery appeared to be: duration of IR pulse =20 ms, flip angle =100 degrees, and inversion time =40 ms. The authors concluded that it was feasible to perform 2D thick-slice MRDSA with time resolution within 1 second. (K.H.)

Genomic Diversity of Burkholderia pseudomallei Clinical Isolates: Subtractive Hybridization Reveals a Burkholderia mallei-Specific Propage in B. pseudomallei 1026b

National Research Council Canada - National Science Library

DeShazer, David

2004-01-01

.... pseudomallei, 1026b and K96243. Numerous mobile genetic elements, including a temperate bacteriophage designated phi1026b, were identified among the 1026b-specific suppression subtractive hybridization products...

Increasing LIGO sensitivity by feedforward subtraction of auxiliary length control noise

International Nuclear Information System (INIS)

Meadors, Grant David; Riles, Keith; Kawabe, Keita

2014-01-01

LIGO, the Laser Interferometer Gravitational-wave Observatory, has been designed and constructed to measure gravitational wave strain via differential arm length. The LIGO 4 km Michelson arms with Fabry–Perot cavities have auxiliary length control servos for suppressing Michelson motion of the beam-splitter and arm cavity input mirrors, which degrades interferometer sensitivity. We demonstrate how a post facto pipeline improves a data sample from LIGO Science Run 6 with feedforward subtraction. Dividing data into 1024 s windows, we numerically fit filter functions representing the frequency-domain transfer functions from Michelson length channels into the gravitational-wave strain data channel for each window, then subtract the filtered Michelson channel noise (witness) from the strain channel (target). In this paper we describe the algorithm, assess achievable improvements in sensitivity to astrophysical sources, and consider relevance to future interferometry. (paper)

X-ray CT high-density artefact suppression in cryosurgery

International Nuclear Information System (INIS)

Wei Jikun; Sandison, George A; Chen Laigao; Liang Yun; Xu, Lisa X

2002-01-01

Advantages of x-ray CT for imaging guidance of cryosurgery include 3D visualization of frozen and unfrozen tissue and calibration of temperature in the tissue water-ice interface (0-10 deg. C) to Hounsfield units. However, use of x-ray CT images and their thermal calibration can be compromised by the cryoprobes generating high-density streak artefacts. A new subtraction technique for artefact suppression is proposed and tested in prostate cryosurgery simulations. By subtracting the measured CT x-ray projection profile without cryoprobes from the profile with cryoprobes plus iceballs, one obtains the combined profile of the cryoprobes and a low value background. Polynomial interpolation to obtain the background profile allows its addition to the original profile without probes. The result may then be fed to a conventional filtered back-projection routine to reconstruct the probe-free image. Finally the cryoprobe pixels in the originally constructed image with probes and iceballs are added back to the probe-free image to get the final artefact-suppressed image. The major advantage of this subtraction technique is that it can successfully suppress the high-density artefacts in bone-abundant body regions such as the pelvis. X-ray CT images of cryoprobe arrays in a homogeneous gelatin phantom and the pelvic region of an anthropomorphic Rando phantom containing a human skeleton were generated. After suppression, cryoprobe metal artefact streaks are reduced and visualization of the positions and dimensions of the cryoprobes are well preserved. (note)

A temporal subtraction method for thoracic CT images based on generalized gradient vector flow

International Nuclear Information System (INIS)

Miyake, Noriaki; Kim, H.; Maeda, Shinya; Itai, Yoshinori; Tan, J.K.; Ishikawa, Seiji; Katsuragawa, Shigehiko

2010-01-01

A temporal subtraction image, which is obtained by subtraction of a previous image from a current one, can be used for enhancing interval changes (such as formation of new lesions and changes in existing abnormalities) on medical images by removing most of the normal structures. If image registration is incorrect, not only the interval changes but also the normal structures would be appeared as some artifacts on the temporal subtraction image. In a temporal subtraction technique for 2-D X-ray image, the effectiveness is shown through a lot of clinical evaluation experiments, and practical use is advancing. Moreover, the MDCT (Multi-Detector row Computed Tomography) can easily introduced on medical field, the development of a temporal subtraction for thoracic CT Images is expected. In our study, a temporal subtraction technique for thoracic CT Images is developed. As the technique, the vector fields are described by use of GGVF (Generalized Gradient Vector Flow) from the previous and current CT images. Afterwards, VOI (Volume of Interest) are set up on the previous and current CT image pairs. The shift vectors are calculated by using nearest neighbor matching of the vector fields in these VOIs. The search kernel on previous CT image is set up from the obtained shift vector. The previous CT voxel which resemble standard the current voxel is detected by voxel value and vector of the GGVF in the kernel. And, the previous CT image is transformed to the same coordinate of standard voxel. Finally, temporal subtraction image is made by subtraction of a warping image from a current one. To verify the proposal method, the result of application to 7 cases and the effectiveness are described. (author)

Advantages and limitations of quantitative PCR (Q-PCR)-based approaches in microbial ecology.

Science.gov (United States)

Smith, Cindy J; Osborn, A Mark

2009-01-01

Quantitative PCR (Q-PCR or real-time PCR) approaches are now widely applied in microbial ecology to quantify the abundance and expression of taxonomic and functional gene markers within the environment. Q-PCR-based analyses combine 'traditional' end-point detection PCR with fluorescent detection technologies to record the accumulation of amplicons in 'real time' during each cycle of the PCR amplification. By detection of amplicons during the early exponential phase of the PCR, this enables the quantification of gene (or transcript) numbers when these are proportional to the starting template concentration. When Q-PCR is coupled with a preceding reverse transcription reaction, it can be used to quantify gene expression (RT-Q-PCR). This review firstly addresses the theoretical and practical implementation of Q-PCR and RT-Q-PCR protocols in microbial ecology, highlighting key experimental considerations. Secondly, we review the applications of (RT)-Q-PCR analyses in environmental microbiology and evaluate the contribution and advances gained from such approaches. Finally, we conclude by offering future perspectives on the application of (RT)-Q-PCR in furthering understanding in microbial ecology, in particular, when coupled with other molecular approaches and more traditional investigations of environmental systems.

99mTc-RBC subtraction scintigraphy

International Nuclear Information System (INIS)

Inagaki, Syoichi; Tonami, Syuichi; Yasui, Masakazu; Kuranishi, Makoto; Sugishita, Kouki; Nakamura, Mamoru

1994-01-01

Sequential abdominal scintigrams with 99m Tc-labelled red blood cells (RBC) were subtracted for observing a site of gastrointestinal bleeding and calculating the bleeding rate. This method is technically very easy and can detect the site of bleeding with the minimum rate, as low as 0.2 ml/min., in a phantom experiment. In 23 cases with final diagnosis of gastrointestinal bleeding, conventional non-subtraction scintigraphy detected only 30% (7/23), but subtraction scintigraphy detected 61% (14/23). It was concluded that subtraction scintigraphy had higher sensitivity than conventional scintigraphy for early diagnosing bleeding. A combination of non-subtraction and subtraction scintigraphy is recommended to detect a site of gastrointestinal bleeding in a clinical setting. (author)

A study on the geometric correction for the digital subtraction radiograph

International Nuclear Information System (INIS)

Lim, Suk Young; Koh, Kwang Joon

2001-01-01

To develop a new subtraction program for registering digital images based on the correspondence of anatomic structures. The digital periapical images were obtained by Digora system with Rinn XCP equipment after translation of 1-16 mm, and rotation of 2-20 at the premolar and molar areas of the human dried mandible. The new subtraction program, NIH Image program and Emago/Advanced program were compared by the peak-signal -to noise ratio (PSNR). The new subtraction program was superior to NIH Images program and Emago/Advanced program up to 16 mm translation and horizontal angulation up to 4. The new subtraction program can be used for subtracting digital periapical images

Cloning of the relative genes of endocrine exophthalmos

International Nuclear Information System (INIS)

Zheng, JG

2004-01-01

Aim: In order to clarify the pathogenesis of endocrine exophthalmos, and lay foundations for finding the new functions of its relative genes, the cloning of its relative genes was carried out. Methods: The thyroid tissues of 10 hyperthyroidism patients, 5 of them with endocrine exophthalmos and 5 without that, were obtained. Their mRNA were collected respectively by using Quick Prep Micro mRNA purification kit. Then the same amount of the mRNA from 5 patients with endocrine exophthalmos was added into an eppendorf tube to form a mRNA pool. And that of the 5 patients without endocrine exophthalmos was also prepared as the other pool. As a model, the pool was used to synthesize the single and double chains of cDNA through SMART Tm PCR cDNA Synthesis Kit. The double chains cDNA from the endocrine exophthalmos patients, being used as tester, and that from the patients without endocrine exophthalmos, being used as driver, were digested by restriction endonucleases Hae III to get the fragments which was less than 500 bases. The tester cDNA was ligated with adapt or 1 or 2 respectively. Then the subtractive suppressive hybridization was performed between tester and driver cDNA. And the efficacies of subtraction were measured. The differential genes between the thyroid tissues of endocrine exophthalmos and the thyroid tissues without endocrine exophthalmos were obtained through two cycles of subtractive hybridization and two cycles PCR. The differential genes were cloned into the vector of pT-Adv, and then transformed into E.coliDH5a. 48 white clonies were selected to build the subtractive suppressive library of the relative genes of endocrine exophthalmos. The primer 2 was applied for the colony PCR of the relative genes. The amplified genes were obtained and purified by using Quaqwich Spine PCR Purification Kit. According to the principle of random primer, the double chains cDNA from the thyroid tissues with or without endocrine exophthalmos were digested by Hae III

Computed tomography lung iodine contrast mapping by image registration and subtraction

Science.gov (United States)

Goatman, Keith; Plakas, Costas; Schuijf, Joanne; Beveridge, Erin; Prokop, Mathias

2014-03-01

Pulmonary embolism (PE) is a relatively common and potentially life threatening disease, affecting around 600,000 people annually in the United States alone. Prompt treatment using anticoagulants is effective and saves lives, but unnecessary treatment risks life threatening haemorrhage. The specificity of any diagnostic test for PE is therefore as important as its sensitivity. Computed tomography (CT) angiography is routinely used to diagnose PE. However, there are concerns it may over-report the condition. Additional information about the severity of an occlusion can be obtained from an iodine contrast map that represents tissue perfusion. Such maps tend to be derived from dual-energy CT acquisitions. However, they may also be calculated by subtracting pre- and post-contrast CT scans. Indeed, there are technical advantages to such a subtraction approach, including better contrast-to-noise ratio for the same radiation dose, and bone suppression. However, subtraction relies on accurate image registration. This paper presents a framework for the automatic alignment of pre- and post-contrast lung volumes prior to subtraction. The registration accuracy is evaluated for seven subjects for whom pre- and post-contrast helical CT scans were acquired using a Toshiba Aquilion ONE scanner. One hundred corresponding points were annotated on the pre- and post-contrast scans, distributed throughout the lung volume. Surface-to-surface error distances were also calculated from lung segmentations. Prior to registration the mean Euclidean landmark alignment error was 2.57mm (range 1.43-4.34 mm), and following registration the mean error was 0.54mm (range 0.44-0.64 mm). The mean surface error distance was 1.89mm before registration and 0.47mm after registration. There was a commensurate reduction in visual artefacts following registration. In conclusion, a framework for pre- and post-contrast lung registration has been developed that is sufficiently accurate for lung subtraction

Hardware Implementation of a Bilateral Subtraction Filter

Science.gov (United States)

Huertas, Andres; Watson, Robert; Villalpando, Carlos; Goldberg, Steven

2009-01-01

A bilateral subtraction filter has been implemented as a hardware module in the form of a field-programmable gate array (FPGA). In general, a bilateral subtraction filter is a key subsystem of a high-quality stereoscopic machine vision system that utilizes images that are large and/or dense. Bilateral subtraction filters have been implemented in software on general-purpose computers, but the processing speeds attainable in this way even on computers containing the fastest processors are insufficient for real-time applications. The present FPGA bilateral subtraction filter is intended to accelerate processing to real-time speed and to be a prototype of a link in a stereoscopic-machine- vision processing chain, now under development, that would process large and/or dense images in real time and would be implemented in an FPGA. In terms that are necessarily oversimplified for the sake of brevity, a bilateral subtraction filter is a smoothing, edge-preserving filter for suppressing low-frequency noise. The filter operation amounts to replacing the value for each pixel with a weighted average of the values of that pixel and the neighboring pixels in a predefined neighborhood or window (e.g., a 9 9 window). The filter weights depend partly on pixel values and partly on the window size. The present FPGA implementation of a bilateral subtraction filter utilizes a 9 9 window. This implementation was designed to take advantage of the ability to do many of the component computations in parallel pipelines to enable processing of image data at the rate at which they are generated. The filter can be considered to be divided into the following parts (see figure): a) An image pixel pipeline with a 9 9- pixel window generator, b) An array of processing elements; c) An adder tree; d) A smoothing-and-delaying unit; and e) A subtraction unit. After each 9 9 window is created, the affected pixel data are fed to the processing elements. Each processing element is fed the pixel value for

Identification of genes differentially expressed in Mikania micrantha during Cuscuta campestris infection by suppression subtractive hybridization.

Science.gov (United States)

Li, Dong-Mei; Staehelin, Christian; Zhang, Yi-Shun; Peng, Shao-Lin

2009-09-01

The influence of Cuscuta campestris on its host Mikania micrantha has been studied with respect to biomass accumulation, physiology and ecology. Molecular events of this parasitic plant-plant interaction are poorly understood, however. In this study, we identified novel genes from M. micrantha induced by C. campestris infection. Genes expressed upon parasitization by C. campestris at early post-penetration stages were investigated by construction and characterization of subtracted cDNA libraries from shoots and stems of M. micrantha. Three hundred and three presumably up-regulated expressed sequence tags (ESTs) were identified and classified in functional categories, such as "metabolism", "cell defence and stress", "transcription factor", "signal transduction", "transportation" and "photosynthesis". In shoots and stems of infected M. micrantha, genes associated with defence responses and cell wall modifications were induced, confirming similar data from other parasitic plant-plant interactions. However, gene expression profiles in infected shoots and stems were found to be different. Compared to infected shoots, more genes induced in response to biotic and abiotic stress factors were identified in infected stems. Furthermore, database comparisons revealed a notable number of M. micrantha ESTs that matched genes with unknown function. Expression analysis by quantitative real-time RT-PCR of 21 genes (from different functional categories) showed significantly increased levels for 13 transcripts in response to C. campestris infection. In conclusion, this study provides an overview of genes from parasitized M. micrantha at early post-penetration stages. The acquired data form the basis for a molecular understanding of host reactions in response to parasitic plants.

Temporal subtraction in chest radiography: Automated assessment of registration accuracy

International Nuclear Information System (INIS)

Armato, Samuel G. III; Doshi, Devang J.; Engelmann, Roger; Croteau, Charles L.; MacMahon, Heber

2006-01-01

Radiologists routinely compare multiple chest radiographs acquired from the same patient over time to more completely understand changes in anatomy and pathology. While such comparisons are achieved conventionally through a side-by-side display of images, image registration techniques have been developed to combine information from two separate radiographic images through construction of a 'temporal subtraction image'. Although temporal subtraction images provide a powerful mechanism for the enhanced visualization of subtle change, errors in the clinical evaluation of these images may arise from misregistration artifacts that can mimic or obscure pathologic change. We have developed a computerized method for the automated assessment of registration accuracy as demonstrated in temporal subtraction images created from radiographic chest image pairs. The registration accuracy of 150 temporal subtraction images constructed from the computed radiography images of 72 patients was rated manually using a five-point scale ranging from '5-excellent' to '1-poor'; ratings of 3, 4, or 5 reflected clinically acceptable subtraction images, and ratings of 1 or 2 reflected clinically unacceptable images. Gray-level histogram-based features and texture measures are computed at multiple spatial scales within a 'lung mask' region that encompasses both lungs in the temporal subtraction images. A subset of these features is merged through a linear discriminant classifier. With a leave-one-out-by-patient training/testing paradigm, the automated method attained an A z value of 0.92 in distinguishing between temporal subtraction images that demonstrated clinically acceptable and clinically unacceptable registration accuracy. A second linear discriminant classifier yielded an A z value of 0.82 based on a feature subset selected from an independent database of digitized film images. These methods are expected to advance the clinical utility of temporal subtraction images for chest

N -jettiness subtractions for g g →H at subleading power

Science.gov (United States)

Moult, Ian; Rothen, Lorena; Stewart, Iain W.; Tackmann, Frank J.; Zhu, Hua Xing

2018-01-01

N -jettiness subtractions provide a general approach for performing fully-differential next-to-next-to-leading order (NNLO) calculations. Since they are based on the physical resolution variable N -jettiness, TN , subleading power corrections in τ =TN/Q , with Q a hard interaction scale, can also be systematically computed. We study the structure of power corrections for 0-jettiness, T0, for the g g →H process. Using the soft-collinear effective theory we analytically compute the leading power corrections αsτ ln τ and αs2τ ln3τ (finding partial agreement with a previous result in the literature), and perform a detailed numerical study of the power corrections in the g g , g q , and q q ¯ channels. This includes a numerical extraction of the αsτ and αs2τ ln2τ corrections, and a study of the dependence on the T0 definition. Including such power suppressed logarithms significantly reduces the size of missing power corrections, and hence improves the numerical efficiency of the subtraction method. Having a more detailed understanding of the power corrections for both q q ¯ and g g initiated processes also provides insight into their universality, and hence their behavior in more complicated processes where they have not yet been analytically calculated.

The parallel-sequential field subtraction technique for coherent nonlinear ultrasonic imaging

Science.gov (United States)

Cheng, Jingwei; Potter, Jack N.; Drinkwater, Bruce W.

2018-06-01

Nonlinear imaging techniques have recently emerged which have the potential to detect cracks at a much earlier stage than was previously possible and have sensitivity to partially closed defects. This study explores a coherent imaging technique based on the subtraction of two modes of focusing: parallel, in which the elements are fired together with a delay law and sequential, in which elements are fired independently. In the parallel focusing a high intensity ultrasonic beam is formed in the specimen at the focal point. However, in sequential focusing only low intensity signals from individual elements enter the sample and the full matrix of transmit-receive signals is recorded and post-processed to form an image. Under linear elastic assumptions, both parallel and sequential images are expected to be identical. Here we measure the difference between these images and use this to characterise the nonlinearity of small closed fatigue cracks. In particular we monitor the change in relative phase and amplitude at the fundamental frequencies for each focal point and use this nonlinear coherent imaging metric to form images of the spatial distribution of nonlinearity. The results suggest the subtracted image can suppress linear features (e.g. back wall or large scatters) effectively when instrumentation noise compensation in applied, thereby allowing damage to be detected at an early stage (c. 15% of fatigue life) and reliably quantified in later fatigue life.

Quantitative threefold allele-specific PCR (QuanTAS-PCR) for highly sensitive JAK2 V617F mutant allele detection

International Nuclear Information System (INIS)

Zapparoli, Giada V; Jorissen, Robert N; Hewitt, Chelsee A; McBean, Michelle; Westerman, David A; Dobrovic, Alexander

2013-01-01

The JAK2 V617F mutation is the most frequent somatic change in myeloproliferative neoplasms, making it an important tumour-specific marker for diagnostic purposes and for the detection of minimal residual disease. Sensitive quantitative assays are required for both applications, particularly for the monitoring of minimal residual disease, which requires not only high sensitivity but also very high specificity. We developed a highly sensitive probe-free quantitative mutant-allele detection method, Quantitative Threefold Allele-Specific PCR (QuanTAS-PCR), that is performed in a closed-tube system, thus eliminating the manipulation of PCR products. QuantTAS-PCR uses a threefold approach to ensure allele-specific amplification of the mutant sequence: (i) a mutant allele-specific primer, (ii) a 3′dideoxy blocker to suppress false-positive amplification from the wild-type template and (iii) a PCR specificity enhancer, also to suppress false-positive amplification from the wild-type template. Mutant alleles were quantified relative to exon 9 of JAK2. We showed that the addition of the 3′dideoxy blocker suppressed but did not eliminate false-positive amplification from the wild-type template. However, the addition of the PCR specificity enhancer near eliminated false-positive amplification from the wild-type allele. Further discrimination between true and false positives was enabled by using the quantification cycle (Cq) value of a single mutant template as a cut-off point, thus enabling robust distinction between true and false positives. As 10,000 JAK2 templates were used per replicate, the assay had a sensitivity of 1/10 -4 per replicate. Greater sensitivity could be reached by increasing the number of replicates analysed. Variation in replicates when low mutant-allele templates were present necessitated the use of a statistics-based approach to estimate the load of mutant JAK2 copies. QuanTAS-PCR showed comparable quantitative results when validated against a

Advanced Background Subtraction Applied to Aeroacoustic Wind Tunnel Testing

Science.gov (United States)

Bahr, Christopher J.; Horne, William C.

2015-01-01

An advanced form of background subtraction is presented and applied to aeroacoustic wind tunnel data. A variant of this method has seen use in other fields such as climatology and medical imaging. The technique, based on an eigenvalue decomposition of the background noise cross-spectral matrix, is robust against situations where isolated background auto-spectral levels are measured to be higher than levels of combined source and background signals. It also provides an alternate estimate of the cross-spectrum, which previously might have poor definition for low signal-to-noise ratio measurements. Simulated results indicate similar performance to conventional background subtraction when the subtracted spectra are weaker than the true contaminating background levels. Superior performance is observed when the subtracted spectra are stronger than the true contaminating background levels. Experimental results show limited success in recovering signal behavior for data where conventional background subtraction fails. They also demonstrate the new subtraction technique's ability to maintain a proper coherence relationship in the modified cross-spectral matrix. Beam-forming and de-convolution results indicate the method can successfully separate sources. Results also show a reduced need for the use of diagonal removal in phased array processing, at least for the limited data sets considered.

Developing a Model to Support Students in Solving Subtraction

Directory of Open Access Journals (Sweden)

Nila Mareta Murdiyani

2013-01-01

Full Text Available Subtraction has two meanings and each meaning leads to the different strategies. The meaning of “taking away something” suggests a direct subtraction, while the meaning of “determining the difference between two numbers” is more likely to be modeled as indirect addition. Many prior researches found that the second meaning and second strategy rarely appeared in the mathematical textbooks and teacher explanations, including in Indonesia. Therefore, this study was conducted to contribute to the development of a local instruction theory for subtraction by designing instructional activities that can facilitate first grade of primary school students to develop a model in solving two digit numbers subtraction. Consequently, design research was chosen as an appropriate approach for achieving the research aim and Realistic Mathematics Education (RME was used as a guide to design the lesson. This study involved 6 students in the pilot experiment, 31 students in the teaching experiment, and a first grade teacher of SDN 179 Palembang. The  result of this study shows that the beads string could bridge students from the contextual problems (taking ginger candies and making grains bracelets to the use of the empty number line. It also shows that the empty number line could promote students to  use different strategies (direct subtraction, indirect addition, and indirect subtraction in solving subtraction problems. Based on these findings, it is recommended to apply RME in the teaching learning process to make it more meaningful for students. Keywords: Subtraction, Design Research, Realistic Mathematics Education, The Beads String, The Empty Number Line DOI: http://dx.doi.org/10.22342/jme.4.1.567.95-112

X-ray image subtracting system

International Nuclear Information System (INIS)

Wesbey, W.H.; Keyes, G.S.; Georges, J.-P.J.

1982-01-01

An X-ray image subtracting system for making low contrast structures in the images more conspicuous is described. An X-ray source projects successive high and low energy X-ray beam pulses through a body and the resultant X-ray images are converted to optical images. Two image pick-up devices such as TV cameras that have synchronously operated shutters receive the alternate images and convert them to corresponding analog video signals. In some embodiments, the analog signals are converted to a matrix of digital pixel signals that are variously processed and subtracted and converted to signals for driving a TV monitor display and analog storage devices. In other embodiments the signals are processed and subtracted in analog form for display. The high and low energy pulses can follow each other immediately so good registration between subtracted images is obtainable even though the anatomy is in motion. The energy levels of the X-ray pulses are chosen to maximize the difference in attenuation between the anatomical structure which is to be subtracted out and that which remains. (author)

Digital subtraction angiography of the heart and lungs

International Nuclear Information System (INIS)

Moodie, D.S.; Yiannikas, J.

1986-01-01

This book contains 12 chapters. Some of the chapter titles are: Physical Principles of Cardiac Digital Subtraction Angiography, The Use of Intravenous Digital Subtraction Angiography in Evaluating Patients with Complex Congenital Heart Disease, Exercise Intravenous Digital Subtraction Angiograpny, Cardiomyopathic and Cardiac Neoplastic Disease, Digital Subtraction Angiography in the Catheterization Laboratory, and Cardiac Digital Subtraction Angiography - Future Directions

Meta-analysis of studies using suppression subtractive hybridization and microarrays to investigate the effects of environmental stress on gene transcription in oysters.

Science.gov (United States)

Anderson, Kelli; Taylor, Daisy A; Thompson, Emma L; Melwani, Aroon R; Nair, Sham V; Raftos, David A

2015-01-01

Many microarray and suppression subtractive hybridization (SSH) studies have analyzed the effects of environmental stress on gene transcription in marine species. However, there have been no unifying analyses of these data to identify common stress response pathways. To address this shortfall, we conducted a meta-analysis of 14 studies that investigated the effects of different environmental stressors on gene expression in oysters. The stressors tested included chemical contamination, hypoxia and infection, as well as extremes of temperature, pH and turbidity. We found that the expression of over 400 genes in a range of oyster species changed significantly after exposure to environmental stress. A repeating pattern was evident in these transcriptional responses, regardless of the type of stress applied. Many of the genes that responded to environmental stress encoded proteins involved in translation and protein processing (including molecular chaperones), the mitochondrial electron transport chain, anti-oxidant activity and the cytoskeleton. In light of these findings, we put forward a consensus model of sub-cellular stress responses in oysters.

Gold nanoparticle-based RT-PCR and real-time quantitative RT-PCR assays for detection of Japanese encephalitis virus

International Nuclear Information System (INIS)

Huang, S-H; Tsai, M-H; Lin, C-W; Yang, T-C; Chuang, P-H; Tsai, I-S; Lu, H-C; Wan Lei; Lin, Y-J; Lai, C-H

2008-01-01

Virus isolation and antibody detection are routinely used for diagnosis of Japanese encephalitis virus (JEV) infection, but the low level of transient viremia in some JE patients makes JEV isolation from clinical and surveillance samples very difficult. We describe the use of gold nanoparticle-based RT-PCR and real-time quantitative RT-PCR assays for detection of JEV from its RNA genome. We tested the effect of gold nanoparticles on four different PCR systems, including conventional PCR, reverse-transcription PCR (RT-PCR), and SYBR green real-time PCR and RT-PCR assays for diagnosis in the acute phase of JEV infection. Gold nanoparticles increased the amplification yield of the PCR product and shortened the PCR time compared to the conventional reaction. In addition, nanogold-based real-time RT-PCR showed a linear relationship between Ct and template amount using ten-fold dilutions of JEV. The nanogold-based RT-PCR and real-time quantitative RT-PCR assays were able to detect low levels (1-10 000 copies) of the JEV RNA genomes extracted from culture medium or whole blood, providing early diagnostic tools for the detection of low-level viremia in the acute-phase infection. The assays described here were simple, sensitive, and rapid approaches for detection and quantitation of JEV in tissue cultured samples as well as clinical samples

Interlaboratory diagnostic accuracy of a Salmonella specific PCR-based method

DEFF Research Database (Denmark)

Malorny, B.; Hoorfar, Jeffrey; Hugas, M.

2003-01-01

A collaborative study involving four European laboratories was conducted to investigate the diagnostic accuracy of a Salmonella specific PCR-based method, which was evaluated within the European FOOD-PCR project (http://www.pcr.dk). Each laboratory analysed by the PCR a set of independent obtained...... presumably naturally contaminated samples and compared the results with the microbiological culture method. The PCR-based method comprised a preenrichment step in buffered peptone water followed by a thermal cell lysis using a closed tube resin-based method. Artificially contaminated minced beef and whole......-based diagnostic methods and is currently proposed as international standard document....

On the usefulness of portal monitor unit subtraction in radiation therapy

International Nuclear Information System (INIS)

Kuperman, Vadim Y; Lubich, Leslie M

2003-01-01

In order to avoid additional dose to patients caused by portal imaging with megavoltage x-rays, portal monitor units (MUs) are frequently subtracted from the actual treatment MUs. This study examines the usefulness of portal MU subtraction in radiation therapy. For 11 prostate cancer patients treated with 23 MV photons, dose to prostate due to portal filming with 6 MV photons was determined. In all 11 patients subtraction of portal MU values from the actual treatment MUs resulted in a small underdosing of the prostate with an average treatment error of -0.5%. Portal filming without MU subtraction would cause small overdosing of the prostate with an average treatment error of 1.2%. The results of this study indicate that the benefits of portal MU subtraction are in doubt if (a) the energy of treatment x-rays is much higher than that of the portal x-rays and/or (b) when radiotherapy is performed with physical wedges. Based on the obtained results, we argue against unconditional use of the portal MU subtraction method to eliminate the dose from portal imaging

Background subtraction theory and practice

CERN Document Server

Elgammal, Ahmed

2014-01-01

Background subtraction is a widely used concept for detection of moving objects in videos. In the last two decades there has been a lot of development in designing algorithms for background subtraction, as well as wide use of these algorithms in various important applications, such as visual surveillance, sports video analysis, motion capture, etc. Various statistical approaches have been proposed to model scene backgrounds. The concept of background subtraction also has been extended to detect objects from videos captured from moving cameras. This book reviews the concept and practice of back

Digital subtraction angiography in traumatology

International Nuclear Information System (INIS)

Steudel, A.; Harder, T.; Lackner, K.; Schneider, B.; Orellano, L.; Bonn Univ.; Bonn Univ.

1986-01-01

The methods, indications and results of digital subtraction angiography in traumatology are presented, based on 56 examinations. The different use of intravenous or intraarterial DSA will be discussed with respect to expanding and localisation of traumatic vascular injury. DSA is recommended as the method of choice for follow-up after vascular reconstructive procedure. (orig.) [de

A subtraction scheme for computing QCD jet cross sections at NNLO: integrating the subtraction terms I

Science.gov (United States)

Somogyi, Gábor; Trócsányi, Zoltán

2008-08-01

In previous articles we outlined a subtraction scheme for regularizing doubly-real emission and real-virtual emission in next-to-next-to-leading order (NNLO) calculations of jet cross sections in electron-positron annihilation. In order to find the NNLO correction these subtraction terms have to be integrated over the factorized unresolved phase space and combined with the two-loop corrections. In this paper we perform the integration of all one-parton unresolved subtraction terms.

A novel approach to background subtraction in contrast-enhanced dual-energy digital mammography with commercially available mammography devices: Noise minimization

International Nuclear Information System (INIS)

Contillo, Adriano; Di Domenico, Giovanni; Cardarelli, Paolo; Gambaccini, Mauro; Taibi, Angelo

2016-01-01

Purpose: Dual-energy image subtraction represents a useful tool to improve the detectability of small lesions, especially in dense breasts. A feature it shares with all x-ray imaging techniques is the appearance of fluctuations in the texture of the background, which can obscure the visibility of interesting details. The aim of the work is to investigate the main noise sources, in order to create a better performing subtraction mechanism. In particular, the structural noise cancellation was achieved by means of a suitable extension of the dual-energy algorithm. Methods: The effect of the cancellation procedure was tested on an analytical simulation of a target with varying structural composition. Subsequently, the subtraction algorithm was also applied to a set of actual radiographs of a breast phantom exhibiting a nonuniform background pattern. The background power spectra of the outcomes were computed and compared to the ones obtained from a standard subtraction algorithm. Results: The comparison between the standard and the proposed cancellations showed an overall suppression of the magnitudes of the spectra, as well as a flattening of the frequency dependence of the structural component of the noise. Conclusions: The proposed subtraction procedure provides an effective cancellation of the residual background fluctuations. When combined with the polychromatic correction already described in a companion publication, it results in a high performing dual-energy subtraction scheme for commercial mammography units.

A novel approach to background subtraction in contrast-enhanced dual-energy digital mammography with commercially available mammography devices: Noise minimization

Energy Technology Data Exchange (ETDEWEB)

Contillo, Adriano, E-mail: contillo@fe.infn.it; Di Domenico, Giovanni; Cardarelli, Paolo; Gambaccini, Mauro; Taibi, Angelo [Dipartimento di Fisica e Scienze della Terra, Università degli Studi di Ferrara, Via Saragat 1, I-44122 Ferrara (Italy)

2016-06-15

Purpose: Dual-energy image subtraction represents a useful tool to improve the detectability of small lesions, especially in dense breasts. A feature it shares with all x-ray imaging techniques is the appearance of fluctuations in the texture of the background, which can obscure the visibility of interesting details. The aim of the work is to investigate the main noise sources, in order to create a better performing subtraction mechanism. In particular, the structural noise cancellation was achieved by means of a suitable extension of the dual-energy algorithm. Methods: The effect of the cancellation procedure was tested on an analytical simulation of a target with varying structural composition. Subsequently, the subtraction algorithm was also applied to a set of actual radiographs of a breast phantom exhibiting a nonuniform background pattern. The background power spectra of the outcomes were computed and compared to the ones obtained from a standard subtraction algorithm. Results: The comparison between the standard and the proposed cancellations showed an overall suppression of the magnitudes of the spectra, as well as a flattening of the frequency dependence of the structural component of the noise. Conclusions: The proposed subtraction procedure provides an effective cancellation of the residual background fluctuations. When combined with the polychromatic correction already described in a companion publication, it results in a high performing dual-energy subtraction scheme for commercial mammography units.

Performance of a video-image-subtraction-based patient positioning system

International Nuclear Information System (INIS)

Milliken, Barrett D.; Rubin, Steven J.; Hamilton, Russell J.; Johnson, L. Scott; Chen, George T.Y.

1997-01-01

Purpose: We have developed and tested an interactive video system that utilizes image subtraction techniques to enable high precision patient repositioning using surface features. We report quantitative measurements of system performance characteristics. Methods and Materials: Video images can provide a high precision, low cost measure of patient position. Image subtraction techniques enable one to incorporate detailed information contained in the image of a carefully verified reference position into real-time images. We have developed a system using video cameras providing orthogonal images of the treatment setup. The images are acquired, processed and viewed using an inexpensive frame grabber and a PC. The subtraction images provide the interactive guidance needed to quickly and accurately place a patient in the same position for each treatment session. We describe the design and implementation of our system, and its quantitative performance, using images both to measure changes in position, and to achieve accurate setup reproducibility. Results: Under clinical conditions (60 cm field of view, 3.6 m object distance), the position of static, high contrast objects could be measured with a resolution of 0.04 mm (rms) in each of two dimensions. The two-dimensional position could be reproduced using the real-time image display with a resolution of 0.15 mm (rms). Two-dimensional measurement resolution of the head of a patient undergoing treatment for head and neck cancer was 0.1 mm (rms), using a lateral view, measuring the variation in position of the nose and the ear over the course of a single radiation treatment. Three-dimensional repositioning accuracy of the head of a healthy volunteer using orthogonal camera views was less than 0.7 mm (systematic error) with an rms variation of 1.2 mm. Setup adjustments based on the video images were typically performed within a few minutes. The higher precision achieved using the system to measure objects than to reposition

Predicting the effect of spectral subtraction on the speech recognition threshold based on the signal-to-noise ratio in the envelope domain

DEFF Research Database (Denmark)

Jørgensen, Søren; Dau, Torsten

2011-01-01

rarely been evaluated perceptually in terms of speech intelligibility. This study analyzed the effects of the spectral subtraction strategy proposed by Berouti at al. [ICASSP 4 (1979), 208-211] on the speech recognition threshold (SRT) obtained with sentences presented in stationary speech-shaped noise....... The SRT was measured in five normal-hearing listeners in six conditions of spectral subtraction. The results showed an increase of the SRT after processing, i.e. a decreased speech intelligibility, in contrast to what is predicted by the Speech Transmission Index (STI). Here, another approach is proposed......, denoted the speech-based envelope power spectrum model (sEPSM) which predicts the intelligibility based on the signal-to-noise ratio in the envelope domain. In contrast to the STI, the sEPSM is sensitive to the increased amount of the noise envelope power as a consequence of the spectral subtraction...

Digital contrast subtraction radiography for proximal caries diagnosis

International Nuclear Information System (INIS)

Kang, Byung Cheol; Yoon, Suk Ja

2002-01-01

To determine whether subtraction images utilizing contrast media can improve the diagnostic performance of proximal caries diagnosis compared to conventional periapical radiographic images. Thirty-six teeth with 57 proximal surfaces were radiographied using a size no.2 RVG-ui sensor (Trophy Radiology, Marne-la-Vallee, France). The teeth immersed in water-soluble contrast media and subtraction images were taken. Each tooth was then sectioned for histologic examination. The digital radiographic images and subtraction images were examined and interpreted by three dentists for proximal caries. The results of the proximal caries diagnosis were then verified with the results of the histologic examination. The proximal caries sensitivity using digital subtraction radiography was significantly higher than simply examining a single digital radiograph. The sensitivity of the proximal dentinal carious lesion when analyzed with the subtraction radiograph and the radiograph together was higher than with the subtraction radiograph or the radiograph alone. The use of subtraction radiography with contrast media may be useful for detecting proximal dentinal carious lesions.

N-jettiness Subtractions for NNLO QCD calculations

International Nuclear Information System (INIS)

Gaunt, Jonathan R.; Stahlhofen, Maximilian; Tackmann, Frank J.; Walsh, Jonathan R.; California Univ., CA

2015-05-01

We present a subtraction method utilizing the N-jettiness observable, Τ N , to perform QCD calculations for arbitrary processes at next-to-next-to-leading order (NNLO). Our method employs soft-collinear effective theory (SCET) to determine the IR singular contributions of N-jet cross sections for Τ N → 0, and uses these to construct suitable Τ N -subtractions. The construction is systematic and economic, due to being based on a physical observable. The resulting NNLO calculation is fully differential and in a form directly suitable for combining with resummation and parton showers. We explain in detail the application to processes with an arbitrary number of massless partons at lepton and hadron colliders together with the required external inputs in the form of QCD amplitudes and lower-order calculations. We provide explicit expressions for the Τ N -subtractions at NLO and NNLO. The required ingredients are fully known at NLO, and at NNLO for processes with two external QCD partons. The remaining NNLO ingredient for three or more external partons can be obtained numerically with existing NNLO techniques. As an example, we employ our method to obtain the NNLO rapidity spectrum for Drell-Yan and gluon-fusion Higgs production. We discuss aspects of numerical accuracy and convergence and the practical implementation. We also discuss and comment on possible extensions, such as more-differential subtractions, necessary steps for going to N 3 LO, and the treatment of massive quarks.

Digital subtraction angiography for breast cancer

International Nuclear Information System (INIS)

Tsurumi, Kiyohiko; Okuyama, Nobuo

1987-01-01

We performed digital subtraction angiography (DSA) on 42 patients with breast diseases to investigate its efficiency. As a result we came to the following conclusions: 1. The sensitivity was well evaluated in intraarterial digital subtraction angiography (IA-DSA) of breast. 2. IA-DSA could diagnose difficult cases like cancer which had undergone augmentation mammoplasty, or like Paget's disease and others. 3. DSA was a safe examination method. 4. The sensitivity of IA-DSA of breast cancer is superior to intravenous digital subtraction angiography (IV-DSA). (author)

An automatic fuzzy-based multi-temporal brain digital subtraction angiography image fusion algorithm using curvelet transform and content selection strategy.

Science.gov (United States)

Momeni, Saba; Pourghassem, Hossein

2014-08-01

Recently image fusion has prominent role in medical image processing and is useful to diagnose and treat many diseases. Digital subtraction angiography is one of the most applicable imaging to diagnose brain vascular diseases and radiosurgery of brain. This paper proposes an automatic fuzzy-based multi-temporal fusion algorithm for 2-D digital subtraction angiography images. In this algorithm, for blood vessel map extraction, the valuable frames of brain angiography video are automatically determined to form the digital subtraction angiography images based on a novel definition of vessel dispersion generated by injected contrast material. Our proposed fusion scheme contains different fusion methods for high and low frequency contents based on the coefficient characteristic of wrapping second generation of curvelet transform and a novel content selection strategy. Our proposed content selection strategy is defined based on sample correlation of the curvelet transform coefficients. In our proposed fuzzy-based fusion scheme, the selection of curvelet coefficients are optimized by applying weighted averaging and maximum selection rules for the high frequency coefficients. For low frequency coefficients, the maximum selection rule based on local energy criterion is applied to better visual perception. Our proposed fusion algorithm is evaluated on a perfect brain angiography image dataset consisting of one hundred 2-D internal carotid rotational angiography videos. The obtained results demonstrate the effectiveness and efficiency of our proposed fusion algorithm in comparison with common and basic fusion algorithms.

A System based on Adaptive Background Subtraction Approach for Moving Object Detection and Tracking in Videos

Directory of Open Access Journals (Sweden)

Bahadır KARASULU

2013-04-01

Full Text Available Video surveillance systems are based on video and image processing research areas in the scope of computer science. Video processing covers various methods which are used to browse the changes in existing scene for specific video. Nowadays, video processing is one of the important areas of computer science. Two-dimensional videos are used to apply various segmentation and object detection and tracking processes which exists in multimedia content-based indexing, information retrieval, visual and distributed cross-camera surveillance systems, people tracking, traffic tracking and similar applications. Background subtraction (BS approach is a frequently used method for moving object detection and tracking. In the literature, there exist similar methods for this issue. In this research study, it is proposed to provide a more efficient method which is an addition to existing methods. According to model which is produced by using adaptive background subtraction (ABS, an object detection and tracking system’s software is implemented in computer environment. The performance of developed system is tested via experimental works with related video datasets. The experimental results and discussion are given in the study

Digital subtraction angiography in ischemic cerebrovascular accidents

Energy Technology Data Exchange (ETDEWEB)

Manelfe, C.; Bonafe, A.; Ducos de Lahitte, M.; Rascol, A.; Prere, J.; Guiraud, B.; Marc-Vergnes, J.P. (Hopital Purpan, 31 - Toulouse (France))

1983-12-29

Recent advances in computer and radiological technology have permitted reassessment of intravenous angiography in the evaluation of cerebrovascular disorders. Although digital subtraction angiography is a relatively new technique, it has rapidly gained a widespread acceptance. It has extended the use of angiography to outpatients and to people in whom conventional angiography is contraindicated. This reliable, safe, and relatively noninvasive technique offers the user two benefits: real-time subtraction and enhanced image quality. The system allows angiographic evaluation of the extracranial and intracranial vessels by means of intravenous injection of contrast material. Extracranial studies clearly demonstrate stenoses and occlusions of the major cervicocephalic arteries. Intracranial studies usually detect major cerebrovascular occlusions and provide insight into the collateral flow patterns. Intravenous digital subtraction angiography permits accurate assessment of cervicocephalic vessels after surgical repair. Although intravenous digital subtraction angiography obviates the need for conventional angiography in many cases, movements from the patients, or superimposition of vascular structures can substantially degrade the quality of the images. Digital subtraction angiography with intra-arterial injection of contrast medium will be contemplated in patients with poor intravenous digital subtraction angiography studies prior to surgery.

Digital subtraction angiography in ischemic cerebrovascular accidents

International Nuclear Information System (INIS)

Manelfe, C.; Bonafe, A.; Ducos de Lahitte, M.; Rascol, A.; Prere, J.; Guiraud, B.; Marc-Vergnes, J.P.

1983-01-01

Recent advances in computer and radiological technology have permitted reassessment of intravenous angiography in the evaluation of cerebrovascular disorders. Although digital subtraction angiography is a relatively new technique, it has rapidly gained a widespread acceptance. It has extended the use of angiography to outpatients and to people in whom conventional angiography is contraindicated. This reliable, safe, and relatively noninvasive technique offers the user two benefits: real-time subtraction and enhanced image quality. The system allows angiographic evaluation of the extracranial and intracranial vessels by means of intravenous injection of contrast material. Extracranial studies clearly demonstrate stenoses and occlusions of the major cervicocephalic arteries. Intracranial studies usually detect major cerebrovascular occlusions and provide insight into the collateral flow patterns. Intravenous digital subtraction angiography permits accurate assessment of cervicocephalic vessels after surgical repair. Although intravenous digital subtraction angiography obviates the need for conventional angiography in many cases, movements from the patients, or superimposition of vascular structures can substantially degrade the quality of the images. Digital subtraction angiography with intra-arterial injection of contrast medium will be contemplated in patients with poor intravenous digital subtraction angiography studies prior to surgery [fr

Novel subtractive transcription-based amplification of mRNA (STAR method and its application in search of rare and differentially expressed genes in AD brains

Directory of Open Access Journals (Sweden)

Walker P Roy

2006-11-01

Full Text Available Abstract Background Alzheimer's disease (AD is a complex disorder that involves multiple biological processes. Many genes implicated in these processes may be present in low abundance in the human brain. DNA microarray analysis identifies changed genes that are expressed at high or moderate levels. Complementary to this approach, we described here a novel technology designed specifically to isolate rare and novel genes previously undetectable by other methods. We have used this method to identify differentially expressed genes in brains affected by AD. Our method, termed Subtractive Transcription-based Amplification of mRNA (STAR, is a combination of subtractive RNA/DNA hybridization and RNA amplification, which allows the removal of non-differentially expressed transcripts and the linear amplification of the differentially expressed genes. Results Using the STAR technology we have identified over 800 differentially expressed sequences in AD brains, both up- and down- regulated, compared to age-matched controls. Over 55% of the sequences represent genes of unknown function and roughly half of them were novel and rare discoveries in the human brain. The expression changes of nearly 80 unique genes were further confirmed by qRT-PCR and the association of additional genes with AD and/or neurodegeneration was established using an in-house literature mining tool (LitMiner. Conclusion The STAR process significantly amplifies unique and rare sequences relative to abundant housekeeping genes and, as a consequence, identifies genes not previously linked to AD. This method also offers new opportunities to study the subtle changes in gene expression that potentially contribute to the development and/or progression of AD.

DNA microarray-based PCR ribotyping of Clostridium difficile.

Science.gov (United States)

Schneeberg, Alexander; Ehricht, Ralf; Slickers, Peter; Baier, Vico; Neubauer, Heinrich; Zimmermann, Stefan; Rabold, Denise; Lübke-Becker, Antina; Seyboldt, Christian

2015-02-01

This study presents a DNA microarray-based assay for fast and simple PCR ribotyping of Clostridium difficile strains. Hybridization probes were designed to query the modularly structured intergenic spacer region (ISR), which is also the template for conventional and PCR ribotyping with subsequent capillary gel electrophoresis (seq-PCR) ribotyping. The probes were derived from sequences available in GenBank as well as from theoretical ISR module combinations. A database of reference hybridization patterns was set up from a collection of 142 well-characterized C. difficile isolates representing 48 seq-PCR ribotypes. The reference hybridization patterns calculated by the arithmetic mean were compared using a similarity matrix analysis. The 48 investigated seq-PCR ribotypes revealed 27 array profiles that were clearly distinguishable. The most frequent human-pathogenic ribotypes 001, 014/020, 027, and 078/126 were discriminated by the microarray. C. difficile strains related to 078/126 (033, 045/FLI01, 078, 126, 126/FLI01, 413, 413/FLI01, 598, 620, 652, and 660) and 014/020 (014, 020, and 449) showed similar hybridization patterns, confirming their genetic relatedness, which was previously reported. A panel of 50 C. difficile field isolates was tested by seq-PCR ribotyping and the DNA microarray-based assay in parallel. Taking into account that the current version of the microarray does not discriminate some closely related seq-PCR ribotypes, all isolates were typed correctly. Moreover, seq-PCR ribotypes without reference profiles available in the database (ribotype 009 and 5 new types) were correctly recognized as new ribotypes, confirming the performance and expansion potential of the microarray. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Specific PCR-based detection of Alternaria helianthi

DEFF Research Database (Denmark)

Udayashankar, A.C.; Nayaka, S. Chandra; Archana, B.

2012-01-01

Alternaria helianthi is an important seed-borne pathogenic fungus responsible for blight disease in sunflower. The current detection methods, which are based on culture and morphological identification, are time-consuming, laborious and are not always reliable. A PCR-based diagnostic method...... tested. The detection limit of the PCR method was of 10 pg from template DNA. The primers could also detect the pathogen in infected sunflower seed. This species-specific PCR method provides a quick, simple, powerful and reliable alternative to conventional methods in the detection and identification...

Optical image encryption based on real-valued coding and subtracting with the help of QR code

Science.gov (United States)

Deng, Xiaopeng

2015-08-01

A novel optical image encryption based on real-valued coding and subtracting is proposed with the help of quick response (QR) code. In the encryption process, the original image to be encoded is firstly transformed into the corresponding QR code, and then the corresponding QR code is encoded into two phase-only masks (POMs) by using basic vector operations. Finally, the absolute values of the real or imaginary parts of the two POMs are chosen as the ciphertexts. In decryption process, the QR code can be approximately restored by recording the intensity of the subtraction between the ciphertexts, and hence the original image can be retrieved without any quality loss by scanning the restored QR code with a smartphone. Simulation results and actual smartphone collected results show that the method is feasible and has strong tolerance to noise, phase difference and ratio between intensities of the two decryption light beams.

BPHZL-subtraction scheme and axial gauges

Energy Technology Data Exchange (ETDEWEB)

Kreuzer, M.; Rebhan, A.; Schweda, M.; Piguet, O.

1986-03-27

The application of the BPHZL subtraction scheme to Yang-Mills theories in axial gauges is presented. In the auxillary mass formulation we show the validity of the convergence theorems for subtracted momentum space integrals, and we give the integral formulae necessary for one-loop calculations. (orig.).

Subtracted versus non-subtracted digital imaging in peripheral angiography

International Nuclear Information System (INIS)

Fink, U.; Heywang, S.; Mayr, B.; Berger, H.

1989-01-01

Digital subtraction angiography (DSA) plays an important role in the management of vascular diseases of the lower extremities. A disadvantage is the lack of an automatically moving table top. We used a 1,024x1,024 matrix with a large-screen intensifier system and an automated 'stepping' facility. In 161 examinations of the arteries of the lower extremity digital peripheral arteriography was performed with and without the subtraction technique. We compared the influence of different iodine concentrations in DA and DSA. Peripheral DA proved to be equal to peripheral DSA in the region of the pelvis, thigh and knee, with no adequate contrasting being obtained merely in the region of the lower leg arteries in about 45%. It is necessary to use contrast medium at a concentration of 300 mg I/ml. The installation of an automated 'stepping' facility reduces the amount of contrast' medium needed and the exposure time. (orig.)

Quantitative analysis of planar technetium-99m-sestamibi myocardial perfusion images using modified background subtraction

International Nuclear Information System (INIS)

Koster, K.; Wackers, F.J.; Mattera, J.A.; Fetterman, R.C.

1990-01-01

Standard interpolative background subtraction, as used for thallium-201 ( 201 Tl), may create artifacts when applied to planar technetium-99m-Sestamibi ( 99m Tc-Sestamibi) images, apparently because of the oversubtraction of relatively high extra-cardiac activity. A modified background subtraction algorithm was developed and compared to standard background subtraction in 16 patients who had both exercise-delayed 201 Tl and exercise-rest 99m Tc-Sestamibi imaging. Furthermore, a new normal data base was generated. Normal 99m Tc-Sestamibi distribution was slightly different compared to 201 Tl. Using standard background subtraction, mean defect reversibility was significantly underestimated by 99m Tc-Sestamibi compared to 201 Tl (2.8 +/- 4.9 versus -1.8 +/- 8.4, p less than 0.05). Using the modified background subtraction, mean defect reversibility on 201 Tl and 99m Tc-Sestamibi images was comparable (2.8 +/- 4.9 versus 1.7 +/- 5.2, p = NS). We conclude, that for quantification of 99m Tc-Sestamibi images a new normal data base, as well as a modification of the interpolative background subtraction method should be employed to obtain quantitative results comparable to those with 201 Tl

Self-masking subtraction tomosynthesis

International Nuclear Information System (INIS)

Chakraborty, D.P.; Yester, M.V.; Barnes, G.T.; Lakshminarayanan, A.V.

1984-01-01

The authors tested the image quality and dose savings of self-masking subtraction tomosynthesis (SST), which combines digital tomosynthesis with subtraction of a blurred self-mask. High-quality images of the inner ear of a head phantom were obtained at moderate dose savings. Although they were taken with linear motion, they did not exhibit the streaking due to off-fulcrum objects that is characteristic of conventional linear tomography. SST could reduce patient dose by a factor of at least 12 in examinations of the inner ear, and the mechanical aspects can be implemented with moderate modifications of existing instrumentation

Left-right subtraction of brain CT

International Nuclear Information System (INIS)

Ishiguchi, Tsuneo; Sakuma, Sadayuki

1986-01-01

A new image-processing method to obtain a left-right subtraction image of CT was designed for the automated detection of abnormalities in brain CT. An original CT image was divided in two by a centerline. Then the right half of the image was subtracted from the left half by calculating the absorption value of the pixels on the symmetrical positions against the centerline. The mean and the standard deviation of the absorption value of the pixels in the subtraction image were used as parameters for analysis, and the detectability of abnormal CT findings was evaluated in 100 cases - 50 cases each with normal and abnormal CT. The presence of abnormalities could be diagnosed with a sensitivity of 86 %, a specificity of 90 %, and an overall accuracy of 88 % when the borderline of these parameters between normal and abnormal CT was set at the mean + 2SD in the normal group. As a further analysis, the CT image was subdivided into several areas from a functional or anatomical viewpoint, such as cerebral vascular territories, and the left-right subtraction image of each area was obtained. The possibilities of diagnosing the location of an abnormality and of detecting smaller lesions with this method were shown. Left-right subtraction was considered to be a useful method for the detection of asymmetric abnormalities in the automated diagnosis of brain CT. (author)

Longitudinal development of subtraction performance in elementary school.

Science.gov (United States)

Artemenko, Christina; Pixner, Silvia; Moeller, Korbinian; Nuerk, Hans-Christoph

2017-10-05

A major goal of education in elementary mathematics is the mastery of arithmetic operations. However, research on subtraction is rather scarce, probably because subtraction is often implicitly assumed to be cognitively similar to addition, its mathematical inverse. To evaluate this assumption, we examined the relation between the borrow effect in subtraction and the carry effect in addition, and the developmental trajectory of the borrow effect in children using a choice reaction paradigm in a longitudinal study. In contrast to the carry effect in adults, carry and borrow effects in children were found to be categorical rather than continuous. From grades 3 to 4, children became more proficient in two-digit subtraction in general, but not in performing the borrow operation in particular. Thus, we observed no specific developmental progress in place-value computation, but a general improvement in subtraction procedures. Statement of contribution What is already known on this subject? The borrow operation increases difficulty in two-digit subtraction in adults. The carry effect in addition, as the inverse operation of borrowing, comprises categorical and continuous processing characteristics. What does this study add? In contrast to the carry effect in adults, the borrow and carry effects are categorical in elementary school children. Children generally improve in subtraction performance from grades 3 to 4 but do not progress in place-value computation in particular. © 2017 The British Psychological Society.

Development of Shimadzu digital subtraction system

International Nuclear Information System (INIS)

Nishioka, Hiroyuki; Shibata, Koichi; Shimizu, Yasumitsu; Shibata, Kenji; Wani, Hidenobu

1985-01-01

Shimadzu has recently developed a digital subtraction system. It can perform intra-arterial digital subtraction angiography (DSA) using low concentration of contrast medium, or can visualize arteries with intravenuous injection. It can extremely reduce patient's pain in angiography. Image quality of DSA has been much improved by the development of high quality image amplifiers, improvement of signal-to-noise ratio of the x-ray television unit and the development of digital disk recorders. The peak-hold subtraction method that is now under clinical study presents images of blood vessels as the trace of the flow of contrast medium. The maximum-hold memory where the maximum value of the brightness in some period is stored for every picture element is subtracted from the minimum-hold memory where the minimum value is stored, and thus images of blood vessels can be obtained. Hardware of this method is rather simple and it is expected that the amount of contrast medium may be reduced or x-ray dose of the patient may be decreased. (author)

Continuous-variable measurement-device-independent quantum key distribution with photon subtraction

Science.gov (United States)

Ma, Hong-Xin; Huang, Peng; Bai, Dong-Yun; Wang, Shi-Yu; Bao, Wan-Su; Zeng, Gui-Hua

2018-04-01

It has been found that non-Gaussian operations can be applied to increase and distill entanglement between Gaussian entangled states. We show the successful use of the non-Gaussian operation, in particular, photon subtraction operation, on the continuous-variable measurement-device-independent quantum key distribution (CV-MDI-QKD) protocol. The proposed method can be implemented based on existing technologies. Security analysis shows that the photon subtraction operation can remarkably increase the maximal transmission distance of the CV-MDI-QKD protocol, which precisely make up for the shortcoming of the original CV-MDI-QKD protocol, and one-photon subtraction operation has the best performance. Moreover, the proposed protocol provides a feasible method for the experimental implementation of the CV-MDI-QKD protocol.

An automated subtraction of NLO EW infrared divergences

Energy Technology Data Exchange (ETDEWEB)

Schoenherr, Marek [CERN, Theoretical Physics Department, Geneva (Switzerland)

2018-02-15

In this paper a generalisation of the Catani-Seymour dipole subtraction method to next-to-leading order electroweak calculations is presented. All singularities due to photon and gluon radiation off both massless and massive partons in the presence of both massless and massive spectators are accounted for. Particular attention is paid to the simultaneous subtraction of singularities of both QCD and electroweak origin which are present in the next-to-leading order corrections to processes with more than one perturbative order contributing at Born level. Similarly, embedding non-dipole-like photon splittings in the dipole subtraction scheme discussed. The implementation of the formulated subtraction scheme in the framework of the Sherpa Monte-Carlo event generator, including the restriction of the dipole phase space through the α-parameters and expanding its existing subtraction for NLO QCD calculations, is detailed and numerous internal consistency checks validating the obtained results are presented. (orig.)

Multiplex PCR-based assay for detection of Bordetella pertussis in nasopharyngeal swab specimens.

Science.gov (United States)

Wadowsky, R M; Michaels, R H; Libert, T; Kingsley, L A; Ehrlich, G D

1996-11-01

A multiplex PCR-based assay was developed for the detection of Bordetella pertussis in nasopharyngeal swab specimens. The assay simultaneously amplified two separate DNA targets (153 and 203 bp) within a B. pertussis repetitive element and a 438-bp target within the beta-actin gene of human DNA (PCR amplification control). PCR products were detected by a sensitive and specific liquid hybridization gel retardation assay. A total of 496 paired nasopharyngeal swab specimens were tested by both the PCR-based assay and culture. Although 30 (6%) of the specimens inhibited the amplification of the beta-actin target, in all 29 specimens studied, the inhibition disappeared on repeat testing or was easily overcome with a 1:8 dilution or less of specimen digest. Of the 495 specimen pairs yielding a final evaluable result by the PCR-based assay, 19.0% were positive by the PCR-based assay, whereas 13.9% were positive by culture (P < 0.0001). After resolving the PCR-positive, culture-negative results by testing an additional aliquot from these specimens by the multiplex PCR-based assay, the PCR-based assay had a sensitivity and specificity of 98.9 and 99.7%, respectively, compared with values of 73.4 and 100%, respectively, for culture. In comparison with patients with culture-confirmed pertussis, those with PCR-positive, culture-negative results were older and more likely to have had prolonged cough, immunization with pertussis vaccine, or treatment with erythromycin. This multiplex PCR-based assay is substantially more sensitive than culture and identifies specimens that contain inhibitors of PCR.

Soft-collinear factorization and zero-bin subtractions

International Nuclear Information System (INIS)

Chiu Juiyu; Fuhrer, Andreas; Kelley, Randall; Manohar, Aneesh V.; Hoang, Andre H.

2009-01-01

We study the Sudakov form factor for a spontaneously broken gauge theory using a (new) Δ-regulator. To be well defined, the effective theory requires zero-bin subtractions for the collinear sectors. The zero-bin subtractions depend on the gauge boson mass M and are not scaleless. They have both finite and 1/ε contributions and are needed to give the correct anomalous dimension and low-scale matching contributions. We also demonstrate the necessity of zero-bin subtractions for soft-collinear factorization. We find that after zero-bin subtractions the form factor is the sum of the collinear contributions minus a soft mass-mode contribution, in agreement with a previous result of Idilbi and Mehen in QCD. This appears to conflict with the method-of-regions approach, where one gets the sum of contributions from different regions.

Improved Savitzky-Golay-method-based fluorescence subtraction algorithm for rapid recovery of Raman spectra.

Science.gov (United States)

Chen, Kun; Zhang, Hongyuan; Wei, Haoyun; Li, Yan

2014-08-20

In this paper, we propose an improved subtraction algorithm for rapid recovery of Raman spectra that can substantially reduce the computation time. This algorithm is based on an improved Savitzky-Golay (SG) iterative smoothing method, which involves two key novel approaches: (a) the use of the Gauss-Seidel method and (b) the introduction of a relaxation factor into the iterative procedure. By applying a novel successive relaxation (SG-SR) iterative method to the relaxation factor, additional improvement in the convergence speed over the standard Savitzky-Golay procedure is realized. The proposed improved algorithm (the RIA-SG-SR algorithm), which uses SG-SR-based iteration instead of Savitzky-Golay iteration, has been optimized and validated with a mathematically simulated Raman spectrum, as well as experimentally measured Raman spectra from non-biological and biological samples. The method results in a significant reduction in computing cost while yielding consistent rejection of fluorescence and noise for spectra with low signal-to-fluorescence ratios and varied baselines. In the simulation, RIA-SG-SR achieved 1 order of magnitude improvement in iteration number and 2 orders of magnitude improvement in computation time compared with the range-independent background-subtraction algorithm (RIA). Furthermore the computation time of the experimentally measured raw Raman spectrum processing from skin tissue decreased from 6.72 to 0.094 s. In general, the processing of the SG-SR method can be conducted within dozens of milliseconds, which can provide a real-time procedure in practical situations.

Capillary-based integrated digital PCR in picoliter droplets.

Science.gov (United States)

Chen, Jinyu; Luo, Zhaofeng; Li, Lin; He, Jinlong; Li, Luoquan; Zhu, Jianwei; Wu, Ping; He, Liqun

2018-01-30

The droplet digital polymerase chain reaction (ddPCR) is becoming more and more popular in diagnostic applications in academia and industry. In commercially available ddPCR systems, after they have been made by a generator, the droplets have to be transferred manually to modules for amplification and detection. In practice, some of the droplets (∼10%) are lost during manual transfer, leading to underestimation of the targets. In addition, the droplets are also at risk of cross-contamination during transfer. By contrast, in labs, some chip-based ddPCRs have been demonstrated where droplets always run in channels. However, the droplets easily coalesce to large ones in chips due to wall wetting as well as thermal oscillation. The loss of droplets becomes serious when such ddPCRs are applied to absolutely quantify rare mutations, such as in early diagnostics in clinical research or when measuring biological diversity at the cell level. Here, we propose a capillary-based integrated ddPCR system that is used for the first time to realize absolute quantification in this way. In this system, a HPLC T-junction is used to generate droplets and a long HPLC capillary connects the generator with both a capillary-based thermocycler and a capillary-based cytometer. The performance of the system is validated by absolute quantification of a gene specific to lung cancer (LunX). The results show that this system has very good linearity (0.9988) at concentrations ranging from NTC to 2.4 × 10 -4 copies per μL. As compared to qPCR, the all-in-one scheme is superior both in terms of the detection limit and the smaller fold changes measurement. The system of ddPCR might provide a powerful approach for clinical or academic applications where rare events are mostly considered.

Subtraction and dynamic MR images of breast cancer

Energy Technology Data Exchange (ETDEWEB)

Murakami, Yoshitaka; Aoki, Manabu; Harada, Junta (Jikei Univ., Tokyo (Japan). School of Medicine)

1993-04-01

The purpose of this study was to evaluate the diagnostic effectiveness of subtraction and dynamic MR imaging in patients with breast masses. In 23 breast cancers and six fibroadenomas, spin echo T1 images were obtained at 0.2 Tesla before and every minute after intravenous injection of Gd-DTPA (0.1 or 0.2 mmol/kg). Subtraction images were obtained sequentially on the CRT monitor. All breast masses were enhanced after gadolinium and stood out as bright lesions on subtraction images. The tumor margin and its extension were more precisely evaluated on subtraction MR images than on conventional postcontrast MR images. Breast cancer showed a characteristic time-intensity curve with an early peak, in contrast to fibroadenoma, which showed a gradual increase in signal intensity. Subtraction MR imaging is a simple method for the evaluation of breast masses, and further, the time-intensity curve obtained by dynamic study is helpful in the differential diagnosis of lesions. (author).

Spectral amplitude coding OCDMA using and subtraction technique.

Science.gov (United States)

Hasoon, Feras N; Aljunid, S A; Samad, M D A; Abdullah, Mohamad Khazani; Shaari, Sahbudin

2008-03-20

An optical decoding technique is proposed for a spectral-amplitude-coding-optical code division multiple access, namely, the AND subtraction technique. The theory is being elaborated and experimental results have been done by comparing a double-weight code against the existing code, Hadamard. We have proved that the and subtraction technique gives better bit error rate performance than the conventional complementary subtraction technique against the received power level.

Bone-suppressed radiography using machine learning

Energy Technology Data Exchange (ETDEWEB)

Park, Jun Beom; Kim, Dae Cheon; Kim, Ho Kyung [KAERI, Daejeon (Korea, Republic of)

2016-05-15

The single-shot dual-energy imaging suffers from reduced contrast-to-noise ratio performance due to poor spectral separation. Tomosynthesis requires more complex motion equipment and may require higher patient dose. An alternative tissue-specific imaging technique was introduced. This alternative technique usually possesses a filter to generate bone-only images for given digital radiographs. Therefore, it provides soft-tissue-enhanced images from the subtraction of given radiographs and filtered bone-only images. Only bone-suppressed imaging capability is a limitation of the method. The filter can be obtained from a machine-learning algorithm, e.g. artificial neural network (ANN), with the dual-energy bone-only images (called 'teaching' images). We suspect the robustness of the filter may be dependent upon the number of teaching images and the number of patients from whose radiographs we obtain the teaching images. In this study, we design an ANN to obtain a bone-extracting filter from a radiograph, and investigate the filter properties with respect to various ANN parameters. Preliminary results are summarized in Fig. 3. We extracted 5,000 subregions in a 21x21 pixel format from the lung region in the bone-enhanced dual-energy image and we used them for teaching images during training the ANN. The resultant bone-enhanced image from the ANN nonlinear filter is shown in Fig. 3 (a). From the weighted logarithmic subtraction between Fig. 2 (a) and Fig. 3 (a), we could obtain the bone-suppressed image as shown in Fig. 3 (b). The quality of the bone-suppressed image is comparable to the ground truth Fig. 2 (c).

Bone-suppressed radiography using machine learning

International Nuclear Information System (INIS)

Park, Jun Beom; Kim, Dae Cheon; Kim, Ho Kyung

2016-01-01

The single-shot dual-energy imaging suffers from reduced contrast-to-noise ratio performance due to poor spectral separation. Tomosynthesis requires more complex motion equipment and may require higher patient dose. An alternative tissue-specific imaging technique was introduced. This alternative technique usually possesses a filter to generate bone-only images for given digital radiographs. Therefore, it provides soft-tissue-enhanced images from the subtraction of given radiographs and filtered bone-only images. Only bone-suppressed imaging capability is a limitation of the method. The filter can be obtained from a machine-learning algorithm, e.g. artificial neural network (ANN), with the dual-energy bone-only images (called 'teaching' images). We suspect the robustness of the filter may be dependent upon the number of teaching images and the number of patients from whose radiographs we obtain the teaching images. In this study, we design an ANN to obtain a bone-extracting filter from a radiograph, and investigate the filter properties with respect to various ANN parameters. Preliminary results are summarized in Fig. 3. We extracted 5,000 subregions in a 21x21 pixel format from the lung region in the bone-enhanced dual-energy image and we used them for teaching images during training the ANN. The resultant bone-enhanced image from the ANN nonlinear filter is shown in Fig. 3 (a). From the weighted logarithmic subtraction between Fig. 2 (a) and Fig. 3 (a), we could obtain the bone-suppressed image as shown in Fig. 3 (b). The quality of the bone-suppressed image is comparable to the ground truth Fig. 2 (c).

Detection of Fusarium verticillioides by PCR-ELISA based on FUM21 gene.

Science.gov (United States)

Omori, Aline Myuki; Ono, Elisabete Yurie Sataque; Bordini, Jaqueline Gozzi; Hirozawa, Melissa Tiemi; Fungaro, Maria Helena Pelegrinelli; Ono, Mario Augusto

2018-08-01

Fusarium verticillioides is a primary corn pathogen and fumonisin producer which is associated with toxic effects in humans and animals. The traditional methods for detection of fungal contamination based on morphological characteristics are time-consuming and show low sensitivity and specificity. Therefore, the objective of this study was to develop a PCR-ELISA based on the FUM21 gene for F. verticillioides detection. The DNA of the F. verticillioides, Fusarium sp., Aspergillus sp. and Penicillium sp. isolates was analyzed by conventional PCR and PCR-ELISA to determine the specificity. The PCR-ELISA was specific to F. verticillioides isolates, showed a 2.5 pg detection limit and was 100-fold more sensitive than conventional PCR. In corn samples inoculated with F. verticillioides conidia, the detection limit of the PCR-ELISA was 1 × 10 4 conidia/g and was also 100-fold more sensitive than conventional PCR. Naturally contaminated corn samples were analyzed by PCR-ELISA based on the FUM21 gene and PCR-ELISA absorbance values correlated positively (p PCR-ELISA developed in this study can be useful for F. verticillioides detection in corn samples. Copyright © 2018 Elsevier Ltd. All rights reserved.

Development of a strain-specific real-time PCR assay for enumeration of a probiotic Lactobacillus reuteri in chicken feed and intestine.

Directory of Open Access Journals (Sweden)

Verity Ann Sattler

Full Text Available A strain-specific real-time PCR assay was developed for quantification of a probiotic Lactobacillus reuteri (DSM 16350 in poultry feed and intestine. The specific primers were designed based on a genomic sequence of the strain derived from suppression subtractive hybridization with the type strain L. reuteri DSM 20016. Specificity was tested using a set of non-target strains from several sources. Applicability of the real-time PCR assay was evaluated in a controlled broiler feeding trial by using standard curves specific for feed and intestinal matrices. The amount of the probiotic L. reuteri was determined in feed from three feeding phases and in intestinal samples of the jejunum, ileum, and caecum of three, 14, and 39 day old birds. L. reuteri DSM 16350 cells were enumerated in all feeds supplemented with the probiotic close to the inclusion rate of 7.0 × 10(3 cfu/g, however, were not detected in L. reuteri DSM 16350 free feed. In three day old birds L. reuteri DSM 16350 was only detected in intestinal samples from probiotic fed animals ranging from 8.2 ± 7.8 × 10(5 cfu/g in the jejunum, 1.0 ± 1.1×10(7 cfu/g in the ileum, and 2.5 ± 5.7 × 10(5 cfu/g in the caecum. Similar results were obtained for intestinal samples of older birds (14 and 39 days. With increasing age of the animals the amount of L. reuteri signals in the control animals, however, also increased, indicating the appearance of highly similar bacterial genomes in the gut microbiota. The L. reuteri DSM 16350 qPCR assay could be used in future for feeding trials to assure the accurate inclusion of the supplement to the feed and to monitor it's uptake into the GIT of young chicken.

Development of a strain-specific real-time PCR assay for enumeration of a probiotic Lactobacillus reuteri in chicken feed and intestine.

Science.gov (United States)

Sattler, Verity Ann; Mohnl, Michaela; Klose, Viviana

2014-01-01

A strain-specific real-time PCR assay was developed for quantification of a probiotic Lactobacillus reuteri (DSM 16350) in poultry feed and intestine. The specific primers were designed based on a genomic sequence of the strain derived from suppression subtractive hybridization with the type strain L. reuteri DSM 20016. Specificity was tested using a set of non-target strains from several sources. Applicability of the real-time PCR assay was evaluated in a controlled broiler feeding trial by using standard curves specific for feed and intestinal matrices. The amount of the probiotic L. reuteri was determined in feed from three feeding phases and in intestinal samples of the jejunum, ileum, and caecum of three, 14, and 39 day old birds. L. reuteri DSM 16350 cells were enumerated in all feeds supplemented with the probiotic close to the inclusion rate of 7.0 × 10(3) cfu/g, however, were not detected in L. reuteri DSM 16350 free feed. In three day old birds L. reuteri DSM 16350 was only detected in intestinal samples from probiotic fed animals ranging from 8.2 ± 7.8 × 10(5) cfu/g in the jejunum, 1.0 ± 1.1×10(7) cfu/g in the ileum, and 2.5 ± 5.7 × 10(5) cfu/g in the caecum. Similar results were obtained for intestinal samples of older birds (14 and 39 days). With increasing age of the animals the amount of L. reuteri signals in the control animals, however, also increased, indicating the appearance of highly similar bacterial genomes in the gut microbiota. The L. reuteri DSM 16350 qPCR assay could be used in future for feeding trials to assure the accurate inclusion of the supplement to the feed and to monitor it's uptake into the GIT of young chicken.

Updates to Constituent Subtraction in Heavy Ions at CMS

CERN Document Server

CMS Collaboration

2018-01-01

The latest upgrades and performance of constituent subtraction in 5.02 TeV PbPb collisions is presented. The constituent subtraction is extended through the full tracker acceptance, increasing the rapidity reach of correctly subtracted jets. A modulation in azimuthal angle is added to the subtraction, accounting for flow on an event-by-event basis and improving jet energy resolution. Closure of jet energy scale after corrections and jet energy resolution is shown for R=0.4 and R=0.8 jets, the latter for the first time in CMS Heavy-Ions.

Shape based kinetic outlier detection in real-time PCR

Directory of Open Access Journals (Sweden)

D'Atri Mario

2010-04-01

Full Text Available Abstract Background Real-time PCR has recently become the technique of choice for absolute and relative nucleic acid quantification. The gold standard quantification method in real-time PCR assumes that the compared samples have similar PCR efficiency. However, many factors present in biological samples affect PCR kinetic, confounding quantification analysis. In this work we propose a new strategy to detect outlier samples, called SOD. Results Richards function was fitted on fluorescence readings to parameterize the amplification curves. There was not a significant correlation between calculated amplification parameters (plateau, slope and y-coordinate of the inflection point and the Log of input DNA demonstrating that this approach can be used to achieve a "fingerprint" for each amplification curve. To identify the outlier runs, the calculated parameters of each unknown sample were compared to those of the standard samples. When a significant underestimation of starting DNA molecules was found, due to the presence of biological inhibitors such as tannic acid, IgG or quercitin, SOD efficiently marked these amplification profiles as outliers. SOD was subsequently compared with KOD, the current approach based on PCR efficiency estimation. The data obtained showed that SOD was more sensitive than KOD, whereas SOD and KOD were equally specific. Conclusion Our results demonstrated, for the first time, that outlier detection can be based on amplification shape instead of PCR efficiency. SOD represents an improvement in real-time PCR analysis because it decreases the variance of data thus increasing the reliability of quantification.

Subtracting and Fitting Histograms using Profile Likelihood

CERN Document Server

D'Almeida, F M L

2008-01-01

It is known that many interesting signals expected at LHC are of unknown shape and strongly contaminated by background events. These signals will be dif cult to detect during the rst years of LHC operation due to the initial low luminosity. In this work, one presents a method of subtracting histograms based on the pro le likelihood function when the background is previously estimated by Monte Carlo events and one has low statistics. Estimators for the signal in each bin of the histogram difference are calculated so as limits for the signals with 68.3% of Con dence Level in a low statistics case when one has a exponential background and a Gaussian signal. The method can also be used to t histograms when the signal shape is known. Our results show a good performance and avoid the problem of negative values when subtracting histograms.

Regulation of gene expression by low levels of ultraviolet-B radiation in Pisum sativum: Isolation of novel genes by suppression subtractive hybridisation

International Nuclear Information System (INIS)

Sävenstrand, H.; Brosché, M.; Strid, A.

2002-01-01

Suppression subtractive hybridisation was used to isolate genes differentially regulated by low levels (UV-B BE,300 0.13 W m -2 ) of ultraviolet-B radiation (UV-B; 290–320 nm) in Pisum sativum. Six genes were regulated, two of which were novel. The mRNA levels for these two (PsTSDC and PsUOS1) were increased and depressed by UV-B treatment, respectively. Domains in the PsTSDC translation product was similar to TIR (Toll-Interleukin-1 receptor-similar) domains and a NB-ARC domain (nucleotide-binding domain in APAF-1, R gene products and CED-4). The PsUOS1 translation product was similar to an open reading frame in Arabidopsis. Genes encoding embryo-abundant protein (PsEMB) and S-adenosyl-l-methionine synthase (PsSAMS) were induced by UV-B, whereas the transcript levels for genes encoding sucrose transport protein (PsSUT) or ribulose-5-phosphate 3-epimerase (PsR5P3E) were decreased. These regulation patterns are novel, and the PsEMB and PsR5P3E sequences are reported for the first time. The stress-specificity of regulation of these genes were tested by ozone fumigation (100 ppb O 3 ). Qualitatively, the similarity of expression after both UV-B and ozone exposure suggests that, for these genes, similar stress-response pathways are in action. (author)

Parallel decompositions of Mueller matrices and polarimetric subtraction

Directory of Open Access Journals (Sweden)

Gil J.J.

2010-06-01

Full Text Available From a general formulation of the physically realizable parallel decompositions of the Mueller matrix M of a given depolarizing system, a procedure for determining the set of pure Mueller matrices susceptible to be subtracted from M is presented. This procedure provides a way to check if a given pure Mueller matrix N can be subtracted from M or not. If this check is positive, the value of the relative cross section of the subtracted component is also determined.

3D temporal subtraction on multislice CT images using nonlinear warping technique

Science.gov (United States)

Ishida, Takayuki; Katsuragawa, Shigehiko; Kawashita, Ikuo; Kim, Hyounseop; Itai, Yoshinori; Awai, Kazuo; Li, Qiang; Doi, Kunio

2007-03-01

The detection of very subtle lesions and/or lesions overlapped with vessels on CT images is a time consuming and difficult task for radiologists. In this study, we have developed a 3D temporal subtraction method to enhance interval changes between previous and current multislice CT images based on a nonlinear image warping technique. Our method provides a subtraction CT image which is obtained by subtraction of a previous CT image from a current CT image. Reduction of misregistration artifacts is important in the temporal subtraction method. Therefore, our computerized method includes global and local image matching techniques for accurate registration of current and previous CT images. For global image matching, we selected the corresponding previous section image for each current section image by using 2D cross-correlation between a blurred low-resolution current CT image and a blurred previous CT image. For local image matching, we applied the 3D template matching technique with translation and rotation of volumes of interests (VOIs) which were selected in the current and the previous CT images. The local shift vector for each VOI pair was determined when the cross-correlation value became the maximum in the 3D template matching. The local shift vectors at all voxels were determined by interpolation of shift vectors of VOIs, and then the previous CT image was nonlinearly warped according to the shift vector for each voxel. Finally, the warped previous CT image was subtracted from the current CT image. The 3D temporal subtraction method was applied to 19 clinical cases. The normal background structures such as vessels, ribs, and heart were removed without large misregistration artifacts. Thus, interval changes due to lung diseases were clearly enhanced as white shadows on subtraction CT images.

Dual-energy subtraction radiography of the breast

International Nuclear Information System (INIS)

Asaga, Taro; Masuzawa, Chihiro; Kawahara, Satoru; Motohashi, Hisahiko; Okamoto, Takashi; Tamura, Nobuo

1988-01-01

Dual-energy projection radiography was applied to breast examination. To perform the dual-energy subtraction radiography using a digital radiography unit, high and low-energy exposures were made at an appropriate time interval under differing X-ray exposure conditions. Dual-energy subtraction radiography was performed in 41 cancer patients in whom the tumor shadow was equivocal or the border of cancer infiltration was not clearly demonstrated by compression mammography, and 15 patients with benign diseases such as fibrocystic disease, cyst and fibroadenoma. In 21 cases out of the 41 cancer patients, the dual-energy subtraction radiography clearly visualized the malignant tumor shadows and the border of cancer infiltration and the daughter nodules by removing the shadows of normal mammary gland. On the other hand, beign diseases such as fibrocystic disease and cyst could be diagnosed as such, because the tumor shadow and the irregularly concentrated image of mammary gland disappeared by the dual-energy subtraction. These results suggest that this new technique will be useful in examination of breast masses. (author)

Dual-energy subtraction radiography of the breast

Energy Technology Data Exchange (ETDEWEB)

Asaga, Taro; Masuzawa, Chihiro; Kawahara, Satoru; Motohashi, Hisahiko; Okamoto, Takashi; Tamura, Nobuo

1988-06-01

Dual-energy projection radiography was applied to breast examination. To perform the dual-energy subtraction radiography using a digital radiography unit, high and low-energy exposures were made at an appropriate time interval under differing X-ray exposure conditions. Dual-energy subtraction radiography was performed in 41 cancer patients in whom the tumor shadow was equivocal or the border of cancer infiltration was not clearly demonstrated by compression mammography, and 15 patients with benign diseases such as fibrocystic disease, cyst and fibroadenoma. In 21 cases out of the 41 cancer patients, the dual-energy subtraction radiography clearly visualized the malignant tumor shadows and the border of cancer infiltration and the daughter nodules by removing the shadows of normal mammary gland. On the other hand, beign diseases such as fibrocystic disease and cyst could be diagnosed as such, because the tumor shadow and the irregularly concentrated image of mammary gland disappeared by the dual-energy subtraction. These results suggest that this new technique will be useful in examination of breast masses.

Digital subtraction angiography

International Nuclear Information System (INIS)

Neuwirth, J. Jr.; Bohutova, J.

1987-01-01

The quality of radiodiagnostic methods to a great extent depends on the quality of the resulting image. The basic technical principles are summed up of the different parts of digital subtraction angiography apparatus and of methods of improving the image. The instrument is based on a videochain consisting of an X-ray tube, an intensifier of the radiographic image, optical parts, a video camera, an analog-to-digital converter and a computer. The main advantage of the digitally processed image is the possibility of optimizing the image into a form which will contain the biggest amount of diagnostically valuable information. Described are the mathematical operations for improving the digital image: spatial filtration, pixel shift, time filtration, image integration, time interval differentation and matched filtering. (M.D.). 8 refs., 3 figs

Digital subtraction angiography system evaluation with phantoms

International Nuclear Information System (INIS)

Wenstrup, R.S.; Sweeney, K.P.; Scholz, F.J.

1985-01-01

Advances in digital subtraction angiography imaging demonstrate the need for critical evaluation of the performance of digital subtraction equipment. The design of a phantom set for noninvasive assessment of the imaging quality of digital subtraction equipment is described; components include a remotely controlled transport system and individual patterns to evaluate the contrast and detail properties of the image intensifier, low-contrast sensitivity and resolution of the system, geometric distortion of image, linearity, mechanical and electronic stability of equipment, and effects of bone and bowel gas on iodine perception. The performance of an add-on digital radiographic system is presented, along with radiation exposure levels at the image intensifier for a range of radiographic techniques

Motion subtraction of the larynx using digital radiography

International Nuclear Information System (INIS)

Kumakawa, Kohzoh; Miyakawa, Kouichi

1990-01-01

The development of digital radiography (DR) has made it possible to analyze the contour of the laryngeal soft tissue structures in more detail than the conventional screen-film method. The authors first used the DR system for time subtraction of the larynx during inspiration and phonation. The images are acquired by means of frontal tomography of the larynx using the imaging plate during inspiration and phonation separately, and stored into the memory of the DR system. The thickness of the slices is 5.0 mm. Time subtraction between the mask image during inspiration and the live image during phonation is performed using digital processing on CRT. Superimposing the two images at the upper trachea and the thyroid cartilage of the same depth, makes it possible to measure movement of the vocal cord and false vocal cord quantitatively in three dimensions. The authors named this time subtraction as motion subtraction of the larynx. This motion subtraction image can be obtained by on-line digital processing without complicated development technique, but has so high spatial resolution. This image processing seems to be useful in functional radiographic analysis of laryngeal diseases. (author)

Digital subtraction cerebral angiography by intraarterial injection: comparison with conventional angiography

International Nuclear Information System (INIS)

Brant-Zawadzki, M.; Gould, R.; Norman, D.; Newton, T.H.; Lane, B.

1983-01-01

For 4 months, a prototype digital subtraction system was used to obtain images of the cerebral vasculature after intraarterial contrast injections. In 12 instances, the intraarterial injections were recorded with both a digital subtraction unit and conventional direct magnification film-screen system. The digital subtraction and conventional film subtraction images were compared and graded for quality and information content by three skilled observers. In addition, quantitative measurements of contrast-detail performance and spatial resolution were obtained on both the digital system and the screen-film imaging chain. In a clinical setting, both the digital subtraction and conventional film-screen systems provided similar quality images and angiographic information. Contrast-detail curves demonstrated that digital subtraction angiography outperformed conventional film technique for low-contrast objects. Digital subtraction angiography also reduced the time required to obtain the angiogram, markedly reduced film cost, and lowered the contrast agent burden

Development of digital subtraction system DAR-1200

International Nuclear Information System (INIS)

Kawai, Masumi; Shimizu, Yasumitsu; Ozaki, Takeshi; Sawada, Hiroshi; Uzuyama, Kazuhiro; Nishioka, Hiroyuki

1989-01-01

Digital subtraction angiography (DSA) has been of widespread use clinically, and it has attracted considerable attention in angiographic examination today. The merits of Shimadzu high resolution digital subtraction system DAR-1200 are reported in this paper. Furthermore, the principle and clinical usefullness of a new method of DSA called the Peak-Hold DSA are explained especially in details. (author)

Introduction to the principles of Digital Subtraction Angiography (DSA)

Energy Technology Data Exchange (ETDEWEB)

Kaplanis, P [Medical Physics Department, Nicosia General Hospital, Nicosia (Cyprus)

1998-12-31

Medical applications of advanced technology have rapidly become more sophisticated and more widespread. The field of diagnostic imaging is by no means an exception. There has been a number of breathtaking developments in the field of medical imaging in recent years. Today higher quality, greater clarity and more minute precision are considered not advantages but necessities. Hence new developments are concentrated in the data acquisition and image processing based on the microprocessor controlled modules interfaced with state of the art radiological imaging equipment. One such development is the subtraction of x-rays vis a computer for better visualization of blood vessels, cavities of the heart and of the coronary and pulmonary vascular system. This procedure is termed Digital Subtraction Angiography (DSA). (author). 5 refs, 3 figs.

Introduction to the principles of Digital Subtraction Angiography (DSA)

International Nuclear Information System (INIS)

Kaplanis, P.

1997-01-01

Medical applications of advanced technology have rapidly become more sophisticated and more widespread. The field of diagnostic imaging is by no means an exception. There has been a number of breathtaking developments in the field of medical imaging in recent years. Today higher quality, greater clarity and more minute precision are considered not advantages but necessities. Hence new developments are concentrated in the data acquisition and image processing based on the microprocessor controlled modules interfaced with state of the art radiological imaging equipment. One such development is the subtraction of x-rays vis a computer for better visualization of blood vessels, cavities of the heart and of the coronary and pulmonary vascular system. This procedure is termed Digital Subtraction Angiography (DSA). (author)

Rapid diagnosis of sepsis with TaqMan-Based multiplex real-time PCR.

Science.gov (United States)

Liu, Chang-Feng; Shi, Xin-Ping; Chen, Yun; Jin, Ye; Zhang, Bing

2018-02-01

The survival rate of septic patients mainly depends on a rapid and reliable diagnosis. A rapid, broad range, specific and sensitive quantitative diagnostic test is the urgent need. Thus, we developed a TaqMan-Based Multiplex real-time PCR assays to identify bloodstream pathogens within a few hours. Primers and TaqMan probes were designed to be complementary to conserved regions in the 16S rDNA gene of different kinds of bacteria. To evaluate accurately, sensitively, and specifically, the known bacteria samples (Standard strains, whole blood samples) are determined by TaqMan-Based Multiplex real-time PCR. In addition, 30 blood samples taken from patients with clinical symptoms of sepsis were tested by TaqMan-Based Multiplex real-time PCR and blood culture. The mean frequency of positive for Multiplex real-time PCR was 96% at a concentration of 100 CFU/mL, and it was 100% at a concentration greater than 1000 CFU/mL. All the known blood samples and Standard strains were detected positively by TaqMan-Based Multiplex PCR, no PCR products were detected when DNAs from other bacterium were used in the multiplex assay. Among the 30 patients with clinical symptoms of sepsis, 18 patients were confirmed positive by Multiplex real-time PCR and seven patients were confirmed positive by blood culture. TaqMan-Based Multiplex real-time PCR assay with highly sensitivity, specificity and broad detection range, is a rapid and accurate method in the detection of bacterial pathogens of sepsis and should have a promising usage in the diagnosis of sepsis. © 2017 Wiley Periodicals, Inc.

Physiological and Molecular Analysis of Aluminium-Induced Organic Acid Anion Secretion from Grain Amaranth (Amaranthus hypochondriacus L.) Roots

OpenAIRE

Fan, Wei; Xu, Jia-Meng; Lou, He-Qiang; Xiao, Chuan; Chen, Wei-Wei; Yang, Jian-Li

2016-01-01

Grain amaranth (Amaranthus hypochondriacus L.) is abundant in oxalate and can secrete oxalate under aluminium (Al) stress. However, the features of Al-induced secretion of organic acid anions (OA) and potential genes responsible for OA secretion are poorly understood. Here, Al-induced OA secretion in grain amaranth roots was characterized by ion charomatography and enzymology methods, and suppression subtractive hybridization (SSH) together with quantitative real-time PCR (qRT-PCR) was used t...

Sky Subtraction with Fiber-Fed Spectrograph

Science.gov (United States)

Rodrigues, Myriam

2017-09-01

"Historically, fiber-fed spectrographs had been deemed inadequate for the observation of faint targets, mainly because of the difficulty to achieve high accuracy on the sky subtraction. The impossibility to sample the sky in the immediate vicinity of the target in fiber instruments has led to a commonly held view that a multi-object fibre spectrograph cannot achieve an accurate sky subtraction under 1% contrary to their slit counterpart. The next generation of multi-objects spectrograph at the VLT (MOONS) and the planed MOS for the E-ELT (MOSAIC) are fiber-fed instruments, and are aimed to observed targets fainter than the sky continuum level. In this talk, I will present the state-of-art on sky subtraction strategies and data reduction algorithm specifically developed for fiber-fed spectrographs. I will also present the main results of an observational campaign to better characterise the sky spatial and temporal variations ( in particular the continuum and faint sky lines)."

[Affine transformation-based automatic registration for peripheral digital subtraction angiography (DSA)].

Science.gov (United States)

Kong, Gang; Dai, Dao-Qing; Zou, Lu-Min

2008-07-01

In order to remove the artifacts of peripheral digital subtraction angiography (DSA), an affine transformation-based automatic image registration algorithm is introduced here. The whole process is described as follows: First, rectangle feature templates are constructed with their centers of the extracted Harris corners in the mask, and motion vectors of the central feature points are estimated using template matching technology with the similarity measure of maximum histogram energy. And then the optimal parameters of the affine transformation are calculated with the matrix singular value decomposition (SVD) method. Finally, bilinear intensity interpolation is taken to the mask according to the specific affine transformation. More than 30 peripheral DSA registrations are performed with the presented algorithm, and as the result, moving artifacts of the images are removed with sub-pixel precision, and the time consumption is less enough to satisfy the clinical requirements. Experimental results show the efficiency and robustness of the algorithm.

Tomography of photon-added and photon-subtracted states

NARCIS (Netherlands)

Bazrafkan, MR; Man'ko, [No Value

The purpose of this paper is to introduce symplectic and optical tomograms of photon-added and photon-subtracted quantum states. Explicit relations for the tomograms of photon-added and photon-subtracted squeezed coherent states and squeezed number states are obtained. Generating functions for the

Expression of immune-response genes in lepidopteran host is suppressed by venom from an endoparasitoid, Pteromalus puparum

Directory of Open Access Journals (Sweden)

Fang Qi

2010-09-01

Full Text Available Abstract Background The relationships between parasitoids and their insect hosts have attracted attention at two levels. First, the basic biology of host-parasitoid interactions is of fundamental interest. Second, parasitoids are widely used as biological control agents in sustainable agricultural programs. Females of the gregarious endoparasitoid Pteromalus puparum (Hymenoptera: Pteromalidae inject venom along with eggs into their hosts. P. puparum does not inject polydnaviruses during oviposition. For this reason, P. puparum and its pupal host, the small white butterfly Pieris rapae (Lepidoptera: Pieridae, comprise an excellent model system for studying the influence of an endoparasitoid venom on the biology of the pupal host. P. puparum venom suppresses the immunity of its host, although the suppressive mechanisms are not fully understood. In this study, we tested our hypothesis that P. puparum venom influences host gene expression in the two main immunity-conferring tissues, hemocytes and fat body. Results At 1 h post-venom injection, we recorded significant decreases in transcript levels of 217 EST clones (revealing 113 genes identified in silico, including 62 unknown contigs derived from forward subtractive libraries of host hemocytes and in transcript levels of 288 EST clones (221 genes identified in silico, including 123 unknown contigs from libraries of host fat body. These genes are related to insect immune response, cytoskeleton, cell cycle and apoptosis, metabolism, transport, stress response and transcriptional and translational regulation. We verified the reliability of the suppression subtractive hybridization (SSH data with semi-quantitative RT-PCR analysis of a set of randomly selected genes. This analysis showed that most of the selected genes were down-regulated after venom injection. Conclusions Our findings support our hypothesis that P. puparum venom influences gene expression in host hemocytes and fat body. Specifically

Higgs boson production in association with a jet using jettiness subtraction

Directory of Open Access Journals (Sweden)

Radja Boughezal

2015-09-01

Full Text Available We use the recently proposed jettiness-subtraction scheme to provide the complete calculation of Higgs boson production in association with a jet in hadronic collisions through next-to-next-to-leading order in perturbative QCD. This method exploits the observation that the N-jettiness event-shape variable completely describes the singularity structure of QCD when final-state colored particles are present. Our results are in agreement with a recent computation of the gg and qg partonic initial states based on sector-improved residue subtraction. We present phenomenological results for both fiducial cross sections and distributions at the LHC.

A web-based adaptive tutor to teach PCR primer design

NARCIS (Netherlands)

van Seters, Janneke R.; Wellink, Joan; Tramper, Johannes; Goedhart, Martin J.; Ossevoort, Miriam A.

2012-01-01

When students have varying prior knowledge, personalized instruction is desirable. One way to personalize instruction is by using adaptive e-learning to offer training of varying complexity. In this study, we developed a web-based adaptive tutor to teach PCR primer design: the PCR Tutor. We used

A Web-based Adaptive Tutor to Teach PCR Primer Design

NARCIS (Netherlands)

Seters, van J.R.; Wellink, J.; Tramper, J.; Goedhart, M.J.; Ossevoort, M.A.

2012-01-01

When students have varying prior knowledge, personalized instruction is desirable. One way to personalize instruction is by using adaptive e-learning to offer training of varying complexity. In this study, we developed a web-based adaptive tutor to teach PCR primer design: the PCR Tutor. We used

Digital subtraction angiography in patients with central vertigo

International Nuclear Information System (INIS)

Inamori, Toru; Takayasu, Yukio; Umetani, Yoshio; Taruoka, Akinori.

1985-01-01

Digital subtraction angiography (DSA) is a recently developed non-invasive intravenous angiography which has become possible through real time digital subtraction of x-ray transmission data from an image intensifier and television system. The output signals of the image intensifier-television camera system are digitized by an analog-digital converter. The digital information, 512x512 pixels and 9 bits deep, is fed into the image processing assembly after logarithmic amplification, where 2-8 frames are added and subtracted from mask images for the final digital images. Intravenous digital subtraction angiography was performed in 21 patients with intractable dizzy spells of central origin resistant to treatment. These patients showed some signs of CNS disturbance, although there were no significant findings on CT scans. Surprisingly, findings were abnormal in 14 of 21 patients (66.7%). DSA is, therefore, considered to be an important aid in the diagnosis of vertigo of the central type. (J.P.N.)

Clinical utility of Gd-DTPA subtraction MR imaging for spinal bone metastasis

International Nuclear Information System (INIS)

Ando, Keiichi; Murakami, Masao; Kuroda, Yasumasa

1993-01-01

Based on reports that Gd-DTPA contributes to the detection of tumors, we used it in 31 cases (97 lesions) of spinal bone metastases. The result was that Gd-DTPA increased the intensity of tumors and the surrounding bone marrow to almost the same level in 53%. To show the metastases clearly, an existing subtraction command system was utilized. The technique included the pixel-by-pixel method, to obtain a Gd-DTPA T1-weighted image (T1WI) subtracted by the original T1WI. The detectability of the subtraction image was improved up to 96%, but was less than the original T1WI (99%). Because of the different imaging rationale between two methods, a means to assess the quality of diagnosis must be proposed. To check the normal background, the same kind of postprocessing was performed in 21 patients without malignancy. Gd-DTPA prefusion was highest in the paravertebral veins, moderate in muscles and epidural fat, and lowest in the spinal cord, intervertebral disk and bone cortex. Gd-DTPA enhanced subtraction MR imaging provides a new diagnostic tool to detect and to assess bone metastasis. (author)

Development of a Single-Step Subtraction Method for Eukaryotic 18S and 28S Ribonucleic Acids

Directory of Open Access Journals (Sweden)

Marie J. Archer

2011-01-01

Full Text Available The abundance of mammalian 18S and 28S ribosomal RNA can decrease the detection sensitivity of bacterial or viral targets in complex host-pathogen mixtures. A method to capture human RNA in a single step was developed and characterized to address this issue. For this purpose, capture probes were covalently attached to magnetic microbeads using a dendrimer linker and the solid phase was tested using rat thymus RNA (mammalian components with Escherichia coli RNA (bacterial target as a model system. Our results indicated that random capture probes demonstrated better performance than specific ones presumably by increasing the number of possible binding sites, and the use of a tetrame-thylammonium-chloride (TMA-Cl- based buffer for the hybridization showed a beneficial effect in the selectivity. The subtraction efficiency determined through real-time RT-PCR revealed capture-efficiencies comparable with commercially available enrichment kits. The performance of the solid phase can be further fine tuned by modifying the annealing time and temperature.

Model Checking Timed Automata with Priorities using DBM Subtraction

DEFF Research Database (Denmark)

David, Alexandre; Larsen, Kim Guldstrand; Pettersson, Paul

2006-01-01

In this paper we describe an extension of timed automata with priorities, and efficient algorithms to compute subtraction on DBMs (difference bounded matrices), needed in symbolic model-checking of timed automata with priorities. The subtraction is one of the few operations on DBMs that result...... in a non-convex set needing sets of DBMs for representation. Our subtraction algorithms are efficient in the sense that the number of generated DBMs is significantly reduced compared to a naive algorithm. The overhead in time is compensated by the gain from reducing the number of resulting DBMs since...... this number affects the performance of symbolic model-checking. The uses of the DBM subtraction operation extend beyond timed automata with priorities. It is also useful for allowing guards on transitions with urgent actions, deadlock checking, and timed games....

Evaluation of the minimum iodine concentration for contrast-enhanced subtraction mammography

International Nuclear Information System (INIS)

Baldelli, P; Bravin, A; Maggio, C Di; Gennaro, G; Sarnelli, A; Taibi, A; Gambaccini, M

2006-01-01

Early manifestation of breast cancer is often very subtle and is displayed in a complex and variable pattern of normal anatomy that may obscure the disease. The use of dual-energy techniques, that can remove the structural noise, and contrast media, that enhance the region surrounding the tumour, could help us to improve the detectability of the lesions. The aim of this work is to investigate the use of an iodine-based contrast medium in mammography with two different double exposure techniques: K-edge subtraction mammography and temporal subtraction mammography. Both techniques have been investigated by using an ideal source, like monochromatic beams produced at a synchrotron radiation facility and a clinical digital mammography system. A dedicated three-component phantom containing cavities filled with different iodine concentrations has been developed and used for measurements. For each technique, information about the minimum iodine concentration, which provides a significant enhancement of the detectability of the pathology by minimizing the risk due to high dose and high concentration of contrast medium, has been obtained. In particular, for cavities of 5 and 8 mm in diameter filled with iodine solutions, the minimum concentration needed to obtain a contrast-to-noise ratio of 5 with a mean glandular dose of 2 mGy has been calculated. The minimum concentrations estimated with monochromatic beams and K-edge subtraction mammography are 0.9 mg ml -1 and 1.34 mg ml -1 for the biggest and smallest details, respectively, while for temporal subtraction mammography they are 0.84 mg ml -1 and 1.31 mg ml -1 . With the conventional clinical system the minimum concentrations for the K-edge subtraction mammography are 4.13 mg ml -1 (8 mm diameter) and 5.75 mg ml -1 (5 mm diameter), while for the temporal subtraction mammography they are 1.01 mg ml -1 (8 mm diameter) and 1.57 mg ml -1 (5 mm diameter)

A multiple regression analysis for accurate background subtraction in 99Tcm-DTPA renography

International Nuclear Information System (INIS)

Middleton, G.W.; Thomson, W.H.; Davies, I.H.; Morgan, A.

1989-01-01

A technique for accurate background subtraction in 99 Tc m -DTPA renography is described. The technique is based on a multiple regression analysis of the renal curves and separate heart and soft tissue curves which together represent background activity. It is compared, in over 100 renograms, with a previously described linear regression technique. Results show that the method provides accurate background subtraction, even in very poorly functioning kidneys, thus enabling relative renal filtration and excretion to be accurately estimated. (author)

A PCR-Based Method to Construct Lentiviral Vector Expressing Double Tough Decoy for miRNA Inhibition.

Directory of Open Access Journals (Sweden)

Huiling Qiu

Full Text Available DNA vector-encoded Tough Decoy (TuD miRNA inhibitor is attracting increased attention due to its high efficiency in miRNA suppression. The current methods used to construct TuD vectors are based on synthesizing long oligonucleotides (~90 mer, which have been costly and problematic because of mutations during synthesis. In this study, we report a PCR-based method for the generation of double Tough Decoy (dTuD vector in which only two sets of shorter oligonucleotides (< 60 mer were used. Different approaches were employed to test the inhibitory potency of dTuDs. We demonstrated that dTuD is the most efficient method in miRNA inhibition in vitro and in vivo. Using this method, a mini dTuD library against 88 human miRNAs was constructed and used for a high-throughput screening (HTS of AP-1 pathway-related miRNAs. Seven miRNAs (miR-18b-5p, -101-3p, -148b-3p, -130b-3p, -186-3p, -187-3p and -1324 were identified as candidates involved in AP-1 pathway regulation. This novel method allows for an accurate and cost-effective generation of dTuD miRNA inhibitor, providing a powerful tool for efficient miRNA suppression in vitro and in vivo.

A Web-Based Adaptive Tutor to Teach PCR Primer Design

Science.gov (United States)

van Seters, Janneke R.; Wellink, Joan; Tramper, Johannes; Goedhart, Martin J.; Ossevoort, Miriam A.

2012-01-01

When students have varying prior knowledge, personalized instruction is desirable. One way to personalize instruction is by using adaptive e-learning to offer training of varying complexity. In this study, we developed a web-based adaptive tutor to teach PCR primer design: the PCR Tutor. We used part of the Taxonomy of Educational Objectives (the…

Immunomagnetic nanoparticle based quantitative PCR for rapid detection of Salmonella

International Nuclear Information System (INIS)

Bakthavathsalam, Padmavathy; Rajendran, Vinoth Kumar; Saran, Uttara; Chatterjee, Suvro; Ali, Baquir Mohammed Jaffar

2013-01-01

We have developed a rapid and sensitive method for immunomagnetic separation (IMS) of Salmonella along with their real time detection via PCR. Silica-coated magnetic nanoparticles were functionalized with carboxy groups to which anti-Salmonella antibody raised against heat-inactivated whole cells of Salmonella were covalently attached. The immuno-captured target cells were detected in beverages like milk and lemon juice by multiplex PCR and real time PCR with a detection limit of 10 4 cfu.mL −1 and 10 3 cfu.mL −1 , respectively. We demonstrate that IMS can be used for selective concentration of target bacteria from beverages for subsequent use in PCR detection. PCR also enables differentiation of Salmonella typhi and Salmonella paratyphi A using a set of four specific primers. In addition, IMS—PCR can be used as a screening tool in the food and beverage industry for the detection of Salmonella within 3–4 h which compares favorably to the time of several days that is needed in case of conventional detection based on culture and biochemical methods. (author)

Inter-plane artifact suppression in tomosynthesis using 3D CT image data

Directory of Open Access Journals (Sweden)

Kim Jae G

2011-12-01

Full Text Available Abstract Background Despite its superb lateral resolution, flat-panel-detector (FPD based tomosynthesis suffers from low contrast and inter-plane artifacts caused by incomplete cancellation of the projection components stemming from outside the focal plane. The incomplete cancellation of the projection components, mostly due to the limited scan angle in the conventional tomosynthesis scan geometry, often makes the image contrast too low to differentiate the malignant tissues from the background tissues with confidence. Methods In this paper, we propose a new method to suppress the inter-plane artifacts in FPD-based tomosynthesis. If 3D whole volume CT images are available before the tomosynthesis scan, the CT image data can be incorporated into the tomosynthesis image reconstruction to suppress the inter-plane artifacts, hence, improving the image contrast. In the proposed technique, the projection components stemming from outside the region-of-interest (ROI are subtracted from the measured tomosynthesis projection data to suppress the inter-plane artifacts. The projection components stemming from outside the ROI are calculated from the 3D whole volume CT images which usually have lower lateral resolution than the tomosynthesis images. The tomosynthesis images are reconstructed from the subtracted projection data which account for the x-ray attenuation through the ROI. After verifying the proposed method by simulation, we have performed both CT scan and tomosynthesis scan on a phantom and a sacrificed rat using a FPD-based micro-CT. Results We have measured contrast-to-noise ratio (CNR from the tomosynthesis images which is an indicator of the residual inter-plane artifacts on the focal-plane image. In both cases of the simulation and experimental imaging studies of the contrast evaluating phantom, CNRs have been significantly improved by the proposed method. In the rat imaging also, we have observed better visual contrast from the tomosynthesis

Inter-plane artifact suppression in tomosynthesis using 3D CT image data

Science.gov (United States)

2011-01-01

Background Despite its superb lateral resolution, flat-panel-detector (FPD) based tomosynthesis suffers from low contrast and inter-plane artifacts caused by incomplete cancellation of the projection components stemming from outside the focal plane. The incomplete cancellation of the projection components, mostly due to the limited scan angle in the conventional tomosynthesis scan geometry, often makes the image contrast too low to differentiate the malignant tissues from the background tissues with confidence. Methods In this paper, we propose a new method to suppress the inter-plane artifacts in FPD-based tomosynthesis. If 3D whole volume CT images are available before the tomosynthesis scan, the CT image data can be incorporated into the tomosynthesis image reconstruction to suppress the inter-plane artifacts, hence, improving the image contrast. In the proposed technique, the projection components stemming from outside the region-of-interest (ROI) are subtracted from the measured tomosynthesis projection data to suppress the inter-plane artifacts. The projection components stemming from outside the ROI are calculated from the 3D whole volume CT images which usually have lower lateral resolution than the tomosynthesis images. The tomosynthesis images are reconstructed from the subtracted projection data which account for the x-ray attenuation through the ROI. After verifying the proposed method by simulation, we have performed both CT scan and tomosynthesis scan on a phantom and a sacrificed rat using a FPD-based micro-CT. Results We have measured contrast-to-noise ratio (CNR) from the tomosynthesis images which is an indicator of the residual inter-plane artifacts on the focal-plane image. In both cases of the simulation and experimental imaging studies of the contrast evaluating phantom, CNRs have been significantly improved by the proposed method. In the rat imaging also, we have observed better visual contrast from the tomosynthesis images reconstructed by

Four-State Continuous-Variable Quantum Key Distribution with Photon Subtraction

Science.gov (United States)

Li, Fei; Wang, Yijun; Liao, Qin; Guo, Ying

2018-06-01

Four-state continuous-variable quantum key distribution (CVQKD) is one of the discretely modulated CVQKD which generates four nonorthogonal coherent states and exploits the sign of the measured quadrature of each state to encode information rather than uses the quadrature \\hat {x} or \\hat {p} itself. It has been proven that four-state CVQKD is more suitable than Gaussian modulated CVQKD in terms of transmission distance. In this paper, we propose an improved four-state CVQKD using an non-Gaussian operation, photon subtraction. A suitable photon-subtraction operation can be exploited to improve the maximal transmission of CVQKD in point-to-point quantum communication since it provides a method to enhance the performance of entanglement-based (EB) CVQKD. Photon subtraction not only can lengthen the maximal transmission distance by increasing the signal-to-noise rate but also can be easily implemented with existing technologies. Security analysis shows that the proposed scheme can lengthen the maximum transmission distance. Furthermore, by taking finite-size effect into account we obtain a tighter bound of the secure distance, which is more practical than that obtained in the asymptotic limit.

Digital subtraction radiographic evaluation of the standardize periapical intraoral radiographs

International Nuclear Information System (INIS)

Cho, Bong Hae; Nah, Kyung Soo

1993-01-01

The geometrically standardized intraoral radiographs using 5 occlusal registration material were taken serially from immediate, 1 day, 2, 4, 8, 12 and 16 weeks after making the bite blocks. The qualities of those subtracted images were evaluated to check the degree of reproducibility of each impression material. The results were as follows: 1. The standard deviations of the grey scales of the overall subtracted images were 4.9 for Exaflex, 7.2 for Pattern resin, 9.0 for Tooth Shade Acrylic, 12.2 for XCP only, 14.8 for Impregum. 2. The standard deviation of the grey scales of the overall subtracted images were grossly related to those of the localized horizontal line of interest. 3. Exaflex which showed the best subtracted image quality had 15 cases of straight, 14 cases of wave, 1 case of canyon shape. Impregum which showed the worst subtracted image quality had 4 cases of straight, 8 cases of wave, 18 cases of canyon shape respectively.

Detection of adenoviruses in shellfish by means of conventional-PCR, nested-PCR, and integrated cell culture PCR (ICC/PCR).

Science.gov (United States)

Rigotto, C; Sincero, T C M; Simões, C M O; Barardi, C R M

2005-01-01

We tested three PCR based methodologies to detect adenoviruses associated with cultivated oysters. Conventional-PCR, nested-PCR, and integrated cell culture-PCR (ICC/PCR) were first optimized using oysters seeded with know amounts of Adenovirus serotype 5 (Ad5). The maximum sensitivity for Ad5 detection was determined for each method, and then used to detect natural adenovirus contamination in oysters from three aquiculture farms in Florianopolis, Santa Catarina State, Brazil, over a period of 6 months. The results showed that the nested-PCR was more sensitive (limit of detection: 1.2 PFU/g of tissue) than conventional-PCR and ICC-PCR (limit of detection for both: 1.2 x 10(2)PFU/g of tissue) for detection of Ad5 in oyster extracts. Nested-PCR was able to detect 90% of Ad5 contamination in harvested oyster samples, while conventional-PCR was unable to detect Ad5 in any of the samples. The present work suggests that detection of human adenoviruses can be used as a tool to monitor the presence of human viruses in marine environments where shellfish grow, and that nested-PCR is the method of choice.

A common base method for analysis of qPCR data and the application of simple blocking in qPCR experiments.

Science.gov (United States)

Ganger, Michael T; Dietz, Geoffrey D; Ewing, Sarah J

2017-12-01

qPCR has established itself as the technique of choice for the quantification of gene expression. Procedures for conducting qPCR have received significant attention; however, more rigorous approaches to the statistical analysis of qPCR data are needed. Here we develop a mathematical model, termed the Common Base Method, for analysis of qPCR data based on threshold cycle values (C q ) and efficiencies of reactions (E). The Common Base Method keeps all calculations in the logscale as long as possible by working with log 10 (E) ∙ C q , which we call the efficiency-weighted C q value; subsequent statistical analyses are then applied in the logscale. We show how efficiency-weighted C q values may be analyzed using a simple paired or unpaired experimental design and develop blocking methods to help reduce unexplained variation. The Common Base Method has several advantages. It allows for the incorporation of well-specific efficiencies and multiple reference genes. The method does not necessitate the pairing of samples that must be performed using traditional analysis methods in order to calculate relative expression ratios. Our method is also simple enough to be implemented in any spreadsheet or statistical software without additional scripts or proprietary components.

Sequence polymorphism can produce serious artefacts in real-time PCR assays: hard lessons from Pacific oysters

Directory of Open Access Journals (Sweden)

Camara Mark D

2008-05-01

Full Text Available Abstract Background Since it was first described in the mid-1990s, quantitative real time PCR (Q-PCR has been widely used in many fields of biomedical research and molecular diagnostics. This method is routinely used to validate whole transcriptome analyses such as DNA microarrays, suppressive subtractive hybridization (SSH or differential display techniques such as cDNA-AFLP (Amplification Fragment Length Polymorphism. Despite efforts to optimize the methodology, misleading results are still possible, even when standard optimization approaches are followed. Results As part of a larger project aimed at elucidating transcriptome-level responses of Pacific oysters (Crassostrea gigas to various environmental stressors, we used microarrays and cDNA-AFLP to identify Expressed Sequence Tag (EST fragments that are differentially expressed in response to bacterial challenge in two heat shock tolerant and two heat shock sensitive full-sib oyster families. We then designed primers for these differentially expressed ESTs in order to validate the results using Q-PCR. For two of these ESTs we tested fourteen primer pairs each and using standard optimization methods (i.e. melt-curve analysis to ensure amplification of a single product, determined that of the fourteen primer pairs tested, six and nine pairs respectively amplified a single product and were thus acceptable for further testing. However, when we used these primers, we obtained different statistical outcomes among primer pairs, raising unexpected but serious questions about their reliability. We hypothesize that as a consequence of high levels of sequence polymorphism in Pacific oysters, Q-PCR amplification is sub-optimal in some individuals because sequence variants in priming sites results in poor primer binding and amplification in some individuals. This issue is similar to the high frequency of null alleles observed for microsatellite markers in Pacific oysters. Conclusion This study highlights

A proline racemase based PCR for identification of Trypanosoma vivax in cattle blood.

Directory of Open Access Journals (Sweden)

Regassa Fikru

Full Text Available A study was conducted to develop a Trypanosoma vivax (T. vivax specific PCR based on the T. vivax proline racemase (TvPRAC gene. Forward and reverse primers were designed that bind at 764-783 bp and 983-1002 bp of the gene. To assess its specificity, TvPRAC PCR was conducted on DNA extracted from different haemotropic pathogens: T. vivax from Nigeria, Ethiopia and Venezuela, T. congolense Savannah type, T. brucei brucei, T. evansi, T. equiperdum, T. theileri, Theileria parva, Anaplasma marginale, Babesia bovis and Babesia bigemina and from bovine, goat, mouse, camel and human blood. The analytical sensitivity of the TvPRAC PCR was compared with that of the ITS-1 PCR and the 18S PCR-RFLP on a dilution series of T. vivax DNA in water. The diagnostic performance of the three PCRs was compared on 411 Ethiopian bovine blood specimens collected in a former study. TvPRAC PCR proved to be fully specific for T. vivax, irrespective of its geographical origin. Its analytical sensitivity was lower than that of ITS-1 PCR. On these bovine specimens, TvPRAC PCR detected 8.3% T. vivax infections while ITS-1 PCR and 18S PCR-RFLP detected respectively 22.6 and 6.1% T. vivax infections. The study demonstrates that a proline racemase based PCR could be used, preferably in combination with ITS-1 PCR, as a species-specific diagnostic test for T. vivax infections worldwide.

High-throughput screening of suppression subtractive hybridization cDNA libraries using DNA microarray analysis

CSIR Research Space (South Africa)

Van den Berg, N

2004-11-01

Full Text Available Efficient construction of cDNA libraries enriched for differentially expressed transcripts is an important first step in many biological investigations. We present a quantitative procedure for screening cDNA libraries constructed by suppression...

Bruchid egg induced transcript dynamics in developing seeds of black gram (Vigna mungo.

Directory of Open Access Journals (Sweden)

Indrani K Baruah

Full Text Available Black gram (Vigna mungo seeds are a rich source of digestible proteins, however, during storage these seeds are severely damaged by bruchids (Callosobruchus spp., reducing seed quality and yield losses. Most of the cultivated genotypes of black gram are susceptible to bruchids, however, few tolerant genotypes have also been identified but the mechanism of tolerance is poorly understood. We employed Suppression Subtractive Hybridization (SSH to identify specifically, but rarely expressed bruchid egg induced genes in black gram. In this study, Suppression Subtractive Hybridization (SSH library was constructed to study the genes involved in defense response in black gram against bruchid infestation. An EST library of 277 clones was obtained for further analyses. Based on CAP3 assembly, 134 unigenes were computationally annotated using Blast2GOPRO software. In all, 20 defense related genes were subject to quantitative PCR analysis (qPCR out of which 12 genes showed up-regulation in developing seeds of the pods oviposited by bruchids. Few major defense genes like defensin, pathogenesis related protein (PR, lipoxygenase (LOX showed high expression levels in the oviposited population when compared with the non-oviposited plants. This is the first report on defense related gene transcript dynamics during the bruchid-black gram interaction using SSH library. This library would be useful to clone defense related gene(s such as defensin as represented in our library for crop improvement.

A new registration method with voxel-matching technique for temporal subtraction images

Science.gov (United States)

Itai, Yoshinori; Kim, Hyoungseop; Ishikawa, Seiji; Katsuragawa, Shigehiko; Doi, Kunio

2008-03-01

A temporal subtraction image, which is obtained by subtraction of a previous image from a current one, can be used for enhancing interval changes on medical images by removing most of normal structures. One of the important problems in temporal subtraction is that subtraction images commonly include artifacts created by slight differences in the size, shape, and/or location of anatomical structures. In this paper, we developed a new registration method with voxel-matching technique for substantially removing the subtraction artifacts on the temporal subtraction image obtained from multiple-detector computed tomography (MDCT). With this technique, the voxel value in a warped (or non-warped) previous image is replaced by a voxel value within a kernel, such as a small cube centered at a given location, which would be closest (identical or nearly equal) to the voxel value in the corresponding location in the current image. Our new method was examined on 16 clinical cases with MDCT images. Preliminary results indicated that interval changes on the subtraction images were enhanced considerably, with a substantial reduction of misregistration artifacts. The temporal subtraction images obtained by use of the voxel-matching technique would be very useful for radiologists in the detection of interval changes on MDCT images.

Effects of global signal regression and subtraction methods on resting-state functional connectivity using arterial spin labeling data.

Science.gov (United States)

Silva, João Paulo Santos; Mônaco, Luciana da Mata; Paschoal, André Monteiro; Oliveira, Ícaro Agenor Ferreira de; Leoni, Renata Ferranti

2018-05-16

Arterial spin labeling (ASL) is an established magnetic resonance imaging (MRI) technique that is finding broader applications in functional studies of the healthy and diseased brain. To promote improvement in cerebral blood flow (CBF) signal specificity, many algorithms and imaging procedures, such as subtraction methods, were proposed to eliminate or, at least, minimize noise sources. Therefore, this study addressed the main considerations of how CBF functional connectivity (FC) is changed, regarding resting brain network (RBN) identification and correlations between regions of interest (ROI), by different subtraction methods and removal of residual motion artifacts and global signal fluctuations (RMAGSF). Twenty young healthy participants (13 M/7F, mean age = 25 ± 3 years) underwent an MRI protocol with a pseudo-continuous ASL (pCASL) sequence. Perfusion-based images were obtained using simple, sinc and running subtraction. RMAGSF removal was applied to all CBF time series. Independent Component Analysis (ICA) was used for RBN identification, while Pearson' correlation was performed for ROI-based FC analysis. Temporal signal-to-noise ratio (tSNR) was higher in CBF maps obtained by sinc subtraction, although RMAGSF removal had a significant effect on maps obtained with simple and running subtractions. Neither the subtraction method nor the RMAGSF removal directly affected the identification of RBNs. However, the number of correlated and anti-correlated voxels varied for different subtraction and filtering methods. In an ROI-to-ROI level, changes were prominent in FC values and their statistical significance. Our study showed that both RMAGSF filtering and subtraction method might influence resting-state FC results, especially in an ROI level, consequently affecting FC analysis and its interpretation. Taking our results and the whole discussion together, we understand that for an exploratory assessment of the brain, one could avoid removing RMAGSF to

A Ribeiroia spp. (Class: Trematoda) - Specific PCR-based diagnostic

Science.gov (United States)

Reinitz, David M.; Yoshino, T.P.; Cole, Rebecca A.

2007-01-01

Increased reporting of amphibian malformations in North America has been noted with concern in light of reports that amphibian numbers and species are declining worldwide. Ribeiroia ondatrae has been shown to cause a variety of types of malformations in amphibians. However, little is known about the prevalence of R. ondatrae in North America. To aid in conducting field studies of Ribeiroia spp., we have developed a polymerase chain reaction (PCR)-based diagnostic. Herein, we describe the development of an accurate, rapid, simple, and cost-effective diagnostic for detection of Ribeiroia spp. infection in snails (Planorbella trivolvis). Candidate oligonucleotide primers for PCR were designed via DNA sequence analyses of multiple ribosomal internal transcribed spacer-2 regions from Ribeiroia spp. and Echinostoma spp. Comparison of consensus sequences determined from both genera identified areas of sequence potentially unique to Ribeiroia spp. The PCR reliably produced a diagnostic 290-base pair (bp) product in the presence of a wide concentration range of snail or frog DNA. Sensitivity was examined with DNA extracted from single R. ondatrae cercaria. The single-tube PCR could routinely detect less than 1 cercariae equivalent, because DNA isolated from a single cercaria could be diluted at least 1:50 and still yield a positive result via gel electrophoresis. An even more sensitive nested PCR also was developed that routinely detected 100 fg of the 290-bp fragment. The assay did not detect furcocercous cercariae of certain Schistosomatidae, Echinostoma sp., or Sphaeridiotrema globulus nor adults of Clinostomum sp. or Cyathocotyle bushiensis. Field testing of 137 P. trivolvis identified 3 positives with no overt environmental cross-reactivity, and results concurred with microscopic examinations in all cases. ?? American Society of Parasitologists 2007.

Multiscale KF Algorithm for Strong Fractional Noise Interference Suppression in Discrete-Time UWB Systems

Directory of Open Access Journals (Sweden)

Liyun Su

2011-01-01

Full Text Available In order to suppress the interference of the strong fractional noise signal in discrete-time ultrawideband (UWB systems, this paper presents a new UWB multi-scale Kalman filter (KF algorithm for the interference suppression. This approach solves the problem of the narrowband interference (NBI as nonstationary fractional signal in UWB communication, which does not need to estimate any channel parameter. In this paper, the received sampled signal is transformed through multiscale wavelet to obtain a state transition equation and an observation equation based on the stationarity theory of wavelet coefficients in time domain. Then through the Kalman filter method, fractional signal of arbitrary scale is easily figured out. Finally, fractional noise interference is subtracted from the received signal. Performance analysis and computer simulations reveal that this algorithm is effective to reduce the strong fractional noise when the sampling rate is low.

Combined nuclear and digital subtraction contrast arthrography in painful knee prosthesis

International Nuclear Information System (INIS)

Namasivayam, J.; Forrester, A.; Poon, F.W.; Cuthbert, G.F.; McKillop, J.H.; Bryan, A.S.

1992-01-01

The evaluation of a painful knee prosthesis remains a difficult problem for both orthopaedic surgeons and radiologists. We have compared digital subtraction arthrography with nuclear-arthrography in 7 patients with a painful knee prosthesis. Three patients showed a loose tibial component, demonstrated by both digital subtraction and nuclear arthrography. All 3 underwent revision of their prosthesis. One patient had an equivocal digital subtraction arthrogram and negative nuclear arthrogram, while both studies were negative in the 3 remaining patients. Nuclear arthrography is a simple procedure and can provide useful additional information when combined with digital subtraction arthrography. (orig.)

Arthrography of painful hips following arthroplasty: Digital versus plain film subtraction

Energy Technology Data Exchange (ETDEWEB)

Walker, C W; FitzRandolph, R L; Dalrymple, G V [Arkansas Univ. for Medical Sciences, Little Rock, AR (USA). Dept. of Radiology John McClellan Memorial Veterans Hospital, Little Rock, AR (USA); Collins, D N [Arkansas Univ. for Medical Sciences, Little Rock, AR (USA). Dept. of Orthopedics John McClellan Memorial Veterans Hospital, Little Rock, AR (USA)

1991-08-01

Digital and manual subtraction images obtained during the arthrographic evaluation of 78 painful hip prostheses were reviewed retrospectively. Revision arthroplasty was performed in 53 of these cases, and the arthrographic and surgical findings were correlated. The digital and manual subtraction images were evaluated without knowledge of the surgical results using established criteria for component loosening. The difference between detection of femoral component loosening on digital as opposed to manual subtraction images was statistically significant (P < 0.05). This study demonstrates that digital subtraction improves the evaluation of femoral component loosening in painful hip prostheses. (orig./GDG).

PCR-based techniques for leprosy diagnosis: from the laboratory to the clinic.

Directory of Open Access Journals (Sweden)

Alejandra Nóbrega Martinez

2014-04-01

Full Text Available In leprosy, classic diagnostic tools based on bacillary counts and histopathology have been facing hurdles, especially in distinguishing latent infection from active disease and diagnosing paucibacillary clinical forms. Serological tests and IFN-gamma releasing assays (IGRA that employ humoral and cellular immune parameters, respectively, are also being used, but recent results indicate that quantitative PCR (qPCR is a key technique due to its higher sensitivity and specificity. In fact, advances concerning the structure and function of the Mycobacterium leprae genome led to the development of specific PCR-based gene amplification assays for leprosy diagnosis and monitoring of household contacts. Also, based on the validation of point-of-care technologies for M. tuberculosis DNA detection, it is clear that the same advantages of rapid DNA detection could be observed in respect to leprosy. So far, PCR has proven useful in the determination of transmission routes, M. leprae viability, and drug resistance in leprosy. However, PCR has been ascertained to be especially valuable in diagnosing difficult cases like pure neural leprosy (PNL, paucibacillary (PB, and patients with atypical clinical presentation and histopathological features compatible with leprosy. Also, the detection of M. leprae DNA in different samples of the household contacts of leprosy patients is very promising. Although a positive PCR result is not sufficient to establish a causal relationship with disease outcome, quantitation provided by qPCR is clearly capable of indicating increased risk of developing the disease and could alert clinicians to follow these contacts more closely or even define rules for chemoprophylaxis.

[sup 99m]Tc-RBC subtraction scintigraphy; Assessmet of bleeding site and rate

Energy Technology Data Exchange (ETDEWEB)

Inagaki, Syoichi; Tonami, Syuichi; Yasui, Masakazu; Kuranishi, Makoto; Sugishita, Kouki; Nakamura, Mamoru (Toyama Medical and Pharmaceutical Univ. (Japan). Hospital)

1994-03-01

Sequential abdominal scintigrams with [sup 99m]Tc-labelled red blood cells (RBC) were subtracted for observing a site of gastrointestinal bleeding and calculating the bleeding rate. This method is technically very easy and can detect the site of bleeding with the minimum rate, as low as 0.2 ml/min., in a phantom experiment. In 23 cases with final diagnosis of gastrointestinal bleeding, conventional non-subtraction scintigraphy detected only 30% (7/23), but subtraction scintigraphy detected 61% (14/23). It was concluded that subtraction scintigraphy had higher sensitivity than conventional scintigraphy for early diagnosing bleeding. A combination of non-subtraction and subtraction scintigraphy is recommended to detect a site of gastrointestinal bleeding in a clinical setting. (author).

Bone marrow edema pattern identification in patients with lytic bone lesions using digital subtraction angiography-like bone subtraction on large-area detector computed tomography.

Science.gov (United States)

Gondim Teixeira, Pedro Augusto; Hossu, Gabriela; Lecocq, Sophie; Razeto, Marco; Louis, Matthias; Blum, Alain

2014-03-01

The objective of this study was to evaluate the performance of digital subtraction angiography (DSA)-like bone subtraction with 2 different registration methods for the identification of bone marrow edema pattern (BMEP) in patients with lytic bone lesions, using magnetic resonance imaging as the criterion standard. Fifty-five patients with a lytic bone lesion were included in this prospective study with approval from the ethics committee. All patients underwent magnetic resonance imaging and low-dose computed tomographic (CT) perfusion after signing an informed consent. Two CT volumes were used for bone subtraction, which was performed with 2 different algorithms (rigid and nonrigid). Enhancement at the nonlytic bone marrow was considered as a sign of BMEP. Two readers evaluated the images blindly. The presence of BMEP on bone-subtracted CT images was evaluated subjectively and quantitatively. Image quality was assessed. Magnetic resonance imaging was used as the criterion standard. Using a rigid registration method, the sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of CT with DSA-like bone subtraction BMEP was 77%, 100%, 100%, 68%, and 85%, respectively. The interobserver agreement was good (κ, 0.782). Image quality was better using a nonrigid registration. With this algorithm, artifacts interfered with image interpretation in only 5% of cases. However, there was a noticeable drop in sensitivity and negative predictive value when a nonrigid algorithm was used: 56% and 52%, respectively. The interobserver agreement was average with a nonrigid subtraction algorithm. Computed tomography with DSA-like bone subtraction is sensitive and highly specific for the identification of BMEP associated with lytic bone lesions. Rigid registering should be preferred, but nonrigid algorithms can be used as a second option when artifacts interfere with image interpretation.

Simultaneous optical digital half-subtraction and -addition using SOAs and a PPLN waveguide.

Science.gov (United States)

McGeehan, John E; Kumar, Saurabh; Willner, Alan E

2007-04-30

We demonstrate an optical half-subtracter and half-adder module that performs simultaneous bit-wise subtraction and addition of two 5 Gbit/s RZ data streams. We generate Borrow (/X*Y) and Difference/Sum (X plus sign in circleY, or XOR) outputs using cross-gain modulation (XGM) in two parallel SOAs. Taking advantage of the gain saturation inherent to SOAs, we generate two signals, /X*Y, and X*/Y, and combine them using a passive optical coupler to generate the XOR Difference/Sum output. We use difference-frequency-generation-based lambda-conversion in a PPLN waveguide to generate the Carry (X*Y) output. The PPLN waveguide allows bit-synchronous wavelength shifting, is wide-bandwidth, and offers no intrinsic chirp. Our module uses three active elements to perform simultaneous half-subtraction and addition, and carries a maximum power penalty of 1.0 dB.

The study of myocardial ischemic quality with weighted-subtraction-bull's-eye analysis

International Nuclear Information System (INIS)

Chen Wuduan; Tian Jiahe; Hou Qingtian

1993-01-01

Weighted-Subtraction-Bull's-eye analysis was studied in 33 normal subjects and 58 patients with coronary artery disease after dipyridamole 99m Tc-MIBI myocardial SPECT imaging. Two kinds of Bull's-eye were produced: (1) subtract rest from 1.2 times dipyridamole from 1.2 times rest Bull's-eye; (2) subtract dipyridamole Bull's-eye. The results showed that the weighted-subtraction-Bull's-eye could clearly displayed the location and puality of ischemic myocardium. And also 74% segments showed so called combined ischemic i.e the blood perfusion reduced, increased and sustained simultaneously after dipyridamole. Therefore weighted-subtraction-Bull's-eye analysis had provided a new method for determination of the quality of ischemia

Research on the algorithm of infrared target detection based on the frame difference and background subtraction method

Science.gov (United States)

Liu, Yun; Zhao, Yuejin; Liu, Ming; Dong, Liquan; Hui, Mei; Liu, Xiaohua; Wu, Yijian

2015-09-01

As an important branch of infrared imaging technology, infrared target tracking and detection has a very important scientific value and a wide range of applications in both military and civilian areas. For the infrared image which is characterized by low SNR and serious disturbance of background noise, an innovative and effective target detection algorithm is proposed in this paper, according to the correlation of moving target frame-to-frame and the irrelevance of noise in sequential images based on OpenCV. Firstly, since the temporal differencing and background subtraction are very complementary, we use a combined detection method of frame difference and background subtraction which is based on adaptive background updating. Results indicate that it is simple and can extract the foreground moving target from the video sequence stably. For the background updating mechanism continuously updating each pixel, we can detect the infrared moving target more accurately. It paves the way for eventually realizing real-time infrared target detection and tracking, when transplanting the algorithms on OpenCV to the DSP platform. Afterwards, we use the optimal thresholding arithmetic to segment image. It transforms the gray images to black-white images in order to provide a better condition for the image sequences detection. Finally, according to the relevance of moving objects between different frames and mathematical morphology processing, we can eliminate noise, decrease the area, and smooth region boundaries. Experimental results proves that our algorithm precisely achieve the purpose of rapid detection of small infrared target.

Digital subtraction cardiopulmonary angiography using FCR (Fuji computed radiography)

International Nuclear Information System (INIS)

Tanimura, Shigeo; Tomoyasu, Hiroshi; Banba, Jiro; Masaki, Mikio; Kanno, Yukio; Abe, Kazuo

1987-01-01

Digital subtraction cardiopulmonary angiography using FCR was performed on 46 patients including lung cancer, mediastinal tumor, giant bullous formation and others. The images of digital subtraction for pulmonary artery, pulmonary vein and thoracic aorta were studied by comparing to the conventional pulmonary angiogram. Good images of pulmonary artery due to digital subtraction were obtained in 80 % of the 45 cases. This method needed only half volume of contrast media compared to the conventional for obtaining good images and thus reduced side effect. Therefore this method seems to be an usefull pre-operative examination in various chest diseases, especially in case of lung cancer. (author)

Array-based techniques for fingerprinting medicinal herbs

Directory of Open Access Journals (Sweden)

Xue Charlie

2011-05-01

Full Text Available Abstract Poor quality control of medicinal herbs has led to instances of toxicity, poisoning and even deaths. The fundamental step in quality control of herbal medicine is accurate identification of herbs. Array-based techniques have recently been adapted to authenticate or identify herbal plants. This article reviews the current array-based techniques, eg oligonucleotides microarrays, gene-based probe microarrays, Suppression Subtractive Hybridization (SSH-based arrays, Diversity Array Technology (DArT and Subtracted Diversity Array (SDA. We further compare these techniques according to important parameters such as markers, polymorphism rates, restriction enzymes and sample type. The applicability of the array-based methods for fingerprinting depends on the availability of genomics and genetics of the species to be fingerprinted. For the species with few genome sequence information but high polymorphism rates, SDA techniques are particularly recommended because they require less labour and lower material cost.

[Development of a digital chest phantom for studies on energy subtraction techniques].

Science.gov (United States)

Hayashi, Norio; Taniguchi, Anna; Noto, Kimiya; Shimosegawa, Masayuki; Ogura, Toshihiro; Doi, Kunio

2014-03-01

Digital chest phantoms continue to play a significant role in optimizing imaging parameters for chest X-ray examinations. The purpose of this study was to develop a digital chest phantom for studies on energy subtraction techniques under ideal conditions without image noise. Computed tomography (CT) images from the LIDC (Lung Image Database Consortium) were employed to develop a digital chest phantom. The method consisted of the following four steps: 1) segmentation of the lung and bone regions on CT images; 2) creation of simulated nodules; 3) transformation to attenuation coefficient maps from the segmented images; and 4) projection from attenuation coefficient maps. To evaluate the usefulness of digital chest phantoms, we determined the contrast of the simulated nodules in projection images of the digital chest phantom using high and low X-ray energies, soft tissue images obtained by energy subtraction, and "gold standard" images of the soft tissues. Using our method, the lung and bone regions were segmented on the original CT images. The contrast of simulated nodules in soft tissue images obtained by energy subtraction closely matched that obtained using the gold standard images. We thus conclude that it is possible to carry out simulation studies based on energy subtraction techniques using the created digital chest phantoms. Our method is potentially useful for performing simulation studies for optimizing the imaging parameters in chest X-ray examinations.

Genomic comparison of the endophyte Herbaspirillum seropedicae SmR1 and the phytopathogen Herbaspirillum rubrisubalbicans M1 by suppressive subtractive hybridization and partial genome sequencing.

Science.gov (United States)

Monteiro, Rose A; Balsanelli, Eduardo; Tuleski, Thalita; Faoro, Helison; Cruz, Leonardo M; Wassem, Roseli; de Baura, Valter A; Tadra-Sfeir, Michelle Z; Weiss, Vinícius; DaRocha, Wanderson D; Muller-Santos, Marcelo; Chubatsu, Leda S; Huergo, Luciano F; Pedrosa, Fábio O; de Souza, Emanuel M

2012-05-01

Herbaspirillum rubrisubalbicans M1 causes the mottled stripe disease in sugarcane cv. B-4362. Inoculation of this cultivar with Herbaspirillum seropedicae SmR1 does not produce disease symptoms. A comparison of the genomic sequences of these closely related species may permit a better understanding of contrasting phenotype such as endophytic association and pathogenic life style. To achieve this goal, we constructed suppressive subtractive hybridization (SSH) libraries to identify DNA fragments present in one species and absent in the other. In a parallel approach, partial genomic sequence from H. rubrisubalbicans M1 was directly compared in silico with the H. seropedicae SmR1 genome. The genomic differences between the two organisms revealed by SSH suggested that lipopolysaccharide and adhesins are potential molecular factors involved in the different phenotypic behavior. The cluster wss probably involved in cellulose biosynthesis was found in H. rubrisubalbicans M1. Expression of this gene cluster was increased in H. rubrisubalbicans M1 cells attached to the surface of maize root, and knockout of wssD gene led to decrease in maize root surface attachment and endophytic colonization. The production of cellulose could be responsible for the maize attachment pattern of H. rubrisubalbicans M1 that is capable of outcompeting H. seropedicae SmR1. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Value of blood-pool subtraction in cardiac indium-111-labeled platelet imaging

Energy Technology Data Exchange (ETDEWEB)

Machac, J.; Vallabhajosula, S.; Goldman, M.E.; Goldsmith, S.J.; Palestro, C.; Strashun, A.; Vaquer, R.; Phillips, R.A.; Fuster, V. (Mt. Sinai Medical Center, New York, NY (USA))

1989-09-01

Blood-pool subtraction has been proposed to enhance {sup 111}In-labeled platelet imaging of intracardiac thrombi. We tested the accuracy of labeled platelet imaging, with and without blood-pool subtraction, in ten subjects with cardiac thrombi of varying age, eight with endocarditis being treated with antimicrobial therapy and ten normal controls. Imaging was performed early after labeled platelet injection (24 hr or less) and late (48 hr or more). Blood-pool subtraction was carried out. All images were graded subjectively by four experienced, blinded readers. Detection accuracy was measured by the sensitivity at three fixed levels of specificity estimated from receiver operator characteristic curve analysis and tested by three-way analysis of variance. Detection accuracy was generally improved on delayed images. Blood-pool subtraction did not improve accuracy. Although blood-pool subtraction increased detection sensitivity, this was offset by decreased specificity. For this population studied, blood-pool subtraction did not improve subjective detection of abnormal platelet deposition by 111In platelet imaging.

Value of blood-pool subtraction in cardiac indium-111-labeled platelet imaging

International Nuclear Information System (INIS)

Machac, J.; Vallabhajosula, S.; Goldman, M.E.; Goldsmith, S.J.; Palestro, C.; Strashun, A.; Vaquer, R.; Phillips, R.A.; Fuster, V.

1989-01-01

Blood-pool subtraction has been proposed to enhance 111 In-labeled platelet imaging of intracardiac thrombi. We tested the accuracy of labeled platelet imaging, with and without blood-pool subtraction, in ten subjects with cardiac thrombi of varying age, eight with endocarditis being treated with antimicrobial therapy and ten normal controls. Imaging was performed early after labeled platelet injection (24 hr or less) and late (48 hr or more). Blood-pool subtraction was carried out. All images were graded subjectively by four experienced, blinded readers. Detection accuracy was measured by the sensitivity at three fixed levels of specificity estimated from receiver operator characteristic curve analysis and tested by three-way analysis of variance. Detection accuracy was generally improved on delayed images. Blood-pool subtraction did not improve accuracy. Although blood-pool subtraction increased detection sensitivity, this was offset by decreased specificity. For this population studied, blood-pool subtraction did not improve subjective detection of abnormal platelet deposition by 111In platelet imaging

Ictal cerebral perfusion patterns in partial epilepsy: SPECT subtraction

International Nuclear Information System (INIS)

Lee, Hyang Woon; Hong, Seung Bong; Tae, Woo Suk; Kim, Sang Eun; Seo, Dae Won; Jeong, Seung Cheol; Yi, Ji Young; Hong, Seung Chyul

2000-01-01

To investigate the various ictal perfusion patterns and find the relationships between clinical factors and different perfusion patterns. Interictal and ictal SPECT and SPECT subtraction were performed in 61 patients with partial epilepsy. Both positive images showing ictal hyperperfusion and negative images revealing ictal hypoperfusion were obtained by SPECT subtraction. The ictal perfusion patterns of subtracted SPECT were classified into focal hyperperfusion, hyperperfusion-plus, combined hyperperfusion-hypoperfusion, and focal hypoperfusion only. The concordance rates with epileptic focus were 91.8% in combined analysis of ictal hyperperfusion and hypoperfusion images of subtracted SPECT, 85.2% in hyperperfusion images only of subtracted SPECT, and 68.9% in conventional ictal SPECT analysis. Ictal hypoperfusion occurred less frequently in temporal lobe epilepsy (TLE) than extratemporal lobe epilepsy. Mesial temporal hyperperfusion alone was seen only in mesial TLE while lateral temporal hyperperfusion alone was observed only in neocortical TLE. Hippocampal sclerosis had much lower incidence of ictal hypoperfusion than any other pathology. Some patients showed ictal hypoperfusion at epileptic focus with ictal hyperperfusion in the neighboring brain regions where ictal discharges propagated. Hypoperfusion as well as hyperperfusion in ictal SPECT should be considered for localizing epileptic focus. Although the mechanism of ictal hypoperfusion could be an intra-ictal early exhaustion of seizure focus or a steal phenomenon by the propagation of ictal discharges to adjacent brain areas, further study is needed to elucidate it.=20

Ictal cerebral perfusion patterns in partial epilepsy: SPECT subtraction

Energy Technology Data Exchange (ETDEWEB)

Lee, Hyang Woon; Hong, Seung Bong; Tae, Woo Suk; Kim, Sang Eun; Seo, Dae Won; Jeong, Seung Cheol; Yi, Ji Young; Hong, Seung Chyul [Sungkyunkwan Univ. School of Medicine, Seoul (Korea, Republic of)

2000-06-01

To investigate the various ictal perfusion patterns and find the relationships between clinical factors and different perfusion patterns. Interictal and ictal SPECT and SPECT subtraction were performed in 61 patients with partial epilepsy. Both positive images showing ictal hyperperfusion and negative images revealing ictal hypoperfusion were obtained by SPECT subtraction. The ictal perfusion patterns of subtracted SPECT were classified into focal hyperperfusion, hyperperfusion-plus, combined hyperperfusion-hypoperfusion, and focal hypoperfusion only. The concordance rates with epileptic focus were 91.8% in combined analysis of ictal hyperperfusion and hypoperfusion images of subtracted SPECT, 85.2% in hyperperfusion images only of subtracted SPECT, and 68.9% in conventional ictal SPECT analysis. Ictal hypoperfusion occurred less frequently in temporal lobe epilepsy (TLE) than extratemporal lobe epilepsy. Mesial temporal hyperperfusion alone was seen only in mesial TLE while lateral temporal hyperperfusion alone was observed only in neocortical TLE. Hippocampal sclerosis had much lower incidence of ictal hypoperfusion than any other pathology. Some patients showed ictal hypoperfusion at epileptic focus with ictal hyperperfusion in the neighboring brain regions where ictal discharges propagated. Hypoperfusion as well as hyperperfusion in ictal SPECT should be considered for localizing epileptic focus. Although the mechanism of ictal hypoperfusion could be an intra-ictal early exhaustion of seizure focus or a steal phenomenon by the propagation of ictal discharges to adjacent brain areas, further study is needed to elucidate it.

Digital subtraction imaging in cardiac investigations

International Nuclear Information System (INIS)

Partridge, J.B.; Dickinson, D.F.

1984-01-01

The role of digital subtraction imaging (DSI) in the investigation of heart disease in patients of all ages, including neonates, was evaluated by the addition of a continuous fluoroscopy system to an existing, single-plane catheterisation laboratory. In some situations, DSI provided diagnostic images where conventional radiography could not and, in general, provided images of comparable quality to cineangiography. The total dose of contrast medium was usually less than that which would have been required for biplane cineangiography and the dose of radiation was always less. Digital subtraction imaging can make a significant contribution to the investigation of congenital heart disease and has some useful features in the study of acquired heart disease. (author)

Improvement of temporal and dynamic subtraction images on abdominal CT using 3D global image matching and nonlinear image warping techniques

International Nuclear Information System (INIS)

Okumura, E; Sanada, S; Suzuki, M; Takemura, A; Matsui, O

2007-01-01

Accurate registration of the corresponding non-enhanced and arterial-phase CT images is necessary to create temporal and dynamic subtraction images for the enhancement of subtle abnormalities. However, respiratory movement causes misregistration at the periphery of the liver. To reduce these misregistration errors, we developed a temporal and dynamic subtraction technique to enhance small HCC by 3D global matching and nonlinear image warping techniques. The study population consisted of 21 patients with HCC. Using the 3D global matching and nonlinear image warping technique, we registered current and previous arterial-phase CT images or current non-enhanced and arterial-phase CT images obtained in the same position. The temporal subtraction image was obtained by subtracting the previous arterial-phase CT image from the warped current arterial-phase CT image. The dynamic subtraction image was obtained by the subtraction of the current non-enhanced CT image from the warped current arterial-phase CT image. The percentage of fair or superior temporal subtraction images increased from 52.4% to 95.2% using the new technique, while on the dynamic subtraction images, the percentage increased from 66.6% to 95.2%. The new subtraction technique may facilitate the diagnosis of subtle HCC based on the superior ability of these subtraction images to show nodular and/or ring enhancement

Rapid and sensitive detection of Feline immunodeficiency virus using an insulated isothermal PCR-based assay with a point-of-need PCR detection platform.

Science.gov (United States)

Wilkes, Rebecca Penrose; Kania, Stephen A; Tsai, Yun-Long; Lee, Pei-Yu Alison; Chang, Hsiu-Hui; Ma, Li-Juan; Chang, Hsiao-Fen Grace; Wang, Hwa-Tang Thomas

2015-07-01

Feline immunodeficiency virus (FIV) is an important infectious agent of cats. Clinical syndromes resulting from FIV infection include immunodeficiency, opportunistic infections, and neoplasia. In our study, a 5' long terminal repeat/gag region-based reverse transcription insulated isothermal polymerase chain reaction (RT-iiPCR) was developed to amplify all known FIV strains to facilitate point-of-need FIV diagnosis. The RT-iiPCR method was applied in a point-of-need PCR detection platform--a field-deployable device capable of generating automatically interpreted RT-iiPCR results from nucleic acids within 1 hr. Limit of detection 95% of FIV RT-iiPCR was calculated to be 95 copies standard in vitro transcription RNA per reaction. Endpoint dilution studies with serial dilutions of an ATCC FIV type strain showed that the sensitivity of lyophilized FIV RT-iiPCR reagent was comparable to that of a reference nested PCR. The established reaction did not amplify any nontargeted feline pathogens, including Felid herpesvirus 1, feline coronavirus, Feline calicivirus, Feline leukemia virus, Mycoplasma haemofelis, and Chlamydophila felis. Based on analysis of 76 clinical samples (including blood and bone marrow) with the FIV RT-iiPCR, test sensitivity was 97.78% (44/45), specificity was 100.00% (31/31), and agreement was 98.65% (75/76), determined against a reference nested-PCR assay. A kappa value of 0.97 indicated excellent correlation between these 2 methods. The lyophilized FIV RT-iiPCR reagent, deployed on a user-friendly portable device, has potential utility for rapid and easy point-of-need detection of FIV in cats. © 2015 The Author(s).

Deblurring in digital tomosynthesis by iterative self-layer subtraction

Science.gov (United States)

Youn, Hanbean; Kim, Jee Young; Jang, SunYoung; Cho, Min Kook; Cho, Seungryong; Kim, Ho Kyung

2010-04-01

Recent developments in large-area flat-panel detectors have made tomosynthesis technology revisited in multiplanar xray imaging. However, the typical shift-and-add (SAA) or backprojection reconstruction method is notably claimed by a lack of sharpness in the reconstructed images because of blur artifact which is the superposition of objects which are out of planes. In this study, we have devised an intuitive simple method to reduce the blur artifact based on an iterative approach. This method repeats a forward and backward projection procedure to determine the blur artifact affecting on the plane-of-interest (POI), and then subtracts it from the POI. The proposed method does not include any Fourierdomain operations hence excluding the Fourier-domain-originated artifacts. We describe the concept of the self-layer subtractive tomosynthesis and demonstrate its performance with numerical simulation and experiments. Comparative analysis with the conventional methods, such as the SAA and filtered backprojection methods, is addressed.

AutoDipole - Automated generation of dipole subtraction terms

International Nuclear Information System (INIS)

Hasegawa, K.; Uwer, P.

2009-11-01

We present an automated generation of the subtraction terms for next-to-leading order QCD calculations in the Catani-Seymour dipole formalism. For a given scattering process with n external particles our Mathematica package generates all dipole terms, allowing for bothmassless and massive dipoles. The numerical evaluation of the subtraction terms proceeds with MadGraph, which provides Fortran code for the necessary scattering amplitudes. Checks of the numerical stability are discussed. (orig.)

AutoDipole - Automated generation of dipole subtraction terms

Energy Technology Data Exchange (ETDEWEB)

Hasegawa, K.; Uwer, P. [Humboldt-Universitaet, Berlin (Germany). Inst. fuer Physik; Moch, S. [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany)

2009-11-15

We present an automated generation of the subtraction terms for next-to-leading order QCD calculations in the Catani-Seymour dipole formalism. For a given scattering process with n external particles our Mathematica package generates all dipole terms, allowing for bothmassless and massive dipoles. The numerical evaluation of the subtraction terms proceeds with MadGraph, which provides Fortran code for the necessary scattering amplitudes. Checks of the numerical stability are discussed. (orig.)

Dicty_cDB: Contig-U05900-1 [Dicty_cDB

Lifescience Database Archive (English)

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Lifescience Database Archive (English)

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Analytical optimization of digital subtraction mammography with contrast medium using a commercial unit.

Science.gov (United States)

Rosado-Méndez, I; Palma, B A; Brandan, M E

2008-12-01

Contrast-medium-enhanced digital mammography (CEDM) is an image subtraction technique which might help unmasking lesions embedded in very dense breasts. Previous works have stated the feasibility of CEDM and the imperative need of radiological optimization. This work presents an extension of a former analytical formalism to predict contrast-to-noise ratio (CNR) in subtracted mammograms. The goal is to optimize radiological parameters available in a clinical mammographic unit (x-ray tube anode/filter combination, voltage, and loading) by maximizing CNR and minimizing total mean glandular dose (D(gT)), simulating the experimental application of an iodine-based contrast medium and the image subtraction under dual-energy nontemporal, and single- or dual-energy temporal modalities. Total breast-entrance air kerma is limited to a fixed 8.76 mGy (1 R, similar to screening studies). Mathematical expressions obtained from the formalism are evaluated using computed mammographic x-ray spectra attenuated by an adipose/glandular breast containing an elongated structure filled with an iodinated solution in various concentrations. A systematic study of contrast, its associated variance, and CNR for different spectral combinations is performed, concluding in the proposal of optimum x-ray spectra. The linearity between contrast in subtracted images and iodine mass thickness is proven, including the determination of iodine visualization limits based on Rose's detection criterion. Finally, total breast-entrance air kerma is distributed between both images in various proportions in order to maximize the figure of merit CNR2/D(gT). Predicted results indicate the advantage of temporal subtraction (either single- or dual-energy modalities) with optimum parameters corresponding to high-voltage, strongly hardened Rh/Rh spectra. For temporal techniques, CNR was found to depend mostly on the energy of the iodinated image, and thus reduction in D(gT) could be achieved if the spectral energy

Development of Quantitative Competitive PCR and Absolute Based Real-Time PCR Assays for Quantification of The Butyrate Producing Bacterium: Butyrivibrio fibrisolvens

Directory of Open Access Journals (Sweden)

Mojtaba Tahmoorespur

2016-04-01

Full Text Available Introduction Butyrivibrio fibrisolvens strains are presently recognized as the major butyrate-producing bacteria found in the rumen and digestive track of many animals and also in the human gut. In this study we reported the development of two DNA based techniques, quantitative competitive (QC PCR and absolute based Real-Time PCR, for enumerating Butyrivibrio fibrisolvens strains. Despite the recent introduction of real-time PCR method for the rapid quantification of the target DNA sequences, use of quantitative competitive PCR (QC-PCR technique continues to play an important role in nucleic acid quantification since it is more cost effective. The procedure relies on the co-amplification of the sequence of interest with a serially diluted synthetic DNA fragment of the known concentration (competitor, using the single set primers. A real-time polymerase chain reaction is a laboratory technique of molecular biology based on the polymerase chain reaction (PCR. It monitors the amplification of a targeted DNA molecule during the PCR. Materials and Methods At first reported species-specific primers targeting the 16S rDNA region of the bacterium Butyrivibrio fibrisolvens were used for amplifying a 213 bp fragment. A DNA competitor differing by 50 bp in length from the 213 bp fragment was constructed and cloned into pTZ57R/T vector. The competitor was quantified by NanoDrop spectrophotometer and serially diluted and co-amplified by PCR with total extracted DNA from rumen fluid samples. PCR products were quantified by photographing agarose gels and analyzed with Image J software and the amount of amplified target DNA was log plotted against the amount of amplified competitor. Coefficient of determination (R2 was used as a criterion of methodology precision. For developing the Real-time PCR technique, the 213 bp fragment was amplified and cloned into pTZ57R/T was used to draw a standard curve. Results and Discussion The specific primers of Butyrivibrio

Big Bang Observer and the neutron-star-binary subtraction problem

International Nuclear Information System (INIS)

Cutler, Curt; Harms, Jan

2006-01-01

The Big Bang Observer (BBO) is a proposed space-based gravitational-wave (GW) mission designed primarily to search for an inflation-generated GW background in the frequency range ∼10 -1 Hz-1 Hz. The major astrophysical foreground in this range is gravitational radiation from inspiralling compact binaries. This foreground is expected to be much larger than the inflation-generated background, so to accomplish its main goal, BBO must be sensitive enough to identify and subtract out practically all such binaries in the observable universe. It is somewhat subtle to decide whether BBO's current baseline design is sufficiently sensitive for this task, since, at least initially, the dominant noise source impeding identification of any one binary is confusion noise from all the others (rather than instrumental noise). Here we present a self-consistent scheme for deciding whether BBO's baseline design is indeed adequate for subtracting out the binary foreground. We conclude that the current baseline should be sufficient. However, if BBO's sensitivity were degraded by a factor 2 from the current baseline, then its ability to detect an underlying primordial background would depend critically on the value of ρ th , the threshold signal-to-noise ratio marking the boundary between detectable and undetectable sources. If BBO's sensitivity were degraded by a factor 4 from the current baseline, it could not detect a primordial background below Ω GW ∼10 -15 . It is impossible to perfectly subtract out each of the binary inspiral waveforms, so an important question is how to deal with the 'residual' errors in the post-subtraction data stream. We sketch a strategy of 'projecting out' these residual errors, at the cost of some effective bandwidth. We also provide estimates of the sizes of various post-Newtonian effects in the inspiral waveforms that must be accounted for in the BBO analysis

ECG-gating in non-cardiac digital subtraction angiography

International Nuclear Information System (INIS)

Gattoni, F.; Baldini, V.; Cairo, F.

1987-01-01

This paper reports the results of the ECG-gating in non-cardiac digital subtraction angiography (DSA). One hundred and fifteen patients underwent DSA (126 examinations); ECG-gating was applied in 66/126 examinations: images recorded at 70% of R wave were subtracted. Artifacts produced by vascular movements were evaluated in all patients: only 40 examinations, carried out whithout ECG-gating, showed vascular artifacts. The major advantage of the ECG-gated DSA is the more efficent subtraction because of the better images superimposition: therefore, ECG-gating can be clinically helpful. On the contrary, it could be a problem in arrhytmic or bradycardic patients. ECG-gating is helpful in DSA imaging of the thoracic and abdominal aorta and of the cervical and renal arteries. In the examinations of peripheral vessels of the limbs it is not so efficent as in the trunk or in the neck

Molecular analysis of single oocyst of Eimeria by whole genome amplification (WGA) based nested PCR.

Science.gov (United States)

Wang, Yunzhou; Tao, Geru; Cui, Yujuan; Lv, Qiyao; Xie, Li; Li, Yuan; Suo, Xun; Qin, Yinghe; Xiao, Lihua; Liu, Xianyong

2014-09-01

PCR-based molecular tools are widely used for the identification and characterization of protozoa. Here we report the molecular analysis of Eimeria species using combined methods of whole genome amplification (WGA) and nested PCR. Single oocyst of Eimeria stiedai or Eimeriamedia was directly used for random amplification of the genomic DNA with either primer extension preamplification (PEP) or multiple displacement amplification (MDA), and then the WGA product was used as template in nested PCR with species-specific primers for ITS-1, 18S rDNA and 23S rDNA of E. stiedai and E. media. WGA-based PCR was successful for the amplification of these genes from single oocyst. For the species identification of single oocyst isolated from mixed E. stiedai or E. media, the results from WGA-based PCR were exactly in accordance with those from morphological identification, suggesting the availability of this method in molecular analysis of eimerian parasites at the single oocyst level. WGA-based PCR method can also be applied for the identification and genetic characterization of other protists. Copyright © 2014 Elsevier Inc. All rights reserved.

Optimization of the GOES-1 Imagers radiometric accuracy: Drift and 1/f noise suppression

International Nuclear Information System (INIS)

Bremer, J.C.; Comeyne, G.J. III

1994-01-01

The raw output of many scanning radiometers is a small, rapidly varying signal superimposed on a large background that varies more slowly, due to thermal drifts and 1/f noise. To isolate the signal, it is necessary to perform a differential measurement: measure a known reference and subtract it from each of the raw outputs, canceling the common-mode background. Calibration is also a differential measurement: the difference between two outputs is divided by the difference between the two known references that produced them to determine the gain. The GOES-I Imager views space as its background subtraction reference and a full-aperture blackbody as its second reference for calibration. The background suppression efficiency of a differential measurement algorithm depends on its timing. The Imager measures space references before and after each scan line and performs interpolated background subtraction: a unique, linearly weighted average of the two references is subtracted from each scene sample in that line, canceling both constant bias and linear drift. One model quantifies the Gaussian noise and 1/f noise terms in the noise equivalent bandwidth, which is minimized to optimize the algorithm. The authors have obtained excellent agreement between the analytical predictions and Monte Carlo computer simulations

Automating dipole subtraction

Energy Technology Data Exchange (ETDEWEB)

Hasegawa, K.; Moch, S. [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany); Uwer, P. [Karlsruhe Univ. (T.H.) (Germany). Inst. fuer Theoretische Teilchenphysik

2008-07-15

We report on automating the Catani-Seymour dipole subtraction which is a general procedure to treat infrared divergences in real emission processes at next-to-leading order in QCD. The automatization rests on three essential steps: the creation of the dipole terms, the calculation of the color linked squared Born matrix elements, and the evaluation of different helicity amplitudes. The routines have been tested for a number of complex processes, such as the real emission process gg{yields}t anti tggg. (orig.)

Automating dipole subtraction

International Nuclear Information System (INIS)

Hasegawa, K.; Moch, S.; Uwer, P.

2008-07-01

We report on automating the Catani-Seymour dipole subtraction which is a general procedure to treat infrared divergences in real emission processes at next-to-leading order in QCD. The automatization rests on three essential steps: the creation of the dipole terms, the calculation of the color linked squared Born matrix elements, and the evaluation of different helicity amplitudes. The routines have been tested for a number of complex processes, such as the real emission process gg→t anti tggg. (orig.)

Colourful FKS subtraction

CERN Document Server

Frixione, Stefano

2011-01-01

I formulate in a colour-friendly way the FKS method for the computation of QCD cross sections at the next-to-leading order accuracy. This is achieved through the definition of subtraction terms for squared matrix elements, constructed with single colour-dressed or pairs of colour-ordered amplitudes. The latter approach relies on the use of colour flows, is exact to all orders in $N$, and is thus particularly suited to being organized as a systematic expansion in 1/N.

A TaqMan real-time PCR-based assay for the identification of Fasciola spp.

Science.gov (United States)

Alasaad, Samer; Soriguer, Ramón C; Abu-Madi, Marawan; El Behairy, Ahmed; Jowers, Michael J; Baños, Pablo Díez; Píriz, Ana; Fickel, Joerns; Zhu, Xing-Quan

2011-06-30

Real time quantitative PCR (qPCR) is one of the key technologies of the post-genome era, with clear advantages compared to normal end-point PCR. In this paper, we report the first qPCR-based assay for the identification of Fasciola spp. Based on sequences of the second internal transcribed spacers (ITS-2) of the ribosomal rRNA gene, we used a set of genus-specific primers for Fasciola ITS-2 amplification, and we designed species-specific internal TaqMan probes to identify F. hepatica and F. gigantica, as well as the hybrid 'intermediate'Fasciola. These primers and probes were used for the highly specific, sensitive, and simple identification of Fasciola species collected from different animal host from China, Spain, Niger and Egypt. The novel qPCR-based technique for the identification of Fasciola spp. may provide a useful tool for the epidemiological investigation of Fasciola infection, including their intermediate snail hosts. Copyright © 2011 Elsevier B.V. All rights reserved.

Nonenhanced magnetic resonance angiography (MRA) of the calf arteries at 3 Tesla: intraindividual comparison of 3D flow-dependent subtractive MRA and 2D flow-independent non-subtractive MRA.

Science.gov (United States)

Knobloch, Gesine; Lauff, Marie-Teres; Hirsch, Sebastian; Schwenke, Carsten; Hamm, Bernd; Wagner, Moritz

2016-12-01

To prospectively compare 3D flow-dependent subtractive MRA vs. 2D flow-independent non-subtractive MRA for assessment of the calf arteries at 3 Tesla. Forty-two patients with peripheral arterial occlusive disease underwent nonenhanced MRA of calf arteries at 3 Tesla with 3D flow-dependent subtractive MRA (fast spin echo sequence; 3D-FSE-MRA) and 2D flow-independent non-subtractive MRA (balanced steady-state-free-precession sequence; 2D-bSSFP-MRA). Moreover, all patients underwent contrast-enhanced MRA (CE-MRA) as standard-of-reference. Two readers performed a per-segment evaluation for image quality (4 = excellent to 0 = non-diagnostic) and severity of stenosis. Image quality scores of 2D-bSSFP-MRA were significantly higher compared to 3D-FSE-MRA (medians across readers: 4 vs. 3; p Tesla with significantly higher image quality and diagnostic accuracy compared to 3D flow-dependent subtractive MRA (3D-FSE-MRA). • 2D flow-independent non-subtractive MRA (2D-bSSFP-MRA) is a robust NE-MRA technique at 3T • 2D-bSSFP-MRA outperforms 3D flow-dependent subtractive MRA (3D-FSE-MRA) as NE-MRA of calf arteries • 2D-bSSFP-MRA is a promising alternative to CE-MRA for calf PAOD evaluation.

Digital subtraction angiography (DSA)

International Nuclear Information System (INIS)

Ludwig, J.W.; Eikelboom, B.C.; Van Schaik, C.C.; Taams, A.J.; Teeuwen, C.

1985-01-01

Besides the non-invasive techniques, angiography remains essential. The disadvantages of angiography are the complexity of the procedure and the possibility of complications. Digital subtraction angiography (DSA) is a considerable improvement in the examination of vessels. In DSA, subtraction combined with enhancement of the signals allows the use of intravenous injection to obtain good images of the arteries. However, when the contrast material is supplied intravenously, a rather large amount of contrast material is necessary to obtain images of good quality. Quantities of 30-40 cc of contrast material are required. The advantage of the intravenous injection of contrast material rather than the use of a catheter to deliver the contrast material in loco is that it is almost non-invasive thus circumventing the complications caused by catheter manipulation in the arterial system. This makes it possible to apply this method on an out-patient basis. DSA can also be applied with intra-arterial selective injection of the contrast material. In this case, the strong enhancement with DSA allows the use of a small quantity of contrast material while still obtaining images of the vessels with good contrast definition

The potential for neurovascular intravenous angiography using K-edge digital subtraction angiography

International Nuclear Information System (INIS)

Schueltke, E.; Fiedler, S.; Kelly, M.; Griebel, R.; Juurlink, B.; LeDuc, G.; Esteve, F.; Le Bas, J.-F.; Renier, M.; Nemoz, C.; Meguro, K.

2005-01-01

Background: Catheterization of small-caliber blood vessels in the central nervous system can be extremely challenging. Alternatively, intravenous (i.v.) administration of contrast agent is minimally invasive and therefore carries a much lower risk for the patient. With conventional X-ray equipment, volumes of contrast agent that could be safely administered to the patient do not allow acquisition of high-quality images after i.v. injection, because the contrast bolus is extremely diluted by passage through the heart. However, synchrotron-based digital K-edge subtraction angiography does allow acquisition of high-quality images after i.v. administration of relatively small doses of contrast agent. Materials and methods: Eight adult male New Zealand rabbits were used for our experiments. Animals were submitted to both angiography with conventional X-ray equipment and synchrotron-based digital subtraction angiography. Results: With conventional X-ray equipment, no contrast was seen in either cerebral or spinal blood vessels after i.v. injection of iodinated contrast agent. However, using K-edge digital subtraction angiography, as little as 1 ml iodinated contrast agent, when administered as i.v. bolus, yielded images of small-caliber blood vessels in the central nervous system (both brain and spinal cord). Conclusions: If it would be possible to image blood vessels of the same diameter in the central nervous system of human patients, the synchrotron-based technique could yield high-quality images at a significantly lower risk for the patient than conventional X-ray imaging. Images could be acquired where catheterization of feeding blood vessels has proven impossible

Development and Evaluation of a PCR and Mass Spectroscopy-based (PCR-MS) Method for Quantitative, Type-specific Detection of Human Papillomavirus

Science.gov (United States)

Patel, Divya A.; Shih, Yang-Jen; Newton, Duane W.; Michael, Claire W.; Oeth, Paul A.; Kane, Michael D.; Opipari, Anthony W.; Ruffin, Mack T.; Kalikin, Linda M.; Kurnit, David M.

2010-01-01

Knowledge of the central role of high-risk human papillomavirus (HPV) in cervical carcinogenesis, coupled with an emerging need to monitor the efficacy of newly introduced HPV vaccines, warrant development and evaluation of type-specific, quantitative HPV detection methods. In the present study, a prototype PCR and mass spectroscopy (PCR-MS)-based method to detect and quantitate 13 high-risk HPV types is compared to the Hybrid Capture 2 High Risk HPV DNA test (HC2; Digene Corp., Gaithersburg, MD) in 199 cervical scraping samples and to DNA sequencing in 77 cervical tumor samples. High-risk HPV types were detected in 76/77 (98.7%) cervical tumor samples by PCR-MS. Degenerate and type-specific sequencing confirmed the types detected by PCR-MS. In 199 cervical scraping samples, all 13 HPV types were detected by PCR-MS. Eighteen (14.5%) of 124 cervical scraping samples that were positive for high-risk HPV by HC2 were negative by PCR-MS. In all these cases, degenerate DNA sequencing failed to detect any of the 13 high-risk HPV types. Nearly half (46.7%) of the 75 cervical scraping samples that were negative for high-risk HPV by the HC2 assay were positive by PCR-MS. Type-specific sequencing in a subset of these samples confirmed the HPV type detected by PCR-MS. Quantitative PCR-MS results demonstrated that 11/75 (14.7%) samples contained as much HPV copies/cell as HC2-positive samples. These findings suggest that this prototype PCR-MS assay performs at least as well as HC2 for HPV detection, while offering the additional, unique advantages of type-specific identification and quantitation. Further validation work is underway to define clinically meaningful HPV detection thresholds and to evaluate the potential clinical application of future generations of the PCR-MS assay. PMID:19410602

Development and evaluation of a PCR and mass spectroscopy (PCR-MS)-based method for quantitative, type-specific detection of human papillomavirus.

Science.gov (United States)

Patel, Divya A; Shih, Yang-Jen; Newton, Duane W; Michael, Claire W; Oeth, Paul A; Kane, Michael D; Opipari, Anthony W; Ruffin, Mack T; Kalikin, Linda M; Kurnit, David M

2009-09-01

Knowledge of the central role of high-risk human papillomavirus (HPV) in cervical carcinogenesis, coupled with an emerging need to monitor the efficacy of newly introduced HPV vaccines, warrant development and evaluation of type-specific, quantitative HPV detection methods. In the present study, a prototype PCR and mass spectroscopy (PCR-MS)-based method to detect and quantitate 13 high-risk HPV types is compared to the Hybrid Capture 2 High-Risk HPV DNA test (HC2; Digene Corp., Gaithersburg, MD) in 199 cervical scraping samples and to DNA sequencing in 77 cervical tumor samples. High-risk HPV types were detected in 76/77 (98.7%) cervical tumor samples by PCR-MS. Degenerate and type-specific sequencing confirmed the types detected by PCR-MS. In 199 cervical scraping samples, all 13 HPV types were detected by PCR-MS. Eighteen (14.5%) of 124 cervical scraping samples that were positive for high-risk HPV by HC2 were negative by PCR-MS. In all these cases, degenerate DNA sequencing failed to detect any of the 13 high-risk HPV types. Nearly half (46.7%) of the 75 cervical scraping samples that were negative for high-risk HPV by the HC2 assay were positive by PCR-MS. Type-specific sequencing in a subset of these samples confirmed the HPV type detected by PCR-MS. Quantitative PCR-MS results demonstrated that 11/75 (14.7%) samples contained as much HPV copies/cell as HC2-positive samples. These findings suggest that this prototype PCR-MS assay performs at least as well as HC2 for HPV detection, while offering the additional, unique advantages of type-specific identification and quantitation. Further validation work is underway to define clinically meaningful HPV detection thresholds and to evaluate the potential clinical application of future generations of the PCR-MS assay.

Subleading power corrections for N -jettiness subtractions

Science.gov (United States)

Moult, Ian; Rothen, Lorena; Stewart, Iain W.; Tackmann, Frank J.; Zhu, Hua Xing

2017-04-01

The N -jettiness observable TN provides a way of describing the leading singular behavior of the N -jet cross section in the τ =TN/Q →0 limit, where Q is a hard interaction scale. We consider subleading-power corrections in the τ ≪1 expansion, and employ soft-collinear effective theory to obtain analytic results for the dominant αsτ ln τ and αs2τ ln3τ subleading terms for thrust in e+e- collisions and 0-jettiness for q q ¯-initiated Drell-Yan-like processes at hadron colliders. These results can be used to significantly improve the numerical accuracy and stability of the N -jettiness subtraction technique for performing fixed-order calculations at next-to-leading order and next-to-next-to-leading order. They reduce the size of missing power corrections in the subtractions by an order of magnitude. We also point out that the precise definition of N -jettiness has an important impact on the size of the power corrections and thus the numerical accuracy of the subtractions. The sometimes employed definition of N -jettiness in the hadronic center-of-mass frame suffers from power corrections that grow exponentially with rapidity, causing the power expansion to deteriorate away from central rapidity. This degradation does not occur for the original N -jettiness definition, which explicitly accounts for the boost of the Born process relative to the frame of the hadronic collision, and has a well-behaved power expansion throughout the entire phase space. Integrated over rapidity, using this N -jettiness definition in the subtractions yields another order of magnitude improvement compared to employing the hadronic-frame definition.

Physical principles of cardiac digital subtraction angiography

International Nuclear Information System (INIS)

Buonocore, E.; Pavlicek, W.

1986-01-01

Advances in the applications of computers with standard radiologic equipment have resulted in the development of electronic, or so-called ''film-less'' imaging. This technique, discussed by the authors, has become of particular value in the visualization of the central vascular system and has become known as digital subtraction angiography (DSA). Commercial products have become increasingly available and are capable of converting T.V. signals, obtained by conventional fluorography, to a computed array of digital values. Addition, subtraction, and averaging of this data, result in images with adequate signal-to-noise ratios that achieve detection of low concentrations of contrast media not possible with conventional screen film techniques. Computer subtraction of unnecessary background information improves the conspicuity of the opacified vessels to permit detection of vascular structures containing a concentration of no more than 1-3 percent of contrast media. This improved visualization is possible even with intravenous peripheral injections or reduced amounts of contrast media given intraarterially. With either method of contrast media administration, DSDA has become an excellent means of anatomic demonstration of the heart and great vessels with decreased morbidity and at lower cost

An analysis of the influence of background subtraction and quenching on jet observables in heavy-ion collisions

CERN Document Server

Apolinario, Liliana; Cunqueiro, Leticia

2013-01-01

Subtraction of the large background in reconstruction is a key ingredient in jet studies in high-energy heavy-ion collisions at RHIC and the LHC. Here we address the question to which extent the most commonly used subtraction techniques are able to eliminate the effects of the background on the most commonly discussed observables at present: single inclusive jet distributions, dijet asymmetry and azimuthal distributions. We consider two different background subtraction methods, an area-based one implemented through the FastJet pack- age and a pedestal subtraction method, that resemble the ones used by the experimental collaborations at the LHC. We also analyze different ways of defining the optimal parame- ters in the second method. We use a toy model that easily allows variations of the background characteristics: average background level and fluctuations and azimuthal structure, but cross- checks are also done with a Monte Carlo simulator. Furthermore, we consider the influence of quenching using Q-PYTHIA o...

Lung nodule detection by microdose CT versus chest radiography (standard and dual-energy subtracted).

Science.gov (United States)

Ebner, Lukas; Bütikofer, Yanik; Ott, Daniel; Huber, Adrian; Landau, Julia; Roos, Justus E; Heverhagen, Johannes T; Christe, Andreas

2015-04-01

The purpose of this study was to investigate the feasibility of microdose CT using a comparable dose as for conventional chest radiographs in two planes including dual-energy subtraction for lung nodule assessment. We investigated 65 chest phantoms with 141 lung nodules, using an anthropomorphic chest phantom with artificial lung nodules. Microdose CT parameters were 80 kV and 6 mAs, with pitch of 2.2. Iterative reconstruction algorithms and an integrated circuit detector system (Stellar, Siemens Healthcare) were applied for maximum dose reduction. Maximum intensity projections (MIPs) were reconstructed. Chest radiographs were acquired in two projections with bone suppression. Four blinded radiologists interpreted the images in random order. A soft-tissue CT kernel (I30f) delivered better sensitivities in a pilot study than a hard kernel (I70f), with respective mean (SD) sensitivities of 91.1%±2.2% versus 85.6%±5.6% (p=0.041). Nodule size was measured accurately for all kernels. Mean clustered nodule sensitivity with chest radiography was 45.7%±8.1% (with bone suppression, 46.1%±8%; p=0.94); for microdose CT, nodule sensitivity was 83.6%±9% without MIP (with additional MIP, 92.5%±6%; pmicrodose CT for readers 1, 2, 3, and 4 were 84.3%, 90.7%, 68.6%, and 45.0%, respectively. Sensitivities with chest radiography for readers 1, 2, 3, and 4 were 42.9%, 58.6%, 36.4%, and 90.7%, respectively. In the per-phantom analysis, respective sensitivities of microdose CT versus chest radiography were 96.2% and 75% (pmicrodose CT, the applied dose was 0.1323 mSv. Microdose CT is better than the combination of chest radiography and dual-energy subtraction for the detection of solid nodules between 5 and 12 mm at a lower dose level of 0.13 mSv. Soft-tissue kernels allow better sensitivities. These preliminary results indicate that microdose CT has the potential to replace conventional chest radiography for lung nodule detection.

Clinical Assessment of a Nocardia PCR-Based Assay for Diagnosis of Nocardiosis.

Science.gov (United States)

Rouzaud, Claire; Rodriguez-Nava, Véronica; Catherinot, Emilie; Méchaï, Frédéric; Bergeron, Emmanuelle; Farfour, Eric; Scemla, Anne; Poirée, Sylvain; Delavaud, Christophe; Mathieu, Daniel; Durupt, Stéphane; Larosa, Fabrice; Lengelé, Jean-Philippe; Christophe, Jean-Louis; Suarez, Felipe; Lortholary, Olivier; Lebeaux, David

2018-06-01

The diagnosis of nocardiosis, a severe opportunistic infection, is challenging. We assessed the specificity and sensitivity of a 16S rRNA Nocardia PCR-based assay performed on clinical samples. In this multicenter study (January 2014 to April 2015), patients who were admitted to three hospitals and had an underlying condition favoring nocardiosis, clinical and radiological signs consistent with nocardiosis, and a Nocardia PCR assay result for a clinical sample were included. Patients were classified as negative control (NC) (negative Nocardia culture results and proven alternative diagnosis or improvement at 6 months without anti- Nocardia treatment), positive control (PC) (positive Nocardia culture results), or probable nocardiosis (positive Nocardia PCR results, negative Nocardia culture results, and no alternative diagnosis). Sixty-eight patients were included; 47 were classified as NC, 8 as PC, and 13 as probable nocardiosis. PCR results were negative for 35/47 NC patients (74%). For the 12 NC patients with positive PCR results, the PCR assay had been performed with respiratory samples. These NC patients had chronic bronchopulmonary disease more frequently than did the NC patients with negative PCR results (8/12 patients [67%] versus 11/35 patients [31%]; P = 0.044). PCR results were positive for 7/8 PC patients (88%). There were 13 cases of probable nocardiosis, diagnosed solely using the PCR results; 9 of those patients (69%) had lung involvement (consolidation or nodule). Nocardia PCR testing had a specificity of 74% and a sensitivity of 88% for the diagnosis of nocardiosis. Nocardia PCR testing may be helpful for the diagnosis of nocardiosis in immunocompromised patients but interpretation of PCR results from respiratory samples is difficult, because the PCR assay may also detect colonization. Copyright © 2018 American Society for Microbiology.

M-BAND IMAGING OF THE HR 8799 PLANETARY SYSTEM USING AN INNOVATIVE LOCI-BASED BACKGROUND SUBTRACTION TECHNIQUE

International Nuclear Information System (INIS)

Galicher, Raphael; Marois, Christian; Macintosh, Bruce; Konopacky, Quinn; Barman, Travis

2011-01-01

Multi-wavelength observations/spectroscopy of exoplanetary atmospheres are the basis of the emerging exciting field of comparative exoplanetology. The HR 8799 planetary system is an ideal laboratory to study our current knowledge gap between massive field brown dwarfs and the cold 5 Gyr old solar system planets. The HR 8799 planets have so far been imaged at J- to L-band, with only upper limits available at M-band. We present here deep high-contrast Keck II adaptive optics M-band observations that show the imaging detection of three of the four currently known HR 8799 planets. Such detections were made possible due to the development of an innovative LOCI-based background subtraction scheme that is three times more efficient than a classical median background subtraction for Keck II AO data, representing a gain in telescope time of up to a factor of nine. These M-band detections extend the broadband photometric coverage out to ∼5 μm and provide access to the strong CO fundamental absorption band at 4.5 μm. The new M-band photometry shows that the HR 8799 planets are located near the L/T-type dwarf transition, similar to what was found by other studies. We also confirm that the best atmospheric fits are consistent with low surface gravity, dusty, and non-equilibrium CO/CH 4 chemistry models.

Gene Expression Profiling in the Pituitary Gland of Laying Period and Ceased Period Huoyan Geese

Directory of Open Access Journals (Sweden)

Xinhong Luan

2013-07-01

Full Text Available Huoyan goose is a Chinese local breed famous for its higher laying performance, but the problems of variety degeneration have emerged recently, especially a decrease in the number of eggs laid. In order to better understand the molecular mechanism that underlies egg laying in Huoyan geese, gene profiles in the pituitary gland of Huoyan geese taken during the laying period and ceased period were investigated using the suppression subtractive hybridization (SSH method. Total RNA was extracted from pituitary glands of ceased period and laying period geese. The cDNA in the pituitary glands of ceased geese was subtracted from the cDNA in the pituitary glands of laying geese (forward subtraction; the reverse subtraction was also performed. After sequencing and annotation, a total of 30 and 24 up and down-regulated genes were obtained from the forward and reverse SSH libraries, respectively. These genes mostly related to biosynthetic process, cellular nitrogen compound metabolic process, transport, cell differentiation, cellular protein modification process, signal transduction, small molecule metabolic process. Furthermore, eleven genes were selected for further analyses by quantitative real-time PCR (qRT-PCR. The qRT-PCR results for the most part were consistent with the SSH results. Among these genes, Synaptotagmin-1 (SYT1 and Stathmin-2 (STMN2 were substantially over-expressed in laying period compared to ceased period. These results could serve as an important reference for elucidating the molecular mechanism of higher laying performance in Huoyan geese.

Partial and Full PCR-Based Reverse Genetics Strategy for Influenza Viruses

Science.gov (United States)

Chen, Hongjun; Ye, Jianqiang; Xu, Kemin; Angel, Matthew; Shao, Hongxia; Ferrero, Andrea; Sutton, Troy; Perez, Daniel R.

2012-01-01

Since 1999, plasmid-based reverse genetics (RG) systems have revolutionized the way influenza viruses are studied. However, it is not unusual to encounter cloning difficulties for one or more influenza genes while attempting to recover virus de novo. To overcome some of these shortcomings we sought to develop partial or full plasmid-free RG systems. The influenza gene of choice is assembled into a RG competent unit by virtue of overlapping PCR reactions containing a cDNA copy of the viral gene segment under the control of RNA polymerase I promoter (pol1) and termination (t1) signals – herein referred to as Flu PCR amplicons. Transfection of tissue culture cells with either HA or NA Flu PCR amplicons and 7 plasmids encoding the remaining influenza RG units, resulted in efficient virus rescue. Likewise, transfections including both HA and NA Flu PCR amplicons and 6 RG plasmids also resulted in efficient virus rescue. In addition, influenza viruses were recovered from a full set of Flu PCR amplicons without the use of plasmids. PMID:23029501

Detection of Histoplasma capsulatum from clinical specimens by cycling probe-based real-time PCR and nested real-time PCR.

Science.gov (United States)

Muraosa, Yasunori; Toyotome, Takahito; Yahiro, Maki; Watanabe, Akira; Shikanai-Yasuda, Maria Aparecida; Kamei, Katsuhiko

2016-05-01

We developed new cycling probe-based real-time PCR and nested real-time PCR assays for the detection of Histoplasma capsulatum that were designed to detect the gene encoding N-acetylated α-linked acidic dipeptidase (NAALADase), which we previously identified as an H. capsulatum antigen reacting with sera from patients with histoplasmosis. Both assays specifically detected the DNAs of all H. capsulatum strains but not those of other fungi or human DNA. The limited of detection (LOD) of the real-time PCR assay was 10 DNA copies when using 10-fold serial dilutions of the standard plasmid DNA and 50 DNA copies when using human serum spiked with standard plasmid DNA. The nested real-time PCR improved the LOD to 5 DNA copies when using human serum spiked with standard plasmid DNA, which represents a 10-fold higher than that observed with the real-time PCR assay. To assess the ability of the two assays to diagnose histoplasmosis, we analyzed a small number of clinical specimens collected from five patients with histoplasmosis, such as sera (n = 4), formalin-fixed paraffin-embedded (FFPE) tissue (n = 4), and bronchoalveolar lavage fluid (BALF) (n = 1). Although clinical sensitivity of the real-time PCR assay was insufficiently sensitive (33%), the nested real-time PCR assay increased the clinical sensitivity (77%), suggesting it has a potential to be a useful method for detecting H. capsulatum DNA in clinical specimens. © The Author 2015. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Reduction of Musical Noise in Spectral Subtraction Method Using Subframe Phase Randomization

Energy Technology Data Exchange (ETDEWEB)

Seok, J.W.; Bae, K.S. [Kyungpook National University, Taegu (Korea)

1999-06-01

The Subframe phase randomization method is applied to the spectral subtraction method to reduce the musical noise in nonvoicing region after speech enhancement. The musical noise in the spectral subtraction method is the result of the narrowband tonal components that appearing somewhat periodically in the spectrogram of unvoiced and silence regions. Thus each synthesis frame in nonvoicing region is divided into several subframes to broaden the narrowband spectrum, and then phases of silence and unvoiced regions are randomized to eliminate the tonal components in the spectrum while keeping the shape of the amplitude spectrum. Performance assessments based on visual inspection of spectrogram, objective measure, and informal subjective listening tests demonstrate the superiority of the proposed algorithm. (author). 7 refs., 5 figs.

Digital image comparison by subtracting contextual transformations—percentile rank order differentiation

Science.gov (United States)

Wehde, M. E.

1995-01-01

The common method of digital image comparison by subtraction imposes various constraints on the image contents. Precise registration of images is required to assure proper evaluation of surface locations. The attribute being measured and the calibration and scaling of the sensor are also important to the validity and interpretability of the subtraction result. Influences of sensor gains and offsets complicate the subtraction process. The presence of any uniform systematic transformation component in one of two images to be compared distorts the subtraction results and requires analyst intervention to interpret or remove it. A new technique has been developed to overcome these constraints. Images to be compared are first transformed using the cumulative relative frequency as a transfer function. The transformed images represent the contextual relationship of each surface location with respect to all others within the image. The process of differentiating between the transformed images results in a percentile rank ordered difference. This process produces consistent terrain-change information even when the above requirements necessary for subtraction are relaxed. This technique may be valuable to an appropriately designed hierarchical terrain-monitoring methodology because it does not require human participation in the process.

A Monte Carlo simulation study of an improved K-edge log-subtraction X-ray imaging using a photon counting CdTe detector

Energy Technology Data Exchange (ETDEWEB)

Lee, Youngjin, E-mail: radioyoungj@gmail.com [Department of Radiological Science, Eulji University, 553, Sanseong-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do (Korea, Republic of); Lee, Amy Candy [Department of Mathematics and Statistics, McGill University (Canada); Kim, Hee-Joung [Department of Radiological Science and Radiation Convergence Engineering, Yonsei University (Korea, Republic of)

2016-09-11

Recently, significant effort has been spent on the development of photons counting detector (PCD) based on a CdTe for applications in X-ray imaging system. The motivation of developing PCDs is higher image quality. Especially, the K-edge subtraction (KES) imaging technique using a PCD is able to improve image quality and useful for increasing the contrast resolution of a target material by utilizing contrast agent. Based on above-mentioned technique, we presented an idea for an improved K-edge log-subtraction (KELS) imaging technique. The KELS imaging technique based on the PCDs can be realized by using different subtraction energy width of the energy window. In this study, the effects of the KELS imaging technique and subtraction energy width of the energy window was investigated with respect to the contrast, standard deviation, and CNR with a Monte Carlo simulation. We simulated the PCD X-ray imaging system based on a CdTe and polymethylmethacrylate (PMMA) phantom which consists of the various iodine contrast agents. To acquired KELS images, images of the phantom using above and below the iodine contrast agent K-edge absorption energy (33.2 keV) have been acquired at different energy range. According to the results, the contrast and standard deviation were decreased, when subtraction energy width of the energy window is increased. Also, the CNR using a KELS imaging technique is higher than that of the images acquired by using whole energy range. Especially, the maximum differences of CNR between whole energy range and KELS images using a 1, 2, and 3 mm diameter iodine contrast agent were acquired 11.33, 8.73, and 8.29 times, respectively. Additionally, the optimum subtraction energy width of the energy window can be acquired at 5, 4, and 3 keV for the 1, 2, and 3 mm diameter iodine contrast agent, respectively. In conclusion, we successfully established an improved KELS imaging technique and optimized subtraction energy width of the energy window, and based on

Late iodine enhancement computed tomography with image subtraction for assessment of myocardial infarction

Energy Technology Data Exchange (ETDEWEB)

Tanabe, Yuki; Kido, Teruhito; Kurata, Akira; Kouchi, Takanori; Fukuyama, Naoki; Yokoi, Takahiro; Miyagawa, Masao; Mochizuki, Teruhito [Ehime University Graduate School of Medicine, Department of Radiology, Toon City, Ehime (Japan); Uetani, Teruyoshi [Department of Cardiology, Ehime University Graduate School of Medicine, Toon City, Ehime (Japan); Yamashita, Natsumi [National Hospital Organization Shikoku Cancer Center, Department of Clinical Biostatistics, Section of Cancer Prevention and Epidemiology, Clinical Research Center, Matsuyama City, Ehime (Japan)

2018-03-15

To evaluate the feasibility of image subtraction in late iodine enhancement CT (LIE-CT) for assessment of myocardial infarction (MI). A comprehensive cardiac CT protocol and late gadolinium enhancement MRI (LGE-MRI) was used to assess coronary artery disease in 27 patients. LIE-CT was performed after stress CT perfusion (CTP) and CT angiography. Subtraction LIE-CT was created by subtracting the mask volume of the left ventricle (LV) cavity from the original LIE-CT using CTP dataset. The %MI volume was quantified as the ratio of LIE to entire LV volume, and transmural extent (TME) of LIE was classified as 0%, 1-24%, 25-49%, 50-74% or 75-100%. These results were compared with LGE-MRI using the Spearman rank test, Bland-Altman method and chi-square test. One hundred twenty-five (29%) of 432 segments were positive on LGE-MRI. Correlation coefficients for original and subtraction LIE-CT to LGE-MRI were 0.79 and 0.85 for %MI volume. Concordances of the 5-point grading scale between original and subtraction LIE-CT with LGE-MRI were 75% and 84% for TME; concordance was significantly improved using the subtraction technique (p <0.05). Subtraction LIE-CT allowed more accurate assessment of MI extent than the original LIE-CT. (orig.)

Decoupling Subtraction Conserving Full Gauge Symmetries : Particles and Fields

OpenAIRE

Noriyasu, OHTSUBO; Hideo, MIYATA; Department of Phycics, Kanazawa Technical College; Department of Information Science, Kanazawa Institute of Technolgy

1984-01-01

A new subtraction scheme (^^^) which realizes the decoupling and conserves the symmetries of full gauge group simultaneously, is proposed. One particle irreducible Green's functions subtracted by ^^^ reveal the effective low energy symmetries at -p^2≪M^2 and the full symmetries at -p^2≫M^2, where M denotes a heavy mass. Also discussed are conditions in order to carry out ^^^ under two-loop approximation.

Quantum dots for a high-throughput Pfu polymerase based multi-round polymerase chain reaction (PCR).

Science.gov (United States)

Sang, Fuming; Zhang, Zhizhou; Yuan, Lin; Liu, Deli

2018-02-26

Multi-round PCR is an important technique for obtaining enough target DNA from rare DNA resources, and is commonly used in many fields including forensic science, ancient DNA analysis and cancer research. However, multi-round PCR is often aborted, largely due to the accumulation of non-specific amplification during repeated amplifications. Here, we developed a Pfu polymerase based multi-round PCR technique assisted by quantum dots (QDs). Different PCR assays, DNA polymerases (Pfu and Taq), DNA sizes and GC amounts were compared in this study. In the presence of QDs, PCR specificity could be retained even in the ninth-round amplification. Moreover, the longer and more complex the targets were, the earlier the abortion happened in multi-round PCR. However, no obvious enhancement of specificity was found in multi-round PCR using Taq DNA polymerase. Significantly, the fidelity of Pfu polymerase based multi-round PCR was not sacrificed in the presence of QDs. Besides, pre-incubation at 50 °C for an hour had no impact on multi-round PCR performance, which further authenticated the hot start effect of QDs modulated in multi-round PCR. The findings of this study demonstrated that a cost-effective and promising multi-round PCR technique for large-scale and high-throughput sample analysis could be established with high specificity, sensibility and accuracy.

Subtraction MR venography acquired from time-resolved contrast-enhanced MR angiography: Comparison with phase-contrast MR venography and single-phase contrast-enhanced MR venography

International Nuclear Information System (INIS)

Jang, Jin Hee; Kim, Bum Soo; KIm, Bom Yi; Choi, Hyun Seok; Jung, So Lyung; Ahn, Kook Jin; Sung, Ji Kyeong

2015-01-01

To evaluate the image characteristics of subtraction magnetic resonance venography (SMRV) from time-resolved contrast-enhanced MR angiography (TRMRA) compared with phase-contrast MR venography (PCMRV) and single-phase contrast-enhanced MR venography (CEMRV). Twenty-one patients who underwent brain MR venography (MRV) using standard protocols (PCMRV, CEMRV, and TRMRA) were included. SMRV was made by subtracting the arterial phase data from the venous phase data in TRMRA. Co-registration and subtraction of the two volume data was done using commercially available software. Image quality and the degree of arterial contamination of the three MRVs were compared. In the three MRVs, 19 pre-defined venous structures (14 dural sinuses and 5 cerebral veins) were evaluated. The signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) of the three MRVs were also compared. Single-phase contrast-enhanced MR venography showed better image quality (median score 4 in both reviewers) than did the other two MRVs (p < 0.001), whereas SMRV (median score 3 in both reviewers) and PCMRV (median score 3 in both reviewers) had similar image quality (p ≥ 0.951). SMRV (median score 0 in both reviewers) suppressed arterial signal better than did the other MRVs (median score 1 in CEMRV, median score 2 in PCMRV, both reviewers) (p < 0.001). The dural sinus score of SMRV (median and interquartile range [IQR] 48, 43-50 for reviewer 1, 47, 43-49 for reviewer 2) was significantly higher than for PCMRV (median and IQR 31, 25-34 for reviewer 1, 30, 23-32 for reviewer 2) (p < 0.01) and did not differ from that of CEMRV (median and IQR 50, 47-52 for reviewer 1, 49, 45-51 for reviewer 2) (p = 0.146 in reviewer 1 and 0.123 in reviewer 2). The SNR and CNR of SMRV (median and IQR 104.5, 83.1-121.2 and 104.1, 74.9-120.5, respectively) were between those of CEMRV (median and IQR 150.3, 111-182.6 and 148.4, 108-178.2) and PCMRV (median and IQR 59.4, 49.2-74.9 and 53.6, 43.8-69.2). Subtraction magnetic

Real-time PCR (qPCR) primer design using free online software.

Science.gov (United States)

Thornton, Brenda; Basu, Chhandak

2011-01-01

Real-time PCR (quantitative PCR or qPCR) has become the preferred method for validating results obtained from assays which measure gene expression profiles. The process uses reverse transcription polymerase chain reaction (RT-PCR), coupled with fluorescent chemistry, to measure variations in transcriptome levels between samples. The four most commonly used fluorescent chemistries are SYBR® Green dyes and TaqMan®, Molecular Beacon or Scorpion probes. SYBR® Green is very simple to use and cost efficient. As SYBR® Green dye binds to any double-stranded DNA product, its success depends greatly on proper primer design. Many types of online primer design software are available, which can be used free of charge to design desirable SYBR® Green-based qPCR primers. This laboratory exercise is intended for those who have a fundamental background in PCR. It addresses the basic fluorescent chemistries of real-time PCR, the basic rules and pitfalls of primer design, and provides a step-by-step protocol for designing SYBR® Green-based primers with free, online software. Copyright © 2010 Wiley Periodicals, Inc.

Intravenous digital subtraction angiography of transplanted kidney artery

International Nuclear Information System (INIS)

Tessier, J.P; Teyssou, H.; Verdier, J.P.; Tison, E.; Meyblum, J.; Marchal, M.

1986-01-01

Results of 351 intravenous digital subtraction angiographs (AN) of transplanted kidneys emphasized reliability of this examination for detection of renal artery stenosis. A prospective study of 219 patients (188 interpretable AN) showed significant stenosis of grafted artery in 22% of cases: 17% of the 126 patients with normal blood pressure and 34% of the 62 cases of hypertension. Digital subtraction allows, with a single injection, assessment of renal artery, nephrogram and excretory cavities, but it is not a substitute for conventional intravenous urography 1 to 2 months after grafting [fr

Development and evaluation of new primers for PCR-based identification of Prevotella intermedia.

Science.gov (United States)

Zhou, Yanbin; Liu, Dali; Wang, Yiwei; Zhu, Cailian; Liang, Jingping; Shu, Rong

2014-08-01

The aim of this study was to develop new Prevotella intermedia-specific PCR primers based on the 16S rRNA. The new primer set, Pi-192 and Pi-468, increased the accuracy of PCR-based P. intermedia identification and could be useful in the detection of P. intermedia as well as epidemiological studies on periodontal disease. Copyright © 2014 Elsevier Ltd. All rights reserved.

Digital subtraction radiography in the study of the lacrimal system

International Nuclear Information System (INIS)

Falaschi, F.; Pieri, L.; Perri, G.; Signorini, G.; Genovese Ebert, F.

1988-01-01

The authors emphasize the usefulness of digital dacrycystography (DCG), as compared with various current technoques. Utilizing a radiographic unit equipped with a video-fluoroscopic system and interfaced to a digital video-processor, several digitalized images are acquired before, during and after the injection of contrast medium. Final images are obtained by subtraction of suitable pairs of source frames. Twenty-six patients affected by epiphora have been examined so far. In 21 cases digital subtraction DCG allowed an accurate visualization of the lacrimal system; in the other five patients the amount of information was acceptable. This methodology allows the assessment of both the normal anatomy of the lacrimal passages and their pathological patterns, such as obstructions, stenoses, fistulas, chronic dacrycystites, lacrimal stones. The examination is easy and quick to perform, with no discomfort for the patient. Digital subtraction DCG proves thus to be a very valuable technique thanks to its possible electronic elaboration - i.e. the subtraction and the magnification of images - to its better contrast resolution, and to the possibility it yields of dynamic studies under radioscopic control

A PCR-based strategy for simple and rapid identification of rough presumptive Salmonella isolates

DEFF Research Database (Denmark)

Hoorfar, Jeffrey; Baggesen, Dorte Lau; Porting, P.H.

1999-01-01

The purpose of the present study was to investigate the application of ready-to-go Salmonella PCR tests, based on dry chemistry, for final identification of rough presumptive Salmonella isolates. The results were compared with two different biotyping methods performed at two different laboratories......, which did not result in any DNA band. A total of 32 out of the 36 rough presumptive isolates were positive in the PCR. All but one isolate were also identified as Salmonella by the two biochemical methods. All 80 Salmonella strains were also tested in the two multiplex serogroup tests based on PCR beads....... The sensitivity of the BAX Salmonella PCR test was assessed by testing a total of 80 Salmonella isolates, covering most serogroups, which correctly identified all the Salmonella strains by resulting in one 800-bp band in the sample tubes. The specificity of the PCR was assessed using 20 non-Salmonella strains...

Detection of intracranial aneurysms using three-dimensional multidetector-row CT angiography: Is bone subtraction necessary?

International Nuclear Information System (INIS)

Hwang, Seung Bae; Kwak, Hyo Sung; Han, Young Min; Chung, Gyung Ho

2011-01-01

Purpose: The aim of this study was to evaluate the usefulness of three-dimensional CT angiography (3D CTA) with bone subtraction in a comparison with 3D CTA without bone subtraction for the detection of intracranial aneurysms. Materials and methods: Among 337 consecutive patients who had intracranial aneurysms detected on 3D CTA, 170 patients who underwent digital subtraction angiography (DSA) were included in the study. CTA was performed with a 16-slice multidetector-row CT (MDCT) scanner. We created the 3D reconstruction images with and without bone subtraction by using the volume rendering technique. Three neuroradiologists in a blinded fashion interpreted both 3D CTA images with and without bone subtraction. The diagnostic accuracy of both techniques was evaluated using the alternative free-response receiver operating characteristic (ROC) analysis. The sensitivity and positive predictive value were also evaluated. Results: A total of 200 aneurysms (size: 2-23 mm) were detected in 170 patients. The area under the receiver operating characteristic curve (Az) for 3D CTA with bone subtraction (mean, Az = 0.933) was significantly higher than that for 3D CTA without bone subtraction (mean, Az = 0.879) for all observers (P < 0.05). The sensitivity of 3D CTA with bone subtraction for three observers was 90.0, 92.0 and 92.5%, respectively, while the sensitivity of 3D CTA without bone subtraction was 83.5, 83.5 and 87.5%, respectively. No significant difference in positive predictive value was observed between the two modalities. Conclusions: 3D CTA with bone subtraction showed significantly higher diagnostic accuracy for the detection of intracranial aneurysms as compared to 3D CTA without bone subtraction.

Incidence of ischemic lesions in diffusion-weighted imaging after transbrachial digital subtraction angiography

International Nuclear Information System (INIS)

Aschenbach, R.; Majeed, A.; Eger, C.; Basche, S.; Kerl, J.M.; Vogl, T.J.

2008-01-01

Purpose: to evaluate the frequency of ischemia after transbrachial digital subtraction angiography under ambulant conditions using diffusion-weighted imaging. Materials and methods: 200 patients were included in a prospective study design and received transbrachial digital subtraction angiography under ambulant conditions. Before and after digital subtraction angiography, diffusion-weighted imaging of the brain was performed. Results: in our study population no new lesions were found in diffusion-weighted imaging after digital subtraction angiography during the 3-hour window after angiography. One new lesion was found 3 days after angiography as a late onset complication. Therefore, the frequency of neurological complications is at the level of the confidence interval of 0 - 1.5%. Conclusion: the transbrachial approach under ambulant conditions is a safe method for digital subtraction angiography resulting in a low rate of ischemic lesions in diffusion-weighted imaging. (orig.)

Clinical evaluation of fat suppressed fast-SPGR sequence of the breast MR imaging

Energy Technology Data Exchange (ETDEWEB)

Takahashi, Mitsuyuki; Hasegawa, Makoto; Matsubara, Tadashi [Yokohama Sakae Kyosai Hospital (Japan)

1998-05-01

MR-mammography by fat suppressed Fast-SPGR was evaluated for diagnosis and determination of invasion of tumor. Dynamic MRIs were performed in 12 phases, such as, before infusion of contrast media, right after and one to ten minutes after infusion with interval of one minute. In 15 patients (breast cancer, fibroadenoma, lymphocytic lobulitits and cystic intraductal papilloma), underwent MRI, the images were compared with pathological findings. Ten cases were confirmed as malignancy among 11 cases of breast cancer (sensitivity 91%). Eleven cases were confirmed as breast cancer among 12 cases diagnosed as breast cancer by MRI (specificity 92%). In 12 of all 15 cases, benignity or malignancy was checked correctly (accuracy 80%). Invasion of breast cancer was defined as the deep color dyeing area which was neighbored with the tumor in early stage of cystography. Eight of 11 cases were diagnosed precisely with fat suppression image, and nine were by subtraction image. Diagnosis was possible only by subtraction image in a case of scirrhous carcinoma accompanied with intradutal invasion. The area of invasion was not defined correctly in the case accompanied by mastopathy. It is difficult to evaluate benignity or malignancy of mammary gland tumor only by dynamic MRI, it is necessary to diagnose the shape and deep color image of tumor generally. (K.H.)

Absolute quantification of DNA methylation using microfluidic chip-based digital PCR.

Science.gov (United States)

Wu, Zhenhua; Bai, Yanan; Cheng, Zule; Liu, Fangming; Wang, Ping; Yang, Dawei; Li, Gang; Jin, Qinghui; Mao, Hongju; Zhao, Jianlong

2017-10-15

Hypermethylation of CpG islands in the promoter region of many tumor suppressor genes downregulates their expression and in a result promotes tumorigenesis. Therefore, detection of DNA methylation status is a convenient diagnostic tool for cancer detection. Here, we reported a novel method for the integrative detection of methylation by the microfluidic chip-based digital PCR. This method relies on methylation-sensitive restriction enzyme HpaII, which cleaves the unmethylated DNA strands while keeping the methylated ones intact. After HpaII treatment, the DNA methylation level is determined quantitatively by the microfluidic chip-based digital PCR with the lower limit of detection equal to 0.52%. To validate the applicability of this method, promoter methylation of two tumor suppressor genes (PCDHGB6 and HOXA9) was tested in 10 samples of early stage lung adenocarcinoma and their adjacent non-tumorous tissues. The consistency was observed in the analysis of these samples using our method and a conventional bisulfite pyrosequencing. Combining high sensitivity and low cost, the microfluidic chip-based digital PCR method might provide a promising alternative for the detection of DNA methylation and early diagnosis of epigenetics-related diseases. Copyright © 2017 Elsevier B.V. All rights reserved.

Subtractive Structural Modification of Morpho Butterfly Wings.

Science.gov (United States)

Shen, Qingchen; He, Jiaqing; Ni, Mengtian; Song, Chengyi; Zhou, Lingye; Hu, Hang; Zhang, Ruoxi; Luo, Zhen; Wang, Ge; Tao, Peng; Deng, Tao; Shang, Wen

2015-11-11

Different from studies of butterfly wings through additive modification, this work for the first time studies the property change of butterfly wings through subtractive modification using oxygen plasma etching. The controlled modification of butterfly wings through such subtractive process results in gradual change of the optical properties, and helps the further understanding of structural optimization through natural evolution. The brilliant color of Morpho butterfly wings is originated from the hierarchical nanostructure on the wing scales. Such nanoarchitecture has attracted a lot of research effort, including the study of its optical properties, its potential use in sensing and infrared imaging, and also the use of such structure as template for the fabrication of high-performance photocatalytic materials. The controlled subtractive processes provide a new path to modify such nanoarchitecture and its optical property. Distinct from previous studies on the optical property of the Morpho wing structure, this study provides additional experimental evidence for the origination of the optical property of the natural butterfly wing scales. The study also offers a facile approach to generate new 3D nanostructures using butterfly wings as the templates and may lead to simpler structure models for large-scale man-made structures than those offered by original butterfly wings. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Digital PCR as a tool to measure HIV persistence.

Science.gov (United States)

Rutsaert, Sofie; Bosman, Kobus; Trypsteen, Wim; Nijhuis, Monique; Vandekerckhove, Linos

2018-01-30

Although antiretroviral therapy is able to suppress HIV replication in infected patients, the virus persists and rebounds when treatment is stopped. In order to find a cure that can eradicate the latent reservoir, one must be able to quantify the persisting virus. Traditionally, HIV persistence studies have used real-time PCR (qPCR) to measure the viral reservoir represented by HIV DNA and RNA. Most recently, digital PCR is gaining popularity as a novel approach to nucleic acid quantification as it allows for absolute target quantification. Various commercial digital PCR platforms are nowadays available that implement the principle of digital PCR, of which Bio-Rad's QX200 ddPCR is currently the most used platform in HIV research. Quantification of HIV by digital PCR is proving to be a valuable improvement over qPCR as it is argued to have a higher robustness to mismatches between the primers-probe set and heterogeneous HIV, and forfeits the need for a standard curve, both of which are known to complicate reliable quantification. However, currently available digital PCR platforms occasionally struggle with unexplained false-positive partitions, and reliable segregation between positive and negative droplets remains disputed. Future developments and advancements of the digital PCR technology are promising to aid in the accurate quantification and characterization of the persistent HIV reservoir.

Digital subtraction angiography: first 900 cases

International Nuclear Information System (INIS)

Rodgers, H.

1984-01-01

The diagnostic technique of digital subtraction angiography (DSA) is briefly outlined. The operational and technical experiences with a DR-960 DSA system used in the examination of the first 900 cases at St. Thomas' Hospital, London are described. (U.K.)

Modified Polyadenylation-Based RT-qPCR Increases Selectivity of Amplification of 3′-MicroRNA Isoforms

Directory of Open Access Journals (Sweden)

Charlotte Nejad

2018-01-01

Full Text Available MicroRNA (miRNA detection by reverse transcription (RT quantitative real-time PCR (RT-qPCR is the most popular method currently used to measure miRNA expression. Although the majority of miRNA families are constituted of several 3′-end length variants (“isomiRs”, little attention has been paid to their differential detection by RT-qPCR. However, recent evidence indicates that 3′-end miRNA isoforms can exhibit 3′-length specific regulatory functions, underlining the need to develop strategies to differentiate 3′-isomiRs by RT-qPCR approaches. We demonstrate here that polyadenylation-based RT-qPCR strategies targeted to 20–21 nt isoforms amplify entire miRNA families, but that primers targeted to >22 nt isoforms were specific to >21 nt isoforms. Based on this observation, we developed a simple method to increase selectivity of polyadenylation-based RT-qPCR assays toward shorter isoforms, and demonstrate its capacity to help distinguish short RNAs from longer ones, using synthetic RNAs and biological samples with altered isomiR stoichiometry. Our approach can be adapted to many polyadenylation-based RT-qPCR technologies already exiting, providing a convenient way to distinguish long and short 3′-isomiRs.

Thallium-201 and technetium-99m pertechnetate subtraction scintigraphy in patients with hyperparathyroidism

International Nuclear Information System (INIS)

Kuwashima, Shigeko; Koizumi, Mitsuru; Goto, Masafumi; Nomura, Toshiharu; Fujioka, Mutsuhisa; Watari, Tsutomu

1992-01-01

A reliable technique for detecting and localizing abnormal parathyroid tissue has been a persistent problem. We evaluated thallium-technetium (Tl/Tc) subtraction scintigraphy in 16 patients with clinical biochemical evidence of hyperparathyroidism prior to other diagnostic methods and surgery. Seven patients had surgery and were confirmed to have parathyroid adenoma or hyperplasia. The other methods included ultrasonography (US) in 6 patients, computed tomography (CT) in 10 patients, magnetic resonance imaging (MRI) in 8 patients, and bone scintigraphy in 7 patients. In patients who had several imaging modalities, the detection rate was significantly better for Tl/Tc subtraction scan than for US, CT or MRI. Bote scintigraphy, though not so sensitive as Tl/Tc subtraction studies, was an important tool for evaluating metabolic bone disorder including hyperparathyroidism and renal osteodystrophy. Thus, Tl/Tc subtraction scan is more useful for diagnosis when hyperparathyroidism is suspected if both Tl/Tc subtraction scan and bone scan are performed. The detectability depended on the mass size, and detection of abnormal glands was greater for adenoma than for hyperplasia. The results suggest that Tl/Tc subtraction scan is a simple, non-invasive and useful tool for locating parathyroid abnormality even when compared with MRI. (author)

Color Addition and Subtraction Apps

Science.gov (United States)

Ruiz, Frances; Ruiz, Michael J.

2015-01-01

Color addition and subtraction apps in HTML5 have been developed for students as an online hands-on experience so that they can more easily master principles introduced through traditional classroom demonstrations. The evolution of the additive RGB color model is traced through the early IBM color adapters so that students can proceed step by step…

Power corrections in the N-jettiness subtraction scheme

Energy Technology Data Exchange (ETDEWEB)

Boughezal, Radja [High Energy Physics Division, Argonne National Laboratory,Argonne, IL 60439 (United States); Liu, Xiaohui [Department of Physics, Beijing Normal University,Beijing, 100875 (China); Center of Advanced Quantum Studies, Beijing Normal University,Beijing, 100875 (China); Center for High-Energy Physics, Peking University,Beijing, 100871 (China); Maryland Center for Fundamental Physics, University of Maryland,College Park, MD 20742 (United States); Petriello, Frank [Department of Physics & Astronomy, Northwestern University,Evanston, IL 60208 (United States); High Energy Physics Division, Argonne National Laboratory,Argonne, IL 60439 (United States)

2017-03-30

We discuss the leading-logarithmic power corrections in the N-jettiness subtraction scheme for higher-order perturbative QCD calculations. We compute the next-to-leading order power corrections for an arbitrary N-jet process, and we explicitly calculate the power correction through next-to-next-to-leading order for color-singlet production for both qq̄ and gg initiated processes. Our results are compact and simple to implement numerically. Including the leading power correction in the N-jettiness subtraction scheme substantially improves its numerical efficiency. We discuss what features of our techniques extend to processes containing final-state jets.

A simple digital subtraction angiographic instrument

International Nuclear Information System (INIS)

Ando, Hiroshi; Kobayashi, Tsuyoshi; Imai, Yutaka; Yanagishita, Akira

1983-01-01

A digital subtraction angiographic instrument was manufactured using a conventional x-ray TV for gastrointestinal series and a computer for processing of nuclear medical data. The results of visualization of the aorta and its primary branches were reviewed with demonstrable cases. (Chiba, N.)

Segmentation of Moving Object Using Background Subtraction Method in Complex Environments

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S. Kumar

2016-06-01

Full Text Available Background subtraction is an extensively used approach to localize the moving object in a video sequence. However, detecting an object under the spatiotemporal behavior of background such as rippling of water, moving curtain and illumination change or low resolution is not a straightforward task. To deal with the above-mentioned problem, we address a background maintenance scheme based on the updating of background pixels by estimating the current spatial variance along the temporal line. The work is focused to immune the variation of local motion in the background. Finally, the most suitable label assignment to the motion field is estimated and optimized by using iterated conditional mode (ICM under a Markovian framework. Performance evaluation and comparisons with the other well-known background subtraction methods show that the proposed method is unaffected by the problem of aperture distortion, ghost image, and high frequency noise.

Summation and subtraction using a modified autoshaping procedure in pigeons.

Science.gov (United States)

Ploog, Bertram O

2008-06-01

A modified autoshaping paradigm (significantly different from those previously reported in the summation literature) was employed to allow for the simultaneous assessment of stimulus summation and subtraction in pigeons. The response requirements and the probability of food delivery were adjusted such that towards the end of training 12 of 48 trials ended in food delivery, the same proportion as under testing. Stimuli (outlines of squares of three sizes and colors: A, B, and C) were used that could be presented separately or in any combination of two or three stimuli. Twelve of the pigeons (summation groups) were trained with either A, B, and C or with AB, BC, and CA, and tested with ABC. The remaining 12 pigeons (subtraction groups) received training with ABC but were tested with A, B, and C or with AB, BC, and CA. These groups were further subdivided according to whether stimulus elements were presented either in a concentric or dispersed manner. Summation did not occur; subtraction occurred in the two concentric groups. For interpretation of the results, configural theory, the Rescorla-Wagner model, and the composite-stimulus control model were considered. The results suggest different mechanisms responsible for summation and subtraction.

Sensitive detection of novel Indian isolate of BTV 21 using ns1 gene based real-time PCR assay

Directory of Open Access Journals (Sweden)

Gaya Prasad

2013-06-01

Full Text Available Aim: The study was conducted to develop ns1 gene based sensitive real-time RT-PCR assay for diagnosis of India isolates of bluetongue virus (BTV. Materials and Methods: The BTV serotype 21 isolate (KMNO7 was isolated from Andhra Pradesh and propagated in BHK-21 cell line in our laboratory. The Nucleic acid (dsRNA of virus was extracted using Trizol method and cDNA was prepared using a standard protocol. The cDNA was allowed to ns1 gene based group specific PCR to confirm the isolate as BTV. The viral RNA was diluted 10 folds and the detection limit of ns1 gene based RT-PCR was determined. Finally the tenfold diluted viral RNA was subjected to real-time RT-PCR using ns1 gene primer and Taq man probe to standardized the reaction and determine the detection limit. Results: The ns1 gene based group specific PCR showed a single 366bp amplicon in agarose gel electrophoresis confirmed the sample as BTV. The ns1 gene RT-PCR using tenfold diluted viral RNA showed the detection limit of 70.0 fg in 1%agarose gel electrophoresis. The ns1 gene based real time RT-PCR was successfully standardized and the detection limit was found to be 7.0 fg. Conclusion: The ns1 gene based real-time RT-PCR was successfully standardized and it was found to be 10 times more sensitive than conventional RT-PCR. Key words: bluetongue, BTV21, RT-PCR, Real time RT-PCR, ns1 gene [Vet World 2013; 6(8.000: 554-557

Appearance of the canine meninges in subtraction magnetic resonance images.

Science.gov (United States)

Lamb, Christopher R; Lam, Richard; Keenihan, Erin K; Frean, Stephen

2014-01-01

The canine meninges are not visible as discrete structures in noncontrast magnetic resonance (MR) images, and are incompletely visualized in T1-weighted, postgadolinium images, reportedly appearing as short, thin curvilinear segments with minimal enhancement. Subtraction imaging facilitates detection of enhancement of tissues, hence may increase the conspicuity of meninges. The aim of the present study was to describe qualitatively the appearance of canine meninges in subtraction MR images obtained using a dynamic technique. Images were reviewed of 10 consecutive dogs that had dynamic pre- and postgadolinium T1W imaging of the brain that was interpreted as normal, and had normal cerebrospinal fluid. Image-anatomic correlation was facilitated by dissection and histologic examination of two canine cadavers. Meningeal enhancement was relatively inconspicuous in postgadolinium T1-weighted images, but was clearly visible in subtraction images of all dogs. Enhancement was visible as faint, small-rounded foci compatible with vessels seen end on within the sulci, a series of larger rounded foci compatible with vessels of variable caliber on the dorsal aspect of the cerebral cortex, and a continuous thin zone of moderate enhancement around the brain. Superimposition of color-encoded subtraction images on pregadolinium T1- and T2-weighted images facilitated localization of the origin of enhancement, which appeared to be predominantly dural, with relatively few leptomeningeal structures visible. Dynamic subtraction MR imaging should be considered for inclusion in clinical brain MR protocols because of the possibility that its use may increase sensitivity for lesions affecting the meninges. © 2014 American College of Veterinary Radiology.

Using the hydrophobic subtraction model to choose orthogonal columns for online comprehensive two-dimensional liquid chromatography

DEFF Research Database (Denmark)

Græsbøll, Rune; Nielsen, Nikoline Juul; Christensen, Jan H.

2014-01-01

A method for choosing orthogonal columns for a specific sample set in on-line comprehensive two-dimensional liquid chromatography (LC×LC) was developed on the basis of the hydrophobic subtraction model. The method takes into account the properties of the sample analytes by estimating new F...... neutral and 4 acidic oxygenated polycyclic aromatic compounds (PACs) and 3 nitrogen-containing PAC bases was measured isocratically on 12 columns. The isocratic runs were used to determine the hydrophobic subtraction model analyte parameters, and these were used to estimate new F-weights and predict...

IR subtraction schemes. Integrating the counterterms at NNLO in QCD

Energy Technology Data Exchange (ETDEWEB)

Bolzoni, Paolo; Somogyi, Gabor

2010-06-15

We briefly review a subtraction scheme for computing radiative corrections to QCD jet cross sections that can be defined at any order in perturbation theory. Hereafter we discuss the computational methods used to evaluate analytically and numerically the integrated counterterms arising from such a subtraction scheme. Basically these methods the Mellin-Barnes (MB) representations technique together with the harmonic summation and the sector decomposition. (orig.)

IR subtraction schemes. Integrating the counterterms at NNLO in QCD

International Nuclear Information System (INIS)

Bolzoni, Paolo; Somogyi, Gabor

2010-06-01

We briefly review a subtraction scheme for computing radiative corrections to QCD jet cross sections that can be defined at any order in perturbation theory. Hereafter we discuss the computational methods used to evaluate analytically and numerically the integrated counterterms arising from such a subtraction scheme. Basically these methods the Mellin-Barnes (MB) representations technique together with the harmonic summation and the sector decomposition. (orig.)

Digital subtraction arthrography in preoperative evaluation of painful total hip arthroplasty

International Nuclear Information System (INIS)

Ginai, A.Z.; Biezen, F.C. van; Kint, P.A.M.; Oei, H.Y.; Hop, W.C.J.

1996-01-01

Digital subtraction arthrograms, scintigrams and plain radiographs of 70 consecutive patients who underwent revision hip arthroplasty were scored individually and in masked fashion for the presence or absence of features indicating loosening of femoral and/or acetabular components. The operative findings acted as the gold standard. Digital subtraction arthrography was best for predicting a loose acetabular component, while no significant additional predictive value was found for plain radiographs and scintigraphy. Digital subtraction arthrography was also the most important modality for predicting a loose femoral component, while the plain radiograph was of significant additional value and scintigraphy was of no additional value on multivariate analysis. (orig./MG)

Temporal digital subtraction radiography with a personal computer digital workstation

International Nuclear Information System (INIS)

Kircos, L.; Holt, W.; Khademi, J.

1990-01-01

Technique have been developed and implemented on a personal computer (PC)-based digital workstation to accomplish temporal digital subtraction radiography (TDSR). TDSR is useful in recording radiologic change over time. Thus, this technique is useful not only for monitoring chronic disease processes but also for monitoring the temporal course of interventional therapies. A PC-based digital workstation was developed on a PC386 platform with add-in hardware and software. Image acquisition, storage, and processing was accomplished using 512 x 512 x 8- or 12-bit frame grabber. Software and hardware were developed to accomplish image orientation, registration, gray scale compensation, subtraction, and enhancement. Temporal radiographs of the jaws were made in a fixed and reproducible orientation between the x-ray source and image receptor enabling TDSR. Temporal changes secondary to chronic periodontal disease, osseointegration of endosseous implants, and wound healing were demonstrated. Use of TDSR for chest imaging was also demonstrated with identification of small, subtle focal masses that were not apparent with routine viewing. The large amount of radiologic information in images of the jaws and chest may obfuscate subtle changes that TDSR seems to identify. TDSR appears to be useful as a tool to record temporal and subtle changes in radiologic images

The Use of Procedural Knowledge in Simple Addition and Subtraction Problems

Science.gov (United States)

Fayol, Michel; Thevenot, Catherine

2012-01-01

In a first experiment, adults were asked to solve one-digit additions, subtractions and multiplications. When the sign appeared 150 ms before the operands, addition and subtraction were solved faster than when the sign and the operands appeared simultaneously on screen. This priming effect was not observed for multiplication problems. A second…

Motion compensation in digital subtraction angiography using graphics hardware.

Science.gov (United States)

Deuerling-Zheng, Yu; Lell, Michael; Galant, Adam; Hornegger, Joachim

2006-07-01

An inherent disadvantage of digital subtraction angiography (DSA) is its sensitivity to patient motion which causes artifacts in the subtraction images. These artifacts could often reduce the diagnostic value of this technique. Automated, fast and accurate motion compensation is therefore required. To cope with this requirement, we first examine a method explicitly designed to detect local motions in DSA. Then, we implement a motion compensation algorithm by means of block matching on modern graphics hardware. Both methods search for maximal local similarity by evaluating a histogram-based measure. In this context, we are the first who have mapped an optimizing search strategy on graphics hardware while paralleling block matching. Moreover, we provide an innovative method for creating histograms on graphics hardware with vertex texturing and frame buffer blending. It turns out that both methods can effectively correct the artifacts in most case, as the hardware implementation of block matching performs much faster: the displacements of two 1024 x 1024 images can be calculated at 3 frames/s with integer precision or 2 frames/s with sub-pixel precision. Preliminary clinical evaluation indicates that the computation with integer precision could already be sufficient.

Temporal subtraction of chest radiographs compensating pose differences

Science.gov (United States)

von Berg, Jens; Dworzak, Jalda; Klinder, Tobias; Manke, Dirk; Kreth, Adrian; Lamecker, Hans; Zachow, Stefan; Lorenz, Cristian

2011-03-01

Temporal subtraction techniques using 2D image registration improve the detectability of interval changes from chest radiographs. Although such methods are well known for some time they are not widely used in radiologic practice. The reason is the occurrence of strong pose differences between two acquisitions with a time interval of months to years in between. Such strong perspective differences occur in a reasonable number of cases. They cannot be compensated by available image registration methods and thus mask interval changes to be undetectable. In this paper a method is proposed to estimate a 3D pose difference by the adaptation of a 3D rib cage model to both projections. The difference between both is then compensated for, thus producing a subtraction image with virtually no change in pose. The method generally assumes that no 3D image data is available from the patient. The accuracy of pose estimation is validated with chest phantom images acquired under controlled geometric conditions. A subtle interval change simulated by a piece of plastic foam attached to the phantom becomes visible in subtraction images generated with this technique even at strong angular pose differences like an anterior-posterior inclination of 13 degrees.

Comparison of PCR-Based Diagnosis with Centrifuged-Based Enrichment Method for Detection of Borrelia persica in Animal Blood Samples.

Science.gov (United States)

Naddaf, S R; Kishdehi, M; Siavashi, Mr

2011-01-01

The mainstay of diagnosis of relapsing fever (RF) is demonstration of the spirochetes in Giemsa-stained thick blood smears, but during non fever periods the bacteria are very scanty and rarely detected in blood smears by microscopy. This study is aimed to evaluate the sensitivity of different methods developed for detection of low-grade spirochetemia. Animal blood samples with low degrees of spirochetemia were tested with two PCRs and a nested PCR targeting flaB, GlpQ, and rrs genes. Also, a centrifuged-based enrichment method and Giemsa staining were performed on blood samples with various degrees of spirochetemia. The flaB-PCR and nested rrs-PCR turned positive with various degrees of spirochetemia including the blood samples that turned negative with dark-field microscopy. The GlpQ-PCR was positive as far as at least one spirochete was seen in 5-10 microscopic fields. The sensitivity of GlpQ-PCR increased when DNA from Buffy Coat Layer (BCL) was used as template. The centrifuged-based enrichment method turned positive with as low concentration as 50 bacteria/ml blood, while Giemsa thick staining detected bacteria with concentrations ≥ 25000 bacteria/ml. Centrifuged-based enrichment method appeared as much as 500-fold more sensitive than thick smears, which makes it even superior to some PCR assays. Due to simplicity and minimal laboratory requirements, this method can be considered a valuable tool for diagnosis of RF in rural health centers.

Wilson expansion in the minimal subtraction scheme

International Nuclear Information System (INIS)

Smirnov, V.A.

1989-01-01

The small distance expansion of the product of composite fields is constructed for an arbitrary renormalization procedure of the type of minimal subtraction scheme. Coefficient functions of the expansion are expressed explicitly through the Green functions of composite fields. The expansion has the explicity finite form: the ultraviolet (UV) divergences of the coefficient functions and composite fields are removed by the initial renormalization procedure while the infrared (IR) divergences in massless diagrams with nonvanishing contribution into the coefficient functions are removed by the R-operation which is the IR part of the R-operation. The latter is the generalization of the dimensional renormalization in the case when both UV and IR divergences are present. To derive the expansion, a ''pre-subtracting operator'' is introduced and formulas of the counter-term technique are exploited

Dynamic contrast-enhanced subtraction MR angiography in intracranial vascular abnormalities

International Nuclear Information System (INIS)

Takano, K.; Ono, H.; Utsunomiya, H.; Okazaki, M.; Tanaka, A.

1999-01-01

We present our clinical experience with dynamic contrast-enhanced MR angiography (MRA) with subtraction for assessing intracranial vascular abnormalities. Ten patients with various cerebrovascular disorders underwent dynamic contrast-enhanced MRA on a 1.0-T system. Thirty sections (2 mm) were acquired in 29-30 s. Maximum intensity projection images and subtracted source images were compared with those obtained by conventional angiography. In all cases, the presence or absence of abnormalities in the targeted vessels, as well as the morphology of the sagittal sinuses, was clearly visualized as in conventional angiography, without any obstructions such as hyperintense hematomas or thrombi, or intraluminal turbulence. Although the temporal and spatial resolutions with current hardware are insufficient, these preliminary results suggest that dynamic contrast-enhanced MRA with subtraction may be useful for assessing vascular lesions with hemorrhage or thrombus, and the dural sinuses. (orig.)

PCR-based detection of a rare linear DNA in cell culture

Directory of Open Access Journals (Sweden)

Saveliev Sergei V.

2002-01-01

Full Text Available The described method allows for detection of rare linear DNA fragments generated during genomic deletions. The predicted limit of the detection is one DNA molecule per 107 or more cells. The method is based on anchor PCR and involves gel separation of the linear DNA fragment and chromosomal DNA before amplification. The detailed chemical structure of the ends of the linear DNA can be defined with the use of additional PCR-based protocols. The method was applied to study the short-lived linear DNA generated during programmed genomic deletions in a ciliate. It can be useful in studies of spontaneous DNA deletions in cell culture or for tracking intracellular modifications at the ends of transfected DNA during gene therapy trials.

PCR-based detection of a rare linear DNA in cell culture.

Science.gov (United States)

Saveliev, Sergei V.

2002-11-11

The described method allows for detection of rare linear DNA fragments generated during genomic deletions. The predicted limit of the detection is one DNA molecule per 10(7) or more cells. The method is based on anchor PCR and involves gel separation of the linear DNA fragment and chromosomal DNA before amplification. The detailed chemical structure of the ends of the linear DNA can be defined with the use of additional PCR-based protocols. The method was applied to study the short-lived linear DNA generated during programmed genomic deletions in a ciliate. It can be useful in studies of spontaneous DNA deletions in cell culture or for tracking intracellular modifications at the ends of transfected DNA during gene therapy trials.

Phage-Mediated Immuno-PCR for Ultrasensitive Detection of Cry1Ac Protein Based on Nanobody.

Science.gov (United States)

Liu, Yuanyuan; Jiang, Dongjian; Lu, Xin; Wang, Wei; Xu, Yang; He, Qinghua

2016-10-11

The widespread use of Cry proteins in transgenic plants for insect control has raised concerns about the environment and food safety in the public. An effective detection method for introduced Cry proteins is of significance for environmental risk assessment and product quality control. This paper describes a novel phage mediated immuno-PCR (iPCR) for the ultrasensitive determination of Cry proteins based on nanobodies. Three nanobodies against Cry1Ac protein were obtained from a naı̈ve phage displayed nanobody library without animal immunization process and were applied to the iPCR assay for Cry1Ac. The phage-mediated iPCR for Cry1Ac based on nanobodies showed a dynamic range of 0.001-100 ng/mL and a limit detection of 0.1 pg/mL. Specific measurement of this established method was performed by testing cross-reativity of other Cry1Ac analogues, and the result showed negligible cross-reactivity with other test Cry proteins (Cry1Ab, Cry1F, Cry3B). Furthermore, the phage-mediated iPCR based on nanobody should be easily applicable to the detection of many other Cry proteins.

DESIGN STUDY: INTEGER SUBTRACTION OPERATION TEACHING LEARNING USING MULTIMEDIA IN PRIMARY SCHOOL

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Rendi Muhammad Aris

2016-12-01

Full Text Available This study aims to develop a learning trajectory to help students understand concept of subtraction of integers using multimedia in the fourth grade. This study is thematic integrative learning in Curriculum 2013 PMRI based. The method used is design research consists of three stages; preparing for the experiment, design experiment, retrospective analysis. The studied was conducted on 20 students of grade four SDN 1 Muara Batun, OKI. The activities of students in this study consisted of six learning trajectories. The first activity asks the students to classify heroism and non-heroism acts, summarize, and classify integers and non-integer. The second activity asks the students to answer the questions in the film given. The third activity asks students to count the remaining gravel in the film. The fourth activity asks students to count remaining spent money in the film. The fifth activity invites students to play rubber seeds in the bag. The last activity asks students to answer the questions in the student worksheet. The media used along the learning activities are a ruler, rubber seed, student worksheet, money, gravel, and film. The results indicate that the learning trajectory using multimedia help students understand the concept of integer subtraction integer. Keywords: Subtraction Integer, PMRI, Multimedia DOI: http://dx.doi.org/10.22342/jme.8.1.3233.95-102

A new trilocus sequence-based multiplex-PCR to detect major Acinetobacter baumannii clones.

Science.gov (United States)

Martins, Natacha; Picão, Renata Cristina; Cerqueira-Alves, Morgana; Uehara, Aline; Barbosa, Lívia Carvalho; Riley, Lee W; Moreira, Beatriz Meurer

2016-08-01

A collection of 163 Acinetobacter baumannii isolates detected in a large Brazilian hospital, was potentially related with the dissemination of four clonal complexes (CC): 113/79, 103/15, 109/1 and 110/25, defined by University of Oxford/Institut Pasteur multilocus sequence typing (MLST) schemes. The urge of a simple multiplex-PCR scheme to specify these clones has motivated the present study. The established trilocus sequence-based typing (3LST, for ompA, csuE and blaOXA-51-like genes) multiplex-PCR rapidly identifies international clones I (CC109/1), II (CC118/2) and III (CC187/3). Thus, the system detects only one (CC109/1) out of four main CC in Brazil. We aimed to develop an alternative multiplex-PCR scheme to detect these clones, known to be present additionally in Africa, Asia, Europe, USA and South America. MLST, performed in the present study to complement typing our whole collection of isolates, confirmed that all isolates belonged to the same four CC detected previously. When typed by 3LST-based multiplex-PCR, only 12% of the 163 isolates were classified into groups. By comparative sequence analysis of ompA, csuE and blaOXA-51-like genes, a set of eight primers was designed for an alternative multiplex-PCR to distinguish the five CC 113/79, 103/15, 109/1, 110/25 and 118/2. Study isolates and one CC118/2 isolate were blind-tested with the new alternative PCR scheme; all were correctly clustered in groups of the corresponding CC. The new multiplex-PCR, with the advantage of fitting in a single reaction, detects five leading A. baumannii clones and could help preventing the spread in healthcare settings. Copyright © 2016 Elsevier B.V. All rights reserved.

Development of a high-throughput real time PCR based on a hot-start alternative for Pfu mediated by quantum dots

Science.gov (United States)

Sang, Fuming; Yang, Yang; Yuan, Lin; Ren, Jicun; Zhang, Zhizhou

2015-09-01

Hot start (HS) PCR is an excellent alternative for high-throughput real time PCR due to its ability to prevent nonspecific amplification at low temperature. Development of a cost-effective and simple HS PCR technique to guarantee high-throughput PCR specificity and consistency still remains a great challenge. In this study, we systematically investigated the HS characteristics of QDs triggered in real time PCR with EvaGreen and SYBR Green I dyes by the analysis of amplification curves, standard curves and melting curves. Two different kinds of DNA polymerases, Pfu and Taq, were employed. Here we showed that high specificity and efficiency of real time PCR were obtained in a plasmid DNA and an error-prone two-round PCR assay using QD-based HS PCR, even after an hour preincubation at 50 °C before real time PCR. Moreover, the results obtained by QD-based HS PCR were comparable to a commercial Taq antibody DNA polymerase. However, no obvious HS effect of QDs was found in real time PCR using Taq DNA polymerase. The findings of this study demonstrated that a cost-effective high-throughput real time PCR based on QD triggered HS PCR could be established with high consistency, sensitivity and accuracy.Hot start (HS) PCR is an excellent alternative for high-throughput real time PCR due to its ability to prevent nonspecific amplification at low temperature. Development of a cost-effective and simple HS PCR technique to guarantee high-throughput PCR specificity and consistency still remains a great challenge. In this study, we systematically investigated the HS characteristics of QDs triggered in real time PCR with EvaGreen and SYBR Green I dyes by the analysis of amplification curves, standard curves and melting curves. Two different kinds of DNA polymerases, Pfu and Taq, were employed. Here we showed that high specificity and efficiency of real time PCR were obtained in a plasmid DNA and an error-prone two-round PCR assay using QD-based HS PCR, even after an hour

Multiplex enrichment quantitative PCR (ME-qPCR): a high-throughput, highly sensitive detection method for GMO identification.

Science.gov (United States)

Fu, Wei; Zhu, Pengyu; Wei, Shuang; Zhixin, Du; Wang, Chenguang; Wu, Xiyang; Li, Feiwu; Zhu, Shuifang

2017-04-01

Among all of the high-throughput detection methods, PCR-based methodologies are regarded as the most cost-efficient and feasible methodologies compared with the next-generation sequencing or ChIP-based methods. However, the PCR-based methods can only achieve multiplex detection up to 15-plex due to limitations imposed by the multiplex primer interactions. The detection throughput cannot meet the demands of high-throughput detection, such as SNP or gene expression analysis. Therefore, in our study, we have developed a new high-throughput PCR-based detection method, multiplex enrichment quantitative PCR (ME-qPCR), which is a combination of qPCR and nested PCR. The GMO content detection results in our study showed that ME-qPCR could achieve high-throughput detection up to 26-plex. Compared to the original qPCR, the Ct values of ME-qPCR were lower for the same group, which showed that ME-qPCR sensitivity is higher than the original qPCR. The absolute limit of detection for ME-qPCR could achieve levels as low as a single copy of the plant genome. Moreover, the specificity results showed that no cross-amplification occurred for irrelevant GMO events. After evaluation of all of the parameters, a practical evaluation was performed with different foods. The more stable amplification results, compared to qPCR, showed that ME-qPCR was suitable for GMO detection in foods. In conclusion, ME-qPCR achieved sensitive, high-throughput GMO detection in complex substrates, such as crops or food samples. In the future, ME-qPCR-based GMO content identification may positively impact SNP analysis or multiplex gene expression of food or agricultural samples. Graphical abstract For the first-step amplification, four primers (A, B, C, and D) have been added into the reaction volume. In this manner, four kinds of amplicons have been generated. All of these four amplicons could be regarded as the target of second-step PCR. For the second-step amplification, three parallels have been taken for

PCR-based detection of gene transfer vectors: application to gene doping surveillance.

Science.gov (United States)

Perez, Irene C; Le Guiner, Caroline; Ni, Weiyi; Lyles, Jennifer; Moullier, Philippe; Snyder, Richard O

2013-12-01

Athletes who illicitly use drugs to enhance their athletic performance are at risk of being banned from sports competitions. Consequently, some athletes may seek new doping methods that they expect to be capable of circumventing detection. With advances in gene transfer vector design and therapeutic gene transfer, and demonstrations of safety and therapeutic benefit in humans, there is an increased probability of the pursuit of gene doping by athletes. In anticipation of the potential for gene doping, assays have been established to directly detect complementary DNA of genes that are top candidates for use in doping, as well as vector control elements. The development of molecular assays that are capable of exposing gene doping in sports can serve as a deterrent and may also identify athletes who have illicitly used gene transfer for performance enhancement. PCR-based methods to detect foreign DNA with high reliability, sensitivity, and specificity include TaqMan real-time PCR, nested PCR, and internal threshold control PCR.

Momentum-subtraction renormalization techniques in curved space-time

Energy Technology Data Exchange (ETDEWEB)

Foda, O.

1987-10-01

Momentum-subtraction techniques, specifically BPHZ and Zimmermann's Normal Product algorithm, are introduced as useful tools in the study of quantum field theories in the presence of background fields. In a model of a self-interacting massive scalar field, conformally coupled to a general asymptotically-flat curved space-time with a trivial topology, momentum-subtractions are shown to respect invariance under general coordinate transformations. As an illustration, general expressions for the trace anomalies are derived, and checked by explicit evaluation of the purely gravitational contributions in the free field theory limit. Furthermore, the trace of the renormalized energy-momentum tensor is shown to vanish at the Gell-Mann Low eigenvalue as it should.

Momentum-subtraction renormalization techniques in curved space-time

International Nuclear Information System (INIS)

Foda, O.

1987-01-01

Momentum-subtraction techniques, specifically BPHZ and Zimmermann's Normal Product algorithm, are introduced as useful tools in the study of quantum field theories in the presence of background fields. In a model of a self-interacting massive scalar field, conformally coupled to a general asymptotically-flat curved space-time with a trivial topology, momentum-subtractions are shown to respect invariance under general coordinate transformations. As an illustration, general expressions for the trace anomalies are derived, and checked by explicit evaluation of the purely gravitational contributions in the free field theory limit. Furthermore, the trace of the renormalized energy-momentum tensor is shown to vanish at the Gell-Mann Low eigenvalue as it should

Subtraction with hadronic initial states at NLO: an NNLO-compatible scheme

Science.gov (United States)

Somogyi, Gábor

2009-05-01

We present an NNLO-compatible subtraction scheme for computing QCD jet cross sections of hadron-initiated processes at NLO accuracy. The scheme is constructed specifically with those complications in mind, that emerge when extending the subtraction algorithm to next-to-next-to-leading order. It is therefore possible to embed the present scheme in a full NNLO computation without any modifications.

Subtraction with hadronic initial states at NLO: an NNLO-compatible scheme

International Nuclear Information System (INIS)

Somogyi, Gabor

2009-01-01

We present an NNLO-compatible subtraction scheme for computing QCD jet cross sections of hadron-initiated processes at NLO accuracy. The scheme is constructed specifically with those complications in mind, that emerge when extending the subtraction algorithm to next-to-next-to-leading order. It is therefore possible to embed the present scheme in a full NNLO computation without any modifications.

Digital subtraction radiography in the study of moving laryngeal structures

International Nuclear Information System (INIS)

Perri, G.; Falaschi, F.; Pieri, L.; Esposito, S.; Ursino, F.

1988-01-01

Digital subtraction radiography (DSR) was applied to the study of the larynx in 11 healthy subjects and 15 pathological cases. The method, consisting in the subtraction of images obtained at rest and during phonation or respiratory phases, allowed a clear definition of the normal moving structures - i.e. vocal cords, false cords, pyriform sinuses, thyroid cartilage. Moreover, several pathological conditions could be demonstrated. DSR asserts thus itself as a suitable technique in the functional evaluation of glottis

SSHscreen and SSHdb, generic software for microarray based gene discovery: application to the stress response in cowpea

Directory of Open Access Journals (Sweden)

Oelofse Dean

2010-04-01

Full Text Available Abstract Background Suppression subtractive hybridization is a popular technique for gene discovery from non-model organisms without an annotated genome sequence, such as cowpea (Vigna unguiculata (L. Walp. We aimed to use this method to enrich for genes expressed during drought stress in a drought tolerant cowpea line. However, current methods were inefficient in screening libraries and management of the sequence data, and thus there was a need to develop software tools to facilitate the process. Results Forward and reverse cDNA libraries enriched for cowpea drought response genes were screened on microarrays, and the R software package SSHscreen 2.0.1 was developed (i to normalize the data effectively using spike-in control spot normalization, and (ii to select clones for sequencing based on the calculation of enrichment ratios with associated statistics. Enrichment ratio 3 values for each clone showed that 62% of the forward library and 34% of the reverse library clones were significantly differentially expressed by drought stress (adjusted p value 88% of the clones in both libraries were derived from rare transcripts in the original tester samples, thus supporting the notion that suppression subtractive hybridization enriches for rare transcripts. A set of 118 clones were chosen for sequencing, and drought-induced cowpea genes were identified, the most interesting encoding a late embryogenesis abundant Lea5 protein, a glutathione S-transferase, a thaumatin, a universal stress protein, and a wound induced protein. A lipid transfer protein and several components of photosynthesis were down-regulated by the drought stress. Reverse transcriptase quantitative PCR confirmed the enrichment ratio values for the selected cowpea genes. SSHdb, a web-accessible database, was developed to manage the clone sequences and combine the SSHscreen data with sequence annotations derived from BLAST and Blast2GO. The self-BLAST function within SSHdb grouped

A method for dynamic subtraction MR imaging of the liver

Directory of Open Access Journals (Sweden)

Setti Ernesto

2006-06-01

Full Text Available Abstract Background Subtraction of Dynamic Contrast-Enhanced 3D Magnetic Resonance (DCE-MR volumes can result in images that depict and accurately characterize a variety of liver lesions. However, the diagnostic utility of subtraction images depends on the extent of co-registration between non-enhanced and enhanced volumes. Movement of liver structures during acquisition must be corrected prior to subtraction. Currently available methods are computer intensive. We report a new method for the dynamic subtraction of MR liver images that does not require excessive computer time. Methods Nineteen consecutive patients (median age 45 years; range 37–67 were evaluated by VIBE T1-weighted sequences (TR 5.2 ms, TE 2.6 ms, flip angle 20°, slice thickness 1.5 mm acquired before and 45s after contrast injection. Acquisition parameters were optimized for best portal system enhancement. Pre and post-contrast liver volumes were realigned using our 3D registration method which combines: (a rigid 3D translation using maximization of normalized mutual information (NMI, and (b fast 2D non-rigid registration which employs a complex discrete wavelet transform algorithm to maximize pixel phase correlation and perform multiresolution analysis. Registration performance was assessed quantitatively by NMI. Results The new registration procedure was able to realign liver structures in all 19 patients. NMI increased by about 8% after rigid registration (native vs. rigid registration 0.073 ± 0.031 vs. 0.078 ± 0.031, n.s., paired t-test and by a further 23% (0.096 ± 0.035 vs. 0.078 ± 0.031, p t-test after non-rigid realignment. The overall average NMI increase was 31%. Conclusion This new method for realigning dynamic contrast-enhanced 3D MR volumes of liver leads to subtraction images that enhance diagnostic possibilities for liver lesions.

Genotyping of PCR-based polymorphisms and linkage-disequilibrium analysis at the NF1 locus

Energy Technology Data Exchange (ETDEWEB)

Purandare, S.M.; Viskochil, D.H.; Cawthon, R. [Univ. of Utah, Salt Lake City, UT (United States)] [and others

1996-07-01

Six polymorphism across the NF1 gene have been adapted for genotyping through application of PCR-based assays. Three exon-based polymorphisms - at positions 702, 2034, and 10647 in the NF1 cDNA - were genotyped by mutagenically separated PCR (MS-PCR). A fourth polymorphism, DV1.9, is an L1 insertion element in intron 30, and the other two polymorphisms, GXAlu and EVI-20, are short tandem repeats in intron 27b. All the polymorphisms were evaluated in a cohort of 110 CEPH individuals who previously had been analyzed by use of eight RFLPs at the NF1 locus. Pairwise linkage-disequilibrium analyses with the six PCR-based polymorphisms and their flanking markers demonstrated disequilibrium between all tested loci. Genotypes of the four diallelic polymorphisms (702, 2034, 10647, and DV1.9) were also evaluated in cohorts from the CEPH, African, and Japanese populations. The CEPH and Japanese cohorts showed similar heterozygosities and linkage-disequilibrium coefficients. The African cohort showed a higher degree of heterozygosity and lower linkage-disequilibrium values, compared with the CEPH and Japanese cohorts. 36 refs., 2 figs., 3 tabs.

Identification of Differentially-Expressed Genes in Response to Mycosphaerella fijiensis in the Resistant Musa Accession 'Calcutta-4' Using Suppression Subtractive Hybridization.

Science.gov (United States)

Sánchez Timm, Eduardo; Hidalgo Pardo, Lisette; Pacheco Coello, Ricardo; Chávez Navarrete, Tatiana; Navarrete Villegas, Oscar; Santos Ordóñez, Efrén

2016-01-01

Bananas and plantains are considered an important crop around the world. Banana production is affected by several constraints, of which Black Sigatoka Disease, caused by the fungus Mycosphaerella fijiensis, is considered one of the most important diseases in banana plantations. The banana accession 'Calcutta-4' has a natural resistance to Black Sigatoka; however, the fruit is not valuable for commercialization. Gene identification and expression studies in 'Calcutta-4' might reveal possible gene candidates for resistant to the disease and elucidate mechanisms for resistance. A subtracted cDNA library was generated from leaves after 6, 9 and 12 days inoculated with M. fijiensis conidia on greenhouse banana plants of the accession 'Calcutta-4'. Bioinformatic analysis revealed 99 good quality sequences. Blast2go analysis revealed that 31% of the sequences could not be categorized and, according to the Biological Process Category, 32 and 28 ESTs are related to general metabolic and cellular processes, respectively; while 10 ESTs response to stimulus. Seven sequences were redundant and one was similar to genes that may be involved in pathogen resistance including the putative disease resistance protein RGA1. Genes encoding zinc finger domains were identified and may play an important role in pathogen resistance by inducing the expression of downstream genes. Expression analysis of four selected genes was performed using RT-qPCR during the early stage of the disease development at 6, 9, 12 and 15 days post inoculation showing a peak of up regulation at 9 or 12 days post inoculation. Three of the four genes showed an up-regulation of expression in 'Calcutta-4' when compared to 'Williams' after inoculation with M. fijiensis, suggesting a fine regulation of specific gene candidates that may lead to a resistance response. The genes identified in early responses in a plant-pathogen interaction may be relevant for the resistance response of 'Calcutta-4' to Black Sigatoka

Identification of Differentially-Expressed Genes in Response to Mycosphaerella fijiensis in the Resistant Musa Accession 'Calcutta-4' Using Suppression Subtractive Hybridization.

Directory of Open Access Journals (Sweden)

Eduardo Sánchez Timm

Full Text Available Bananas and plantains are considered an important crop around the world. Banana production is affected by several constraints, of which Black Sigatoka Disease, caused by the fungus Mycosphaerella fijiensis, is considered one of the most important diseases in banana plantations. The banana accession 'Calcutta-4' has a natural resistance to Black Sigatoka; however, the fruit is not valuable for commercialization. Gene identification and expression studies in 'Calcutta-4' might reveal possible gene candidates for resistant to the disease and elucidate mechanisms for resistance. A subtracted cDNA library was generated from leaves after 6, 9 and 12 days inoculated with M. fijiensis conidia on greenhouse banana plants of the accession 'Calcutta-4'. Bioinformatic analysis revealed 99 good quality sequences. Blast2go analysis revealed that 31% of the sequences could not be categorized and, according to the Biological Process Category, 32 and 28 ESTs are related to general metabolic and cellular processes, respectively; while 10 ESTs response to stimulus. Seven sequences were redundant and one was similar to genes that may be involved in pathogen resistance including the putative disease resistance protein RGA1. Genes encoding zinc finger domains were identified and may play an important role in pathogen resistance by inducing the expression of downstream genes. Expression analysis of four selected genes was performed using RT-qPCR during the early stage of the disease development at 6, 9, 12 and 15 days post inoculation showing a peak of up regulation at 9 or 12 days post inoculation. Three of the four genes showed an up-regulation of expression in 'Calcutta-4' when compared to 'Williams' after inoculation with M. fijiensis, suggesting a fine regulation of specific gene candidates that may lead to a resistance response. The genes identified in early responses in a plant-pathogen interaction may be relevant for the resistance response of 'Calcutta-4' to

Influence of DNA isolation on Q-PCR-based quantification of methanogenic Archaea in biogas fermenters.

Science.gov (United States)

Bergmann, I; Mundt, K; Sontag, M; Baumstark, I; Nettmann, E; Klocke, M

2010-03-01

Quantitative real-time PCR (Q-PCR) is commonly applied for the detection of certain microorganisms in environmental samples. However, some environments, like biomass-degrading biogas fermenters, are enriched with PCR-interfering substances. To study the impact of the DNA extraction protocol on the results of Q-PCR-based analysis of the methane-producing archaeal community in biogas fermenters, nine different protocols with varying cell disruption and DNA purification approaches were tested. Differences in the quantities of the isolated DNA and the purity parameters were found, with the best cell lysis efficiencies being obtained by a combined lysozyme/SDS-based lysis. When DNA was purified by sephacryl columns, the amount of DNA decreased by one log cycle but PCR inhibitors were eliminated sufficiently. In the case of detection of methanogenic Archaea, the chosen DNA isolation protocol strongly influenced the Q-PCR-based determination of 16S rDNA copy numbers. For example, with protocols including mechanical cell disruption, the 16S rDNA of Methanobacteriales were predominantly amplified (81-90% of the total 16S rDNA copy numbers), followed by the 16S rDNA of Methanomicrobiales (9-18%). In contrast, when a lysozyme/SDS-based cell lysis was applied, the 16S rDNA copy numbers determined for these two orders were the opposite (Methanomicrobiales 82-95%, Methanobacteriales 4-18%). In extreme cases, the DNA isolation method led to discrimination of some groups of methanogens (e.g. members of the Methanosaetaceae). In conclusion, for extraction of high amounts of microbial DNA with high purity from samples of biogas plants, a combined lysozyme/SDS-based cell lysis followed by a purification step with sephacryl columns is recommended. Copyright 2010 Elsevier GmbH. All rights reserved.

Mental Computation or Standard Algorithm? Children's Strategy Choices on Multi-Digit Subtractions

Science.gov (United States)

Torbeyns, Joke; Verschaffel, Lieven

2016-01-01

This study analyzed children's use of mental computation strategies and the standard algorithm on multi-digit subtractions. Fifty-eight Flemish 4th graders of varying mathematical achievement level were individually offered subtractions that either stimulated the use of mental computation strategies or the standard algorithm in one choice and two…

Removal of arterial wall calcifications in CT angiography by local subtraction

International Nuclear Information System (INIS)

Straten, Marcel van; Venema, Henk W.; Streekstra, Geert J.; Reekers, Jim A.; Heeten, Gerard J. den; Grimbergen, Cornelis A.

2003-01-01

CT Angiography (CTA) is an established technique for the minimally invasive imaging of arteries. The technique of maximum intensity projection (MIP) is often used to get a comprehensive overview of the vascular anatomy. On a MIP, however, arterial wall calcifications may hinder the visualization of the arterial lumen. These calcifications are in direct contact with the contrast-enhanced blood, which makes removal difficult. We present a local subtraction method for the automatic removal of these calcifications. In our approach a second CT scan has to be made, prior to contrast injection. The calcifications in both scans are registered prior to subtraction to compensate for displacements in between the two scans. Local subtraction results are compared with results obtained by thresholding. The method was tested in a phantom and with data from four patients. The phantom represented an artery with different types of stenosis. Data were used from patients for which CTA of the renal arteries was performed. For two patients the electrocardiogram (ECG) was recorded during the CTA examination, making retrospective cardiac gated reconstructions possible. Both the phantom and the patient study showed that the local subtraction method is capable of removing calcifications and visualizing the residual lumen. In the patient study it appeared that some artifacts remained for higher pitch values. We conclude that the local subtraction method is less subjective and more accurate than thresholding. Best results are obtained by use of a small pitch, at the expense of the volume covered during a single breath hold

Nonenhanced magnetic resonance angiography (MRA) of the calf arteries at 3 Tesla: intraindividual comparison of 3D flow-dependent subtractive MRA and 2D flow-independent non-subtractive MRA

Energy Technology Data Exchange (ETDEWEB)

Knobloch, Gesine; Lauff, Marie-Teres; Hirsch, Sebastian; Hamm, Bernd; Wagner, Moritz [Charite - Universitaetsmedizin Berlin, Department of Radiology, Berlin (Germany); Schwenke, Carsten [SCO:SSiS Statistical Consulting, Berlin (Germany)

2016-12-15

To prospectively compare 3D flow-dependent subtractive MRA vs. 2D flow-independent non-subtractive MRA for assessment of the calf arteries at 3 Tesla. Forty-two patients with peripheral arterial occlusive disease underwent nonenhanced MRA of calf arteries at 3 Tesla with 3D flow-dependent subtractive MRA (fast spin echo sequence; 3D-FSE-MRA) and 2D flow-independent non-subtractive MRA (balanced steady-state-free-precession sequence; 2D-bSSFP-MRA). Moreover, all patients underwent contrast-enhanced MRA (CE-MRA) as standard-of-reference. Two readers performed a per-segment evaluation for image quality (4 = excellent to 0 = non-diagnostic) and severity of stenosis. Image quality scores of 2D-bSSFP-MRA were significantly higher compared to 3D-FSE-MRA (medians across readers: 4 vs. 3; p < 0.0001) with lower rates of non-diagnostic vessel segments on 2D-bSSFP-MRA (reader 1: <1 % vs. 15 %; reader 2: 1 % vs. 29 %; p < 0.05). Diagnostic performance of 2D-bSSFP-MRA and 3D-FSE-MRA across readers showed sensitivities of 89 % (214/240) vs. 70 % (168/240), p = 0.0153; specificities: 91 % (840/926) vs. 63 % (585/926), p < 0.0001; and diagnostic accuracies of 90 % (1054/1166) vs. 65 % (753/1166), p < 0.0001. 2D flow-independent non-subtractive MRA (2D-bSSFP-MRA) is a robust nonenhanced MRA technique for assessment of the calf arteries at 3 Tesla with significantly higher image quality and diagnostic accuracy compared to 3D flow-dependent subtractive MRA (3D-FSE-MRA). (orig.)

Digital subtraction angiography of carotid bifurcation

International Nuclear Information System (INIS)

Vries, A.R. de.

1984-01-01

This study demonstrates the reliability of digital subtraction angiography (DSA) by means of intra- and interobserver investigations as well as indicating the possibility of substituting catheterangiography by DSA in the diagnosis of carotid bifurcation. Whenever insufficient information is obtained from the combination of non-invasive investigation and DSA, a catheterangiogram will be necessary. (Auth.)

Digital subtraction angiography: myths and reality

International Nuclear Information System (INIS)

Levin, D.C.

1984-01-01

Some of the claims made about digital subtraction angiography (DSA) when it was first developed have turned out to be greatly exaggerated, and some members of the radiologic community have become disillusioned with its capabilities. The author discusses some of the limitations of DSA, and concludes that the advantages of DSA outweigh its limitations

The contribution of chemical shift imaging with digital subtracting images to the diagnosis of steatohepatitis

International Nuclear Information System (INIS)

Guo Xinghua; Wang Juanping; Zhang Chongjie; Zheng Guofang; Fan Ruiqiang; Zhu Sumei; Liu Qiwang

2006-01-01

Objective: To investigate the diagnosis value of chemical shift imaging with digital subtracting in steatohepatitis. Methods: The in-phase images were subtracted by the out-phase ones in 34 cases of steatohepatitis, and the CNR were measured on these subtracted images to estimate the steatosis of the liver. The relationship of CT grade of steatohepatitis and CNR from the subtracted images was analyzed to evaluate the relationship between CNR and the degree of hepatic steatosis. The sensitivity and specificity of the subtracting and eyeballing methods were compared with chi-square test. Results: On the subtracted images, the liver and spleen were seen nearly the same aspects as low signals, CNR=0.98±0.06, meanwhile the spongy vertebra and the subcutaneous or abdominal lipid were seen as obvious higher signals in 52 normal cases. On the 34 steatohepatitis, scattered high signals were seen in the liver, which made the signal of liver higher than that of spleen, CNR=3.25±0.91--14.35±6.10. There was positive correlation between CNR and CT grade in the 34 cases of steatohepatitis, r=0.893, P<0.01. The sensitivity and specificity of the subtracting method were 88.24% and 94. 23%, significantly higher than that of the eyeballing results, 32.35% and 80.77%, P<0.01 and P<0.05. Conclusion: Chemical shift imaging with digital subtracting is a sensitive, specific, objective method to diagnose steatohepatitis and it is of potential ability for quantitative diagnosis. (authors)

An adaptive demodulation approach for bearing fault detection based on adaptive wavelet filtering and spectral subtraction

Science.gov (United States)

Zhang, Yan; Tang, Baoping; Liu, Ziran; Chen, Rengxiang

2016-02-01

Fault diagnosis of rolling element bearings is important for improving mechanical system reliability and performance. Vibration signals contain a wealth of complex information useful for state monitoring and fault diagnosis. However, any fault-related impulses in the original signal are often severely tainted by various noises and the interfering vibrations caused by other machine elements. Narrow-band amplitude demodulation has been an effective technique to detect bearing faults by identifying bearing fault characteristic frequencies. To achieve this, the key step is to remove the corrupting noise and interference, and to enhance the weak signatures of the bearing fault. In this paper, a new method based on adaptive wavelet filtering and spectral subtraction is proposed for fault diagnosis in bearings. First, to eliminate the frequency associated with interfering vibrations, the vibration signal is bandpass filtered with a Morlet wavelet filter whose parameters (i.e. center frequency and bandwidth) are selected in separate steps. An alternative and efficient method of determining the center frequency is proposed that utilizes the statistical information contained in the production functions (PFs). The bandwidth parameter is optimized using a local ‘greedy’ scheme along with Shannon wavelet entropy criterion. Then, to further reduce the residual in-band noise in the filtered signal, a spectral subtraction procedure is elaborated after wavelet filtering. Instead of resorting to a reference signal as in the majority of papers in the literature, the new method estimates the power spectral density of the in-band noise from the associated PF. The effectiveness of the proposed method is validated using simulated data, test rig data, and vibration data recorded from the transmission system of a helicopter. The experimental results and comparisons with other methods indicate that the proposed method is an effective approach to detecting the fault-related impulses

An adaptive demodulation approach for bearing fault detection based on adaptive wavelet filtering and spectral subtraction

International Nuclear Information System (INIS)

Zhang, Yan; Tang, Baoping; Chen, Rengxiang; Liu, Ziran

2016-01-01

Fault diagnosis of rolling element bearings is important for improving mechanical system reliability and performance. Vibration signals contain a wealth of complex information useful for state monitoring and fault diagnosis. However, any fault-related impulses in the original signal are often severely tainted by various noises and the interfering vibrations caused by other machine elements. Narrow-band amplitude demodulation has been an effective technique to detect bearing faults by identifying bearing fault characteristic frequencies. To achieve this, the key step is to remove the corrupting noise and interference, and to enhance the weak signatures of the bearing fault. In this paper, a new method based on adaptive wavelet filtering and spectral subtraction is proposed for fault diagnosis in bearings. First, to eliminate the frequency associated with interfering vibrations, the vibration signal is bandpass filtered with a Morlet wavelet filter whose parameters (i.e. center frequency and bandwidth) are selected in separate steps. An alternative and efficient method of determining the center frequency is proposed that utilizes the statistical information contained in the production functions (PFs). The bandwidth parameter is optimized using a local ‘greedy’ scheme along with Shannon wavelet entropy criterion. Then, to further reduce the residual in-band noise in the filtered signal, a spectral subtraction procedure is elaborated after wavelet filtering. Instead of resorting to a reference signal as in the majority of papers in the literature, the new method estimates the power spectral density of the in-band noise from the associated PF. The effectiveness of the proposed method is validated using simulated data, test rig data, and vibration data recorded from the transmission system of a helicopter. The experimental results and comparisons with other methods indicate that the proposed method is an effective approach to detecting the fault-related impulses

Comparison of kDNA PCR-hybridization assay with three PCR methods for canines visceral Leishmaniasis diagnosis

Energy Technology Data Exchange (ETDEWEB)

Pilatti, Marcia M.; Andrade, Antero S.R. [Centro de Desenvolvimento da Tecnologia Nuclear (CDTN/CNEN-MG), Belo Horizonte, MG (Brazil)], e-mail: marciapilatti@yahoo.com.br, e-mail: antero@cdtn.br; Ferreira, Sidney A. [Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG (Brazil). Dept. de Parasitologia], e-mail: saninoalmeida@gmail.com

2009-07-01

The sensitivity of the kDNA PCR-Hybridization assay, which uses radioactive DNA probes (labeled with {sup 32}P), was compared with three conventional PCR methods used for canine visceral leishmaniasis diagnosis. All PCR methods had two steps: a first amplification followed by hybridization or by a new amplification (nested or semi nested). Two methods (kDNA PCR-Hybridization and kDNA snPCR) used primers addressed to kinetoplast minicircles and the other two methods to the coding (LnPCR) and intergenic noncoding regions (ITS-1 nPCR) of the ribosomal rRNA genes. The comparison was accomplished in two groups of 23 infected dogs using samples collected by the conjunctival swab procedure. In the Group 1 the DNA was extracted from cotton swabs by phenol-chloroform and in Group 2 by boiling. The most efficient PCR methods in the Group 1 were those based on kDNA targets. The kDNA PCR-Hybridization was able to detect parasites in 22/23 dogs (95.6%) and in 40/46 samples (86.9%). The kDNA snPCR was positive for 21/23 dogs (91.3%) and for 40/46 samples (86.9%). The positivities of the kDNA based methods were significantly higher than the positivities verified for the methods based on ribosomal rRNA genes (p<0.05). In the Group 2 the kDNA PCR- Hybridization showed a better performance detecting parasites in 18/23 dogs (78.3%) and in 31/46 samples (67.4%), significantly higher than the other three methods (p<0.05). The higher sensitivity of the minicircle kDNA based assays reported by others was confirmed in this study and kDNA PCR-Hybridization showed the best sensitivity among the assays evaluated. (author)

Comparison of kDNA PCR-hybridization assay with three PCR methods for canines visceral Leishmaniasis diagnosis

International Nuclear Information System (INIS)

Pilatti, Marcia M.; Andrade, Antero S.R.; Ferreira, Sidney A.

2009-01-01

The sensitivity of the kDNA PCR-Hybridization assay, which uses radioactive DNA probes (labeled with 32 P), was compared with three conventional PCR methods used for canine visceral leishmaniasis diagnosis. All PCR methods had two steps: a first amplification followed by hybridization or by a new amplification (nested or semi nested). Two methods (kDNA PCR-Hybridization and kDNA snPCR) used primers addressed to kinetoplast minicircles and the other two methods to the coding (LnPCR) and intergenic noncoding regions (ITS-1 nPCR) of the ribosomal rRNA genes. The comparison was accomplished in two groups of 23 infected dogs using samples collected by the conjunctival swab procedure. In the Group 1 the DNA was extracted from cotton swabs by phenol-chloroform and in Group 2 by boiling. The most efficient PCR methods in the Group 1 were those based on kDNA targets. The kDNA PCR-Hybridization was able to detect parasites in 22/23 dogs (95.6%) and in 40/46 samples (86.9%). The kDNA snPCR was positive for 21/23 dogs (91.3%) and for 40/46 samples (86.9%). The positivities of the kDNA based methods were significantly higher than the positivities verified for the methods based on ribosomal rRNA genes (p<0.05). In the Group 2 the kDNA PCR- Hybridization showed a better performance detecting parasites in 18/23 dogs (78.3%) and in 31/46 samples (67.4%), significantly higher than the other three methods (p<0.05). The higher sensitivity of the minicircle kDNA based assays reported by others was confirmed in this study and kDNA PCR-Hybridization showed the best sensitivity among the assays evaluated. (author)

Comparison of PCR-Based Diagnosis with Centrifuged-Based Enrichment Method for Detection of Borrelia Persica in Animal Blood Samples

Directory of Open Access Journals (Sweden)

SR Naddaf

2011-06-01

Full Text Available Background: The mainstay of diagnosis of relapsing fever (RF is demonstration of the spirochetes in Giemsa-stained thick blood smears, but during non fever periods the bacteria are very scanty and rarely detected in blood smears by mi­cros­copy. This study is aimed to evaluate the sensitivity of different methods developed for detection of low-grade spi­ro­chetemia. Methods: Animal blood samples with low degrees of spirochetemia were tested with two PCRs and a nested PCR tar­get­ing flaB, GlpQ, and rrs genes. Also, a centrifuged-based enrichment method and Giemsa staining were per­formed on blood samples with various degrees of spirochetemia. Results: The flaB-PCR and nested rrs-PCR turned positive with various degrees of spirochetemia including the blood samples that turned negative with dark-field microscopy. The GlpQ-PCR was positive as far as at least one spi­ro­chete was seen in 5-10 microscopic fields. The sensitivity of GlpQ-PCR increased when DNA from Buffy Coat Layer (BCL was used as template. The centrifuged-based enrichment method turned positive with as low concentra­tion as 50 bacteria/ml blood, while Giemsa thick staining detected bacteria with concentrations ≥ 25000 bacteria/ml. Conclusion: Centrifuged-based enrichment method appeared as much as 500-fold more sensitive than thick smears, which makes it even superior to some PCR assays. Due to simplicity and minimal laboratory requirements, this method can be considered a valuable tool for diagnosis of RF in rural health centers.

Comparison of PCR-Based Diagnosis with Centrifuged-Based Enrichment Method for Detection of Borrelia persica in Animal Blood Samples

Directory of Open Access Journals (Sweden)

SR Naddaf

2011-06-01

Background: The mainstay of diagnosis of relapsing fever (RF is demonstration of the spirochetes in Giemsa-stained thick blood smears, but during non fever periods the bacteria are very scanty and rarely detected in blood smears by mi­cros­copy. This study is aimed to evaluate the sensitivity of different methods developed for detection of low-grade spi­ro­chetemia. Methods: Animal blood samples with low degrees of spirochetemia were tested with two PCRs and a nested PCR tar­get­ing flaB, GlpQ, and rrs genes. Also, a centrifuged-based enrichment method and Giemsa staining were per­formed on blood samples with various degrees of spirochetemia. Results: The flaB-PCR and nested rrs-PCR turned positive with various degrees of spirochetemia including the blood samples that turned negative with dark-field microscopy. The GlpQ-PCR was positive as far as at least one spi­ro­chete was seen in 5-10 microscopic fields. The sensitivity of GlpQ-PCR increased when DNA from Buffy Coat Layer (BCL was used as template. The centrifuged-based enrichment method turned positive with as low concentra­tion as 50 bacteria/ml blood, while Giemsa thick staining detected bacteria with concentrations ≥ 25000 bacteria/ml.  Conclusion: Centrifuged-based enrichment method appeared as much as 500-fold more sensitive than thick smears, which makes it even superior to some PCR assays. Due to simplicity and minimal laboratory requirements, this method can be considered a valuable tool for diagnosis of RF in rural health centers.  

[The backgroud sky subtraction around [OIII] line in LAMOST QSO spectra].

Science.gov (United States)

Shi, Zhi-Xin; Comte, Georges; Luo, A-Li; Tu, Liang-Ping; Zhao, Yong-Heng; Wu, Fu-Chao

2014-11-01

At present, most sky-subtraction methods focus on the full spectrum, not the particular location, especially for the backgroud sky around [OIII] line which is very important to low redshift quasars. A new method to precisely subtract sky lines in local region is proposed in the present paper, which sloves the problem that the width of Hβ-[OIII] line is effected by the backgroud sky subtraction. The exprimental results show that, for different redshift quasars, the spectral quality has been significantly improved using our method relative to the original batch program by LAMOST. It provides a complementary solution for the small part of LAMOST spectra which are not well handled by LAMOST 2D pipeline. Meanwhile, This method has been used in searching for candidates of double-peaked Active Galactic Nuclei.

PCR Based Microbial Monitor for Analysis of Recycled Water Aboard the ISSA: Issues and Prospects

Science.gov (United States)

Cassell, Gail H.; Lefkowitz, Elliot J.; Glass, John I.

1995-01-01

The monitoring of spacecraft life support systems for the presence of health threatening microorganisms is paramount for crew well being and successful completion of missions. Development of technology to monitor spacecraft recycled water based on detection and identification of the genetic material of contaminating microorganisms and viruses would be a substantial improvement over current NASA plans to monitor recycled water samples that call for the use of conventional microbiology techniques which are slow, insensitive, and labor intensive. The union of the molecular biology techniques of DNA probe hybridization and polymerase chain reaction (PCR) offers a powerful method for the detection, identification, and quantification of microorganisms and viruses. This technology is theoretically capable of assaying samples in as little as two hours with specificity and sensitivity unmatched by any other method. A major advance in probe-hybridization/PCR has come about in a technology called TaqMan(TM), which was invented by Perkin Elmer. Instrumentation using TaqMan concepts is evolving towards devices that could meet NASA's needs of size, low power use, and simplicity of operation. The chemistry and molecular biology needed to utilize these probe-hybridization/PCR instruments must evolve in parallel with the hardware. The following issues of chemistry and biology must be addressed in developing a monitor: Early in the development of a PCR-based microbial monitor it will be necessary to decide how many and which organisms does the system need the capacity to detect. We propose a set of 17 different tests that would detect groups of bacteria and fungus, as well as specific eukaryotic parasites and viruses; In order to use the great sensitivity of PCR it will be necessary to concentrate water samples using filtration. If a lower limit of detection of 1 microorganism per 100 ml is required then the microbes in a 100 ml sample must be concentrated into a volume that can be

A study of transverse image reconstruction with digital subtraction angiography

International Nuclear Information System (INIS)

Sakamoto, Kiyoshi; Kotoura, Noriko; Terasawa, Yuuji; Oda, Masahiko; Gotou, Hiroshi; Nasada, Toshiya; Tanooka, Masao

1995-01-01

For digital subtraction angiography (DSA) with C-type equipment, it is possible to radiate an X-ray during rotation and to collect data at different angular settings. We tried to reconstruct transverse image from data obtained by scanning DSA images at different angular settings. 88 projection data were obtained by rotating the object at 180deg during radiation. Reconstruction was made using the convolution method with pixel value distribution for each projection. Similarly, the image quality of the reconstructed images were compared with the unsubtracted and subtracted ones. In case a part object was outside the calculating region, artifacts were generally produced. However, the artifacts were reduced by subtracting the background from the image. In addition, the cupping phenomenon caused by beam hardening was relaxed and high-quality imaging could be achieved. This method will become even more effective, if we will use it with selective angiography in which the limited area is enhanced. (author)

Tomographic image via background subtraction using an x-ray projection image and a priori computed tomography

International Nuclear Information System (INIS)

Zhang Jin; Yi Byongyong; Lasio, Giovanni; Suntharalingam, Mohan; Yu, Cedric

2009-01-01

Kilovoltage x-ray projection images (kV images for brevity) are increasingly available in image guided radiotherapy (IGRT) for patient positioning. These images are two-dimensional (2D) projections of a three-dimensional (3D) object along the x-ray beam direction. Projecting a 3D object onto a plane may lead to ambiguities in the identification of anatomical structures and to poor contrast in kV images. Therefore, the use of kV images in IGRT is mainly limited to bony landmark alignments. This work proposes a novel subtraction technique that isolates a slice of interest (SOI) from a kV image with the assistance of a priori information from a previous CT scan. The method separates structural information within a preselected SOI by suppressing contributions to the unprocessed projection from out-of-SOI-plane structures. Up to a five-fold increase in the contrast-to-noise ratios (CNRs) was observed in selected regions of the isolated SOI, when compared to the original unprocessed kV image. The tomographic image via background subtraction (TIBS) technique aims to provide a quick snapshot of the slice of interest with greatly enhanced image contrast over conventional kV x-ray projections for fast and accurate image guidance of radiation therapy. With further refinements, TIBS could, in principle, provide real-time tumor localization using gantry-mounted x-ray imaging systems without the need for implanted markers.

Comparative study between rib imaging of DR dual energy subtraction technology and chest imaging

International Nuclear Information System (INIS)

Yu Jianming; Lei Ziqiao; Kong Xiangchuang

2006-01-01

Objective: To investigate the application value of DR dual energy subtraction technology in rib lesions. Methods: 200 patients were performed with chest DR dual energy subtraction, comparing the rib imaging between DR of thorax and chest imaging using ROC analysis. Results: Among the total of 200 patients, there are 50 cases of rib calcification, 7 cases of rib destruction, 22 cases of rib fracture. The calcification, destruction and fracture were displayed respectively by ribs below diaphragm and rib markings. The analytic parameter of rib imaging of DR dual energy subtraction Az is 0.9367, while that of rib imaging of chest Az is 0.6830. Conclusion: DR dual energy subtraction technology is superior to chest imaging in the displaying of rib lesion and ribs below diaphragm. (authors)

Subtractive fabrication of ferroelectric thin films with precisely controlled thickness

Science.gov (United States)

Ievlev, Anton V.; Chyasnavichyus, Marius; Leonard, Donovan N.; Agar, Joshua C.; Velarde, Gabriel A.; Martin, Lane W.; Kalinin, Sergei V.; Maksymovych, Petro; Ovchinnikova, Olga S.

2018-04-01

The ability to control thin-film growth has led to advances in our understanding of fundamental physics as well as to the emergence of novel technologies. However, common thin-film growth techniques introduce a number of limitations related to the concentration of defects on film interfaces and surfaces that limit the scope of systems that can be produced and studied experimentally. Here, we developed an ion-beam based subtractive fabrication process that enables creation and modification of thin films with pre-defined thicknesses. To accomplish this we transformed a multimodal imaging platform that combines time-of-flight secondary ion mass spectrometry with atomic force microscopy to a unique fabrication tool that allows for precise sputtering of the nanometer-thin layers of material. To demonstrate fabrication of thin-films with in situ feedback and control on film thickness and functionality we systematically studied thickness dependence of ferroelectric switching of lead-zirconate-titanate, within a single epitaxial film. Our results demonstrate that through a subtractive film fabrication process we can control the piezoelectric response as a function of film thickness as well as improve on the overall piezoelectric response versus an untreated film.

Subtraction of random coincidences in γ-ray spectroscopy: A new approach

International Nuclear Information System (INIS)

Pattabiraman, N.S.; Ghugre, S.S.; Basu, S.K.; Garg, U.; Ray, S.; Sinha, A.K.; Zhu, S.

2006-01-01

A new analytical method for estimation and subsequent subtraction of random coincidences has been developed. It utilizes the knowledge of the counts in the main diagonal of a background-subtracted symmetric data set for the estimation of the events originating from random coincidences. This procedure has been successfully applied to several data sets. It could be a valuable tool for low-fold data sets, especially for low-cross-section events

Efflux inhibitor suppresses Streptococcus mutans virulence properties.

Science.gov (United States)

Zeng, Huihui; Liu, Jia; Ling, Junqi

2017-04-01

It is well established that efflux pumps play important roles in bacterial pathogenicity and efflux inhibitors (EIs) have been proved to be effective in suppressing bacterial virulence properties. However, little is known regarding the EI of Streptococcus mutans, a well-known caries-inducing bacterium. In this study, we identified the EI of S. mutans through ethidium bromide efflux assay and investigated how EI affected S. mutans virulence regarding the cariogenicity and stress response. Results indicated that reserpine, the identified EI, suppressed acid tolerance, mutacin production and transformation efficiency of S. mutans, and modified biofilm architecture and extracellular polysaccharide distribution. Suppressed glycosyltransferase activity was also noted after reserpine exposure. The data from quantitative real-time-PCR demonstrated that reserpine significantly altered the expression profile of quorum-sensing and virulence-associated genes. These findings suggest that reserpine represents a promising adjunct anticariogenic agent in that it suppresses virulence properties of S. mutans. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

A rapid and direct real time PCR-based method for identification of Salmonella spp

DEFF Research Database (Denmark)

Rodriguez-Lazaro, D.; Hernández, Marta; Esteve, T.

2003-01-01

The aim of this work was the validation of a rapid, real-time PCR assay based on TaqMan((R)) technology for the unequivocal identification of Salmonella spp. to be used directly on an agar-grown colony. A real-time PCR system targeting at the Salmonella spp. invA gene was optimized and validated ...

A method for subtraction of the extrarenal 'background' in dynamic 131I-hippurate renoscintigraphy

International Nuclear Information System (INIS)

Mlodkowska, E.; Liniecki, J.; Surma, M.

1979-01-01

Using a Toshiba GC-401 gamma camera with MDS computer Trinary a new method was developed for subtracting the extrarenal (extracanalicular) 'background' from the count rate recorded over the kidneys after intravenous administration of 131 I-hippurate. Mean subtraction factors of the 'blood' activity curve were calculated from a study of 27 patients who were given 51 Cr-HSA for purposes of conventional renography with 'background' subtraction. The values of the mean subtraction factors anti Fsub(R,L) for the right and left kidney, by which a blood count rate should be multiplied amounted to 0.86 +- 0.12 and 0.79 +- 0.13, respectively. A comparison of the coefficients of variation of the pure renal signal when mean vs. individually determined subtraction factors were used, and the verification of the method in unilaterally nephrectomized patients have demonstrated that determination of the factors, anti Fsub(R,L), for each patient individually is not required and sufficient precision can be obtained by using the method and factors reported in this study. (orig.) [de

TU-CD-BRA-11: Application of Bone Suppression Technique to Inspiratory/expiratory Chest Radiography

Energy Technology Data Exchange (ETDEWEB)

Tanaka, R; Sanada, S [Kanazawa University, Kanazawa, Ishikawa (Japan); Sakuta, K; Kawashima, H [Kanazawa University Hospital, Kanazawa, Ishikawa (Japan); Kishitani, Y [TOYO Corporation, Chuoh-ku, Tokyo (Japan)

2015-06-15

Purpose: The bone suppression technique based on advanced image processing can suppress the conspicuity of bones on chest radiographs, creating soft tissue images normally obtained by the dual-energy subtraction technique. This study was performed to investigate the usefulness of bone suppression technique in quantitative analysis of pulmonary function in inspiratory/expiratory chest radiography. Methods: Commercial bone suppression image processing software (ClearRead; Riverain Technologies) was applied to paired inspiratory/expiratory chest radiographs of 107 patients (normal, 33; abnormal, 74) to create corresponding bone suppression images. The abnormal subjects had been diagnosed with pulmonary diseases, such as pneumothorax, pneumonia, emphysema, asthma, and lung cancer. After recognition of the lung area, the vectors of respiratory displacement were measured in all local lung areas using a cross-correlation technique. The measured displacement in each area was visualized as displacement color maps. The distribution pattern of respiratory displacement was assessed by comparison with the findings of lung scintigraphy. Results: Respiratory displacement of pulmonary markings (soft tissues) was able to be quantified separately from the rib movements on bone suppression images. The resulting displacement map showed a left-right symmetric distribution increasing from the lung apex to the bottom region of the lung in many cases. However, patients with ventilatory impairments showed a nonuniform distribution caused by decreased displacement of pulmonary markings, which were confirmed to correspond to area with ventilatory impairments found on the lung scintigrams. Conclusion: The bone suppression technique was useful for quantitative analysis of respiratory displacement of pulmonary markings without any interruption of the rib shadows. Abnormal areas could be detected as decreased displacement of pulmonary markings. Inspiratory/expiratory chest radiography combined

The digital subtraction technique in lateral urethrocystography. Die laterale Urethrozystographie in digitaler Subtraktionstechnik

Energy Technology Data Exchange (ETDEWEB)

Wolf, K. (Radiologische Abt., Caritas-Krankenhaus, Bad Mergentheim (Germany)); Peterseim, H. (Frauenklinik, Caritas-Krankenhaus, Bad Mergentheim (Germany)); Grehn, S. (Radiologische Abt., Caritas-Krankenhaus, Bad Mergentheim (Germany))

1994-09-01

The first application of the digital subtraction technique to lateral urethrocystography is described. This methodology facilitates gynecological-urological operations by providing reliable investigation results and an unambiguous image interpretation. Methods and first experiences with the digital subtraction technique in gynecological-urological diagnosis are reported. (orig.)

Intraarterial digital subtraction angiography

International Nuclear Information System (INIS)

Davis, P.C.

1987-01-01

Digital subtraction angiography (DSA) refers to a radiographic technique of amplifying low levels of contrast from intravascular iodine into an acceptable image of vascular anatomy. Initial enthusiasm suggested that DSA using intravenous injections (IV-DSA) would eliminate most conventional film-screen angiographic studies. It was soon apparent, however, that IV-DSA examinations were often compromised in those patients who most needed a less invasive study. Indeed, only a 70 to 85 percent accuracy rate was achieved with IV-DSA, primarily due to motion artifact, poor cardiac output, overlap of pertinent vessels, and inability to resolve smaller vessels

Baicalein and U0126 suppress bladder cancer proliferation via ...

African Journals Online (AJOL)

RT-PCR) and western blot. Results: Baicalein and U0126 suppressed bladder cancer cell T24 proliferation by blocking cell cycle in G0~G1 phase. TUNEL and Annexin V/PI detection showed both baicalein and U0126 induced T24 cell ...

On a gauge invariant subtraction scheme for massive quantum electrodynamics

International Nuclear Information System (INIS)

Abdalla, E.; Gomes, M.; Koeberle, R.

A momentum-space subtraction scheme for massive quantum electrodynamics is proposed which respects gauge invariance, in contrast to ordinary normal product techniques. As a consequence the dependence of Green functions on the ghost mass becomes very simple and formally gauge invariant normal products of degree up to four, when subtracted according to the proposed scheme, are automatically gauge invariant. As an aplication we discuss the proof of the Adler-Bardeen theorem. Zero mass limits can be taken for Green function after the integration over intermediate states has been carried out [pt

Digital subtraction arthrography of the hips and of the shoulders

International Nuclear Information System (INIS)

Fink, B.K.; Schedel, J.; Fink, U.; Hansen, M.; Hilbertz, T.; Hagena, F.W.

1991-01-01

In a study on 60 patients, it could be shown that very good results can be achieved in the region of the shoulder joint with the use of the digital subtraction technique and of digital image intensifier radiography. A further possibility of using the digital subtraction technique for proving endoprosthesis loosenings of the hip demonstrated its importance after a short time and has become a routine method in the meantime. These two examination techniques are displayed methodologically and their clinical possibilities of use are assessed in this contribution. (orig.)

Improvement of DSA, reduction of acquisition images and suppression of halation

International Nuclear Information System (INIS)

Yamada, Kinichi; Kaga, Yuji; Eguchi, Yoichi; Kinai, Shigeo; Asahina, Hiroshi; Fujita, Hitoshi; Ogura, Ichiro; Yasuhara, Hiroshi.

1991-01-01

Recently, digital subtraction angiography (DSA) is seeing widespread use. Especially, intraarterial DSA (IA-DSA) makes good use of interventional radiology. However, we know that the skin dose for DSA is so much larger than general angiography, and halations often appearing on DSA images. In this report, we show two improvements of DSA. First, the skin dose for DSA is successfully decreased to one-sixth compared with the late DSA of cerebral artery by a reduction in acquisition images. Secondly, we are doing well in suppressing halation by exchanging the control point of automatic exposure control (AEC) from one-half to one-fourth. (author)

Radionuclide identification using subtractive clustering method

International Nuclear Information System (INIS)

Farias, Marcos Santana; Mourelle, Luiza de Macedo

2011-01-01

Radionuclide identification is crucial to planning protective measures in emergency situations. This paper presents the application of a method for a classification system of radioactive elements with a fast and efficient response. To achieve this goal is proposed the application of subtractive clustering algorithm. The proposed application can be implemented in reconfigurable hardware, a flexible medium to implement digital hardware circuits. (author)

Development of PCR-based detection methods for the quarantine phytopathogen Synchytrium endobioticum, causal agent of wart disease

NARCIS (Netherlands)

Boogert, van den P.H.J.F.; Gent-Pelzer, van M.P.E.; Bonants, P.J.M.; Boer, de S.H.; Wander, J.G.N.; Lévesque, C.A.; Leeuwen, van G.C.M.; Baayen, R.P.

2005-01-01

Abstract PCR-based methods were developed for the detection and quantification of the potato pathogen Synchytrium endobioticum in soil extracts and in planta. PCR primers, based on the internal transcribed spacer region of the multi-copy gene rDNA were tested for specificity, sensitivity and

Subtraction imaging of the ECG gated cardiac CT

Energy Technology Data Exchange (ETDEWEB)

Tanegashima, K.; Fukui, M.; Hyodo, H.

1987-05-01

The subtracting manipulation of contrast-enhanced gated cardiac CT (GCCT) images was experimentally studied with TCT 60A - 30 type (Toshiba) for clinical use, thereby reducing the amount of contrast medium (CM). Initially the optimum relationship between the concentration of CM and its injected velocity was determined using the model of resected canine hearts and in actual dogs. The emphasized good-subtracted images were obtained when the difference of CT values was approximately 40 H.U. between cardiac cavity and myocardium. Such condition was feasible in the use of 25 % Diatrizoic acid and its injected velocity of 0.02 ml/kg/sec. Finally the reduction of the amount of CM by 1/3 became possible in clinical settings. The method is applicable to multi-slice GCCT in various heart diseases.

Ion energy recovery experiment based on magnetic electro suppression

International Nuclear Information System (INIS)

Kim, J.; Stirling, W.L.; Dagenhart, W.K.; Barber, G.C.; Ponte, N.S.

1980-05-01

A proof-of-principle experiment on direct recovery of residual hydrogen ions based on a magnetic electron suppression scheme is described. Ions extracted from a source plasma a few kilovolts above the ground potential (approx. 20 A) are accelerated to 40 keV by a negative potential maintained on a neutralizer gas cell. As the residual ions exit the gas cell, they are deflected from the neutral beam by a magnetic field that also suppresses gas cell electrons and then recovered on a ground-potential surface. Under optimum conditions, a recovery efficiency (the ratio of the net recovered current to the available full-energy ion current) of 80% +- 20% has been obtained. Magnetic suppression of the beam plasma electrons was rather easily achieved; however, handling the fractional-energy ions originating from molecular species (H 2 + and H 3 + ) proved to be extremely important to recovery efficiency

Preliminary study of lateral cerebral angiography with reverse rotation in the digital image registration and subtraction

International Nuclear Information System (INIS)

Shen Zhenglin; Liu Dongyang; Shen Zhenghai; Li Shuping; Zhang Ziyan; Wu Yongjuan; Liu Peijun

2012-01-01

Objective: Investigate the value and feasibility of image registration with reverse rotation in lateral cerebral DSA. Methods: (1) Experimental study: the target images were subtracted directly, and subtracted again after reverse rotation. Software of registration and subtraction with reverse rotation edited by the author utilizing Visual Basic. The function of the automatic angle detection by the software were evaluated to see whether it detected the angle of line. The subtraction function of DSA by the software was evaluated. (2) Clinical retrospective study: the untreated mask and target images of 15 patients with motion along vertical axis during lateral cerebral DSA were uploaded to the software. The target images were processed with and without the software to get two sets of images. (3) Evaluation: four experienced radiologists read and compared the two sets of the images,and graded their findings. Results: (1) The automatic detection by the software suggested that the target images should be rotated counterclockwise 1.3°. The subtraction result of the software was satisfactory. (2) In the 15 sets of images, there were only three sets of images deemed optimal after traditional subtraction. After reverse rotation, artifacts were significantly reduced and the image sharper. There were ten cases with significant artifacts after traditional subtraction, and those images were sharper and showed more peripheral vessels after reverse rotation. The traditional subtraction images of two sets could not be interpreted,the reverse rotation registration images reached the diagnostic quality. (3) Subjective evaluation: there were more information and less noise and distortion in the registration images with reverse rotation than in the traditional subtraction. But the image resolution decreased slightly after reverse rotation registration. Conclusion: The registration of digital angiography with reverse rotation can improve the image quality in lateral cerebral DSA

Diagnosis of clinical samples spotted on FTA cards using PCR-based methods.

Science.gov (United States)

Jamjoom, Manal; Sultan, Amal H

2009-04-01

The broad clinical presentation of Leishmaniasis makes the diagnosis of current and past cases of this disease rather difficult. Differential diagnosis is important because diseases caused by other aetiologies and a clinical spectrum similar to that of leishmaniasis (e.g. leprosy, skin cancers and tuberculosis for CL; malaria and schistosomiasis for VL) are often present in endemic areas of endemicity. Presently, a variety of methods have been developed and tested to aid the identification and diagnosis of Leishmania. The advent of the PCR technology has opened new channels for the diagnosis of leishmaniasis in a variety of clinical materials. PCR is a simple, rapid procedure that has been adapted for diagnosis of leishmaniasis. A range of tools is currently available for the diagnosis and identification of leishmaniasis and Leishmania species, respectively. However, none of these diagnostic tools are examined and tested using samples spotted on FTA cards. Three different PCR-based approaches were examined including: kDNA minicircle, Leishmania 18S rRNA gene and PCR-RFLP of Intergenic region of ribosomal protein. PCR primers were designed that sit within the coding sequences of genes (relatively well conserved) but which amplify across the intervening intergenic sequence (relatively variable). These were used in PCR-RFLP on reference isolates of 10 of the most important Leishmania species: L. donovani, L. infantum, L. major & L. tropica. Digestion of PCR products with restriction enzymes produced species-specific restriction patterns allowed discrimination of reference isolates. The kDNA minicircle primers are highly sensitive in diagnosis of both bone marrow and skin smears from FTA cards. Leishmania 18S rRNA gene conserved region is sensitive in identification of bone marrow smear but less sensitive in diagnosing skin smears. The intergenic nested PCR-RFLP using P5 & P6 as well as P1 & P2 newly designed primers showed high level of reproducibility and sensitivity

Exercise intravenous digital subtraction angiography

International Nuclear Information System (INIS)

Yiannikas, J.

1986-01-01

Attempts to use exercise ventriculography have been made, not only to give diagnostic and perhaps even prognostic information in patients with coronary artery disease, but also in patients with valvular heart disease both before and after surgical intervention. Clearly an accurate method of assessing ventricular function under conditions of stress in various cardiac diseases would provide important information that would help in patient management. Exercise ventriculography using gated blood pool equilibrium technetium studies are widely used, but are limited by spatial resolution and by the foreshortening affects of visualizing the left ventricular chamber in the left anterior oblique view. First pass radionuclide studies have the added advantage of being able to visualize the ventricular chamber in the anterior or even the right anterior oblique view, but are even more limited by their spatial resolution problems. Several investigations have shown that digital subtraction angiography produces left ventricular images with a spatial resolution almost identical to that of conventional contrast ventriculography, but without the inherent problems of cardiac arrhythmias, which often limit the assessment of left ventricular function. Because of its ability to accurately delineate wall motion abnormalities, the technique may provide an adequate assessment of global and regional left ventricular function after exercise. Digital subtraction angiography may identify ischemic wall motion abnormalities produced by exercise in patients who already had significant permanent left ventricular damage from myocardial infarction

Use of PCR-Based Methods for Rapid Differentiation of Lactobacillus delbrueckii subsp. bulgaricus and L. delbrueckii subsp. lactis

OpenAIRE

Torriani, Sandra; Zapparoli, Giacomo; Dellaglio, Franco

1999-01-01

Two PCR-based methods, specific PCR and randomly amplified polymorphic DNA PCR (RAPD-PCR), were used for rapid and reliable differentiation of Lactobacillus delbrueckii subsp. bulgaricus and L. delbrueckii subsp. lactis. PCR with a single combination of primers which targeted the proline iminopeptidase (pepIP) gene of L. delbrueckii subsp. bulgaricus allowed amplification of genomic fragments specific for the two subspecies when either DNA from a single colony or cells extracted from dairy pr...

A comparative study of additive and subtractive manufacturing for dental restorations.

Science.gov (United States)

Bae, Eun-Jeong; Jeong, Il-Do; Kim, Woong-Chul; Kim, Ji-Hwan

2017-08-01

Digital systems have recently found widespread application in the fabrication of dental restorations. For the clinical assessment of dental restorations fabricated digitally, it is necessary to evaluate their accuracy. However, studies of the accuracy of inlay restorations fabricated with additive manufacturing are lacking. The purpose of this in vitro study was to evaluate and compare the accuracy of inlay restorations fabricated by using recently introduced additive manufacturing with the accuracy of subtractive methods. The inlay (distal occlusal cavity) shape was fabricated using 3-dimensional image (reference data) software. Specimens were fabricated using 4 different methods (each n=10, total N=40), including 2 additive manufacturing methods, stereolithography apparatus and selective laser sintering; and 2 subtractive methods, wax and zirconia milling. Fabricated specimens were scanned using a dental scanner and then compared by overlapping reference data. The results were statistically analyzed using a 1-way analysis of variance (α=.05). Additionally, the surface morphology of 1 randomly (the first of each specimen) selected specimen from each group was evaluated using a digital microscope. The results of the overlap analysis of the dental restorations indicated that the root mean square (RMS) deviation observed in the restorations fabricated using the additive manufacturing methods were significantly different from those fabricated using the subtractive methods (Padditive manufacturing methods (P=.466). Similarly, no significant differences were found between wax and zirconia, the subtractive methods (P=.986). The observed RMS values were 106 μm for stereolithography apparatus, 113 μm for selective laser sintering, 116 μm for wax, and 119 μm for zirconia. Microscopic evaluation of the surface revealed a fine linear gap between the layers of restorations fabricated using stereolithography apparatus and a grooved hole with inconsistent weak scratches

The analysis of novel microRNA mimic sequences in cancer cells reveals lack of specificity in stem-loop RT-qPCR-based microRNA detection.

Science.gov (United States)

Winata, Patrick; Williams, Marissa; McGowan, Eileen; Nassif, Najah; van Zandwijk, Nico; Reid, Glen

2017-11-17

MicroRNAs are frequently downregulated in cancer, and restoring expression has tumour suppressive activity in tumour cells. Our recent phase I clinical trial investigated microRNA-based therapy in patients with malignant pleural mesothelioma. Treatment with TargomiRs, microRNA mimics with novel sequence packaged in EGFR antibody-targeted bacterial minicells, revealed clear signs of clinical activity. In order to detect delivery of microRNA mimics to tumour cells in future clinical trials, we tested hydrolysis probe-based assays specific for the sequence of the novel mimics in transfected mesothelioma cell lines using RT-qPCR. The custom assays efficiently and specifically amplified the consensus mimics. However, we found that these assays gave a signal when total RNA from untransfected and control mimic-transfected cells were used as templates. Further investigation revealed that the reverse transcription step using stem-loop primers appeared to introduce substantial non-specific amplification with either total RNA or synthetic RNA templates. This suggests that reverse transcription using stem-loop primers suffers from an intrinsic lack of specificity for the detection of highly similar microRNAs in the same family, especially when analysing total RNA. These results suggest that RT-qPCR is unlikely to be an effective means to detect delivery of microRNA mimic-based drugs to tumour cells in patients.

Subtractions in the Adler sum rule and violation of charge symmetry

International Nuclear Information System (INIS)

Dominguez, C.A.; Moreno, H.; Zepeda, A.

1976-01-01

The consequences of a once-subtracted dispersion relation in the derivation of the Adler sum rule are investigated. It is shown that one can expect a breakdown of charge symmetry, of the isotriplet-current hypothesis, and of scaling of the structure functions. These breakdowns are related to the possible presence of a nonzero subtraction function at asymptotic energies and arbitrary q 2 . We also comment about second-class currents and PCAC (partial conservation of axial-vector current) relations

IMPROVED BACKGROUND SUBTRACTION FOR THE SLOAN DIGITAL SKY SURVEY IMAGES

International Nuclear Information System (INIS)

Blanton, Michael R.; Kazin, Eyal; Muna, Demitri; Weaver, Benjamin A.; Price-Whelan, Adrian

2011-01-01

We describe a procedure for background subtracting Sloan Digital Sky Survey (SDSS) imaging that improves the resulting detection and photometry of large galaxies on the sky. Within each SDSS drift scan run, we mask out detected sources and then fit a smooth function to the variation of the sky background. This procedure has been applied to all SDSS-III Data Release 8 images, and the results are available as part of that data set. We have tested the effect of our background subtraction on the photometry of large galaxies by inserting fake galaxies into the raw pixels, reanalyzing the data, and measuring them after background subtraction. Our technique results in no size-dependent bias in galaxy fluxes up to half-light radii r 50 ∼ 100 arcsec; in contrast, for galaxies of that size the standard SDSS photometric catalog underestimates fluxes by about 1.5 mag. Our results represent a substantial improvement over the standard SDSS catalog results and should form the basis of any analysis of nearby galaxies using the SDSS imaging data.

Enhanced capillary electrophoretic screening of Alzheimer based on direct apolipoprotein E genotyping and one-step multiplex PCR.

Science.gov (United States)

Woo, Nain; Kim, Su-Kang; Sun, Yucheng; Kang, Seong Ho

2018-01-01

Human apolipoprotein E (ApoE) is associated with high cholesterol levels, coronary artery disease, and especially Alzheimer's disease. In this study, we developed an ApoE genotyping and one-step multiplex polymerase chain reaction (PCR) based-capillary electrophoresis (CE) method for the enhanced diagnosis of Alzheimer's. The primer mixture of ApoE genes enabled the performance of direct one-step multiplex PCR from whole blood without DNA purification. The combination of direct ApoE genotyping and one-step multiplex PCR minimized the risk of DNA loss or contamination due to the process of DNA purification. All amplified PCR products with different DNA lengths (112-, 253-, 308-, 444-, and 514-bp DNA) of the ApoE genes were analyzed within 2min by an extended voltage programming (VP)-based CE under the optimal conditions. The extended VP-based CE method was at least 120-180 times faster than conventional slab gel electrophoresis methods In particular, all amplified DNA fragments were detected in less than 10 PCR cycles using a laser-induced fluorescence detector. The detection limits of the ApoE genes were 6.4-62.0pM, which were approximately 100-100,000 times more sensitive than previous Alzheimer's diagnosis methods In addition, the combined one-step multiplex PCR and extended VP-based CE method was also successfully applied to the analysis of ApoE genotypes in Alzheimer's patients and normal samples and confirmed the distribution probability of allele frequencies. This combination of direct one-step multiplex PCR and an extended VP-based CE method should increase the diagnostic reliability of Alzheimer's with high sensitivity and short analysis time even with direct use of whole blood. Copyright © 2017 Elsevier B.V. All rights reserved.

Improved olefinic fat suppression in skeletal muscle DTI using a magnitude-based dixon method.

Science.gov (United States)

Burakiewicz, Jedrzej; Hooijmans, Melissa T; Webb, Andrew G; Verschuuren, Jan J G M; Niks, Erik H; Kan, Hermien E

2018-01-01

To develop a method of suppressing the multi-resonance fat signal in diffusion-weighted imaging of skeletal muscle. This is particularly important when imaging patients with muscular dystrophies, a group of diseases which cause gradual replacement of muscle tissue by fat. The signal from the olefinic fat peak at 5.3 ppm can significantly confound diffusion-tensor imaging measurements. Dixon olefinic fat suppression (DOFS), a magnitude-based chemical-shift-based method of suppressing the olefinic peak, is proposed. It is verified in vivo by performing diffusion tensor imaging (DTI)-based quantification in the lower leg of seven healthy volunteers, and compared to two previously described fat-suppression techniques in regions with and without fat contamination. In the region without fat contamination, DOFS produces similar results to existing techniques, whereas in muscle contaminated by subcutaneous fat signal moved due to the chemical shift artefact, it consistently showed significantly higher (P = 0.018) mean diffusivity (MD). Because fat presence lowers MD, this suggests improved fat suppression. DOFS offers superior fat suppression and enhances quantitative measurements in the muscle in the presence of fat. DOFS is an alternative to spectral olefinic fat suppression. Magn Reson Med 79:152-159, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Hybrid intravenous digital subtraction angiography of the carotid bifurcation

International Nuclear Information System (INIS)

Burbank, F.H.; Enzmann, D.; Keyes, G.S.; Brody, W.R.

1984-01-01

A hybrid digital subtraction angiography technique and noise-reduction algorithm were used to evaluate the carotid bifurcation. Temporal, hybrid, and reduced-noise hybrid images were obtained in right and left anterior oblique projections, and both single- and multiple-frame images were created with each method. The resulting images were graded on a scale of 1 to 5 by three experienced neuroradiologists. Temporal images were preferred over hybrid images. The percentage of nondiagnostic examinations, as agreed upon by two readers, was higher for temporal alone than temporal + hybrid. In addition, also by agreement between two readers, temporal + hybrid images significantly increased the number of bifurcations seen in two views (87%) compared to temporal subtraction alone

Evaluation of PCR-based preimplantation genetic diagnosis applied to monogenic diseases: a collaborative ESHRE PGD consortium study

Science.gov (United States)

Dreesen, Jos; Destouni, Aspasia; Kourlaba, Georgia; Degn, Birte; Mette, Wulf Christensen; Carvalho, Filipa; Moutou, Celine; Sengupta, Sioban; Dhanjal, Seema; Renwick, Pamela; Davies, Steven; Kanavakis, Emmanouel; Harton, Gary; Traeger-Synodinos, Joanne

2014-01-01

Preimplantation genetic diagnosis (PGD) for monogenic disorders currently involves polymerase chain reaction (PCR)-based methods, which must be robust, sensitive and highly accurate, precluding misdiagnosis. Twelve adverse misdiagnoses reported to the ESHRE PGD-Consortium are likely an underestimate. This retrospective study, involving six PGD centres, assessed the validity of PCR-based PGD through reanalysis of untransferred embryos from monogenic-PGD cycles. Data were collected on the genotype concordance at PGD and follow-up from 940 untransferred embryos, including details on the parameters of PGD cycles: category of monogenic disease, embryo morphology, embryo biopsy and genotype assay strategy. To determine the validity of PCR-based PGD, the sensitivity (Se), specificity (Sp) and diagnostic accuracy were calculated. Stratified analyses were also conducted to assess the influence of the parameters above on the validity of PCR-based PGD. The analysis of overall data showed that 93.7% of embryos had been correctly classified at the time of PGD, with Se of 99.2% and Sp of 80.9%. The stratified analyses found that diagnostic accuracy is statistically significantly higher when PGD is performed on two cells versus one cell (P=0.001). Se was significantly higher when multiplex protocols versus singleplex protocols were applied (P=0.005), as well as for PGD applied on cells from good compared with poor morphology embryos (P=0.032). Morphology, however, did not affect diagnostic accuracy. Multiplex PCR-based methods on one cell, are as robust as those on two cells regarding false negative rate, which is the most important criteria for clinical PGD applications. Overall, this study demonstrates the validity, robustness and high diagnostic value of PCR-based PGD. PMID:24301057

Tomosynthesis applied to digital subtraction angiography

International Nuclear Information System (INIS)

Kruger, R.A.; Sedaghati, M.; Roy, D.G.; Liu, P.; Nelson, J.A.; Kubal, W.; Del Rio, P.

1984-01-01

This extension of the author's previous work on tomographic digital subtraction angiography (DSA) describes the theory of tomosynthetic DSA image reconstruction techniques. In addition to developing the resolution limits resulting from x-ray exposure length and image intensifier field curvature, the authors describe one method of image formation and show tomosynthetic DSA images of animal and human anatomy. Methods for improving the present technique are discussed

Improvement of Dimensional Accuracy of 3-D Printed Parts using an Additive/Subtractive Based Hybrid Prototyping Approach

Science.gov (United States)

Amanullah Tomal, A. N. M.; Saleh, Tanveer; Raisuddin Khan, Md.

2017-11-01

At present, two important processes, namely CNC machining and rapid prototyping (RP) are being used to create prototypes and functional products. Combining both additive and subtractive processes into a single platform would be advantageous. However, there are two important aspects need to be taken into consideration for this process hybridization. First is the integration of two different control systems for two processes and secondly maximizing workpiece alignment accuracy during the changeover step. Recently we have developed a new hybrid system which incorporates Fused Deposition Modelling (FDM) as RP Process and CNC grinding operation as subtractive manufacturing process into a single setup. Several objects were produced with different layer thickness for example 0.1 mm, 0.15 mm and 0.2 mm. It was observed that pure FDM method is unable to attain desired dimensional accuracy and can be improved by a considerable margin about 66% to 80%, if finishing operation by grinding is carried out. It was also observed layer thickness plays a role on the dimensional accuracy and best accuracy is achieved with the minimum layer thickness (0.1 mm).

Blood grouping based on PCR methods and agarose gel electrophoresis.

Science.gov (United States)

Sell, Ana Maria; Visentainer, Jeane Eliete Laguila

2015-01-01

The study of erythrocyte antigens continues to be an intense field of research, particularly after the development of molecular testing methods. More than 300 specificities have been described by the International Society for Blood Transfusion as belonging to 33 blood group systems. The polymerase chain reaction (PCR) is a central tool for red blood cells (RBC) genotyping. PCR and agarose gel electrophoresis are low cost, easy, and versatile in vitro methods for amplifying defined target DNA (RBC polymorphic region). Multiplex-PCR, AS-PCR (Specific Allele Polymerase Chain Reaction), and RFLP-PCR (Restriction Fragment Length Polymorphism-Polymerase Chain Reaction) techniques are usually to identify RBC polymorphisms. Furthermore, it is an easy methodology to implement. This chapter describes the PCR methodology and agarose gel electrophoresis to identify the polymorphisms of the Kell, Duffy, Kidd, and MNS blood group systems.

Use of amplicon sequencing to improve sensitivity in PCR-based detection of microbial pathogen in environmental samples.

Science.gov (United States)

Saingam, Prakit; Li, Bo; Yan, Tao

2018-06-01

DNA-based molecular detection of microbial pathogens in complex environments is still plagued by sensitivity, specificity and robustness issues. We propose to address these issues by viewing them as inadvertent consequences of requiring specific and adequate amplification (SAA) of target DNA molecules by current PCR methods. Using the invA gene of Salmonella as the model system, we investigated if next generation sequencing (NGS) can be used to directly detect target sequences in false-negative PCR reaction (PCR-NGS) in order to remove the SAA requirement from PCR. False-negative PCR and qPCR reactions were first created using serial dilutions of laboratory-prepared Salmonella genomic DNA and then analyzed directly by NGS. Target invA sequences were detected in all false-negative PCR and qPCR reactions, which lowered the method detection limits near the theoretical minimum of single gene copy detection. The capability of the PCR-NGS approach in correcting false negativity was further tested and confirmed under more environmentally relevant conditions using Salmonella-spiked stream water and sediment samples. Finally, the PCR-NGS approach was applied to ten urban stream water samples and detected invA sequences in eight samples that would be otherwise deemed Salmonella negative. Analysis of the non-target sequences in the false-negative reactions helped to identify primer dime-like short sequences as the main cause of the false negativity. Together, the results demonstrated that the PCR-NGS approach can significantly improve method sensitivity, correct false-negative detections, and enable sequence-based analysis for failure diagnostics in complex environmental samples. Copyright © 2018 Elsevier B.V. All rights reserved.

Preoperative radiological diagnosis by 99mTc·MIBI-99mTc subtraction scintigraphy for primary hyperparathyroidism

International Nuclear Information System (INIS)

Inouye, Takahiro; Tomita, Toshiki; Shinden, Seiichi; Takagi, Hitoshi; Kano, Shigeru.

1996-01-01

Preoperative radiological diagnosis constitutes the most important factor for the surgical treatment of hyperparathyroidism. In this regard, MRI is useful for detecting the abnormal parathyroid, but it is often difficult to localize it using MRI only. It is thus necessary to combine this procedure with excellent subtraction scintigraphy. We performed both 201 Tl- 99m Tc and 99m Tc·MIBI- 99m Tc subtraction scintigraphy in seven patients with primary hyperparathyroidism and compared them the radiological results. Five patients presented parathyroid adenomas and the rest hypertrophy of the parathyroid. We could detect the abnormal parathyroid in four patients (57.1%) by 201 Tl- 99m Tc subtraction scintigraphy and in six patients (85.7%) by 99m Tc·MIBI- 99m Tc subtraction scintigraphy. We therefore believe that 99m Tc·MIBI- 99m Tc subtraction scintigraphy will become an essential examination for primary hyperparathyroidism rather than the presently employed 201 Tl- 99m Tc subtraction scintigraphy. (author)

Quantitative (real-time) PCR

International Nuclear Information System (INIS)

Denman, S.E.; McSweeney, C.S.

2005-01-01

Many nucleic acid-based probe and PCR assays have been developed for the detection tracking of specific microbes within the rumen ecosystem. Conventional PCR assays detect PCR products at the end stage of each PCR reaction, where exponential amplification is no longer being achieved. This approach can result in different end product (amplicon) quantities being generated. In contrast, using quantitative, or real-time PCR, quantification of the amplicon is performed not at the end of the reaction, but rather during exponential amplification, where theoretically each cycle will result in a doubling of product being created. For real-time PCR, the cycle at which fluorescence is deemed to be detectable above the background during the exponential phase is termed the cycle threshold (Ct). The Ct values obtained are then used for quantitation, which will be discussed later

Dispersed-fringe-accumulation-based left-subtract-right method for fine co-phasing of a dispersed fringe sensor.

Science.gov (United States)

Li, Yang; Wang, Shengqian; Rao, Changhui

2017-05-20

In this paper, a dispersed-fringe-accumulation (DFA)-based left-subtract-right (LSR) piston estimation method (DFA-LSR), in which the dispersed fringe image is accumulated in the dispersed direction, and then the LSR method is used to estimate the piston error, is proposed for dispersed fringe sensors (DFS) in the fine co-phasing stage. The DFS is usually used to detect the piston errors (optical path difference) between different segmented mirrors or synthetic aperture telescopes. The DFA-LSR makes up for the shortcomings of the main peak position (MPP) method, which suffers from the constant offset in the pixel counts. The analysis and experiment results show that the proposed method can keep relatively better performance even at the condition of poor signal-to-noise ratio, compared with the MPP method in fine co-phasing stage.

Parathyroid localizlation by 201Tl-99mTc subtraction scintigraphy

International Nuclear Information System (INIS)

Rademaker, P.; Meijer, S.; Piers, D.A.

1990-01-01

Subtraction scintigraphy with 201 Tl and 99m Tc for parathyroid localization was performed preoperatively in 13 patients with chronic renal failure and secondary hyperparathyroidism. Twenty of the 37 examined pathological glands were predicted correctly (sensitivity 54%). In 3 patients with recurrent hyperparathyroidism after surgery all pathological glands found at second operation had been detected correctly by subtraction scintigraphy. We conclude that this localization method has a limited value when used prior to first neck exploration in secondary hyperparathyroidism. In persistent hyperparathyroidism after surgery it may play a useful role in localizing missed and ectopic glands. (author)

Cloning of the koi herpesvirus (KHV gene encoding thymidine kinase and its use for a highly sensitive PCR based diagnosis

Directory of Open Access Journals (Sweden)

Gilad Oren

2005-03-01

Full Text Available Abstract Background Outbreaks with mass mortality among common carp Cyprinus carpio carpio and koi Cyprinus carpio koi have occurred worldwide since 1998. The herpes-like virus isolated from diseased fish is different from Herpesvirus cyprini and channel catfish virus and was accordingly designated koi herpesvirus (KHV. Diagnosis of KHV infection based on viral isolation and current PCR assays has a limited sensitivity and therefore new tools for the diagnosis of KHV infections are necessary. Results A robust and sensitive PCR assay based on a defined gene sequence of KHV was developed to improve the diagnosis of KHV infection. From a KHV genomic library, a hypothetical thymidine kinase gene (TK was identified, subcloned and expressed as a recombinant protein. Preliminary characterization of the recombinant TK showed that it has a kinase activity using dTTP but not dCTP as a substrate. A PCR assay based on primers selected from the defined DNA sequence of the TK gene was developed and resulted in a 409 bp amplified fragment. The TK based PCR assay did not amplify the DNAs of other fish herpesviruses such as Herpesvirus cyprini (CHV and the channel catfish virus (CCV. The TK based PCR assay was specific for the detection of KHV and was able to detect as little as 10 fentograms of KHV DNA corresponding to 30 virions. The TK based PCR was compared to previously described PCR assays and to viral culture in diseased fish and was shown to be the most sensitive method of diagnosis of KHV infection. Conclusion The TK based PCR assay developed in this work was shown to be specific for the detection of KHV. The TK based PCR assay was more sensitive for the detection of KHV than previously described PCR assays; it was as sensitive as virus isolation which is the golden standard method for KHV diagnosis and was able to detect as little as 10 fentograms of KHV DNA corresponding to 30 virions.

Informed baseline subtraction of proteomic mass spectrometry data aided by a novel sliding window algorithm.

Science.gov (United States)

Stanford, Tyman E; Bagley, Christopher J; Solomon, Patty J

2016-01-01

Proteomic matrix-assisted laser desorption/ionisation (MALDI) linear time-of-flight (TOF) mass spectrometry (MS) may be used to produce protein profiles from biological samples with the aim of discovering biomarkers for disease. However, the raw protein profiles suffer from several sources of bias or systematic variation which need to be removed via pre-processing before meaningful downstream analysis of the data can be undertaken. Baseline subtraction, an early pre-processing step that removes the non-peptide signal from the spectra, is complicated by the following: (i) each spectrum has, on average, wider peaks for peptides with higher mass-to-charge ratios ( m / z ), and (ii) the time-consuming and error-prone trial-and-error process for optimising the baseline subtraction input arguments. With reference to the aforementioned complications, we present an automated pipeline that includes (i) a novel 'continuous' line segment algorithm that efficiently operates over data with a transformed m / z -axis to remove the relationship between peptide mass and peak width, and (ii) an input-free algorithm to estimate peak widths on the transformed m / z scale. The automated baseline subtraction method was deployed on six publicly available proteomic MS datasets using six different m/z-axis transformations. Optimality of the automated baseline subtraction pipeline was assessed quantitatively using the mean absolute scaled error (MASE) when compared to a gold-standard baseline subtracted signal. Several of the transformations investigated were able to reduce, if not entirely remove, the peak width and peak location relationship resulting in near-optimal baseline subtraction using the automated pipeline. The proposed novel 'continuous' line segment algorithm is shown to far outperform naive sliding window algorithms with regard to the computational time required. The improvement in computational time was at least four-fold on real MALDI TOF-MS data and at least an order of

SASqPCR: robust and rapid analysis of RT-qPCR data in SAS.

Directory of Open Access Journals (Sweden)

Daijun Ling

Full Text Available Reverse transcription quantitative real-time PCR (RT-qPCR is a key method for measurement of relative gene expression. Analysis of RT-qPCR data requires many iterative computations for data normalization and analytical optimization. Currently no computer program for RT-qPCR data analysis is suitable for analytical optimization and user-controllable customization based on data quality, experimental design as well as specific research aims. Here I introduce an all-in-one computer program, SASqPCR, for robust and rapid analysis of RT-qPCR data in SAS. This program has multiple macros for assessment of PCR efficiencies, validation of reference genes, optimization of data normalizers, normalization of confounding variations across samples, and statistical comparison of target gene expression in parallel samples. Users can simply change the macro variables to test various analytical strategies, optimize results and customize the analytical processes. In addition, it is highly automatic and functionally extendable. Thus users are the actual decision-makers controlling RT-qPCR data analyses. SASqPCR and its tutorial are freely available at http://code.google.com/p/sasqpcr/downloads/list.

Identifying genes and gene networks involved in chromium metabolism and detoxification in Crambe abyssinica

International Nuclear Information System (INIS)

Zulfiqar, Asma; Paulose, Bibin; Chhikara, Sudesh; Dhankher, Om Parkash

2011-01-01

Chromium pollution is a serious environmental problem with few cost-effective remediation strategies available. Crambe abyssinica (a member of Brassicaseae), a non-food, fast growing high biomass crop, is an ideal candidate for phytoremediation of heavy metals contaminated soils. The present study used a PCR-Select Suppression Subtraction Hybridization approach in C. abyssinica to isolate differentially expressed genes in response to Cr exposure. A total of 72 differentially expressed subtracted cDNAs were sequenced and found to represent 43 genes. The subtracted cDNAs suggest that Cr stress significantly affects pathways related to stress/defense, ion transporters, sulfur assimilation, cell signaling, protein degradation, photosynthesis and cell metabolism. The regulation of these genes in response to Cr exposure was further confirmed by semi-quantitative RT-PCR. Characterization of these differentially expressed genes may enable the engineering of non-food, high-biomass plants, including C. abyssinica, for phytoremediation of Cr-contaminated soils and sediments. - Highlights: → Molecular mechanism of Cr uptake and detoxification in plants is not well known. → We identified differentially regulated genes upon Cr exposure in Crambe abyssinica. → 72 Cr-induced subtracted cDNAs were sequenced and found to represent 43 genes. → Pathways linked to stress, ion transport, and sulfur assimilation were affected. → This is the first Cr transcriptome study in a crop with phytoremediation potential. - This study describes the identification and isolation of differentially expressed genes involved in chromium metabolism and detoxification in a non-food industrial oil crop Crambe abyssinica.

Identifying genes and gene networks involved in chromium metabolism and detoxification in Crambe abyssinica

Energy Technology Data Exchange (ETDEWEB)

Zulfiqar, Asma, E-mail: asmazulfiqar08@yahoo.com [Department of Plant, Soil, and Insect Sciences, 270 Stockbridge Road, University of Massachusetts Amherst, MA 01003 (United States); Paulose, Bibin, E-mail: bpaulose@psis.umass.edu [Department of Plant, Soil, and Insect Sciences, 270 Stockbridge Road, University of Massachusetts Amherst, MA 01003 (United States); Chhikara, Sudesh, E-mail: sudesh@psis.umass.edu [Department of Plant, Soil, and Insect Sciences, 270 Stockbridge Road, University of Massachusetts Amherst, MA 01003 (United States); Dhankher, Om Parkash, E-mail: parkash@psis.umass.edu [Department of Plant, Soil, and Insect Sciences, 270 Stockbridge Road, University of Massachusetts Amherst, MA 01003 (United States)

2011-10-15

Chromium pollution is a serious environmental problem with few cost-effective remediation strategies available. Crambe abyssinica (a member of Brassicaseae), a non-food, fast growing high biomass crop, is an ideal candidate for phytoremediation of heavy metals contaminated soils. The present study used a PCR-Select Suppression Subtraction Hybridization approach in C. abyssinica to isolate differentially expressed genes in response to Cr exposure. A total of 72 differentially expressed subtracted cDNAs were sequenced and found to represent 43 genes. The subtracted cDNAs suggest that Cr stress significantly affects pathways related to stress/defense, ion transporters, sulfur assimilation, cell signaling, protein degradation, photosynthesis and cell metabolism. The regulation of these genes in response to Cr exposure was further confirmed by semi-quantitative RT-PCR. Characterization of these differentially expressed genes may enable the engineering of non-food, high-biomass plants, including C. abyssinica, for phytoremediation of Cr-contaminated soils and sediments. - Highlights: > Molecular mechanism of Cr uptake and detoxification in plants is not well known. > We identified differentially regulated genes upon Cr exposure in Crambe abyssinica. > 72 Cr-induced subtracted cDNAs were sequenced and found to represent 43 genes. > Pathways linked to stress, ion transport, and sulfur assimilation were affected. > This is the first Cr transcriptome study in a crop with phytoremediation potential. - This study describes the identification and isolation of differentially expressed genes involved in chromium metabolism and detoxification in a non-food industrial oil crop Crambe abyssinica.

Application of droplet digital PCR for quantitative detection of Spiroplasma citri in comparison with real time PCR.

Directory of Open Access Journals (Sweden)

Yogita Maheshwari

Full Text Available Droplet digital polymerase chain reaction (ddPCR is a method for performing digital PCR that is based on water-oil emulsion droplet technology. It is a unique approach to measure the absolute copy number of nucleic acid targets without the need of external standards. This study evaluated the applicability of ddPCR as a quantitative detection tool for the Spiroplasma citri, causal agent of citrus stubborn disease (CSD in citrus. Two sets of primers, SP1, based on the spiral in housekeeping gene, and a multicopy prophage gene, SpV1 ORF1, were used to evaluate ddPCR in comparison with real time (quantitative PCR (qPCR for S. citri detection in citrus tissues. Standard curve analyses on tenfold dilution series showed that both ddPCR and qPCR exhibited good linearity and efficiency. However, ddPCR had a tenfold greater sensitivity than qPCR and accurately quantified up to one copy of spiralin gene. Receiver operating characteristic analysis indicated that the ddPCR methodology was more robust for diagnosis of CSD and the area under the curve was significantly broader compared to qPCR. Field samples were used to validate ddPCR efficacy and demonstrated that it was equal or better than qPCR to detect S. citri infection in fruit columella due to a higher pathogen titer. The ddPCR assay detected both the S. citri spiralin and the SpV1 ORF1 targets quantitatively with high precision and accuracy compared to qPCR assay. The ddPCR was highly reproducible and repeatable for both the targets and showed higher resilience to PCR inhibitors in citrus tissue extract for the quantification of S. citri compare to qPCR.

Novel PCR Assays Complement Laser Biosensor-Based Method and Facilitate Listeria Species Detection from Food

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Kwang-Pyo Kim

2015-09-01

Full Text Available The goal of this study was to develop the Listeria species-specific PCR assays based on a house-keeping gene (lmo1634 encoding alcohol acetaldehyde dehydrogenase (Aad, previously designated as Listeria adhesion protein (LAP, and compare results with a label-free light scattering sensor, BARDOT (bacterial rapid detection using optical scattering technology. PCR primer sets targeting the lap genes from the species of Listeria sensu stricto were designed and tested with 47 Listeria and 8 non-Listeria strains. The resulting PCR primer sets detected either all species of Listeria sensu stricto or individual L. innocua, L. ivanovii and L. seeligeri, L. welshimeri, and L. marthii without producing any amplified products from other bacteria tested. The PCR assays with Listeria sensu stricto-specific primers also successfully detected all species of Listeria sensu stricto and/or Listeria innocua from mixed culture-inoculated food samples, and each bacterium in food was verified by using the light scattering sensor that generated unique scatter signature for each species of Listeria tested. The PCR assays based on the house-keeping gene aad (lap can be used for detection of either all species of Listeria sensu stricto or certain individual Listeria species in a mixture from food with a detection limit of about 104 CFU/mL.

3D printing of intracranial aneurysm based on intracranial digital subtraction angiography and its clinical application.

Science.gov (United States)

Wang, Jian-Li; Yuan, Zi-Gang; Qian, Guo-Liang; Bao, Wu-Qiao; Jin, Guo-Liang

2018-06-01

The study aimed to develop simulation models including intracranial aneurysmal and parent vessel geometries, as well as vascular branches, through 3D printing technology. The simulation models focused on the benefits of aneurysmal treatments and clinical education. This prospective study included 13 consecutive patients who suffered from intracranial aneurysms confirmed by digital subtraction angiography (DSA) in the Neurosurgery Department of Shaoxing People's Hospital. The original 3D-DSA image data were extracted through the picture archiving and communication system and imported into Mimics. After reconstructing and transforming to Binary STL format, the simulation models of the hollow vascular tree were printed using 3D devices. The intracranial aneurysm 3D printing simulation model was developed based on DSA to assist neurosurgeons in aneurysmal treatments and residency training. Seven neurosurgical residents and 15 standardization training residents received their simulation model training and gave high assessments for the educational course with the follow-up qualitative questionnaire. 3D printed simulation models based on DSA can perfectly reveal target aneurysms and help neurosurgeons select therapeutic strategies precisely. As an educational tool, the 3D aneurysm vascular simulation model is useful for training residents.

Addition and Subtraction but Not Multiplication and Division Cause Shifts of Spatial Attention

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Mengjin Li

2018-05-01

Full Text Available Many studies have shown that solving addition and subtraction problems can induce overt shifts of spatial attention. In particular, right-side targets are detected faster than left-side targets when preceded by an addition operation, while left-side targets are detected faster than right-side targets when preceded by a subtraction operation. However, the interaction between space and arithmetic in multiplication or division is hardly studied and remains controversial. In order to make a strong case for the interaction between space and mental arithmetic, we attempted to replicate the spatial-arithmetic association in addition and subtraction (Experiment 1, and at the same time investigated whether shift of spatial attention would also be induced by multiplication or division operations (Experiment 2. We found that solving addition problems facilitated the detection of right-side targets, whereas left-side targets were detected faster after solving subtraction problems. However, no interaction between space and arithmetic operation was observed in multiplication or division. The implication of these findings is discussed.

Proximal caries detection using digital subtraction radiography in the artificial caries activity model

Energy Technology Data Exchange (ETDEWEB)

Park, Jong Hoon; Lee, Gi Ja; Choi, Sam Jin; Park, Young Ho; Kim, Kyung Soo; Jin, Hyun Seok; Hong, Kyung Won; Oh, Berm Seok; Park, Hun Kuk [Department of Biomedical Engineering, School of Medicine, Kyung Hee University, Seoul (Korea, Republic of); Choi, Yong Suk; Hwang, Eui Hwan [Department of Oral and Maxillofacial Radiology, Institute of Oral Biology, School of Dentistry, Kyung Hee University, Seoul (Korea, Republic of)

2009-03-15

The purpose of the experiment was to evaluating the diagnostic ability of dental caries detection using digital subtraction in the artificial caries activity model. Digital radiographs of five teeth with 8 proximal surfaces were obtained by CCD sensor (Kodak RVG 6100 using a size no.2). The digital radiographic images and subtraction images from artificial proximal caries were examined and interpreted. In this study, we proposed novel caries detection method which could diagnose the dental proximal caries from single digital radiographic image. In artificial caries activity model, the range of lesional depth was 572-1,374 {mu}m and the range of lesional area was 36.95-138.52 mm{sup 2}. The lesional depth and the area were significantly increased with demineralization time (p<0.001). Furthermore, the proximal caries detection using digital subtraction radiography showed high detection rate compared to the proximal caries examination using simple digital radiograph. The results demonstrated that the digital subtraction radiography from single radiographic image of artificial caries was highly efficient in the detection of dental caries compared to the data from simple digital radiograph.

Proximal caries detection using digital subtraction radiography in the artificial caries activity model

International Nuclear Information System (INIS)

Park, Jong Hoon; Lee, Gi Ja; Choi, Sam Jin; Park, Young Ho; Kim, Kyung Soo; Jin, Hyun Seok; Hong, Kyung Won; Oh, Berm Seok; Park, Hun Kuk; Choi, Yong Suk; Hwang, Eui Hwan

2009-01-01

The purpose of the experiment was to evaluating the diagnostic ability of dental caries detection using digital subtraction in the artificial caries activity model. Digital radiographs of five teeth with 8 proximal surfaces were obtained by CCD sensor (Kodak RVG 6100 using a size no.2). The digital radiographic images and subtraction images from artificial proximal caries were examined and interpreted. In this study, we proposed novel caries detection method which could diagnose the dental proximal caries from single digital radiographic image. In artificial caries activity model, the range of lesional depth was 572-1,374 μm and the range of lesional area was 36.95-138.52 mm 2 . The lesional depth and the area were significantly increased with demineralization time (p<0.001). Furthermore, the proximal caries detection using digital subtraction radiography showed high detection rate compared to the proximal caries examination using simple digital radiograph. The results demonstrated that the digital subtraction radiography from single radiographic image of artificial caries was highly efficient in the detection of dental caries compared to the data from simple digital radiograph.

PCR-Based Seamless Genome Editing with High Efficiency and Fidelity in Escherichia coli

DEFF Research Database (Denmark)

Liu, Yilan; Yang, Maohua; Yan, Daojiang

2016-01-01

Efficiency and fidelity are the key obstacles for genome editing toolboxes. In the present study, a PCR-based tandem repeat assisted genome editing (TRAGE) method with high efficiency and fidelity was developed. The design of TRAGE is based on the mechanism of repair of spontaneous double...... for seamlessly deleting, substituting and inserting targeted genes using PCR products. The effects of different manipulations including sucrose addition time, subculture times in LB with sucrose and stages of inoculation on the efficiency were investigated. With our recommended procedure, seamless excision...... of cat-sacB cassette can be realized in 48 h efficiently. We believe that the developed method has great potential for seamless genome editing in E. coli....

Mung bean nuclease treatment increases capture specificity of microdroplet-PCR based targeted DNA enrichment.

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Zhenming Yu

Full Text Available Targeted DNA enrichment coupled with next generation sequencing has been increasingly used for interrogation of select sub-genomic regions at high depth of coverage in a cost effective manner. Specificity measured by on-target efficiency is a key performance metric for target enrichment. Non-specific capture leads to off-target reads, resulting in waste of sequencing throughput on irrelevant regions. Microdroplet-PCR allows simultaneous amplification of up to thousands of regions in the genome and is among the most commonly used strategies for target enrichment. Here we show that carryover of single-stranded template genomic DNA from microdroplet-PCR constitutes a major contributing factor for off-target reads in the resultant libraries. Moreover, treatment of microdroplet-PCR enrichment products with a nuclease specific to single-stranded DNA alleviates off-target load and improves enrichment specificity. We propose that nuclease treatment of enrichment products should be incorporated in the workflow of targeted sequencing using microdroplet-PCR for target capture. These findings may have a broad impact on other PCR based applications for which removal of template DNA is beneficial.

Novel Ratio Subtraction and Isoabsorptive Point Methods for ...

African Journals Online (AJOL)

Purpose: To develop and validate two innovative spectrophotometric methods used for the simultaneous determination of ambroxol hydrochloride and doxycycline in their binary mixture. Methods: Ratio subtraction and isoabsorptive point methods were used for the simultaneous determination of ambroxol hydrochloride ...

Determining the analytical specificity of PCR-based assays for the diagnosis of IA: What is Aspergillus?

NARCIS (Netherlands)

Morton, C.O.; White, P.L.; Barnes, R.A.; Klingspor, L.; Cuenca-Estrella, M.; Lagrou, K.; Bretagne, S.; Melchers, W.J.; Mengoli, C.; Caliendo, A.M.; Cogliati, M.; Debets-Ossenkopp, Y.; Gorton, R.; Hagen, F.; Halliday, C.; Hamal, P.; Harvey-Wood, K.; Jaton, K.; Johnson, G.; Kidd, S.; Lengerova, M.; Lass-Florl, C.; Linton, C.; Millon, L.; Morrissey, C.O.; Paholcsek, M.; Talento, A.F.; Ruhnke, M.; Willinger, B.; Donnelly, J.P.; Loeffler, J.

2017-01-01

A wide array of PCR tests has been developed to aid the diagnosis of invasive aspergillosis (IA), providing technical diversity but limiting standardisation and acceptance. Methodological recommendations for testing blood samples using PCR exist, based on achieving optimal assay sensitivity to help

A simultaneous all-optical half/full-subtraction strategy using cascaded highly nonlinear fibers

Science.gov (United States)

Singh, Karamdeep; Kaur, Gurmeet; Singh, Maninder Lal

2018-02-01

Using non-linear effects such as cross-gain modulation (XGM) and cross-phase modulation (XPM) inside two highly non-linear fibres (HNLF) arranged in cascaded configuration, a simultaneous half/full-subtracter is proposed. The proposed simultaneous half/full-subtracter design is attractive due to several features such as input data pattern independence and usage of minimal number of non-linear elements i.e. HNLFs. Proof of concept simulations have been conducted at 100 Gbps rate, indicating fine performance, as extinction ratio (dB) > 6.28 dB and eye opening factors (EO) > 77.1072% are recorded for each implemented output. The proposed simultaneous half/full-subtracter can be used as a key component in all-optical information processing circuits.

Development and application of a universal Hemoplasma screening assay based on the SYBR green PCR principle.

Science.gov (United States)

Willi, Barbara; Meli, Marina L; Lüthy, Ruedi; Honegger, Hanspeter; Wengi, Nicole; Hoelzle, Ludwig E; Reusch, Claudia E; Lutz, Hans; Hofmann-Lehmann, Regina

2009-12-01

Hemotropic mycoplasmas (hemoplasmas) are the causative agents of infectious anemia in several mammalian species. Their zoonotic potential has recently been substantiated by the identification of a feline hemoplasma isolate in an immunocompromised human patient. Although species-specific diagnostic molecular methods have been developed, their application as screening tools is limited due to the species diversity of hemoplasmas. The goals of this study were to develop a universal hemoplasma screening assay with broad specificity based on the SYBR green PCR principle, to compare the assay with hemoplasma-specific TaqMan PCR, and to analyze potential tick vectors and human blood samples to address the zoonotic potential. The newly developed PCR assay based on the 16S rRNA gene amplified feline, canine, bovine, porcine, camelid, and murine hemoplasmas, as well as Mycoplasma penetrans and Mycoplasma pneumoniae. The lower detection limit for feline and canine hemoplasmas was 1 to 10 copies/PCR. The assay exhibited 98.2% diagnostic sensitivity and 92.1% diagnostic specificity for feline hemoplasmas. All 1,950 Ixodes ticks were PCR negative, suggesting that Ixodes ticks are not relevant vectors for the above-mentioned hemoplasma species in Switzerland. None of the 414 blood samples derived from anemic or immunocompromised human patients revealed a clear positive result. The SYBR green PCR assay described here is a suitable tool to screen for known and so-far-undiscovered hemoplasma species. Positive results should be confirmed by specific TaqMan PCR or sequencing.

Background dose subtraction in personnel dosimetry

International Nuclear Information System (INIS)

Picazo, T.; Llorca, N.; Alabau, J.

1997-01-01

In this paper it is proposed to consider the mode of the frequency distribution of the low dose dosemeters from each clinic that uses X rays as the background environmental dose that should be subtracted from the personnel dosimetry to evaluate the doses due to practice. The problems and advantages of this indirect method to estimate the environmental background dose are discussed. The results for 60 towns are presented. (author)

Bone images from dual-energy subtraction chest radiography in the detection of rib fractures.

Science.gov (United States)

Szucs-Farkas, Zsolt; Lautenschlager, Katrin; Flach, Patricia M; Ott, Daniel; Strautz, Tamara; Vock, Peter; Ruder, Thomas D

2011-08-01

To assess the sensitivity and image quality of chest radiography (CXR) with or without dual-energy subtracted (ES) bone images in the detection of rib fractures. In this retrospective study, 39 patients with 204 rib fractures and 24 subjects with no fractures were examined with a single exposure dual-energy subtraction digital radiography system. Three blinded readers first evaluated the non-subtracted posteroanterior and lateral chest radiographs alone, and 3 months later they evaluated the non-subtracted images together with the subtracted posteroanterior bone images. The locations of rib fractures were registered with confidence levels on a 3-grade scale. Image quality was rated on a 5-point scale. Marks by readers were compared with fracture localizations in CT as a standard of reference. The sensivity for fracture detection using both methods was very similar (34.3% with standard CXR and 33.5% with ES-CXR, p=0.92). At the patient level, both sensitivity (71.8%) and specificity (92.9%) with or without ES were identical. Diagnostic confidence was not significantly different (2.61 with CXR and 2.75 with ES-CXR, p=0.063). Image quality with ES was rated higher than that on standard CXR (4.08 vs. 3.74, prib fractures. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

The PCR-Based Diagnosis of Central Nervous System Tuberculosis: Up to Date

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Teruyuki Takahashi

2012-01-01

Full Text Available Central nervous system (CNS tuberculosis, particularly tuberculous meningitis (TBM, is the severest form of Mycobacterium tuberculosis (M.Tb infection, causing death or severe neurological defects in more than half of those affected, in spite of recent advancements in available anti-tuberculosis treatment. The definitive diagnosis of CNS tuberculosis depends upon the detection of M.Tb bacilli in the cerebrospinal fluid (CSF. At present, the diagnosis of CNS tuberculosis remains a complex issue because the most widely used conventional “gold standard” based on bacteriological detection methods, such as direct smear and culture identification, cannot rapidly detect M.Tb in CSF specimens with sufficient sensitivity in the acute phase of TBM. Recently, instead of the conventional “gold standard”, the various molecular-based methods including nucleic acid amplification (NAA assay technique, particularly polymerase chain reaction (PCR assay, has emerged as a promising new method for the diagnosis of CNS tuberculosis because of its rapidity, sensitivity and specificity. In addition, the innovation of nested PCR assay technique is worthy of note given its contribution to improve the diagnosis of CNS tuberculosis. In this review, an overview of recent progress of the NAA methods, mainly highlighting the PCR assay technique, was presented.

A survey of tools for the analysis of quantitative PCR (qPCR) data.

Science.gov (United States)

Pabinger, Stephan; Rödiger, Stefan; Kriegner, Albert; Vierlinger, Klemens; Weinhäusel, Andreas

2014-09-01

Real-time quantitative polymerase-chain-reaction (qPCR) is a standard technique in most laboratories used for various applications in basic research. Analysis of qPCR data is a crucial part of the entire experiment, which has led to the development of a plethora of methods. The released tools either cover specific parts of the workflow or provide complete analysis solutions. Here, we surveyed 27 open-access software packages and tools for the analysis of qPCR data. The survey includes 8 Microsoft Windows, 5 web-based, 9 R-based and 5 tools from other platforms. Reviewed packages and tools support the analysis of different qPCR applications, such as RNA quantification, DNA methylation, genotyping, identification of copy number variations, and digital PCR. We report an overview of the functionality, features and specific requirements of the individual software tools, such as data exchange formats, availability of a graphical user interface, included procedures for graphical data presentation, and offered statistical methods. In addition, we provide an overview about quantification strategies, and report various applications of qPCR. Our comprehensive survey showed that most tools use their own file format and only a fraction of the currently existing tools support the standardized data exchange format RDML. To allow a more streamlined and comparable analysis of qPCR data, more vendors and tools need to adapt the standardized format to encourage the exchange of data between instrument software, analysis tools, and researchers.

Antisense-induced suppression of taxoid 14β- hydroxylase gene ...

African Journals Online (AJOL)

Reverse transcription-polymerase chain reaction (RT-PCR) analysis showed that the 14OH mRNA level in transgenic cells dropped dramatically, suggesting that the expression of endogenous14OH gene was significantly suppressed by the exogenous as14OH gene. Correspondingly, the total yield of three major C-14 ...

Chaos suppression based on adaptive observer for a P-class of chaotic systems

International Nuclear Information System (INIS)

Rodriguez, Angel; Leon, Jesus de; Femat, Ricardo

2007-01-01

A feedback approach is presented to suppress chaos in a P-class of chaotic system. The approach is based on an adaptive observer; which provides estimated values of both the unmeasured states and the uncertain model parameters. A continuous-time feedback law is taken as suppressing force. The feedback law attains chaos suppression as the observer provides estimated values close to the actual state/parameter values along time. The proposed scheme is robust in the sense that suppression is achieved despite only some states are measured and uncertainties in parameters are compensated. Results are corroborated experimentally by implementation in chaotic circuits

Chaos suppression based on adaptive observer for a P-class of chaotic systems

Energy Technology Data Exchange (ETDEWEB)

Rodriguez, Angel [Universidad Autonoma de Nuevo Leon, Facultad de Ingenieria Mecanica y Electrica, Av. Pedro de Alba s/n Cd. Universitaria, CP 66450 San Nicolas de los Garza, NL (Mexico); Leon, Jesus de [Universidad Autonoma de Nuevo Leon, Facultad de Ingenieria Mecanica y Electrica, Av. Pedro de Alba s/n Cd. Universitaria, CP 66450 San Nicolas de los Garza, NL (Mexico); Femat, Ricardo [Division de Matematicas Aplicadas y Sistemas Computacionales, IPICyT, Camino a la Presa San Jose 2055 Col. Lomas 4a. Secc. CP 78216 San Luis Potosi, SLP (Mexico)]. E-mail: rfemat@ipicyt.edu.mx

2007-05-15

A feedback approach is presented to suppress chaos in a P-class of chaotic system. The approach is based on an adaptive observer; which provides estimated values of both the unmeasured states and the uncertain model parameters. A continuous-time feedback law is taken as suppressing force. The feedback law attains chaos suppression as the observer provides estimated values close to the actual state/parameter values along time. The proposed scheme is robust in the sense that suppression is achieved despite only some states are measured and uncertainties in parameters are compensated. Results are corroborated experimentally by implementation in chaotic circuits.

Digital subtraction angiography in the assessment of cardiovascular disease

International Nuclear Information System (INIS)

Harrington, D.P.; Boxt, L.M.

1985-01-01

Digital subtraction angiography (DSA) is a new radiographic method for evaluating the cardiovascular system. It represents another in a continuing series of computer-assisted diagnostic imaging modalities. The advantages of this technique are its relatively noninvasive nature combined with diagnostically acceptable angiographic images of a variety of cardiovascular structures. Major clinical applications of DSA include its use in imaging of localized regions of peripheral arterial disease and as a screening procedure in evaluating extracranial carotid and vertebral artery disease and renovascular hypertension. Cardiac applications of DSA include assessment of ventricular function, recognition and quantification of intracardiac shunts, visualization of coronary artery bypass grafts, and the study of complex congenital cardiac malformations. Digital subtraction angiography may also be used to evaluate intracranial aneurysms and vascular tumors

Spinal pedicle subtraction osteotomy for fixed sagittal imbalance patients

Science.gov (United States)

Hyun, Seung-Jae; Kim, Yongjung J; Rhim, Seung-Chul

2013-01-01

In addressing spinal sagittal imbalance through a posterior approach, the surgeon now may choose from among a variety of osteotomy techniques. Posterior column osteotomies such as the facetectomy or Ponte or Smith-Petersen osteotomy provide the least correction, but can be used at multiple levels with minimal blood loss and a lower operative risk. Pedicle subtraction osteotomies provide nearly 3 times the per-level correction of Ponte/Smith-Petersen osteotomies; however, they carry increased technical demands, longer operative time, and greater blood loss and associated significant morbidity, including neurological injury. The literature focusing on pedicle subtraction osteotomy for fixed sagittal imbalance patients is reviewed. The long-term overall outcomes, surgical tips to reduce the complications and suggestions for their proper application are also provided. PMID:24340276

Development of Nested PCR, Multiplex PCR, and Loop-Mediated Isothermal Amplification Assays for Rapid Detection of Cylindrocladium scoparium on Eucalyptus

Directory of Open Access Journals (Sweden)

Tian-Min Qiao

2016-10-01

Full Text Available Eucalyptus dieback disease, caused by Cylindrocladium scoparium, has occurred in last few years in large Eucalyptus planting areas in China and other countries. Rapid, simple, and reliable diagnostic techniques are desired for the early detection of Eucalyptus dieback of C. scoparium prior to formulation of efficient control plan. For this purpose, three PCR-based methods of nested PCR, multiplex PCR, loop-mediated isothermal amplification (LAMP were developed for detection of C. scoparium based on factor 1-alpha (tef1 and beta-tubulin gene in this study. All of the three methods showed highly specific to C. scoparium. The sensitivities of the nested PCR and LAMP were much higher than the multiplex PCR. The sensitivity of multiplex PCR was also higher than regular PCR. C. scoparium could be detected within 60 min from infected Eucalyptus plants by LAMP, while at least 2 h was needed by the rest two methods. Using different Eucalyptus tissues as samples for C. scoparium detection, all of the three PCR-based methods showed much better detection results than regular PCR. Base on the results from this study, we concluded that any of the three PCR-based methods could be used as diagnostic technology for the development of efficient strategies of Eucalyptus dieback disease control. Particularly, LAMP was the most practical method in field application because of its one-step and rapid reaction, simple operation, single-tube utilization, and simple visualization of amplification products.

Development of Nested PCR, Multiplex PCR, and Loop-Mediated Isothermal Amplification Assays for Rapid Detection of Cylindrocladium scoparium on Eucalyptus

Science.gov (United States)

Qiao, Tian-Min; Zhang, Jing; Li, Shu-Jiang; Han, Shan; Zhu, Tian-Hui

2016-01-01

Eucalyptus dieback disease, caused by Cylindrocladium scoparium, has occurred in last few years in large Eucalyptus planting areas in China and other countries. Rapid, simple, and reliable diagnostic techniques are desired for the early detection of Eucalyptus dieback of C. scoparium prior to formulation of efficient control plan. For this purpose, three PCR-based methods of nested PCR, multiplex PCR, loop-mediated isothermal amplification (LAMP) were developed for detection of C. scoparium based on factor 1-alpha (tef1) and beta-tubulin gene in this study. All of the three methods showed highly specific to C. scoparium. The sensitivities of the nested PCR and LAMP were much higher than the multiplex PCR. The sensitivity of multiplex PCR was also higher than regular PCR. C. scoparium could be detected within 60 min from infected Eucalyptus plants by LAMP, while at least 2 h was needed by the rest two methods. Using different Eucalyptus tissues as samples for C. scoparium detection, all of the three PCR-based methods showed much better detection results than regular PCR. Base on the results from this study, we concluded that any of the three PCR-based methods could be used as diagnostic technology for the development of efficient strategies of Eucalyptus dieback disease control. Particularly, LAMP was the most practical method in field application because of its one-step and rapid reaction, simple operation, single-tube utilization, and simple visualization of amplification products. PMID:27721691

Development of Nested PCR, Multiplex PCR, and Loop-Mediated Isothermal Amplification Assays for Rapid Detection of Cylindrocladium scoparium on Eucalyptus.

Science.gov (United States)

Qiao, Tian-Min; Zhang, Jing; Li, Shu-Jiang; Han, Shan; Zhu, Tian-Hui

2016-10-01

Eucalyptus dieback disease, caused by Cylindrocladium scoparium , has occurred in last few years in large Eucalyptus planting areas in China and other countries. Rapid, simple, and reliable diagnostic techniques are desired for the early detection of Eucalyptus dieback of C. scoparium prior to formulation of efficient control plan. For this purpose, three PCR-based methods of nested PCR, multiplex PCR, loop-mediated isothermal amplification (LAMP) were developed for detection of C. scoparium based on factor 1-alpha (tef1) and beta-tubulin gene in this study. All of the three methods showed highly specific to C. scoparium . The sensitivities of the nested PCR and LAMP were much higher than the multiplex PCR. The sensitivity of multiplex PCR was also higher than regular PCR. C. scoparium could be detected within 60 min from infected Eucalyptus plants by LAMP, while at least 2 h was needed by the rest two methods. Using different Eucalyptus tissues as samples for C. scoparium detection, all of the three PCR-based methods showed much better detection results than regular PCR. Base on the results from this study, we concluded that any of the three PCR-based methods could be used as diagnostic technology for the development of efficient strategies of Eucalyptus dieback disease control. Particularly, LAMP was the most practical method in field application because of its one-step and rapid reaction, simple operation, single-tube utilization, and simple visualization of amplification products.

A subtraction scheme for computing QCD jet cross sections at NNLO: integrating the doubly unresolved subtraction terms

CERN Document Server

Somogyi, Gabor

2013-01-01

We finish the definition of a subtraction scheme for computing NNLO corrections to QCD jet cross sections. In particular, we perform the integration of the soft-type contributions to the doubly unresolved counterterms via the method of Mellin-Barnes representations. With these final ingredients in place, the definition of the scheme is complete and the computation of the regularised doubly virtual contribution to the NNLO cross section becomes feasible.

Misconception on Addition and Subtraction of Fraction at Primary School Students in Fifth-Grade

Science.gov (United States)

Trivena, V.; Ningsih, A. R.; Jupri, A.

2017-09-01

This study aims to investigate the mastery concept of the student in mathematics learning especially in addition and subtraction of fraction at primary school level. By using qualitative research method, the data were collected from 23 grade five students (10-11-year-old). Instruments included a test, that is accompanied by Certainty Response Index (CRI) and interview with students and teacher. The result of the test has been obtained, then processed by analyzing the student’s answers for each item and then grouped by the CRI categories that combined with the results of the interview with students and teacher. The results showed that student’s mastery-concept on additional and subtraction dominated by category ‘misconception’. So, we can say that mastery-concept on addition and subtraction of fraction at fifth-grade students is still low. Finally, the impact can make most of primary student think that learning addition and subtraction of fraction in mathematics is difficult.

Multinuclide digital subtraction imaging in symptomatic prostnetic joints

International Nuclear Information System (INIS)

Chafetz, N.; Hattner, R.S.; Ruarke, W.C.; Helms, C.A.; Genant, H.K.; Murray, W.R.

1985-01-01

One hundred eleven patients with symptomatic prosthetic joints (86 hips, 23 knees, and two shoulders) were evaluated for prosthetic loosening and infection by combined technetium-99m-MDP/gallium-67 digital subtraction imaging. Clinical correlation was based on the assessment of loosening and bacterial cultures obtained at the time of surgery in 54 patients, joint aspiration cultures obtained in 37 patients, and long-term clinical follow-up for greater than 1.5 years in an additional 15 patients. Results revealed an 80-90% predictive value of a positive test for loosening, and a 95% predictive value of a negative test for infection. However, because of the low sensitivities and specificities observed, this approach to the evaluation of symptomatic prosthetic joints does not seem cost effective

Analysis of luminosity distributions of strong lensing galaxies: subtraction of diffuse lensed signal

Science.gov (United States)

Biernaux, J.; Magain, P.; Hauret, C.

2017-08-01

Context. Strong gravitational lensing gives access to the total mass distribution of galaxies. It can unveil a great deal of information about the lenses' dark matter content when combined with the study of the lenses' light profile. However, gravitational lensing galaxies, by definition, appear surrounded by lensed signal, both point-like and diffuse, that is irrelevant to the lens flux. Therefore, the observer is most often restricted to studying the innermost portions of the galaxy, where classical fitting methods show some instabilities. Aims: We aim at subtracting that lensed signal and at characterising some lenses' light profile by computing their shape parameters (half-light radius, ellipticity, and position angle). Our objective is to evaluate the total integrated flux in an aperture the size of the Einstein ring in order to obtain a robust estimate of the quantity of ordinary (luminous) matter in each system. Methods: We are expanding the work we started in a previous paper that consisted in subtracting point-like lensed images and in independently measuring each shape parameter. We improve it by designing a subtraction of the diffuse lensed signal, based only on one simple hypothesis of symmetry. We apply it to the cases where it proves to be necessary. This extra step improves our study of the shape parameters and we refine it even more by upgrading our half-light radius measurement method. We also calculate the impact of our specific image processing on the error bars. Results: The diffuse lensed signal subtraction makes it possible to study a larger portion of relevant galactic flux, as the radius of the fitting region increases by on average 17%. We retrieve new half-light radii values that are on average 11% smaller than in our previous work, although the uncertainties overlap in most cases. This shows that not taking the diffuse lensed signal into account may lead to a significant overestimate of the half-light radius. We are also able to measure

Real-time PCR to supplement gold-standard culture-based detection of Legionella in environmental samples.

Science.gov (United States)

Collins, S; Jorgensen, F; Willis, C; Walker, J

2015-10-01

Culture remains the gold-standard for the enumeration of environmental Legionella. However, it has several drawbacks including long incubation and poor sensitivity, causing delays in response times to outbreaks of Legionnaires' disease. This study aimed to validate real-time PCR assays to quantify Legionella species (ssrA gene), Legionella pneumophila (mip gene) and Leg. pneumophila serogroup-1 (wzm gene) to support culture-based detection in a frontline public health laboratory. Each qPCR assay had 100% specificity, excellent sensitivity (5 GU/reaction) and reproducibility. Comparison of the assays to culture-based enumeration of Legionella from 200 environmental samples showed that they had a negative predictive value of 100%. Thirty eight samples were positive for Legionella species by culture and qPCR. One hundred samples were negative by both methods, whereas 62 samples were negative by culture but positive by qPCR. The average log10 increase between culture and qPCR for Legionella spp. and Leg. pneumophila was 0·72 (P = 0·0002) and 0·51 (P = 0·006), respectively. The qPCR assays can be conducted on the same 1 l water sample as culture thus can be used as a supplementary technique to screen out negative samples and allow more rapid indication of positive samples. The assay could prove informative in public health investigations to identify or rule out sources of Legionella as well as to specifically identify Leg. pneumophila serogroup 1 in a timely manner not possible with culture. © 2015 The Society for Applied Microbiology.

Two-dimensional real-time imaging system for subtraction angiography using an iodine filter

Science.gov (United States)

Umetani, Keiji; Ueda, Ken; Takeda, Tohoru; Anno, Izumi; Itai, Yuji; Akisada, Masayoshi; Nakajima, Teiichi

1992-01-01

A new type of subtraction imaging system was developed using an iodine filter and a single-energy broad bandwidth monochromatized x ray. The x-ray images of coronary arteries made after intravenous injection of a contrast agent are enhanced by an energy-subtraction technique. Filter chopping of the x-ray beam switches energies rapidly, so that a nearly simultaneous pair of filtered and nonfiltered images can be made. By using a high-speed video camera, a pair of two 512 × 512 pixel images can be obtained within 9 ms. Three hundred eighty-four images (raw data) are stored in a 144-Mbyte frame memory. After phantom studies, in vivo subtracted images of coronary arteries in dogs were obtained at a rate of 15 images/s.

Venous digital subtraction angiography for diagnosis of renal artery stenosis in arterial hypertony

International Nuclear Information System (INIS)

Schoerner, W.; Kempter, H.; Banzer, D.; Aviles, C.; Weiss, T.; Felix, R.

1984-01-01

Venous digital subtraction angiography was performed in 248 patients for the diagnosis of renal arterial stenosis. In 88% of the investigations the stenosis could be found. Comparison of digital angiography and conventional angiography was made for 57 renal arteries (25 investigations). In 52 renal arteries we found the same results with both methods, in 5 renal arteries we found the same results with both methods, in 5 renal arteries the digital angiography showed false positive results. The spatial resolution of digital subtraction angiography is sufficient for the correct diagnosis of significant renal arterial stenosis. With regard to the lower invasion of digital subtraction angiography compared to conventional angiography the first method should be used for clarification of renal arterial hypertension. (orig.)

European validation of a real-time PCR-based method for detection of Listeria monocytogenes in soft cheese.

Science.gov (United States)

Gianfranceschi, Monica Virginia; Rodriguez-Lazaro, David; Hernandez, Marta; González-García, Patricia; Comin, Damiano; Gattuso, Antonietta; Delibato, Elisabetta; Sonnessa, Michele; Pasquali, Frederique; Prencipe, Vincenza; Sreter-Lancz, Zuzsanna; Saiz-Abajo, María-José; Pérez-De-Juan, Javier; Butrón, Javier; Kozačinski, Lidija; Tomic, Danijela Horvatek; Zdolec, Nevijo; Johannessen, Gro S; Jakočiūnė, Džiuginta; Olsen, John Elmerdahl; De Santis, Paola; Lovari, Sarah; Bertasi, Barbara; Pavoni, Enrico; Paiusco, Antonella; De Cesare, Alessandra; Manfreda, Gerardo; De Medici, Dario

2014-08-01

The classical microbiological method for detection of Listeria monocytogenes requires around 7 days for final confirmation, and due to perishable nature of RTE food products, there is a clear need for an alternative methodology for detection of this pathogen. This study presents an international (at European level) ISO 16140-based validation trial of a non-proprietary real-time PCR-based methodology that can generate final results in the following day of the analysis. This methodology is based on an ISO compatible enrichment coupled to a bacterial DNA extraction and a consolidated real-time PCR assay. Twelve laboratories from six European countries participated in this trial, and soft cheese was selected as food model since it can represent a difficult matrix for the bacterial DNA extraction and real-time PCR amplification. The limit of detection observed was down to 10 CFU per 25 of sample, showing excellent concordance and accordance values between samples and laboratories (>75%). In addition, excellent values were obtained for relative accuracy, specificity and sensitivity (82.75%, 96.70% and 97.62%, respectively) when the results obtained for the real-time PCR-based methods were compared to those of the ISO 11290-1 standard method. An interesting observation was that the L. monocytogenes detection by the real-time PCR method was less affected in the presence of Listeria innocua in the contaminated samples, proving therefore to be more reliable than the reference method. The results of this international trial demonstrate that the evaluated real-time PCR-based method represents an excellent alterative to the ISO standard since it shows a higher performance as well as reduce the extent of the analytical process, and can be easily implemented routinely by the competent authorities and food industry laboratories. Copyright © 2014 Elsevier B.V. All rights reserved.

Use of PCR-based methods for rapid differentiation of Lactobacillus delbrueckii subsp. bulgaricus and L. delbrueckii subsp. lactis.

Science.gov (United States)

Torriani, S; Zapparoli, G; Dellaglio, F

1999-10-01

Two PCR-based methods, specific PCR and randomly amplified polymorphic DNA PCR (RAPD-PCR), were used for rapid and reliable differentiation of Lactobacillus delbrueckii subsp. bulgaricus and L. delbrueckii subsp. lactis. PCR with a single combination of primers which targeted the proline iminopeptidase (pepIP) gene of L. delbrueckii subsp. bulgaricus allowed amplification of genomic fragments specific for the two subspecies when either DNA from a single colony or cells extracted from dairy products were used. A numerical analysis of the RAPD-PCR patterns obtained with primer M13 gave results that were consistent with the results of specific PCR for all strains except L. delbrueckii subsp. delbrueckii LMG 6412(T), which clustered with L. delbrueckii subsp. lactis strains. In addition, RAPD-PCR performed with primer 1254 provided highly polymorphic profiles and thus was superior for distinguishing individual L. delbrueckii strains.

Use of PCR-Based Methods for Rapid Differentiation of Lactobacillus delbrueckii subsp. bulgaricus and L. delbrueckii subsp. lactis

Science.gov (United States)

Torriani, Sandra; Zapparoli, Giacomo; Dellaglio, Franco

1999-01-01

Two PCR-based methods, specific PCR and randomly amplified polymorphic DNA PCR (RAPD-PCR), were used for rapid and reliable differentiation of Lactobacillus delbrueckii subsp. bulgaricus and L. delbrueckii subsp. lactis. PCR with a single combination of primers which targeted the proline iminopeptidase (pepIP) gene of L. delbrueckii subsp. bulgaricus allowed amplification of genomic fragments specific for the two subspecies when either DNA from a single colony or cells extracted from dairy products were used. A numerical analysis of the RAPD-PCR patterns obtained with primer M13 gave results that were consistent with the results of specific PCR for all strains except L. delbrueckii subsp. delbrueckii LMG 6412T, which clustered with L. delbrueckii subsp. lactis strains. In addition, RAPD-PCR performed with primer 1254 provided highly polymorphic profiles and thus was superior for distinguishing individual L. delbrueckii strains. PMID:10508059

Detection of hepatitis C virus RNA: comparison of one-stage polymerase chain reaction (PCR) with nested-set PCR.

OpenAIRE

Gretch, D R; Wilson, J J; Carithers, R L; dela Rosa, C; Han, J H; Corey, L

1993-01-01

We evaluated a new hepatitis C virus RNA assay based on one-stage PCR followed by liquid hybridization with an oligonucleotide probe and compared it with nested-set PCR. The one-stage and nested-set PCR assays had identical sensitivities in analytical experiments and showed 100% concordance when clinical specimens were used. One-stage PCR may be less prone to contamination than nested-set PCR.

Efficacy of a novel PCR- and microarray-based method in diagnosis of a prosthetic joint infection

Science.gov (United States)

2014-01-01

Background and purpose Polymerase chain reaction (PCR) methods enable detection and species identification of many pathogens. We assessed the efficacy of a new PCR and microarray-based platform for detection of bacteria in prosthetic joint infections (PJIs). Methods This prospective study involved 61 suspected PJIs in hip and knee prostheses and 20 negative controls. 142 samples were analyzed by Prove-it Bone and Joint assay. The laboratory staff conducting the Prove-it analysis were not aware of the results of microbiological culture and clinical findings. The results of the analysis were compared with diagnosis of PJIs defined according to the Musculoskeletal Infection Society (MSIS) criteria and with the results of microbiological culture. Results 38 of 61 suspected PJIs met the definition of PJI according to the MSIS criteria. Of the 38 patients, the PCR detected bacteria in 31 whereas bacterial culture was positive in 28 patients. 15 of the PJI patients were undergoing antimicrobial treatment as the samples for analysis were obtained. When antimicrobial treatment had lasted 4 days or more, PCR detected bacteria in 6 of the 9 patients, but positive cultures were noted in only 2 of the 9 patients. All PCR results for the controls were negative. Of the 61 suspected PJIs, there were false-positive PCR results in 6 cases. Interpretation The Prove-it assay was helpful in PJI diagnostics during ongoing antimicrobial treatment. Without preceding treatment with antimicrobials, PCR and microarray-based assay did not appear to give any additional information over culture. PMID:24564748

Establishment of a minor groove binder-probe based quantitative real time PCR to detect Borrelia burgdorferi sensu lato and differentiation of Borrelia spielmanii by ospA-specific conventional PCR

Directory of Open Access Journals (Sweden)

Strube Christina

2010-08-01

Full Text Available Abstract Background Borrelia burgdorferi sensu lato (sl, the causative agent of Lyme borreliosis, is transmitted by ticks of the genus Ixodes as vector. For identification of Borrelia infections in ticks a TaqMan™ minor groove binder (MGB probe-based quantitative real time PCR (qPCR was established targeting the 5S-23S intergenic spacer. Extension to a duplex qPCR included an Ixodes spp. positive control to verify successful DNA isolation. Besides qPCR, an ospA-specific conventional PCR for species-specific identification of B. spielmanii was established. Afterwards 1000 I. ricinus flagged in the city of Hanover, Germany, were investigated for B. burgdorferi sl infections followed by species identification. Furthermore, I. hexagonus ticks were investigated to proof applicability of the PCRs. Results Quantitative real time PCR (qPCR identifying B. burgdorferi sl in ticks was able to detect 1-10 copies per reaction. B. spielmanii ospA-specific conventional PCR was also highly specific and showed no cross reactions with the other tested Borrelia species. From 1000 hanoveranian ticks 24.3% were positive compared to only 7.4% positives by dark-field microscopy. Related to tick stage 1.7% larvae, 18.1% nymphs, and 34.6% adults were positive. The most frequent species was B. garinii, followed by B. afzelii, B. spielmanii, B. valaisiana and B. burgdorferi sensu stricto (ss. 70.6% of I. ricinus were mono-infected, whereas 28.0% and 1.4% were infected with two and three Borrelia species, respectively. From 232 I. hexagonus collected from hedgehogs in different sites of Germany, qPCR detected 5.7% to be infected with B. burgdorferi sl, which were identified as B. afzelii, B. garinii and B. spielmanii. Conclusions The evaluated qPCR to detect B. burgdorferi sl in Ixodes spp. is highly specific and sensitive. As a duplex qPCR including detection of Ixodes spp. DNA it is the first DNA based technique incorporating a control for successful DNA isolation from

Digital subtraction angiography in 105 living renal transplant donors

International Nuclear Information System (INIS)

Suh, Ho Jong; Oh, Kyung Seung; Kim, So Sun; Huh, Jin Do; Kim, Ho Joon; Chun, Byung Hee; Joh, Young Duck

1989-01-01

In order to analyze the number and length of the renal arteries and to evaluate abnormalities of the renal parenchyma and vessel, digital subtraction angiogram images of 105 potential renal donors (45 men and 60 women aged 17-66 years) were studied retrospectively. For the entire series, 31 donors had multiple renal arteries on one side (15 on the left, 11 on the right) and 5 donors on the both sides. 89 donors were family related either parents or siblings of recipients. The estimation of the length of the renal artery was based on the mean height of the second lumbar vertebral body (L2). The right renal artery is significant longer than on the left and measured more than the height of L2 vertebral body in 84 cases on the right and 60 cases on the left. Twenty two donors underwent right nephrectomy due to presence of multiple renal arteries on the left (N=14), proximal bifurcation of left main renal artery (N=3), and young females in reproductive age (N=5). Unexpected abnormalities found with angiogram were seen in 7 cases and they include renal artery stenosis (N=2), renal cysts (N=4) and focal infarction (N=1). In cases of the renal cysts and focal infarction, there were no serious complications related to the abnormalities. It is conclude that intra-arterial digital subtraction angiography is safe and efficient method to image renal anatomy of the potential renal donors

Digital Subtraction Angiography (DSA) "Road Map": An Angiographic Tool

Science.gov (United States)

Turski, P. A.; Stieghorst, M. F.; Strother, C. M.; Crummy, A. B.; Lieberman, R. P.; Mistretta, C. A.

1982-12-01

Continuous Digital subtraction combined with intraarterial injections of contrast medium permits the display of arterial structures during real time fluoroscopy. This DSA "road map" facilitates selective catheterization and has proved useful in interventional procedures.

Comparison of two interpolative background subtraction methods using phantom and clinical data

International Nuclear Information System (INIS)

Houston, A.S.; Sampson, W.F.D.

1989-01-01

Two interpolative background subtraction methods used in scintigraphy are tested using both phantom and clinical data. Cauchy integral subtraction was found to be relatively free of artefacts but required more computing time than bilinear interpolation. Both methods may be used with reasonable confidence for the quantification of relative measurements such as left ventricular ejection fraction and myocardial perfusion index but should be avoided if at all possible in the quantification of absolute measurements such as glomerular filtration rate. (author)

A novel PCR-based system for the detection of four species of human malaria parasites and Plasmodium knowlesi

Science.gov (United States)

Komaki-Yasuda, Kanako; Vincent, Jeanne Perpétue; Nakatsu, Masami; Kato, Yasuyuki; Ohmagari, Norio

2018-01-01

A microscopy-based diagnosis is the gold standard for the detection and identification of malaria parasites in a patient’s blood. However, the detection of cases involving a low number of parasites and the differentiation of species sometimes requires a skilled microscopist. Although PCR-based diagnostic methods are already known to be very powerful tools, the time required to apply such methods is still much longer in comparison to traditional microscopic observation. Thus, improvements to PCR systems are sought to facilitate the more rapid and accurate detection of human malaria parasites Plasmodium falciparum, P. vivax, P. ovale, and P. malariae, as well as P. knowlesi, which is a simian malaria parasite that is currently widely distributed in Southeast Asia. A nested PCR that targets the small subunit ribosomal RNA genes of malaria parasites was performed using a “fast PCR enzyme”. In the first PCR, universal primers for all parasite species were used. In the second PCR, inner-specific primers, which targeted sequences from P. falciparum, P. vivax, P. ovale, P. malariae, and P. knowlesi, were used. The PCR reaction time was reduced with the use of the “fast PCR enzyme”, with only 65 minutes required to perform the first and second PCRs. The specific primers only reacted with the sequences of their targeted parasite species and never cross-reacted with sequences from other species under the defined PCR conditions. The diagnoses of 36 clinical samples that were obtained using this new PCR system were highly consistent with the microscopic diagnoses. PMID:29370297

A novel PCR-based system for the detection of four species of human malaria parasites and Plasmodium knowlesi.

Directory of Open Access Journals (Sweden)

Kanako Komaki-Yasuda

Full Text Available A microscopy-based diagnosis is the gold standard for the detection and identification of malaria parasites in a patient's blood. However, the detection of cases involving a low number of parasites and the differentiation of species sometimes requires a skilled microscopist. Although PCR-based diagnostic methods are already known to be very powerful tools, the time required to apply such methods is still much longer in comparison to traditional microscopic observation. Thus, improvements to PCR systems are sought to facilitate the more rapid and accurate detection of human malaria parasites Plasmodium falciparum, P. vivax, P. ovale, and P. malariae, as well as P. knowlesi, which is a simian malaria parasite that is currently widely distributed in Southeast Asia. A nested PCR that targets the small subunit ribosomal RNA genes of malaria parasites was performed using a "fast PCR enzyme". In the first PCR, universal primers for all parasite species were used. In the second PCR, inner-specific primers, which targeted sequences from P. falciparum, P. vivax, P. ovale, P. malariae, and P. knowlesi, were used. The PCR reaction time was reduced with the use of the "fast PCR enzyme", with only 65 minutes required to perform the first and second PCRs. The specific primers only reacted with the sequences of their targeted parasite species and never cross-reacted with sequences from other species under the defined PCR conditions. The diagnoses of 36 clinical samples that were obtained using this new PCR system were highly consistent with the microscopic diagnoses.

Identification of circulating miRNA biomarkers based on global quantitative real-time PCR profiling

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Kang Kang

2012-02-01

Full Text Available Abstract MicroRNAs (miRNAs are small noncoding RNAs (18-25 nucleotides that regulate gene expression at the post-transcriptional level. Recent studies have demonstrated the presence of miRNAs in the blood circulation. Deregulation of miRNAs in serum or plasma has been associated with many diseases including cancers and cardiovascular diseases, suggesting the possible use of miRNAs as diagnostic biomarkers. However, the detection of the small amount of miRNAs found in serum or plasma requires a method with high sensitivity and accuracy. Therefore, the current study describes polymerase chain reaction (PCR-based methods for measuring circulating miRNAs. Briefly, the procedure involves four major steps: (1 sample collection and preparation; (2 global miRNAs profiling using quantitative real-time PCR (qRT-PCR; (3 data normalization and analysis; and (4 selection and validation of miRNA biomarkers. In conclusion, qRT-PCR is a promising method for profiling of circulating miRNAs as biomarkers.

Clinical application of subtraction CT imaging for evaluation of pulmonary vascular permeability

International Nuclear Information System (INIS)

Kato, Shiro; Asai, Toshihiko; Yatagai, Shigeo; Oonuma, Noboru; Ohno, Kunihiko; Nakamoto, Takaaki; Iizuka, Masahiko

1991-01-01

In this clinical study, one normal subject, one patient with primary interstitial pneumonia, one patient with segmental pneumonia due to Staphylococcus aureus, one patient with post-operative esophageal carcinoma, and two patients with mitral stenosis were studied. Dynamic CT scan images under continuous injection of low osmotic contrast medium were analyzed in series, in an attempt to evaluate vascular permeability quantitatively. The following results were obtained. Subtraction CT scan image 10 minutes after the start of contrast medium injection in two patients with pneumonia, showed a reduction of pulmonary vascular permeability following therapy. Subtraction CT scan image of the patient with post-operative esophageal carcinoma treated with 25 Gy radiation showed a discrepancy between pulmonary vascular permeability and other findings. In hemodynamically stable patients with mitral stenosis, subtraction CT images demonstrated that pulmonary vascular permeability was not affected by pulmonary congestion, irrespective of its severity. (author)

A subtraction scheme for computing QCD jet cross sections at NNLO: integrating the doubly unresolved subtraction terms

Science.gov (United States)

Somogyi, Gábor

2013-04-01

We finish the definition of a subtraction scheme for computing NNLO corrections to QCD jet cross sections. In particular, we perform the integration of the soft-type contributions to the doubly unresolved counterterms via the method of Mellin-Barnes representations. With these final ingredients in place, the definition of the scheme is complete and the computation of fully differential rates for electron-positron annihilation into two and three jets at NNLO accuracy becomes feasible.

A subtraction scheme for computing QCD jet cross sections at NNLO: integrating the doubly unresolved subtraction terms

OpenAIRE

Somogyi, Gabor

2013-01-01

We finish the definition of a subtraction scheme for computing NNLO corrections to QCD jet cross sections. In particular, we perform the integration of the soft-type contributions to the doubly unresolved counterterms via the method of Mellin-Barnes representations. With these final ingredients in place, the definition of the scheme is complete and the computation of fully differential rates for electron-positron annihilation into two and three jets at NNLO accuracy becomes feasible.

Performance of Droplet Digital PCR in Non-Invasive Fetal RHD Genotyping - Comparison with a Routine Real-Time PCR Based Approach.

Directory of Open Access Journals (Sweden)

Iveta Svobodová

Full Text Available Detection and characterization of circulating cell-free fetal DNA (cffDNA from maternal circulation requires an extremely sensitive and precise method due to very low cffDNA concentration. In our study, droplet digital PCR (ddPCR was implemented for fetal RHD genotyping from maternal plasma to compare this new quantification alternative with real-time PCR (qPCR as a golden standard for quantitative analysis of cffDNA. In the first stage of study, a DNA quantification standard was used. Clinical samples, including 10 non-pregnant and 35 pregnant women, were analyzed as a next step. Both methods' performance parameters-standard curve linearity, detection limit and measurement precision-were evaluated. ddPCR in comparison with qPCR has demonstrated sufficient sensitivity for analysing of cffDNA and determination of fetal RhD status from maternal circulation, results of both methods strongly correlated. Despite the more demanding workflow, ddPCR was found to be slightly more precise technology, as evaluated using quantitative standard. Regarding the clinical samples, the precision of both methods equalized with decreasing concentrations of tested DNA samples. In case of cffDNA with very low concentrations, variance parameters of both techniques were comparable. Detected levels of fetal cfDNA in maternal plasma were slightly higher than expected and correlated significantly with gestational age as measured by both methods (ddPCR r = 0.459; qPCR r = 0.438.

Enriching Addition and Subtraction Fact Mastery through Games

Science.gov (United States)

Bay-Williams, Jennifer M.; Kling, Gina

2014-01-01

The learning of "basic facts"--single-digit combinations for addition, subtraction, multiplication, and division--has long been a focus of elementary school mathematics. Many people remember completing endless worksheets, timed tests, and flash card drills as they attempted to "master" their basic facts as children. However,…

Improvement in visibility of simulated lung nodules on computed radiography (CR) chest images by use of temporal subtraction technique

International Nuclear Information System (INIS)

Oda, Nobuhiro; Fujimoto, Keiji; Murakami, Seiichi; Katsuragawa, Shigehiko; Doi, Kunio; Nakata, Hajime

1999-01-01

A temporal subtraction image obtained by subtraction of a previous image from a current one can enhance interval change on chest images. In this study, we compared the visibility of simulated lung nodules on CR images with and without temporal subtraction. Chest phantom images without and with simulated nodules were obtained as previous and current images, respectively, by a CR system. Then, subtraction images were produced with an iterative image warping technique. Twelve simulated nodules were attached on various locations of the chest phantom. The diameter of nodules having a CT number of 47 ranged from 3 mm to 10 mm. Seven radiologists subjectively evaluated the visibility of simulated nodules on CR images with and without temporal subtraction using a three-point rating scale (0: invisible, +1: questionable, +2:visible). The minimum diameter of simulated nodules visible at a frequency greater than 50% was 4 mm on the CR images with temporal subtraction and 6 mm on those without. Our results indicated that the subtraction images clearly improved the visibility of simulated nodules. (author)

Simulation and experimental validation of a SU-8 based PCR thermocycler chip with integrated heaters and temperature sensor

DEFF Research Database (Denmark)

El-Ali, Jamil; Perch-Nielsen, Ivan R.; Poulsen, Claus Riber

2004-01-01

We present a SU-8 based polymerase chain reaction (PCR) chip with integrated platinum thin film heaters and temperature sensor. The device is fabricated in SU-8 on a glass substrate. The use of SU-8 provides a simple microfabrication process for the PCR chamber, controllable surface properties......C/s, respectively, the performance of the chip is comparable with the best silicon micromachined PCR chips presented in the literature. The SU-8 chamber surface was found to be PCR compatible by amplification of yeast gene ribosomal protein S3 and Campylobacter gene cadF. The PCR compatibility of the chamber...

Pediatric head and neck lesions: assessment of vascularity by MR digital subtraction angiography.

Science.gov (United States)

Chooi, Weng Kong; Woodhouse, Neil; Coley, Stuart C; Griffiths, Paul D

2004-08-01

Pediatric head and neck lesions can be difficult to characterize on clinical grounds alone. We investigated the use of dynamic MR digital subtraction angiography as a noninvasive adjunct for the assessment of the vascularity of these abnormalities. Twelve patients (age range, 2 days to 16 years) with known or suspected vascular abnormalities were studied. Routine MR imaging, time-of-flight MR angiography, and MR digital subtraction angiography were performed in all patients. The dynamic sequence was acquired in two planes at one frame per second by using a thick section (6-10 cm) selective radio-frequency spoiled fast gradient-echo sequence and an IV administered bolus of contrast material. The images were subtracted from a preliminary mask sequence and viewed as a video-inverted cine loop. In all cases, MR digital subtraction angiography was successfully performed. The technique showed the following: 1) slow flow lesions (two choroidal angiomas, eyelid hemangioma, and scalp venous malformation); 2) high flow lesions that were not always suspected by clinical examination alone (parotid hemangioma, scalp, occipital, and eyelid arteriovenous malformations plus a palatal teratoma); 3) a hypovascular tumor for which a biopsy could be safely performed (Burkitt lymphoma); and 4) a hypervascular tumor of the palate (cystic teratoma). Our early experience suggests that MR digital subtraction angiography can be reliably performed in children of all ages without complication. The technique provided a noninvasive assessment of the vascularity of each lesion that could not always have been predicted on the basis of clinical examination or routine MR imaging alone.

Detection of 22 common leukemic fusion genes using a single-step multiplex qRT-PCR-based assay.

Science.gov (United States)

Lyu, Xiaodong; Wang, Xianwei; Zhang, Lina; Chen, Zhenzhu; Zhao, Yu; Hu, Jieying; Fan, Ruihua; Song, Yongping

2017-07-25

Fusion genes generated from chromosomal translocation play an important role in hematological malignancies. Detection of fusion genes currently employ use of either conventional RT-PCR methods or fluorescent in situ hybridization (FISH), where both methods involve tedious methodologies and require prior characterization of chromosomal translocation events as determined by cytogenetic analysis. In this study, we describe a real-time quantitative reverse transcription PCR (qRT-PCR)-based multi-fusion gene screening method with the capacity to detect 22 fusion genes commonly found in leukemia. This method does not require pre-characterization of gene translocation events, thereby facilitating immediate diagnosis and therapeutic management. We performed fluorescent qRT-PCR (F-qRT-PCR) using a commercially-available multi-fusion gene detection kit on a patient cohort of 345 individuals comprising 108 cases diagnosed with acute myeloid leukemia (AML) for initial evaluation; remaining patients within the cohort were assayed for confirmatory diagnosis. Results obtained by F-qRT-PCR were compared alongside patient analysis by cytogenetic characterization. Gene translocations detected by F-qRT-PCR in AML cases were diagnosed in 69.4% of the patient cohort, which was comparatively similar to 68.5% as diagnosed by cytogenetic analysis, thereby demonstrating 99.1% concordance. Overall gene fusion was detected in 53.7% of the overall patient population by F-qRT-PCR, 52.9% by cytogenetic prediction in leukemia, and 9.1% in non-leukemia patients by both methods. The overall concordance rate was calculated to be 99.0%. Fusion genes were detected by F-qRT-PCR in 97.3% of patients with CML, followed by 69.4% with AML, 33.3% with acute lymphoblastic leukemia (ALL), 9.1% with myelodysplastic syndromes (MDS), and 0% with chronic lymphocytic leukemia (CLL). We describe the use of a F-qRT-PCR-based multi-fusion gene screening method as an efficient one-step diagnostic procedure as an

Digital subtraction in gadolinium-enhanced MR imaging of the brain: a method to reduce contrast dosage

International Nuclear Information System (INIS)

Chan, J.H.M.; Tsui, E.Y.K.; Chan, C.Y.; Lai, K.F.; Cheung, Y.K.; Wong, K.P.C.; Yuen, M.K.; Chau, L.F.; Fong, D.; Mok, C.K.

2002-01-01

The aim of the study was to investigate the feasibility of using digital subtraction in contrast-enhanced MR imaging of the brain to reduce the MR contrast dosage without jeopardizing patient care. Fifty-two patients with intracranial lesions, either intra-axial or extra-axial, detected by computerized tomography were selected for contrast-enhanced MR imaging with half-dose and full-dose of gadopentetate dimeglumine. The half-dose unsubtracted, full-dose unsubtracted, and half-dose subtracted MR images were visually assessed by counting the number of enhancing brain lesions in the images and quantitatively analyzed by computing their lesion contrast-to-background ratios (CBR). The visual conspicuity of the half-dose subtracted MR images was comparable to that of the full-dose unsubtracted MR images (p>0.05), whereas the CBR of the half-dose subtracted images was approximately two to three times higher than that of the full-dose unsubtracted images. The half-dose subtracted T1-weighted spin-echo images might be able to replace the conventional standard-dose T1-weighted spin-echo images in MR imaging of the brain. (orig.)

A digital subtraction radiography based tool for periodontal bone resorption analysis

Energy Technology Data Exchange (ETDEWEB)

Schiabel, Homero; Rodrigues, Eveline B., E-mail: homero@sc.usp.br [University of Sao Paulo (EESC/USP), Sao Carlos, SP (Brazil). Dept. of Electrical Engineering; Rubira-Bullen, Izabel R.F. [University of Sao Paulo (USP), Bauru, SP (Brazil). Bauru Dentistry School

2011-07-01

The aim of this paper was to describe an aided diagnosis scheme for periodontal bone resorption so that the dentist can make an early diagnosis of the periodontal disease and establish the best treatment plan to increase the success of healing. Three ways of displaying the results are provided: qualitative, simple quantitative and colored-percentage quantitative views. A total of 72 pairs of in vitro radiographic images were used. The main procedure registers the images perspective projection aimed to align them in rotation and translation, and is followed by the application of a contrast correction technique. The results from the subtraction were evaluated firstly by the comparison between the actual and the digital sizes corresponding to the holes made by drills in phantoms. The mean error was 4.2%. The method was also applied to actual tooth radiographic images and could detect clearly the effect of treatment of periodontal diseases. It is dependent on the reproducibility of the process of radiographs acquisition and digitization, but the calculated mean error allows to conclude its better efficacy compared to usual procedures in this field. (author)

A digital subtraction radiography based tool for periodontal bone resorption analysis

International Nuclear Information System (INIS)

Schiabel, Homero; Rodrigues, Eveline B.; Rubira-Bullen, Izabel R.F.

2011-01-01

The aim of this paper was to describe an aided diagnosis scheme for periodontal bone resorption so that the dentist can make an early diagnosis of the periodontal disease and establish the best treatment plan to increase the success of healing. Three ways of displaying the results are provided: qualitative, simple quantitative and colored-percentage quantitative views. A total of 72 pairs of in vitro radiographic images were used. The main procedure registers the images perspective projection aimed to align them in rotation and translation, and is followed by the application of a contrast correction technique. The results from the subtraction were evaluated firstly by the comparison between the actual and the digital sizes corresponding to the holes made by drills in phantoms. The mean error was 4.2%. The method was also applied to actual tooth radiographic images and could detect clearly the effect of treatment of periodontal diseases. It is dependent on the reproducibility of the process of radiographs acquisition and digitization, but the calculated mean error allows to conclude its better efficacy compared to usual procedures in this field. (author)

Moving object detection using background subtraction

CERN Document Server

Shaikh, Soharab Hossain; Chaki, Nabendu

2014-01-01

This Springer Brief presents a comprehensive survey of the existing methodologies of background subtraction methods. It presents a framework for quantitative performance evaluation of different approaches and summarizes the public databases available for research purposes. This well-known methodology has applications in moving object detection from video captured with a stationery camera, separating foreground and background objects and object classification and recognition. The authors identify common challenges faced by researchers including gradual or sudden illumination change, dynamic bac

Practical applications and methods in performing cardiac digital subtraction angiography

International Nuclear Information System (INIS)

Markovic, D.M.; Withrow, S.; Moodie, D.S.

1986-01-01

One of the purposes of this book is to outline the utility of digital subtraction angiography (DSA) in common clinical practice. No text has dealt with the actual physical setup of the room or the patient prior and during a digital subtraction angiographic study at rest and with exercise. This chapter outlines the steps commonly used when cardiac DSA is performed on patients in the authors' laboratory. The authors have learned over the last few years the best way to prepare the patient and the equipment and it is hoped that utilizing this experience, other centers may avoid the mistakes the authors have made in the past and develop new techniques for the future

PCR-based methods for the detection of L1014 kdr mutation in Anopheles culicifacies sensu lato

Science.gov (United States)

Singh, Om P; Bali, Prerna; Hemingway, Janet; Subbarao, Sarala K; Dash, Aditya P; Adak, Tridibes

2009-01-01

Background Anopheles culicifacies s.l., a major malaria vector in India, has developed widespread resistance to DDT and is becoming resistant to pyrethroids–the only insecticide class recommended for the impregnation of bed nets. Knock-down resistance due to a point mutation in the voltage gated sodium channel at L1014 residue (kdr) is a common mechanism of resistance to DDT and pyrethroids. The selection of this resistance may pose a serious threat to the success of the pyrethroid-impregnated bed net programme. This study reports the presence of kdr mutation (L1014F) in a field population of An. culicifacies s.l. and three new PCR-based methods for kdr genotyping. Methods The IIS4-IIS5 linker to IIS6 segments of the para type voltage gated sodium channel gene of DDT and pyrethroid resistant An. culicifacies s.l. population from the Surat district of India was sequenced. This revealed the presence of an A-to-T substitution at position 1014 leading to a leucine-phenylalanine mutation (L1014F) in a few individuals. Three molecular methods viz. Allele Specific PCR (AS-PCR), an Amplification Refractory Mutation System (ARMS) and Primer Introduced Restriction Analysis-PCR (PIRA-PCR) were developed and tested for kdr genotyping. The specificity of the three assays was validated following DNA sequencing of the samples genotyped. Results The genotyping of this An. culicifacies s.l. population by the three PCR based assays provided consistent result and were in agreement with DNA sequencing result. A low frequency of the kdr allele mostly in heterozygous condition was observed in the resistant population. Frequencies of the different genotypes were in Hardy-Weinberg equilibrium. Conclusion The Leu-Phe mutation, which generates the kdr phenotype in many insects, was detected in a pyrethroid and DDT resistant An. culicifacies s.l. population. Three PCR-based methods were developed for kdr genotyping. All the three assays were specific. The ARMS method was refractory to non

PCR-based methods for the detection of L1014 kdr mutation in Anopheles culicifacies sensu lato

Directory of Open Access Journals (Sweden)

Dash Aditya P

2009-07-01

Full Text Available Abstract Background Anopheles culicifacies s.l., a major malaria vector in India, has developed widespread resistance to DDT and is becoming resistant to pyrethroids–the only insecticide class recommended for the impregnation of bed nets. Knock-down resistance due to a point mutation in the voltage gated sodium channel at L1014 residue (kdr is a common mechanism of resistance to DDT and pyrethroids. The selection of this resistance may pose a serious threat to the success of the pyrethroid-impregnated bed net programme. This study reports the presence of kdr mutation (L1014F in a field population of An. culicifacies s.l. and three new PCR-based methods for kdr genotyping. Methods The IIS4-IIS5 linker to IIS6 segments of the para type voltage gated sodium channel gene of DDT and pyrethroid resistant An. culicifacies s.l. population from the Surat district of India was sequenced. This revealed the presence of an A-to-T substitution at position 1014 leading to a leucine-phenylalanine mutation (L1014F in a few individuals. Three molecular methods viz. Allele Specific PCR (AS-PCR, an Amplification Refractory Mutation System (ARMS and Primer Introduced Restriction Analysis-PCR (PIRA-PCR were developed and tested for kdr genotyping. The specificity of the three assays was validated following DNA sequencing of the samples genotyped. Results The genotyping of this An. culicifacies s.l. population by the three PCR based assays provided consistent result and were in agreement with DNA sequencing result. A low frequency of the kdr allele mostly in heterozygous condition was observed in the resistant population. Frequencies of the different genotypes were in Hardy-Weinberg equilibrium. Conclusion The Leu-Phe mutation, which generates the kdr phenotype in many insects, was detected in a pyrethroid and DDT resistant An. culicifacies s.l. population. Three PCR-based methods were developed for kdr genotyping. All the three assays were specific. The ARMS method

In vivo optical imaging of amblyopia: Digital subtraction autofluorescence and split-spectrum amplitude-decorrelation angiography.

Science.gov (United States)

Guo, Lei; Tao, Jun; Xia, Fan; Yang, Zhi; Ma, Xiaoli; Hua, Rui

2016-09-01

Amblyopia is a visual impairment that is attributed to either abnormal binocular interactions or visual deprivation. The retina and choroids have been shown to be involved in the development of amblyopia. The purpose of this study was to investigate the retinal and choroidal microstructural abnormalities of amblyopia using digital subtraction autofluorescence and split-spectrum amplitude-decorrelation angiography (SSADA) approaches. This prospective study included 44 eyes of 22 patients with unilateral amblyopia. All patients who received indirect ophthalmoscopy, combined depth imaging spectral domain optical coherence tomography (OCT), SSADA-OCT, and macular blue light (BL-) and near-infrared (NIR-) autofluorescences underwent pupil dilation. The subfoveal choroidal thickness (SFCT) was measured. BL- and NIR-autofluorescences were determined for all patients and used to generate subtraction images with ImageJ software. The superficial, deep layers of the retina, and inner choroid layer were required for SSADA-OCT. For the normal eyes, a regularly increasing signal was observed in the central macula based on the subtraction images. In contrast, a decreased signal for the central patch or a reduced peak was detected in 16 of 22 amblyopic eyes (72.7%). The mean SFCT of the amblyopic eyes was greater than that of the fellow normal eyes (399.25 ± 4.944 µm vs. 280.58 ± 6.491 µm, respectively, P autofluorescence. The mechanistic relationship of a thicker choroid and choroidal capillary atrophy with amblyopia remains to be described. The digital subtraction image confirmed the changes in the microstructure of the amblyopic retina as a supplementary approach to detect the progression of amblyopia. Lasers Surg. Med. 48:660-667, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Subtracted Dispersion Relations for In-medium Meson Correlators in QCD Sum Rules

Energy Technology Data Exchange (ETDEWEB)

Florkowski, W; Broniowski, W [The H. Niewodniczanski Institute of Nuclear Physics, Cracow (Poland)

1999-01-01

We analyze subtracted dispersion relations for meson correlators at finite baryon density and temperature. Such relations are needed for QCD sum rules. We point out that importance of scattering terms, as well as finite, well-defined subtraction constants. Both are necessary for consistency, in particular for the equality of the longitudinal and transverse correlators in the limit of the vanishing three-momentum of mesons relative to the medium. We present detailed calculations in various mesonic channels of the Fermi gas of nucleons. (author)

Genomic Characterization of Flavobacterium psychrophilum Serotypes and Development of a Multiplex PCR-Based Serotyping Scheme

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Tatiana Rochat

2017-09-01

Full Text Available Flavobacterium psychrophilum is a devastating bacterial pathogen of salmonids reared in freshwater worldwide. So far, serological diversity between isolates has been described but the underlying molecular factors remain unknown. By combining complete genome sequence analysis and the serotyping method proposed by Lorenzen and Olesen (1997 for a set of 34 strains, we identified key molecular determinants of the serotypes. This knowledge allowed us to develop a robust multiplex PCR-based serotyping scheme, which was applied to 244 bacterial isolates. The results revealed a striking association between PCR-serotype and fish host species and illustrate the use of this approach as a simple and cost-effective method for the determination of F. psychrophilum serogroups. PCR-based serotyping could be a useful tool in a range of applications such as disease surveillance, selection of salmonids for bacterial coldwater disease resistance and future vaccine formulation.

Inverse fusion PCR cloning.

Directory of Open Access Journals (Sweden)

Markus Spiliotis

Full Text Available Inverse fusion PCR cloning (IFPC is an easy, PCR based three-step cloning method that allows the seamless and directional insertion of PCR products into virtually all plasmids, this with a free choice of the insertion site. The PCR-derived inserts contain a vector-complementary 5'-end that allows a fusion with the vector by an overlap extension PCR, and the resulting amplified insert-vector fusions are then circularized by ligation prior transformation. A minimal amount of starting material is needed and experimental steps are reduced. Untreated circular plasmid, or alternatively bacteria containing the plasmid, can be used as templates for the insertion, and clean-up of the insert fragment is not urgently required. The whole cloning procedure can be performed within a minimal hands-on time and results in the generation of hundreds to ten-thousands of positive colonies, with a minimal background.

Subtraction method of computing QCD jet cross sections at NNLO accuracy

Science.gov (United States)

Trócsányi, Zoltán; Somogyi, Gábor

2008-10-01

We present a general subtraction method for computing radiative corrections to QCD jet cross sections at next-to-next-to-leading order accuracy. The steps needed to set up this subtraction scheme are the same as those used in next-to-leading order computations. However, all steps need non-trivial modifications, which we implement such that that those can be defined at any order in perturbation theory. We give a status report of the implementation of the method to computing jet cross sections in electron-positron annihilation at the next-to-next-to-leading order accuracy.

Subtraction method of computing QCD jet cross sections at NNLO accuracy

Energy Technology Data Exchange (ETDEWEB)

Trocsanyi, Zoltan [University of Debrecen and Institute of Nuclear Research of the Hungarian Academy of Sciences, H-4001 Debrecen P.O.Box 51 (Hungary)], E-mail: Zoltan.Trocsanyi@cern.ch; Somogyi, Gabor [University of Zuerich, Winterthurerstrasse 190, CH-8057 Zuerich (Switzerland)], E-mail: sgabi@physik.unizh.ch

2008-10-15

We present a general subtraction method for computing radiative corrections to QCD jet cross sections at next-to-next-to-leading order accuracy. The steps needed to set up this subtraction scheme are the same as those used in next-to-leading order computations. However, all steps need non-trivial modifications, which we implement such that that those can be defined at any order in perturbation theory. We give a status report of the implementation of the method to computing jet cross sections in electron-positron annihilation at the next-to-next-to-leading order accuracy.

Increasing Entanglement between Gaussian States by Coherent Photon Subtraction

DEFF Research Database (Denmark)

Ourjoumtsev, Alexei; Dantan, Aurelien Romain; Tualle Brouri, Rosa

2007-01-01

We experimentally demonstrate that the entanglement between Gaussian entangled states can be increased by non-Gaussian operations. Coherent subtraction of single photons from Gaussian quadrature-entangled light pulses, created by a nondegenerate parametric amplifier, produces delocalized states...

Mindfulness-based cognitive therapy for depressed individuals improves suppression of irrelevant mental-sets.

Science.gov (United States)

Greenberg, Jonathan; Shapero, Benjamin G; Mischoulon, David; Lazar, Sara W

2017-04-01

An impaired ability to suppress currently irrelevant mental-sets is a key cognitive deficit in depression. Mindfulness-based cognitive therapy (MBCT) was specifically designed to help depressed individuals avoid getting caught in such irrelevant mental-sets. In the current study, a group assigned to MBCT plus treatment-as-usual (n = 22) exhibited significantly lower depression scores and greater improvements in irrelevant mental-set suppression compared to a wait-list plus treatment-as-usual (n = 18) group. Improvements in mental-set-suppression were associated with improvements in depression scores. Results provide the first evidence that MBCT can improve suppression of irrelevant mental-sets and that such improvements are associated with depressive alleviation.

Thallium-technetium-subtraction scintigraphy in secondary hyperparathyroidism

International Nuclear Information System (INIS)

Adalet, I.; Hawkins, T.; Clark, F.; Wilkinson, R.

1994-01-01

Between 1983 and 1992 thallium-technetium subtraction scintigraphy (TTS) was performed on 74 patients with clinical and biochemical evidence of hyperparathyroidism. Twenty-five of the 53 investigations since 1988 were conducted on patients with renal failure with a suspicion of secondary hyperparathyroidism. In a retrospective study we have evaluated radioisotope scintigraphy for patients with adenoma and for renal failure patients with possible parathyroid hyperplasia. Thirty of 74 patients underwent neck exploration. Scintigraphy detected 17 of 24 parathyroid adenomas (sensitivity 71%). In contrast, in six renal patients who came to operation, scintigraphy localised only 5 of 20 hyperplastic parathyroid glands (sensitivity 25%) and in one renal patient we localised a parathyroid adenoma. A review of the literature shows low detection rates for hyperplasia by TTS to be a common observation. Based on these findings a rational approach is offered for parathyroid localisation in renal patients prior to neck exploration. (orig.)

Comparative evaluation of conventional RT-PCR and real-time RT-PCR (RRT-PCR for detection of avian metapneumovirus subtype A Comparação entre as técnicas de RT-PCR convencional e RT-PCR em tempo real para a detecção do metapneumovírus aviários subtipo A

Directory of Open Access Journals (Sweden)

Helena Lage Ferreira

2009-08-01

Full Text Available Avian metapneumovirus (AMPV belongs to Metapneumovirus genus of Paramyxoviridae family. Virus isolation, serology, and detection of genomic RNA are used as diagnostic methods for AMPV. The aim of the present study was to compare the detection of six subgroup A AMPV isolates (AMPV/A viral RNA by using different conventional and real time RT-PCR methods. Two new RT-PCR tests and two real time RT-PCR tests, both detecting fusion (F gene and nucleocapsid (N gene were compared with an established test for the attachment (G gene. All the RT-PCR tested assays were able to detect the AMPV/A. The lower detection limits were observed using the N-, F- based RRT-PCR and F-based conventional RT-PCR (10(0.3 to 10¹ TCID50 mL-1. The present study suggests that the conventional F-based RT-PCR presented similar detection limit when compared to N- and F-based RRT-PCR and they can be successfully used for AMPV/A detection.O metapneumovírus aviário (AMPV pertence ao gênero Metapneumovirus, família Paramyxoviridae. Isolamento viral, sorologia e detecção do RNA genômico são atualmente as técnicas utilizadas para o diagnóstico desse agente. O objetivo do presente estudo foi comparar a detecção de RNA viral de seis isolados de AMPV, subtipo A (AMPV/A, utilizando diferentes métodos de RT-PCR convencional e real time RT-PCR (RRT-PCR. Duas novas técnicas de RT-PCR convencional e duas técnicas de RRT-PCR, ambas para a detecção dos genes da nucleoproteína (N e da proteína de fusão (F, foram comparadas com um RT-PCR previamente estabelecido para a detecção do AMPV (gene da glicoproteína -G. Todos esses métodos foram capazes de detectar os isolados AMPV/A. As técnicas RRT-PCR (genes F e N mostraram os menores limites de detecção (10(0.3 to 10¹ TCID50 mL-1. Os resultados sugerem que as técnicas RT-PCR convencional (gene F e as técnicas de RRT-PCR (gene F e N desenvolvidas no presente estudo podem ser utilizadas com sucesso para a detecção do

Molecular genotyping of Colletotrichum species based on arbitrarily primed PCR, A + T-Rich DNA, and nuclear DNA analyses

Science.gov (United States)

Freeman, S.; Pham, M.; Rodriguez, R.J.

1993-01-01

Molecular genotyping of Colletotrichum species based on arbitrarily primed PCR, A + T-rich DNA, and nuclear DNA analyses. Experimental Mycology 17, 309-322. Isolates of Colletotrichum were grouped into 10 separate species based on arbitrarily primed PCR (ap-PCR), A + T-rich DNA (AT-DNA) and nuclear DNA banding patterns. In general, the grouping of Colletotrichum isolates by these molecular approaches corresponded to that done by classical taxonomic identification, however, some exceptions were observed. PCR amplification of genomic DNA using four different primers allowed for reliable differentiation between isolates of the 10 species. HaeIII digestion patterns of AT-DNA also distinguished between species of Colletotrichum by generating species-specific band patterns. In addition, hybridization of the repetitive DNA element (GcpR1) to genomic DNA identified a unique set of Pst 1-digested nuclear DNA fragments in each of the 10 species of Colletotrichum tested. Multiple isolates of C. acutatum, C. coccodes, C. fragariae, C. lindemuthianum, C. magna, C. orbiculare, C. graminicola from maize, and C. graminicola from sorghum showed 86-100% intraspecies similarity based on ap-PCR and AT-DNA analyses. Interspecies similarity determined by ap-PCR and AT-DNA analyses varied between 0 and 33%. Three distinct banding patterns were detected in isolates of C. gloeosporioides from strawberry. Similarly, three different banding patterns were observed among isolates of C. musae from diseased banana.

Evaluation of PCR and multiplex PCR in relation to nested PCR for diagnosing Theileria equi

Directory of Open Access Journals (Sweden)

Danielle C. Leal

2011-07-01

Full Text Available Conventional PCR (PCRTeq for diagnosing Theileria equi and multiplex PCR (M/PCRTeq-Bc for diagnosing T. equi and Babesia caballi were comparatively evaluated with nested PCR (N/PCR-Teq for diagnosing equine piroplasmosis. In DNA sensitivity determinations, in multiple dilutions of equine blood that had tested positive for T. equi, PCR-Teq and N/PCR-Teq detected hemoparasite DNA in the larger dilutions (1:128, but did not differ significantly from the M/PCRTeq-Bc (1:64. In analyses on equine serum tested by ELISA, there was high agreement between this serological test and PCR-Teq (k = 0.780 and moderate agreement with N/PCR-Teq (k = 0.562 and M/PCRTeq-Bc (k = 0.488. PCR-Teq found a higher frequency of T. equi both in extensively and intensively reared horses, but this was not significant in relation to N/PCR-Teq (P>0.05, and both PCRs indicated that there was an endemic situation regarding T. equi in the population of horses of this sample. PCR-Teq was only significantly different from M/PCR-Teq-Bc (P<0.05. PCR-Teq presented high sensitivity and specificity, comparable to N/PCR-Teq, but with the advantage of higher speed in obtaining results and lower costs and risks of laboratory contamination. This accredits PCR-Teq for epidemiological studies and for determinations on affected horses.

The Effects of Mind Subtraction Meditation on Depression, Social Anxiety, Aggression, and Salivary Cortisol Levels of Elementary School Children in South Korea.

Science.gov (United States)

Yoo, Yang-Gyeong; Lee, Duck-Joo; Lee, In-Soo; Shin, Namin; Park, Ju-Yeon; Yoon, Mi-Ra; Yu, Boas

2016-01-01

This study analyzed the effects of a school-based mind subtraction meditation program on depression, social anxiety, aggression, and salivary cortisol levels of 42 elementary school children in South Korea. The research design was a nonequivalent group comparison with pretest and post-test. The experimental group was given 8weeks of the meditation program. The results showed social anxiety, aggression, and salivary cortisol levels were significantly lowered in the experimental group. This demonstrated that the school-based mind subtraction meditation program could be effective in improving psychosocial and behavioral aspects of mental health in elementary school children. Copyright © 2016 Elsevier Inc. All rights reserved.

Alpha efficiency under TL and OSL - A subtraction technique using OSL and TL to detect artificial irradiation

International Nuclear Information System (INIS)

Zink, A.J.C.; Dabis, S.; Porto, E.; Castaing, J.

2010-01-01

With the development of thermoluminescence (TL) and optically stimulated luminescence (OSL) to determine the authenticity of old ceramics, forgers use artificial irradiation by gamma ray to age modern productions. Besides fraudulent action, objects can be exposed to various sources of X-rays (e.g. radiography, security control at airports). For all these reasons, the determination of artificial irradiation is an important topic for dating art objects. The main technique to identify artificial irradiations is the subtraction technique. It is based on the fact that alpha efficiency varies according to the luminescence technique (fine grain, coarse grains, predose, OSL). Having observed a rather significant difference of alpha efficiency for TL and OSL, we propose a new subtraction technique using OSL and TL of fine grains.

PCR melting profile (PCR MP - a new tool for differentiation of Candida albicans strains

Directory of Open Access Journals (Sweden)

Nowak Magdalena

2009-11-01

Full Text Available Abstract Background We have previously reported the use of PCR Melting Profile (PCR MP technique based on using low denaturation temperatures during ligation mediated PCR (LM PCR for bacterial strain differentiation. The aim of the current study was to evaluate this method for intra-species differentiation of Candida albicans strains. Methods In total 123 Candida albicans strains (including 7 reference, 11 clinical unrelated, and 105 isolates from patients of two hospitals in Poland were examined using three genotyping methods: PCR MP, macrorestriction analysis of the chromosomal DNA by pulsed-field gel electrophoresis (REA-PFGE and RAPD techniques. Results The genotyping results of the PCR MP were compared with results from REA-PFGE and RAPD techniques giving 27, 26 and 25 unique types, respectively. The results showed that the PCR MP technique has at least the same discriminatory power as REA-PFGE and RAPD. Conclusion Data presented here show for the first time the evaluation of PCR MP technique for candidial strains differentiation and we propose that this can be used as a relatively simple and cheap technique for epidemiological studies in short period of time in hospital.

Multivariate spatial condition mapping using subtractive fuzzy cluster means.

Science.gov (United States)

Sabit, Hakilo; Al-Anbuky, Adnan

2014-10-13

Wireless sensor networks are usually deployed for monitoring given physical phenomena taking place in a specific space and over a specific duration of time. The spatio-temporal distribution of these phenomena often correlates to certain physical events. To appropriately characterise these events-phenomena relationships over a given space for a given time frame, we require continuous monitoring of the conditions. WSNs are perfectly suited for these tasks, due to their inherent robustness. This paper presents a subtractive fuzzy cluster means algorithm and its application in data stream mining for wireless sensor systems over a cloud-computing-like architecture, which we call sensor cloud data stream mining. Benchmarking on standard mining algorithms, the k-means and the FCM algorithms, we have demonstrated that the subtractive fuzzy cluster means model can perform high quality distributed data stream mining tasks comparable to centralised data stream mining.

New electronic filtering technique in digital subtraction angiography

Energy Technology Data Exchange (ETDEWEB)

Stacul, F; Pozzi-Mucelli, R; Predonzan, F; Magnaldi, S; Godina, G

1986-01-01

The authors report their experience with a new electronic filtering technique in digital subtraction angiography (DSA). The principles of the technique are reported and the advantages in comparison with conventional filters are stressed (accurate and fast placement without fluoroscopic exposure). The system provided excellent results in about 900 DSA examinations.

Bone images from dual-energy subtraction chest radiography in the detection of rib fractures

Energy Technology Data Exchange (ETDEWEB)

Szucs-Farkas, Zsolt, E-mail: zsolt.szuecs@insel.ch [Department of Diagnostic, Interventional and Pediatric Radiology, University Hospital Bern, Freiburgstrasse 4, Bern CH-3010 (Switzerland); Lautenschlager, Katrin, E-mail: katrin@students.unibe.ch [Department of Diagnostic, Interventional and Pediatric Radiology, University Hospital Bern, Freiburgstrasse 4, Bern CH-3010 (Switzerland); Flach, Patricia M., E-mail: patricia.flach@irm.unibe.ch [Institute of Forensic Medicine, University of Bern, Freiburgstrasse 4, Bern CH-3010 (Switzerland); Ott, Daniel, E-mail: daniel.ott@insel.ch [Department of Diagnostic, Interventional and Pediatric Radiology, University Hospital Bern, Freiburgstrasse 4, Bern CH-3010 (Switzerland); Strautz, Tamara, E-mail: tamara.strautz@insel.ch [Department of Diagnostic, Interventional and Pediatric Radiology, University Hospital Bern, Freiburgstrasse 4, Bern CH-3010 (Switzerland); Vock, Peter, E-mail: peter.vock@insel.ch [Department of Diagnostic, Interventional and Pediatric Radiology, University Hospital Bern, Freiburgstrasse 4, Bern CH-3010 (Switzerland); Ruder, Thomas D., E-mail: thomas.ruder@irm.unibe.ch [Institute of Forensic Medicine, University of Bern, Freiburgstrasse 4, Bern CH-3010 (Switzerland)

2011-08-15

Objective: To assess the sensitivity and image quality of chest radiography (CXR) with or without dual-energy subtracted (ES) bone images in the detection of rib fractures. Materials and methods: In this retrospective study, 39 patients with 204 rib fractures and 24 subjects with no fractures were examined with a single exposure dual-energy subtraction digital radiography system. Three blinded readers first evaluated the non-subtracted posteroanterior and lateral chest radiographs alone, and 3 months later they evaluated the non-subtracted images together with the subtracted posteroanterior bone images. The locations of rib fractures were registered with confidence levels on a 3-grade scale. Image quality was rated on a 5-point scale. Marks by readers were compared with fracture localizations in CT as a standard of reference. Results: The sensivity for fracture detection using both methods was very similar (34.3% with standard CXR and 33.5% with ES-CXR, p = 0.92). At the patient level, both sensitivity (71.8%) and specificity (92.9%) with or without ES were identical. Diagnostic confidence was not significantly different (2.61 with CXR and 2.75 with ES-CXR, p = 0.063). Image quality with ES was rated higher than that on standard CXR (4.08 vs. 3.74, p < 0.001). Conclusions: Despite a better image quality, adding ES bone images to standard radiographs of the chest does not provide better sensitivity or improved diagnostic confidence in the detection of rib fractures.

201Tl-99mTc subtraction scintigraphy as a preoperative localization procedure for persistent primary and secondary hyperparathyroidism

International Nuclear Information System (INIS)

Geipel, D.; Mischke, W.; Deckart, H.; Weiss, M.L.

1989-01-01

5 patients with a persistent hyperparathyroidism underwent thallium-technetium subtraction scintigraphy prior to reoperation. In all cases the fidings obtained by scintigraphy were confirmed by operation. Based on the preoperative localization of parathyroid adenomas and hyperplastic parathyroid bodies, respectively, their extirpation could be performed in short time. This new nuclear medicine localization procedure for identifying hyperparathyroidism has proved to be useful both in the cervical region and the mediastinum. Thus, as a sensitive method with a non-invasive character this procedure should be applied to reoperations before any other localization method. The indication for performing thallium-technetium subtraction scintigraphy as well as its evaluation have to be carried out in close collaboration between surgeons and nuclear medicine specialists. (author)

Evaluation of DNA extraction methods for PCR-based detection of Listeria monocytogenes from vegetables.

Science.gov (United States)

Vojkovska, H; Kubikova, I; Kralik, P

2015-03-01

Epidemiological data indicate that raw vegetables are associated with outbreaks of Listeria monocytogenes. Therefore, there is a demand for the availability of rapid and sensitive methods, such as PCR assays, for the detection and accurate discrimination of L. monocytogenes. However, the efficiency of PCR methods can be negatively affected by inhibitory compounds commonly found in vegetable matrices that may cause false-negative results. Therefore, the sample processing and DNA isolation steps must be carefully evaluated prior to the introduction of such methods into routine practice. In this study, we compared the ability of three column-based and four magnetic bead-based commercial DNA isolation kits to extract DNA of the model micro-organism L. monocytogenes from raw vegetables. The DNA isolation efficiency of all isolation kits was determined using a triplex real-time qPCR assay designed to specifically detect L. monocytogenes. The kit with best performance, the PowerSoil(™) Microbial DNA Isolation Kit, is suitable for the extraction of amplifiable DNA from L. monocytogenes cells in vegetable with efficiencies ranging between 29.6 and 70.3%. Coupled with the triplex real-time qPCR assay, this DNA isolation kit is applicable to the samples with bacterial loads of 10(3) bacterial cells per gram of L. monocytogenes. Several recent outbreaks of Listeria monocytogenes have been associated with the consumption of fruits and vegetables. Real-time PCR assays allow fast detection and accurate quantification of microbes. However, the success of real-time PCR is dependent on the success with which template DNA can be extracted. The results of this study suggest that the PowerSoil(™) Microbial DNA Isolation Kit can be used for the extraction of amplifiable DNA from L. monocytogenes cells in vegetable with efficiencies ranging between 29.6 and 70.3%. This method is applicable to samples with bacterial loads of 10(3) bacterial cells per gram of L. monocytogenes. © 2014

NNLO jet cross sections by subtraction

International Nuclear Information System (INIS)

Somogyi, G.; Bolzoni, P.; Trocsanyi, Z.

2010-06-01

We report on the computation of a class of integrals that appear when integrating the so-called iterated singly-unresolved approximate cross section of an earlier NNLO subtraction scheme over the factorised phase space of unresolved partons. The integrated approximate cross section itself can be written as the product of an insertion operator (in colour space) times the Born cross section. We give selected results for the insertion operator for processes with two and three hard partons in the final state. (orig.)

NNLO jet cross sections by subtraction

Energy Technology Data Exchange (ETDEWEB)

Somogyi, G.; Bolzoni, P. [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany); Trocsanyi, Z. [CERN, Geneva (Switzerland)

2010-06-15

We report on the computation of a class of integrals that appear when integrating the so-called iterated singly-unresolved approximate cross section of an earlier NNLO subtraction scheme over the factorised phase space of unresolved partons. The integrated approximate cross section itself can be written as the product of an insertion operator (in colour space) times the Born cross section. We give selected results for the insertion operator for processes with two and three hard partons in the final state. (orig.)

NNLO jet cross sections by subtraction

CERN Document Server

Somogyi, Gabor; Trocsanyi, Zoltan

2010-01-01

We report on the computation of a class of integrals that appear when integrating the so-called iterated singly-unresolved approximate cross section of the NNLO subtraction scheme of [1-4], over the factorised phase space of unresolved partons. The integrated approximate cross section itself can be written as the product of an insertion operator (in colour space) times the Born cross section. We give selected results for the insertion operator for processes with two and three hard partons in the final state.

PCR-Based EST Mapping in Wheat (Triticum aestivum L.

Directory of Open Access Journals (Sweden)

J. PERRY GUSTAFSON

2009-04-01

Full Text Available Mapping expressed sequence tags (ESTs to hexaploid wheat is aimed to reveal the structure and function of the hexaploid wheat genome. Sixty eight ESTs representing 26 genes were mapped into all seven homologous chromosome groups of wheat (Triticum aestivum L using a polymerase chain reaction technique. The majority of the ESTs were mapped to homologous chromosome group 2, and the least were mapped to homologous chromosome group 6. Comparative analysis between the EST map from this study and the EST map based on RFLPs showed 14 genes that have been mapped by both approaches were mapped to the same arm of the same homologous chromosome, which indicated that using PCR-based ESTs was a reliable approach in mapping ESTs in hexaploid wheat.

Digital subtraction angiography

International Nuclear Information System (INIS)

Gmelin, E.; Arlart, I.P.

1987-01-01

The introduction explains the technical and physical fundamentals of digital radiography, the principles of digital subtraction, and the various filtering methods. The authors then define the requirements to be met by a DSA equipment in terms of technical components and operational performance. A very extensive chapter deals with the indications supporting intravenous or intraarterial DSA and compares the two methods, showing advantages and drawbacks with respect to practical results. Another chapter discusses the applications of DSA for cardiological diagnostics, as e.g. imaging of the coronary arteries or arterial bypasses, and explains the densitometric and planimetric evaluation of the coronary functional processes. The book also discusses less customary applications of DSA such as the sialography or dacryocystography, as well as angiologic examinations in children. The limits of the DSA methods are discussed in the last chapter, together with aspects such as the radiation exposure of the patient, and cost-benefit analyses, and potential future improvements. With 204 figs., 44 tabs [de

An Evidence-Based Approach to Detection by DASI-ELISA and RT-PCR in Dormant Period

Directory of Open Access Journals (Sweden)

Antonio Olmos

2008-01-01

Full Text Available An evidence-based approach, such as those developed in clinical and veterinary medicine, was applied to the detection of Plum pox virus (PPV during the dormant period. A standardized methodology was used for the calculation of parameters of the operational capacity of DASI-ELISA and RT-PCR in wintertime. These methods are routinely handled to test the sanitary status of plants in national or international trading and in those cases concerning export-import of plant materials. Diagnosis often has to be performed during the dormant period, when plant material is commercialized. Some guidelines to interpret diagnostic results of wintertime are provided in an attempt to minimize risks associated with the methods and over-reliance on the binary outcome of a single assay. In order to evaluate if a complementary test increased the confidence of PPV diagnosis when discordant results between DASI-ELISA and RT-PCR are obtained, NASBA-FH also was included. Likelihood ratios of each method were estimated based on the sensitivity and specificity obtained in wintertime. Subsequently, a Bayesian approach was performed to calculate post-test probability of PPV infection in spring. Results of evidence-based approach show that different PPV prevalences require different screening tests. Thus, at very low PPV prevalence levels DASI-ELISA should be used as the election method, whilst at the highest PPV prevalence levels RT-PCR should be performed. NASBA-FH could be used at medium prevalences to clarify discordances between DASI-ELISA and RT-PCR.

Nested PCR and RFLP analysis based on the 16S rRNA gene

Science.gov (United States)

Current phytoplasma detection and identification method is primarily based on nested PCR followed by restriction fragment length polymorphism analysis and gel electrophoresis. This method can potentially detect and differentiate all phytoplasmas including those previously not described. The present ...

qPCR-based mitochondrial DNA quantification: Influence of template DNA fragmentation on accuracy

International Nuclear Information System (INIS)

Jackson, Christopher B.; Gallati, Sabina; Schaller, André

2012-01-01

Highlights: ► Serial qPCR accurately determines fragmentation state of any given DNA sample. ► Serial qPCR demonstrates different preservation of the nuclear and mitochondrial genome. ► Serial qPCR provides a diagnostic tool to validate the integrity of bioptic material. ► Serial qPCR excludes degradation-induced erroneous quantification. -- Abstract: Real-time PCR (qPCR) is the method of choice for quantification of mitochondrial DNA (mtDNA) by relative comparison of a nuclear to a mitochondrial locus. Quantitative abnormal mtDNA content is indicative of mitochondrial disorders and mostly confines in a tissue-specific manner. Thus handling of degradation-prone bioptic material is inevitable. We established a serial qPCR assay based on increasing amplicon size to measure degradation status of any DNA sample. Using this approach we can exclude erroneous mtDNA quantification due to degraded samples (e.g. long post-exicision time, autolytic processus, freeze–thaw cycles) and ensure abnormal DNA content measurements (e.g. depletion) in non-degraded patient material. By preparation of degraded DNA under controlled conditions using sonification and DNaseI digestion we show that erroneous quantification is due to the different preservation qualities of the nuclear and the mitochondrial genome. This disparate degradation of the two genomes results in over- or underestimation of mtDNA copy number in degraded samples. Moreover, as analysis of defined archival tissue would allow to precise the molecular pathomechanism of mitochondrial disorders presenting with abnormal mtDNA content, we compared fresh frozen (FF) with formalin-fixed paraffin-embedded (FFPE) skeletal muscle tissue of the same sample. By extrapolation of measured decay constants for nuclear DNA (λ nDNA ) and mtDNA (λ mtDNA ) we present an approach to possibly correct measurements in degraded samples in the future. To our knowledge this is the first time different degradation impact of the two

qPCR-based mitochondrial DNA quantification: Influence of template DNA fragmentation on accuracy

Energy Technology Data Exchange (ETDEWEB)

Jackson, Christopher B., E-mail: Christopher.jackson@insel.ch [Division of Human Genetics, Departements of Pediatrics and Clinical Research, Inselspital, University of Berne, Freiburgstrasse, CH-3010 Berne (Switzerland); Gallati, Sabina, E-mail: sabina.gallati@insel.ch [Division of Human Genetics, Departements of Pediatrics and Clinical Research, Inselspital, University of Berne, Freiburgstrasse, CH-3010 Berne (Switzerland); Schaller, Andre, E-mail: andre.schaller@insel.ch [Division of Human Genetics, Departements of Pediatrics and Clinical Research, Inselspital, University of Berne, Freiburgstrasse, CH-3010 Berne (Switzerland)

2012-07-06

Highlights: Black-Right-Pointing-Pointer Serial qPCR accurately determines fragmentation state of any given DNA sample. Black-Right-Pointing-Pointer Serial qPCR demonstrates different preservation of the nuclear and mitochondrial genome. Black-Right-Pointing-Pointer Serial qPCR provides a diagnostic tool to validate the integrity of bioptic material. Black-Right-Pointing-Pointer Serial qPCR excludes degradation-induced erroneous quantification. -- Abstract: Real-time PCR (qPCR) is the method of choice for quantification of mitochondrial DNA (mtDNA) by relative comparison of a nuclear to a mitochondrial locus. Quantitative abnormal mtDNA content is indicative of mitochondrial disorders and mostly confines in a tissue-specific manner. Thus handling of degradation-prone bioptic material is inevitable. We established a serial qPCR assay based on increasing amplicon size to measure degradation status of any DNA sample. Using this approach we can exclude erroneous mtDNA quantification due to degraded samples (e.g. long post-exicision time, autolytic processus, freeze-thaw cycles) and ensure abnormal DNA content measurements (e.g. depletion) in non-degraded patient material. By preparation of degraded DNA under controlled conditions using sonification and DNaseI digestion we show that erroneous quantification is due to the different preservation qualities of the nuclear and the mitochondrial genome. This disparate degradation of the two genomes results in over- or underestimation of mtDNA copy number in degraded samples. Moreover, as analysis of defined archival tissue would allow to precise the molecular pathomechanism of mitochondrial disorders presenting with abnormal mtDNA content, we compared fresh frozen (FF) with formalin-fixed paraffin-embedded (FFPE) skeletal muscle tissue of the same sample. By extrapolation of measured decay constants for nuclear DNA ({lambda}{sub nDNA}) and mtDNA ({lambda}{sub mtDNA}) we present an approach to possibly correct measurements in

Internal quality control of PCR-based genotyping methods

DEFF Research Database (Denmark)

Bladbjerg, Else-Marie; Gram, Jørgen; Jespersen, Jørgen

2002-01-01

Internal quality control programmes for genetic analyses are needed. We have focused on quality control aspects of selected polymorphism analyses used in thrombosis research. DNA was isolated from EDTA-blood (n = 500) and analysed for 18 polymorphisms by polymerase chain reaction (PCR), i...... because of positive reagent blanks (controls (Control of data handling revealed 0.1% reading mistakes and 0.5% entry mistakes. Based on our experiences, we propose an internal quality control programme......, electrophoresis (analytical factors), result reading and entry into a database (post-analytical factors). Furthermore, we evaluated a procedure for result confirmation. Isolated DNA was of good quality (42 micrograms/ml blood, A260/A280 ratio > 1.75, negative DNAsis tests). Occasionally, results were reanalysed...

Comparison of iodine K-edge subtraction and fluorescence subtraction imaging in an animal system

International Nuclear Information System (INIS)

Zhang, H.; Zhu, Y.; Bewer, B.; Zhang, L.; Korbas, M.; Pickering, I.J.; George, G.N.; Gupta, M.; Chapman, D.

2008-01-01

K-Edge Subtraction (KES) utilizes the discontinuity in the X-ray absorption across the absorption edge of the selected contrast element and creates an image of the projected density of the contrast element from two images acquired just above and below the K-edge of the contrast element. KES has proved to be powerful in coronary angiography, micro-angiography, bronchography, and lymphatic imaging. X-ray fluorescence imaging is a successful technique for the detection of dilute quantities of elements in specimens. However, its application at high X-ray energies (e.g. at the iodine K-edge) is complicated by significant Compton background, which may enter the energy window set for the contrast material's fluorescent X-rays. Inspired by KES, Fluorescence Subtraction Imaging (FSI) is a technique for high-energy (>20 keV) fluorescence imaging using two different incident beam energies just above and below the absorption edge of a contrast element (e.g. iodine). The below-edge image can be assumed as a 'background' image, which includes Compton scatter and fluorescence from other elements. The above-edge image will contain nearly identical spectral content as the below-edge image but will contain the additional fluorescence of the contrast element. This imaging method is especially promising with thick objects with dilute contrast materials, significant Compton background, and/or competing fluorescence lines from other materials. A quality factor is developed to facilitate the comparison. The theoretical value of the quality factor sets the upper limit that an imaging method can achieve when the noise is Poisson limited. The measured value of this factor makes two or more imaging methods comparable. Using the Hard X-ray Micro-Analysis (HXMA) beamline at the Canadian Light Source (CLS), the techniques of FSI and KES were critically compared, with reference to radiation dose, image acquisition time, resolution, signal-to-noise ratios, and quality factor

A PCR-based method for identification of bifidobacteria from the human alimentary tract at the species level

NARCIS (Netherlands)

Venema, K.; Maathuis, A.J.H.

2003-01-01

A polymerase chain reaction (PCR)-based method was developed for the identification of isolates of Bifidobacterium at the species level. Using two Bifidobacterium-specific primers directed against the 16S ribosomal gene (Bif164 and Bif662), a PCR product was obtained from the type strains of 12

Clinical usefulness of subtraction scintigraphy of the liver with Ga-67-citrate and Tc-99m-colloid

International Nuclear Information System (INIS)

Oyamada, H.; Terui, S.; Nagaiwa, K.; Kawai, H.; Fukukita, H.

1983-01-01

Subtraction scintigraphy of the liver with Ga-67-citrate and Tc-99m-colloid was performed for the radionuclide image diagnosis of intrahepatic masses, especially hepatoma. In this method the Tc-99m image was subtracted from the Ga-67 image. After normalizing both images, 4 different factors (0.6, 0.8, 1.0, and 1.2) were applied to the Tc-99m image before the subtraction. Finally, 4 subtraction images with different contrasts were obtained in one X-ray film. This method was found to be very useful in the assessment of intrahepatic focal accumulation of Ga-67, especially in cases with hepatoma, because it eliminated the uncertainty in the former method in which only visual judgment was done

Speech Enhancement by Multichannel Crosstalk Resistant ANC and Improved Spectrum Subtraction

Directory of Open Access Journals (Sweden)

Zeng Qingning

2006-01-01

Full Text Available A scheme combining multichannel crosstalk resistant adaptive noise cancellation (MCRANC algorithm and improved spectrum subtraction (ISS algorithm is presented to enhance noise carrying speech signals. The scheme would permit locating the microphones in close proximity by virtue of using MCRANC which has the capability of removing the crosstalk effect. MCRANC would also permit canceling out nonstationary noise and making the residual noise more stationary for further treatment by ISS algorithm. Experimental results have indicated that this scheme outperforms many commonly used techniques in the sense of SNR improvement and music effect reduction which is an inevitable byproduct of the spectrum subtraction algorithm.

Single tube genotyping of sickle cell anaemia using PCR-based SNP analysis.

Science.gov (United States)

Waterfall, C M; Cobb, B D

2001-12-01

Allele-specific amplification (ASA) is a generally applicable technique for the detection of known single nucleotide polymorphisms (SNPs), deletions, insertions and other sequence variations. Conventionally, two reactions are required to determine the zygosity of DNA in a two-allele system, along with significant upstream optimisation to define the specific test conditions. Here, we combine single tube bi-directional ASA with a 'matrix-based' optimisation strategy, speeding up the whole process in a reduced reaction set. We use sickle cell anaemia as our model SNP system, a genetic disease that is currently screened using ASA methods. Discriminatory conditions were rapidly optimised enabling the unambiguous identification of DNA from homozygous sickle cell patients (HbS/S), heterozygous carriers (HbA/S) or normal DNA in a single tube. Simple downstream mathematical analyses based on product yield across the optimisation set allow an insight into the important aspects of priming competition and component interactions in this competitive PCR. This strategy can be applied to any polymorphism, defining specific conditions using a multifactorial approach. The inherent simplicity and low cost of this PCR-based method validates bi-directional ASA as an effective tool in future clinical screening and pharmacogenomic research where more expensive fluorescence-based approaches may not be desirable.

Comparison of culture-based, vital stain and PMA-qPCR methods for the quantitative detection of viable hookworm ova.

Science.gov (United States)

Gyawali, P; Sidhu, J P S; Ahmed, W; Jagals, P; Toze, S

2017-06-01

Accurate quantitative measurement of viable hookworm ova from environmental samples is the key to controlling hookworm re-infections in the endemic regions. In this study, the accuracy of three quantitative detection methods [culture-based, vital stain and propidium monoazide-quantitative polymerase chain reaction (PMA-qPCR)] was evaluated by enumerating 1,000 ± 50 Ancylostoma caninum ova in the laboratory. The culture-based method was able to quantify an average of 397 ± 59 viable hookworm ova. Similarly, vital stain and PMA-qPCR methods quantified 644 ± 87 and 587 ± 91 viable ova, respectively. The numbers of viable ova estimated by the culture-based method were significantly (P methods. Therefore, both PMA-qPCR and vital stain methods appear to be suitable for the quantitative detection of viable hookworm ova. However, PMA-qPCR would be preferable over the vital stain method in scenarios where ova speciation is needed.

Comparison of RT-PCR-Dot blot hybridization based on radioisotope 32P with conventional RT-PCR and commercial ELISA Assays for blood screening of HIV-1

International Nuclear Information System (INIS)

Maria Lina R; Andi Yasmon

2011-01-01

There are many commercial ELISA and rapid test kits that have been used for blood screening; however, the kits can give false positive and negative results. Therefore, RT-PCR (Reverse Transcription Polymerase Chain Reaction) - Dot Blot Hybridization based on radioisotope 32 P (RDBR) method was developed in this research, to compare the method with the conventional RT-PCR and commercial ELISA Enzyme-Linked lmmunosorbent Assay) kit. This method is efficient for screening of large blood specimens and surveillance study. Eighty seven samples were used and serum of the samples were tested by ELISA to detect HIV-1. The HIV-l RNA genome was extracted from plasma samples and tested using the RT-PCR and RDBR methods. Of 87 samples that were tested, the rates of positive testing of the RT-PCR, the RDBR, and the ELISA were 71.26%, 74.71%, and 80.46%, respectively. The RDBR (a combination of RTPCR and dot blot hybridization) was more sensitive than conventional RT-PCR by showing 3.45% in increase number of positive specimens. The results showed that of 9 samples (10.34%) were negative RDBR and positive ELISA, while 4 samples (4.60%) were negative ELISA and positive RDBR. The two methods showed slightly difference in the results but further validation is still needed. However, RDBR has high potential as an alternative method for screening of blood in large quantities when compared to method of conventional RT-PCR and ELISA. (author)

Bias in the Cq value observed with hydrolysis probe based quantitative PCR can be corrected with the estimated PCR efficiency value

NARCIS (Netherlands)

Tuomi, Jari Michael; Voorbraak, Frans; Jones, Douglas L.; Ruijter, Jan M.

2010-01-01

For real-time monitoring of PCR amplification of DNA, quantitative PCR (qPCR) assays use various fluorescent reporters. DNA binding molecules and hybridization reporters (primers and probes) only fluoresce when bound to DNA and result in the non-cumulative increase in observed fluorescence.

Review: Diagnostic accuracy of PCR-based detection tests for Helicobacter Pylori in stool samples.

Science.gov (United States)

Khadangi, Fatemeh; Yassi, Maryam; Kerachian, Mohammad Amin

2017-12-01

Although different methods have been established to detect Helicobacter pylori (H. pylori) infection, identifying infected patients is an ongoing challenge. The aim of this meta-analysis was to provide pooled diagnostic accuracy measures for stool PCR test in the diagnosis of H. pylori infection. In this study, a systematic review and meta-analysis were carried out on various sources, including MEDLINE, Web of Sciences, and the Cochrane Library from April 1, 1999, to May 1, 2016. This meta-analysis adheres to the guidelines provided by the Preferred Reporting Items for Systematic Reviews and Meta-Analyses report (PRISMA Statement). The clinical value of DNA stool PCR test was based on the pooled false positive, false negative, true positive, and true negative of different genes. Twenty-six of 328 studies identified met the eligibility criteria. Stool PCR test had a performance of 71% (95% CI: 68-73) sensitivity, 96% (95% CI: 94-97) specificity, and 65.6 (95% CI: 30.2-142.5) diagnostic odds ratio (DOR) in diagnosis of H. pylori. The DOR of genes which showed the highest performance of stool PCR tests was as follows: 23S rRNA 152.5 (95% CI: 55.5-418.9), 16S rRNA 67.9 (95%CI: 6.4-714.3), and glmM 68.1 (95%CI: 20.1-231.7). The sensitivity and specificity of stool PCR test are relatively in the same spectrum of other diagnostic methods for the detection of H. pylori infection. In descending order of significance, the most diagnostic candidate genes using PCR detection were 23S rRNA, 16S rRNA, and glmM. PCR for 23S rRNA gene which has the highest performance could be applicable to detect H. pylori infection. © 2017 John Wiley & Sons Ltd.

Improved detection of pulmonary nodules on energy-subtracted chest radiographs with a commercial computer-aided diagnosis software: comparison with human observers

International Nuclear Information System (INIS)

Szucs-Farkas, Zsolt; Patak, Michael A.; Yuksel-Hatz, Seyran; Ruder, Thomas; Vock, Peter

2010-01-01

To retrospectively analyze the performance of a commercial computer-aided diagnosis (CAD) software in the detection of pulmonary nodules in original and energy-subtracted (ES) chest radiographs. Original and ES chest radiographs of 58 patients with 105 pulmonary nodules measuring 5-30 mm and images of 25 control subjects with no nodules were randomized. Five blinded readers evaluated firstly the original postero-anterior images alone and then together with the subtracted radiographs. In a second phase, original and ES images were analyzed by a commercial CAD program. CT was used as reference standard. CAD results were compared to the readers' findings. True-positive (TP) and false-positive (FP) findings with CAD on subtracted and non-subtracted images were compared. Depending on the reader's experience, CAD detected between 11 and 21 nodules missed by readers. Human observers found three to 16 lesions missed by the CAD software. CAD used with ES images produced significantly fewer FPs than with non-subtracted images: 1.75 and 2.14 FPs per image, respectively (p=0.029). The difference for the TP nodules was not significant (40 nodules on ES images and 34 lesions in non-subtracted radiographs, p = 0.142). CAD can improve lesion detection both on energy subtracted and non-subtracted chest images, especially for less experienced readers. The CAD program marked less FPs on energy-subtracted images than on original chest radiographs. (orig.)

Resolution Enhancement Algorithm for Spaceborn SAR Based on Hanning Function Weighted Sidelobe Suppression

Science.gov (United States)

Li, C.; Zhou, X.; Tang, D.; Zhu, Z.

2018-04-01

Resolution and sidelobe are mutual restrict for SAR image. Usually sidelobe suppression is based on resolution reduction. This paper provide a method for resolution enchancement using sidelobe opposition speciality of hanning window and SAR image. The method can keep high resolution on the condition of sidelobe suppression. Compare to traditional method, this method can enchance 50 % resolution when sidelobe is -30dB.

FPGA implementation for real-time background subtraction based on Horprasert model.

Science.gov (United States)

Rodriguez-Gomez, Rafael; Fernandez-Sanchez, Enrique J; Diaz, Javier; Ros, Eduardo

2012-01-01

Background subtraction is considered the first processing stage in video surveillance systems, and consists of determining objects in movement in a scene captured by a static camera. It is an intensive task with a high computational cost. This work proposes an embedded novel architecture on FPGA which is able to extract the background on resource-limited environments and offers low degradation (produced because of the hardware-friendly model modification). In addition, the original model is extended in order to detect shadows and improve the quality of the segmentation of the moving objects. We have analyzed the resource consumption and performance in Spartan3 Xilinx FPGAs and compared to others works available on the literature, showing that the current architecture is a good trade-off in terms of accuracy, performance and resources utilization. With less than a 65% of the resources utilization of a XC3SD3400 Spartan-3A low-cost family FPGA, the system achieves a frequency of 66.5 MHz reaching 32.8 fps with resolution 1,024 × 1,024 pixels, and an estimated power consumption of 5.76 W.

FPGA Implementation for Real-Time Background Subtraction Based on Horprasert Model

Directory of Open Access Journals (Sweden)

Eduardo Ros

2012-01-01

Full Text Available Background subtraction is considered the first processing stage in video surveillance systems, and consists of determining objects in movement in a scene captured by a static camera. It is an intensive task with a high computational cost. This work proposes an embedded novel architecture on FPGA which is able to extract the background on resource-limited environments and offers low degradation (produced because of the hardware-friendly model modification. In addition, the original model is extended in order to detect shadows and improve the quality of the segmentation of the moving objects. We have analyzed the resource consumption and performance in Spartan3 Xilinx FPGAs and compared to others works available on the literature, showing that the current architecture is a good trade-off in terms of accuracy, performance and resources utilization. With less than a 65% of the resources utilization of a XC3SD3400 Spartan-3A low-cost family FPGA, the system achieves a frequency of 66.5 MHz reaching 32.8 fps with resolution 1,024 x 1,024 pixels, and an estimated power consumption of 5.76 W.

Optimal construction and delivery of dual-functioning lentiviral vectors for type I collagen-suppressed chondrogenesis in synovium-derived mesenchymal stem cells.

Science.gov (United States)

Zhang, Feng; Yao, Yongchang; Zhou, Ruijie; Su, Kai; Citra, Fudiman; Wang, Dong-An

2011-06-01

This study aims to deliver both transforming growth factor β3 (TGF-β3) and shRNA targeting type I collagen (Col I) by optimal construction and application of various dual-functioning lentiviral vectors to induce Col I-suppressed chondrogenesis in synovium-derived mesenchymal stem cells (SMSCs). We constructed four lentiviral vectors (LV-1, LV-2, LV-3 and LV-4) with various arrangements of the two expression cassettes in different positions and orientations. Col I inhibition efficiency and chondrogenic markers were assessed with qPCR, ELISA and staining techniques. Among the four vectors, LV-1 has two distant and reversely oriented cassettes, LV-2 has two distant and same-oriented cassettes, LV-3 has two proximal and reversely oriented cassettes, and LV-4 has two proximal and same-oriented cassettes. Col I and chondrogenic markers, including type II collagen (Col II), aggrecan and glycosaminoglycan (GAG), were examined in SMSCs cultured in 3-D alginate hydrogel. All of the four vectors showed distinct effects in Col I level as well as diverse inductive efficiencies in upregulation of the cartilaginous markers. Based on real-time PCR results, LV-1 was optimal towards Col I-suppressed chondrogenesis. LV-1 vector is competent to promote Col I-suppressed chondrogenesis in SMSCs.

Can approximate mental calculation account for operational momentum in addition and subtraction?

Science.gov (United States)

Knops, André; Dehaene, Stanislas; Berteletti, Ilaria; Zorzi, Marco

2014-01-01

The operational momentum (OM) effect describes a cognitive bias whereby we overestimate the results of mental addition problems while underestimating for subtraction. To test whether the OM emerges from psychophysical characteristics of the mental magnitude representation we measured two basic parameters (Weber fraction and numerical estimation accuracy) characterizing the mental magnitude representation and participants' performance in cross-notational addition and subtraction problems. Although participants were able to solve the cross-notational problems, they consistently chose relatively larger results in addition problems than in subtraction problems, thus replicating and extending previous results. Combining the above measures in a psychophysical model allowed us to partially predict the chosen results. Most crucially, however, we were not able to fully model the OM bias on the basis of these psychophysical parameters. Our results speak against the idea that the OM is due to basic characteristics of the mental magnitude representation. In turn, this might be interpreted as evidence for the assumption that the OM effect is better explained by attentional shifts along the mental magnitude representation during mental calculation.

Detection of aneurysms in subarachnoidal hemorrhage - CT-angiography versus digital subtraction angiography

International Nuclear Information System (INIS)

Roehnert, W.; Haenig, V.; Hietschold, V.; Abolmaali, N.

1998-01-01

Purpose: The value of CT-angiography (CT-A) for the visualization of intracranial aneurysms was more closely defined by comparison with digital subtraction angiography (DSA). Methods: Over a period of 18 months a total of 106 patients in whom a subarachnoidal hemorrhage had been detected on native CT were examined in parallel by spiral CT and DSA. CT-angiography was performed under standardized parameters and included processing with 3D surface reconstructions. Results: In 64 patients (60.4%) at total of 72 aneurysms were detected. In four cases (6.2%) there were two and in two cases (3.1%) even three aneurysms. The findings of DSA and CTA agreed in 98 cases (92.5%). In four patients (3.8%) a false negative results was obtained in CTA and the initial DSA. Conclusions: Digital subtraction angiography must still be considered as the gold standard in the diagnosis of cerebral aneurysms. On account of its excellent spatial delineation of aneurysms and possibilities for exact measurements, CT-angiography represents a valuable, supplementary method - in some cases also an alternative method - to digital subtraction angiography. (orig.) [de

Children's Understanding of the Addition/Subtraction Complement Principle

Science.gov (United States)

Torbeyns, Joke; Peters, Greet; De Smedt, Bert; Ghesquière, Pol; Verschaffel, Lieven

2016-01-01

Background: In the last decades, children's understanding of mathematical principles has become an important research topic. Different from the commutativity and inversion principles, only few studies have focused on children's understanding of the addition/subtraction complement principle (if a - b = c, then c + b = a), mainly relying on verbal…

Visualization of the renal venous system by renal arteriography with digital subtraction angiography

International Nuclear Information System (INIS)

Nagai, Jun

1989-01-01

The purpose of this study was to obtain vivid and precise images of intrarenal venous branching using DSA for renal arteriography. The type of system used was an ADAC DPS-4100C with 70-80 kVp, and 320 mA, 25-50 msec at 6 frames/sec. The duration was 10 sec and the matrix size was 512x512. In order to retain clear subtracted images of intrarenal venous branching with minimal noise the three frames were selected on the time-density curve of DSA: (Fig.3). 1) a frame on which renal arteries disappear (frame X), 2) the frame with highest renal venous density value as (frame Y), 3) the difference of the nephrogram density between X and Y frames in which only the density of the nephrogram decreases (frame Z). The mask image is the image subtracted by the equation of the weighted averaging method on X and Z frame and is subtracted from the image of Y frame in the final step. By this method, 40 kidneys in 36 patients were studied, and the intrarenal venous branches up to the interlobar vein was clearly demonstrated in 28 of these cases (70%). This method is useful to estimate the extent of intrarenal lesions and detect abnormal renal blood flow compared with conventional temporal subtraction method. (author)

The role of contrast-enhanced digital subtraction MRI in the diagnosis of vertebral metastasic tumors

International Nuclear Information System (INIS)

Xiao Yeyu; Yang Jun; Qi Weili; Liu Qize; Hong Bikai; Wu Renhua

2008-01-01

Objective: To evaluate the contrast-enhanced digital subtraction MRI in the diagnosis of vertebral metastasic tumors. Methods 66 vertebral metastasic tumors in 43 patients were examined with conventional MRI (T 1 WI, STIR and Contrast-enhanced T 1 WI) and contrast-enhanced digital subtraction MR imaging. All lesions were histologically proved. The quantity and characteristic imaging signs (including spiculation, bull eye sign and irregular edge) of lesions were detected separately by different sequences. K independent samples test was used. Results: The detection rates of 35 vertebral metastasic tumors with vertebral morphological changes were same in all MR sequences. But in the other 31 lesions without vertebral morphological changes, the detection rates were different and STIR was the highest in all sequences. Contrast-enhanced digital subtraction MRI was more sensitive than all the conventional MR sequences in finding characteristic imaging signs with statistically significant differences. Conclusion: Contrast enhanced subtraction MRI is an useful and convenient technique which has great value in finding vertebral metastasic tumors and depicting the characteristic imaging signs. (authors)

Genetic sequences derived from suppression subtractive ...

African Journals Online (AJOL)

STORAGESEVER

2008-06-17

Jun 17, 2008 ... their possible roles in Xanthomonas albilineans ... Technology, P. O. Box 1334, Durban 4000, Republic of South Africa. Accepted 4 ... Clones selected were sequenced (using a Perkin Elmer ABI PRISM Dye terminator cycle.

Magnetization transfer contrast (MTC) and MTC-subtraction: enhancement of cartilage lesions and intracartilaginous degeneration in vitro

International Nuclear Information System (INIS)

Vahlensieck, M.; Dombrowski, F.; Leutner, C.; Wagner, U.; Reiser, M.

1994-01-01

Human articular cartilage from 16 cadaveric or amputated knees was studied using standard magnetic resonance imaging (MRI), on-resonance magnetization transfer contrast (MTC) and MTC-subtraction MRI. Results were compared with subsequent macroscopic and histopathological findings. MTC-subtraction and T2-weighted spin-echo images visualized cartilaginous surface defects with high sensitivity and specificity. MTC and T2-weighted spin-echo images revealed intra-cartilaginous signal loss without surface defects in 80% of the cases, corresponding to an increased collagen concentration. It is concluded that MTC is sensitive to early cartilage degeneration and MTC-subtraction can be helpful in detecting cartilage defects. (orig.)

Evaluation of the pulmonary vascular bed by digital subtraction angiography