Detectability comparison of simulated tumors in digital breast tomosynthesis using high-energy X-ray inline phase sensitive and commercial imaging systems

This study compared the detectability of simulated tumors using a high-energy X-ray inline phase sensitive digital breast tomosynthesis (DBT) prototype and a commercial attenuation-based DBT system. Each system imaged a 5-cm thick modular breast phantom with 50–50 adipose-glandular percentage density containing contrast-detail (CD) test objects to simulate different tumor sizes. A commercial DBT system acquired 15 projection views over 15 degrees (15d-15p) was used to acquire the attenuation-based projection views and to reconstruct the conventional DBT slices. Attenuation-based projection views were acquired at 32 kV, 46 mAs with a mean glandular dose (D_g) of 1.6 mGy. For acquiring phase sensitive projection views, the prototype utilized two acquisition geometries: 11 projection views were acquired over 15 degrees (15d-11p), and 17 projection views were acquired over 16 degrees (16d-17p) at 120 kV, 5.27 mAs with 1.51 mGy under the magnification (M) of 2. A phase retrieval algorithm based on the phase-attenuation duality (PAD) was applied to each projection view, and a modified Feldkamp-Davis-Kress (FDK) algorithm was used to reconstruct the phase sensitive DBT slices. Simulated tumor margins were rated as more conspicuous and better visualized for both phase sensitive acquisition geometries versus conventional DBT imaging. The CD curves confirmed the improvement in both contrast and spatial resolutions with the phase sensitive DBT imaging. The superiority of the phase sensitive DBT imaging was further endorsed by higher contrast to noise ratio (CNR) and figure-of-merit (FOM) values. The CNR improvements provided by the phase sensitive DBT prototype were sufficient to offset the noise reduction provided by the attenuation-based DBT imaging.     

Characterization of the imaging settings in screening mammography using a tracking and reporting system: A multi-center and multi-vendor analysis

A tracking and reporting system was developed to monitor radiation dose in X-ray breast imaging. We used our tracking system to characterize and compare the mammographic practices of five breast imaging centers located in the United States and Brazil. Clinical data were acquired using eight mammography systems comprising three modalities: computed radiography (CR), full-field digital mammography (FFDM), and digital breast tomosynthesis (DBT). Our database consists of metadata extracted from 334,234 images. We analyzed distributions and correlations of compressed breast thickness (CBT), compression force, target-filter combinations, X-ray tube voltage, and average glandular dose (AGD). AGD reference curves were calculated based on AGD distributions as a function of CBT. These curves represent an AGD reference for a particular population and system. Differences in AGD and imaging settings were attributed to a combination of factors, such as improvements in technology, imaging protocol, and patient demographics. The tracking system allows the comparison of various imaging settings used in screening mammography, as well as the tracking of patient- and population-specific breast data collected from different populations.     

Normalized glandular dose coefficients in mammography,digital breast tomosynthesis and dedicated breast CT

PurposeTo provide mean glandular dose (MGD) estimates via Monte Carlo (MC) simulations as a function of the breast models and scan parameters in mammography, digital breast tomosynthesis (DBT) and dedicated breast CT (BCT).MethodsThe MC code was based on GEANT4 toolkit. The simulated compressed breast was either a cylinder with a semi-circular section or ad hoc shaped for oblique view (MLO). In DBT we studied the influence of breast models and exam parameters on the T-factors (i.e. the conversion factor for the calculation of the MGD in DBT from that for a 0-degree projection), and in BCT we investigated the influence on the MGD estimates of the ion chamber volume used for the air kerma measurements.ResultsIn mammography, a model representative of a breast undergoing an MLO view exam did not produce substantial differences (0.4%) in MGD estimates, when compared to a conventional cranio-caudal (CC) view breast model. The beam half value layer did not present a significant influence on T-factors in DBT (<0.8%), while the skin model presented significant influence on MGD estimates (up to 3.3% at 30 degrees scan angle), increasing for larger scan angles. We derived a correction factor for taking into account the different ion chamber volume used in MGD estimates in BCT.ConclusionsA series of MC code modules for MGD estimates in 2D and 3D breast imaging have been developed in order to take into account the most recent advances in breast models.     

Optimal photon energy comparison between digital breast tomosynthesis and mammography: A case study

A comparison, in terms of the optimal energy that maximizes the image quality between digital breast tomosynthesis (DBT) and digital mammography (DM) was performed in a MAMMOMAT Inspiration system (Siemens) based on amorphous selenium flat panel detector. In this paper we measured the image quality by the signal difference-to-noise ratio (SDNR), and the patient risk by the mean glandular dose (MGD). Using these quantities we compared the optimal voltage that maximizes the image quality both in breast tomosynthesis and standard mammography acquisition mode. The comparison for the two acquisition modes was performed for a W/Rh anode filter combinations by using a 4.5 cm tissue equivalent mammography phantom. Moreover, in order to check if the used equipment was quantum noise limited, the relation of the relative noise with respect to the detector dose was evaluated. Results showed that in the tomosynthesis acquisition mode the optimal voltage is 28 kV, whereas in standard mammography the optimal voltage is 30 kV. The automatic exposure control (AEC) of the system selects 28 kV as optimal voltage both for DBT and DM. Monte Carlo simulations showed a qualitative agreement with the AEC selection system, since an optimal monochromatic energy of 20 keV was found both for DBT and DM. Moreover, the check about the noise showed that the system is not completely quantum noise limited, and this issue could explain the experimental slight difference in terms of optimal voltage between DBT and DM. According to these results, the use of higher voltage settings is not justified for the improvement of the image quality during a DBT examination.     

Visualizing the internal structure of polyethylene glycol-impregnated wood by digital breast tomosynthesis

This study proposes digital breast tomosynthesis (DBT) as a low-tube-voltage method for imaging wood artifacts treated with polyethylene glycol (PEG). In case of general clinical X-ray Computed Tomography (X-CT), PEG-impregnated wood images typically suffer from low contrast between the PEG and the tree-ring. Because X-CT uses high-tube-voltage X-rays that have high energy, they are transmitted regardless of the X-ray absorption difference of the substance, and therefore, it is not suitable for imaging PEG-impregnated wood. Mammography uses low-tube-voltage X-rays, and therefore, it is suitable for delineating substances with small X-ray absorption differences. However, although mammography can produce high-contrast images of wood, it cannot distinguish three-dimensional (3D) structures such as tree rings, because those are projection images. DBT is a type of mammography used to enhance contrast using low-tube voltage, and it enables imaging 3D structures by exposure X-rays to objects several times changing the exposure angle, and it can obtain quasi-computed tomography. Therefore, we believe that by applying DBT to dendroarchaeology, it would be possible to obtain high-contrast, high-resolution images in the visualization of the internal structure of wood.In this study, we used clinical X-CT, mammography, and DBT to obtain images of wood after PEG impregnation, and we evaluated the internal structure of the wood and the visibility of annual rings. We obtained DBT images as a tomogram with a thickness of 1 mm, which eliminated the distortion of tree rings in the sagittal direction and duplication of the PEG and the tree-ring. Further, tree-rings were easily visualized without a noticeable blur, and the DBT contrast was improved compared to clinical X-CT contrast because DBT was performed at low voltage. Important wooden artifacts excavated from ruins were preserved by PEG. Therefore, this method can be expected to become a very useful tool for dendroarchaeology when used as a complementary tool for microfocus X-CT.     

A deep learning classifier for digital breast tomosynthesis

PurposeTo develop a computerized detection system for the automatic classification of the presence/absence of mass lesions in digital breast tomosynthesis (DBT) annotated exams, based on a deep convolutional neural network (DCNN).Materials and MethodsThree DCNN architectures working at image-level (DBT slice) were compared: two state-of-the-art pre-trained DCNN architectures (AlexNet and VGG19) customized through transfer learning, and one developed from scratch (DBT-DCNN). To evaluate these DCNN-based architectures we analysed their classification performance on two different datasets provided by two hospital radiology departments. DBT slice images were processed following normalization, background correction and data augmentation procedures. The accuracy, sensitivity, and area-under-the-curve (AUC) values were evaluated on both datasets, using receiver operating characteristic curves. A Grad-CAM technique was also implemented providing an indication of the lesion position in the DBT slice.Results Accuracy, sensitivity and AUC for the investigated DCNN are in-line with the best performance reported in the field. The DBT-DCNN network developed in this work showed an accuracy and a sensitivity of (90% ± 4%) and (96% ± 3%), respectively, with an AUC as good as 0.89 ± 0.04. A k-fold cross validation test (with k = 4) showed an accuracy of 94.0% ± 0.2%, and a F1-score test provided a value as good as 0.93 ± 0.03. Grad-CAM maps show high activation in correspondence of pixels within the tumour regions.Conclusions We developed a deep learning-based framework (DBT-DCNN) to classify DBT images from clinical exams. We investigated also a possible application of the Grad-CAM technique to identify the lesion position.     

Digital breast tomosynthesis: Dose and image quality assessment

The aim of this work was to evaluate how different acquisition geometries and reconstruction parameters affect the performance of four digital breast tomosynthesis (DBT) systems (Senographe Essential – GE, Mammomat Inspiration – Siemens, Selenia Dimensions – Hologic and Amulet Innovality – Fujifilm) on the basis of a physical characterization.Average Glandular Dose (AGD) and image quality parameters such as in-plane/in-depth resolution, signal difference to noise ratio (SDNR) and artefact spread function (ASF) were examined.Measured AGD values resulted below EUREF limits for 2D imaging. A large variability was recorded among the investigated systems: the mean dose ratio DBT/2D ranged between 1.1 and 1.9.In-plane resolution was in the range: 2.2 mm⁻¹–3.8 mm⁻¹ in chest wall-nipple direction. A worse resolution was found for all devices in tube travel direction.In-depth resolution improved with increasing scan angle but was also affected by the choice of reconstruction and post-processing algorithms. The highest z-resolution was provided by Siemens (50°, FWHM = 2.3 mm) followed by GE (25°, FWHM = 2.8 mm), while the Fujifilm HR showed the lowest one, despite its wide scan angle (40°, FWHM = 4.1 mm).The ASF was dependent on scan angle: smaller range systems showed wider ASF curves; however a clear relationship was not found between scan angle and ASF, due to the different post processing and reconstruction algorithms.SDNR analysis, performed on Fujifilm system, demonstrated that pixel binning improves detectability for a fixed dose/projection.In conclusion, we provide a performance comparison among four DBT systems under a clinical acquisition mode.     

Variations in slice sensitivity profile for various height settings in tomosynthesis imaging: Phantom study

Understanding the properties of slice sensitivity profile (SSP), or slice thickness, is crucial for an accurate and highly reproducible diagnosis using tomosynthesis imaging. The objectives of the present study are therefore to quantitatively evaluate how the SSP with the use of a small metal bead is affected by different settings of the height from the table and the height of the center of rotation (COR) in tomosynthesis imaging except for the digital breast tomosynthesis, and visually verify the effects on tomosynthesis images. The reconstruction filters used were three types of filtered back-projection and iterative reconstructions. The SSP was measured from the full width at half maximum (FWHM-SSP) of the profile curve of the bead in the perpendicular direction (z direction) relative to the table. Two types of anthropomorphic phantoms simulating the human body, with bones and soft tissues, were used to study the effects of different settings for the COR height. In all reconstruction filters, the FWHM-SSP changed as the height of the bead varied when the bead and COR were set to the same height from the table. If the bead and the COR were set to different heights, the FWHM-SSP increased (decreased) when the height of the bead was set to be greater (less) than the height of the COR. These changes were also confirmed on the anthropomorphic phantom images of the bones and soft tissues.     

Evaluation of the technical performance of three different commercial digital breast tomosynthesis systems in the clinical environment

The aim of this work was to research and evaluate the performance of three different digital breast tomosynthesis (DBT) systems in the clinical environment (Siemens Mammomat Inspiration, Hologic Selenia Dimensions, and Fujifilm Amulet Innovality). The characterization included the study of the detector, the automatic exposure control, and the resolution of DBT projections and reconstructed planes.The modulation transfer function (MTF) of the DBT projections was measured with a 1 mm thick steel edge, showing a strong anisotropy (30–40% lower MTF_0.5 frequencies in the tube travel direction). The in-plane MTF_0.5, measured with a 25 μm tungsten wire, ranges from 1.3 to 1.8 lp/mm in the tube-travel direction and between 2.4 and 3.7 lp/mm in the chest wall–nipple. In the latter direction, the MTF peak shift is more emphasized for large angular range systems (2.0 versus 1.0 lp/mm). In-depth resolution of the planes, via the full width at half maximum (FWHM) from the point spread function of a 25 μm tungsten wire, is not only influenced by angular range and yields 1.3–4.6 mm among systems. The artifact spread function from 1 mm diameter tungsten beads depends mainly on angular range, yielding two tendencies whether large (FWHM is 4.5 mm) or small (FWHM is 10 mm) angular range is used. DBT delivers per scan a mean glandular dose between 1.4 and 2.7 mGy for a 45 mm thick polymethyl methacrylate (PMMA) block.In conclusion, we have identified and analysed specific metrics that can be used for quality assurance of DBT systems.     

A cell-free framework for rapid biosynthetic pathway prototyping and enzyme discovery

Speeding up design-build-test (DBT) cycles is a fundamental challenge facing biochemical engineering. To address this challenge, we report a new cell-free protein synthesis driven metabolic engineering (CFPS-ME) framework for rapid biosynthetic pathway prototyping. In our framework, cell-free cocktails for synthesizing target small molecules are assembled in a mix-and-match fashion from crude cell lysates either containing selectively enriched pathway enzymes from heterologous overexpression or directly producing pathway enzymes in lysates by CFPS. As a model, we apply our approach to n-butanol biosynthesis showing that Escherichia coli lysates support a highly active 17-step CoA-dependent n-butanol pathway in vitro. The elevated degree of flexibility in the cell-free environment allows us to manipulate physiochemical conditions, access enzymatic nodes, discover new enzymes, and prototype enzyme sets with linear DNA templates to study pathway performance. We anticipate that CFPS-ME will facilitate efforts to define, manipulate, and understand metabolic pathways for accelerated DBT cycles without the need to reengineer organisms.     

Proteomics and Metabolomics Analyses to Elucidate the Desulfurization Pathway of Chelatococcus sp.

Desulfurization of dibenzothiophene (DBT) and alkylated DBT derivatives present in transport fuel through specific cleavage of carbon-sulfur (C-S) bonds by a newly isolated bacterium Chelatococcus sp. is reported for the first time. Gas chromatography-mass spectrometry (GC-MS) analysis of the products of DBT degradation by Chelatococcus sp. showed the transient formation of 2-hydroxybiphenyl (2-HBP) which was subsequently converted to 2-methoxybiphenyl (2-MBP) by methylation at the hydroxyl group of 2-HBP. The relative ratio of 2-HBP and 2-MBP formed after 96 h of bacterial growth was determined at 4:1 suggesting partial conversion of 2-HBP or rapid degradation of 2-MBP. Nevertheless, the enzyme involved in this conversion process remains to be identified. This production of 2-MBP rather than 2-HBP from DBT desulfurization has a significant metabolic advantage for enhancing the growth and sulfur utilization from DBT by Chelatococcus sp. and it also reduces the environmental pollution by 2-HBP. Furthermore, desulfurization of DBT derivatives such as 4-M-DBT and 4, 6-DM-DBT by Chelatococcus sp. resulted in formation of 2-hydroxy-3-methyl-biphenyl and 2-hydroxy –3, 3^/- dimethyl-biphenyl, respectively as end product. The GC and X-ray fluorescence studies revealed that Chelatococcus sp. after 24 h of treatment at 37°C reduced the total sulfur content of diesel fuel by 12% by per gram resting cells, without compromising the quality of fuel. The LC-MS/MS analysis of tryptic digested intracellular proteins of Chelatococcus sp. when grown in DBT demonstrated the biosynthesis of 4S pathway desulfurizing enzymes viz. monoxygenases (DszC, DszA), desulfinase (DszB), and an NADH-dependent flavin reductase (DszD). Besides, several other intracellular proteins of Chelatococcus sp. having diverse biological functions were also identified by LC-MS/MS analysis. Many of these enzymes are directly involved with desulfurization process whereas the other enzymes/proteins support growth of bacteria at an expense of DBT. These combined results suggest that Chelatococcus sp. prefers sulfur-specific extended 4S pathway for deep-desulphurization which may have an advantage for its intended future application as a promising biodesulfurizing agent.     

Statistical learning methods as a preprocessing step for survival analysis: evaluation of concept using lung cancer data

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 the proposed method.

Conclusions

The proposed tomosynthesis technique can improve image contrast with aids of 3D whole volume CT images. Even though local tomosynthesis needs extra 3D CT scanning, it may find clinical applications in special situations in which extra 3D CT scan is already available or allowed.     

Evaluating the usefulness of the direct density reconstruction algorithm for intensity modulated and passively scattered proton therapy: Validation using an anthropomorphic phantom

PurposeAccurate calculation of the proton beam range inside a patient is an important topic in proton therapy. In recent times, a computed tomography (CT) image reconstruction algorithm was developed for treatment planning to reduce the impact of the variation of the CT number with changes in imaging conditions. In this study, we investigated the usefulness of this new reconstruction algorithm (DirectDensity™: DD) in proton therapy based on its comparison with filtered back projection (FBP).MethodsWe evaluated the effects of variations in the X-ray tube potential and target size on the FBP- and DD-image values and investigated the usefulness of the DD algorithm based on the range variations and dosimetric quantity variations.ResultsFor X-ray tube potential variations, the range variation in the case of FBP was up to 12.5 mm (20.8%), whereas that of DD was up to 3.3 mm (5.6%). Meanwhile, for target size variations, the range variation in the case of FBP was up to 2.2 mm (2.5%), whereas that of DD was up to 0.9 mm (1.4%). Moreover, the variations observed in the case of DD were smaller than those of FBP for all dosimetric quantities.ConclusionThe dose distributions obtained using DD were more robust against variations in the CT imaging conditions (X-ray tube potential and target size) than those obtained using FBP, and the range variations were often less than the dose calculation grid (2 mm). Therefore, the DD algorithm is effective in a robust workflow and reduces uncertainty in range calculations.     

Homogeneous vs. patient specific breast models for Monte Carlo evaluation of mean glandular dose in mammography

PurposeTo compare, via Monte Carlo simulations, homogeneous and non-homogenous breast models adopted for mean glandular dose (MGD) estimates in mammography vs. patient specific digital breast phantoms.MethodsWe developed a GEANT4 Monte Carlo code simulating four homogenous cylindrical breast models featured as follows: (1) semi-cylindrical section enveloped in a 5-mm adipose layer; (2) semi-elliptical section with a 4-mm thick skin; (3) semi-cylindrical section with a 1.45-mm skin layer; (4) semi-cylindrical section in a 1.45-mm skin layer and 2-mm subcutaneous adipose layer. Twenty patient specific digital breast phantoms produced from a dedicated CT scanner were assumed as reference in the comparison. We simulated two spectra produced from two anode/filter combinations. An additional digital breast phantom was produced via BreastSimulator software.ResultsWith reference to the results for patient-specific breast phantoms and for W/Al spectra, models #1 and #3 showed higher MGD values by about 1% (ranges [–33%; +28%] and [−31%; +30%], respectively), while for model #4 it was 2% lower (range [−34%; +26%]) and for model #2 –11% (range [−39%; +14%]), on average. On the other hand, for W/Rh spectra, models #1 and #4 showed lower MGD values by 2% and 1%, while for model #2 and #3 it was 14% and 8% lower, respectively (ranges [−43%; +13%] and [−41%; +21%]). The simulation with the digital breast phantom produced with BreastSimulator showed a MGD overestimation of +33%.ConclusionsThe homogeneous breast models led to maximum MGD underestimation and overestimation of 43% and 28%, respectively, when compared to patient specific breast phantoms derived from clinical CT scans.     

钼靶X射线与彩色多普勒超声对乳腺癌的影像学特征及诊断价值比较分析

摘要 目的：探讨乳腺癌患者钼靶X射线与彩色多普勒超声（CDUs）的影像学特征及联合应用的诊断价值。方法：前瞻性选取 2018年1月至2021年6月收入安徽医科大学附属巢湖医院且疑似为乳腺癌患者120例,所有患者均接受钼靶X射线与CDUs技术检查,以手术病理为金标准,分别观察钼靶X射线与CDUs对不同大小乳腺癌的诊断价值、比较乳腺癌钼靶X射线与CDUs的影像特征,探讨钼靶X射线及CDUs单独应用及联合应用的诊断效能。结果：120例患者确诊乳腺癌者106例,证实为良性病变者14例。对于不同直径的乳腺癌诊断比较中,CDUs检查直径<1 cm病灶31个（29.25%）,钼靶X射线检查直径<1 cm病灶23个（21.70%）,组间比较具有统计学差异（P<0.05）;对于直径>3 cm病灶,钼靶X射线检查22个（20.75%）,CDUs检查为14个（13.21%）,组间比较具有统计学差异（P<0.05）。乳腺癌钼靶X射线与CDUs的影像特征比较显示,钼靶X射线对于点状微小钙化检查72个（67.92%）、边缘模糊伴毛刺病灶检查84个（79.25%）,二者征象检出率明显高于CDUs检查40个（37.36%）、47个（44.34%）,组间比较具有统计学差异（P<0.05）;CDUs对于肿块影检查个（76.42%）、增粗血管影或血流信号异常病灶检查79个（74.53%）,二者征象检出率明显高于钼靶X射线检查54（50.94%）个、57（53.77%）个,组间比较具有统计学差异（P<0.05）。钼靶X射线及CDUs诊断效能研究显示钼靶X射线联合CDUs技术检查的敏感度、特异度、准确度、阴性预测值（NPV）以及阳性预测值（PPV）分别为93.40%、93.41%、95.83%、64.29%及76.98%,均高于钼靶X射线的83.02%、88.89%、80.19%、15.81%及51.88%,亦高于CDUs技术的78.30%、75.47%、85.83%、28.57%及30.98%,多组数据单因素方差分析具有统计学差异（P<0.05）。结论：钼靶X射线与CDUs技术在诊断乳腺癌方面各有优缺点,二者联合检查利于提升对乳腺癌的诊断准确性,减少误诊漏诊的情况发生。     

Drosophila DBT lacking protein kinase activity produces long-period and arrhythmic circadian behavioral and molecular rhythms

A mutation (K38R) which specifically eliminates kinase activity was created in the Drosophila melanogaster ckI gene (doubletime [dbt]). In vitro, DBT protein carrying the K38R mutation (DBT^K/R) interacted with Period protein (PER) but lacked kinase activity. In cell culture and in flies, DBT^K/R antagonized the phosphorylation and degradation of PER, and it damped the oscillation of PER in vivo. Overexpression of short-period, long-period, or wild-type DBT in flies produced the same circadian periods produced by the corresponding alleles of the endogenous gene. These mutations therefore dictate an altered “set point” for period length that is not altered by overexpression. Overexpression of the DBT^K/R produced effects proportional to the titration of endogenous DBT, with long circadian periods at lower expression levels and arrhythmicity at higher levels. This first analysis of adult flies with a virtual lack of DBT activity demonstrates that DBT's kinase activity is necessary for normal circadian rhythms and that a general reduction of DBT kinase activity does not produce short periods.     

Design and testing of 'genome-proxy' microarrays to profile marine microbial communities

Microarrays are useful tools for detecting and quantifying specific functional and phylogenetic genes in natural microbial communities. In order to track uncultivated microbial genotypes and their close relatives in an environmental context, we designed and implemented a 'genome-proxy' microarray that targets microbial genome fragments recovered directly from the environment. Fragments consisted of sequenced clones from large-insert genomic libraries from microbial communities in Monterey Bay, the Hawaii Ocean Time-series station ALOHA, and Antarctic coastal waters. In a prototype array, we designed probe sets to 13 of the sequenced genome fragments and to genomic regions of the cultivated cyanobacterium Prochlorococcus MED4. Each probe set consisted of multiple 70-mers, each targeting an individual open reading frame, and distributed along each approximately 40-160 kbp contiguous genomic region. The targeted organisms or clones, and close relatives, were hybridized to the array both as pure DNA mixtures and as additions of cells to a background of coastal seawater. This prototype array correctly identified the presence or absence of the target organisms and their relatives in laboratory mixes, with negligible cross-hybridization to organisms having 相似文献   

Pin-photodiode array for the measurement of fan-beam energy and air kerma distributions of X-ray CT scanners

PurposePatient dose estimation in X-ray computed tomography (CT) is generally performed by Monte Carlo simulation of photon interactions within anthropomorphic or cylindrical phantoms. An accurate Monte Carlo simulation requires an understanding of the effects of the bow-tie filter equipped in a CT scanner, i.e. the change of X-ray energy and air kerma along the fan-beam arc of the CT scanner. To measure the effective energy and air kerma distributions, we devised a pin-photodiode array utilizing eight channels of X-ray sensors arranged at regular intervals along the fan-beam arc of the CT scanner.MethodsEach X-ray sensor consisted of two plate type of pin silicon photodiodes in tandem – front and rear photodiodes – and of a lead collimator, which only allowed X-rays to impinge vertically to the silicon surface of the photodiodes. The effective energy of the X-rays was calculated from the ratio of the output voltages of the photodiodes and the dose was calculated from the output voltage of the front photodiode using the energy and dose calibration curves respectively.ResultsThe pin-photodiode array allowed the calculation of X-ray effective energies and relative doses, at eight points simultaneously along the fan-beam arc of a CT scanner during a single rotation of the scanner.ConclusionsThe fan-beam energy and air kerma distributions of CT scanners can be effectively measured using this pin-photodiode array.     

Development and Evaluation of Functional Gene Arrays for Detection of Selected Genes in the Environment

To determine the potential of DNA array technology for assessing functional gene diversity and distribution, a prototype microarray was constructed with genes involved in nitrogen cycling: nitrite reductase (nirS and nirK) genes, ammonia mono-oxygenase (amoA) genes, and methane mono-oxygenase (pmoA) genes from pure cultures and those cloned from marine sediments. In experiments using glass slide microarrays, genes possessing less than 80 to 85% sequence identity were differentiated under hybridization conditions of high stringency (65°C). The detection limit for nirS genes was approximately 1 ng of pure genomic DNA and 25 ng of soil community DNA using our optimized protocol. A linear quantitative relationship (r² = 0.89 to 0.94) was observed between signal intensity and target DNA concentration over a range of 1 to 100 ng for genomic DNA (or genomic DNA equivalent) from both pure cultures and mixed communities. However, the quantitative capacity of microarrays for measuring the relative abundance of targeted genes in complex environmental samples is less clear due to divergent target sequences. Sequence divergence and probe length affected hybridization signal intensity within a certain range of sequence identity and size, respectively. This prototype functional gene array did reveal differences in the apparent distribution of nir and amoA and pmoA gene families in sediment and soil samples. Our results indicate that glass-based microarray hybridization has potential as a tool for revealing functional gene composition in natural microbial communities; however, more work is needed to improve sensitivity and quantitation and to understand the associated issue of specificity.     

Two-dimensional imaging of tumour control probabilities and normal tissue complication probabilities

Aim

To create a presentation method of TCP and NTCP distributions calculated based on dose distribution for a selected CT slice.

Materials and methods

Three 24-bit colour maps – of dose distribution, delineated structures and CT information – were converted into m-by-n-by-3 data arrays, containing intensities of red, green, and blue colour components for each pixel. All calculations were performed with Matlab v.6.5. The transformation function, which consists of five linear functions, was prepared to translate the colour map into a one-dimensional data array of dose values. A menu-driven application based on the transformation function and mathematical models of complication risk (NTCP) and treatment control probability (TCP) was designed to allow pixel-by-pixel translation of colour maps into one-dimensional arrays of TCP and NTCP values.

Results

The result of this work is an application created to visualize the TCP and NTCP distribution for a single CT scan based on the spatial dose distribution calculated in the treatment planning system. The application allows 10 targets (PTV) and 10 organs at risks (OaR) to be defined. The interface allows alpha/beta values to be inserted for each delineated structure. The application computes TCP and NTCP matrices, which are presented as colour maps superimposed on the corresponding CT slice. There is a set of parameters used for TCP/NTCP calculations which can be defined by the user.

Conclusion

Our application is a prototype of an evaluation tool. Although limited to a single plane of the treatment plan, it is believed to be a starting point for further development.