Monitoring Radiofrequency Ablation Using Real-Time Ultrasound Nakagami Imaging Combined with Frequency and Temporal Compounding Techniques

Gas bubbles induced during the radiofrequency ablation (RFA) of tissues can affect the detection of ablation zones (necrosis zone or thermal lesion) during ultrasound elastography. To resolve this problem, our previous study proposed ultrasound Nakagami imaging for detecting thermal-induced bubble formation to evaluate ablation zones. To prepare for future applications, this study (i) created a novel algorithmic scheme based on the frequency and temporal compounding of Nakagami imaging for enhanced ablation zone visualization, (ii) integrated the proposed algorithm into a clinical scanner to develop a real-time Nakagami imaging system for monitoring RFA, and (iii) investigated the applicability of Nakagami imaging to various types of tissues. The performance of the real-time Nakagami imaging system in visualizing RFA-induced ablation zones was validated by measuring porcine liver (n = 18) and muscle tissues (n = 6). The experimental results showed that the proposed algorithm can operate on a standard clinical ultrasound scanner to monitor RFA in real time. The Nakagami imaging system effectively monitors RFA-induced ablation zones in liver tissues. However, because tissue properties differ, the system cannot visualize ablation zones in muscle fibers. In the future, real-time Nakagami imaging should be focused on the RFA of the liver and is suggested as an alternative monitoring tool when advanced elastography is unavailable or substantial bubbles exist in the ablation zone.     

Comparison of methods for staining microvessels in bone

Detection of microvessels is critical for studying bone tissue. We developed an intravascular ink-based method coupled with Van Gieson (VG) staining and compared it with other commonly used methods for capillary visualization. The ink perfusate was formulated as 10% ink, 10% formaldehyde and 20% mannitol. The ink solution was perfused into a healthy goat and the tibia was subjected to decalcification, dehydration, paraffin embedding, de-waxing and staining to observe microvessels. Angiogenesis was assessed by vascular area image analysis and the hematoxylin and eosin (HE), Masson, and VG staining techniques were compared to determine the reliability of these methods for counting microvessels. We found that HE, Masson, and VG staining produced poor contrast between the microvessels and surrounding tissues. By contrast, ink coupled with VG staining permitted clear discrimination between the microvessels and surrounding tissues. Our results indicate that ink-VG staining could be more useful than other methods for detecting tissue microvessels.     

基于遥感的夏季西安城市公园"冷效应"研究

城市公园景观作为城市绿洲区对城市生态环境特别是局地热环境的调节和改善起着极其重要的作用.以热红外遥感数据为信息源,以遥感定量反演和地理信息空间分析技术为支撑,对西安市城区7个主要公园对周边区域热环境的降温效应进行了研究.结果表明:降温幅度(△T)与远离公园的距离(L)两者间呈现非线性的关系特征;不同形态参数的公园对其周边区域的热环境影响不同,公园降温范围与公园绿地面积和水体面积呈现较强的正相关关系;公园水体面积比例≥30％时,其平均降温影响范围和降温幅度均高于水体面积比例低于30％的公园.因此,城市公园建设,不仅要考虑公园面积和形状,亦要考虑水体比例,一般说来,水体面积占公园面积30％以上为佳.基于热红外遥感数据对城市公园影响周边区域的范围和强度进行了定量探讨,所得结论对指导城市公园的规划与建设具有实用价值和参考意义.     

MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis

Shotgun proteomics experiments are dependent upon database search engines to identify peptides from tandem mass spectra. Many of these algorithms score potential identifications by evaluating the number of fragment ions matched between each peptide sequence and an observed spectrum. These systems, however, generally do not distinguish between matching an intense peak and matching a minor peak. We have developed a statistical model to score peptide matches that is based upon the multivariate hypergeometric distribution. This scorer, part of the "MyriMatch" database search engine, places greater emphasis on matching intense peaks. The probability that the best match for each spectrum has occurred by random chance can be employed to separate correct matches from random ones. We evaluated this software on data sets from three different laboratories employing three different ion trap instruments. Employing a novel system for testing discrimination, we demonstrate that stratifying peaks into multiple intensity classes improves the discrimination of scoring. We compare MyriMatch results to those of Sequest and X!Tandem, revealing that it is capable of higher discrimination than either of these algorithms. When minimal peak filtering is employed, performance plummets for a scoring model that does not stratify matched peaks by intensity. On the other hand, we find that MyriMatch discrimination improves as more peaks are retained in each spectrum. MyriMatch also scales well to tandem mass spectra from high-resolution mass analyzers. These findings may indicate limitations for existing database search scorers that count matched peaks without differentiating them by intensity. This software and source code is available under Mozilla Public License at this URL: http://www.mc.vanderbilt.edu/msrc/bioinformatics/.     

Comparison of methods for staining microvessels in bone

Abstract

Detection of microvessels is critical for studying bone tissue. We developed an intravascular ink-based method coupled with Van Gieson (VG) staining and compared it with other commonly used methods for capillary visualization. The ink perfusate was formulated as 10% ink, 10% formaldehyde and 20% mannitol. The ink solution was perfused into a healthy goat and the tibia was subjected to decalcification, dehydration, paraffin embedding, de-waxing and staining to observe microvessels. Angiogenesis was assessed by vascular area image analysis and the hematoxylin and eosin (HE), Masson, and VG staining techniques were compared to determine the reliability of these methods for counting microvessels. We found that HE, Masson, and VG staining produced poor contrast between the microvessels and surrounding tissues. By contrast, ink coupled with VG staining permitted clear discrimination between the microvessels and surrounding tissues. Our results indicate that ink-VG staining could be more useful than other methods for detecting tissue microvessels.     

Thermographic mapping of the skin surface of the head in bald-headed male subjects

Thermal patterns on the skin are related to skin blood perfusion. While knowledge concerning thermal distribution patterns of the face are well established, the thermal distribution patterns of the skin surface of other aspects of the head has only been investigated once previously in a study employing low resolution thermographic equipment [van Dulken, H., van Voss, S.F.C.H, 1971. The normal thermographic patterns of the human head. Acta Neurochir. 23, 247–58.] The purpose of the study was to re-examine the thermal distribution patterns of the surface of the entire head in 12 healthy bald headed male subjects (mean age 39±7.8 (SD) years) using a high definition infrared (IR) thermographic camera. The thermal distribution patterns were monitored using dynamic infrared thermography (DIRT) before, during and after a 2 min local skin cooling procedure with a pair of fans. Infrared thermal images (thermograms) were taken of the superior, anterior, lateral and posterior aspects of the head. The thermal patterns in general followed the anatomical location of the main superficial arteries and veins of the head as described in anatomy books although there were some variations, especially with regard to the forehead and top of the head (superior aspect), ranging from an asymmetrical distribution pattern to a lack of a clear thermal pattern. The thermal patterns in the left and right lateral thermograms in each individual were relatively symmetrical. During the rewarming period the helix, auricular lobule of the auricles and the nose were relatively cold. The frontal thermograms were characterized by cool nasal and cheek areas and a clear warm area surrounding the eyes, especially around the inner canthus.     

蛋白质组学研究中的无标记定量方法

蛋白质定量是探索疾病发生发展状况和寻找新药靶标的重要手段.该领域最常用的技术是比较染色后的二维凝胶上蛋白点的光密度值或综合同位素标记后的质谱峰强度方法.但此二者的样品处理方法都比较麻烦,不利于进行大规模蛋白质组的定量研究.最近几年出现了利用质谱数据进行无标记定量的方法, 根据数据类型这些方法可以分为2类：基于鉴定蛋白的肽段数的方法和基于质谱峰强度的方法,在高通量大规模蛋白组定量研究中有很大优势.本综述主要介绍了这2类无标记定量方法的模型及优缺点,并比较了2类方法的灵敏度和准确度.肽段计数方法在检测蛋白丰度变化时更灵敏,而峰面积强度在评估蛋白比率时更准确.     

Detecting overlapping coding sequences with pairwise alignments

MOTIVATION: Overlapping gene coding sequences (CDSs) are particularly common in viruses but also occur in more complex genomes. Detecting such genes with conventional gene-finding algorithms can be difficult for several reasons. If an overlapping CDS is on the same read-strand as a known CDS, then there may not be a distinct promoter or mRNA. Furthermore, the constraints imposed by double-coding can result in atypical codon biases. However, these same constraints lead to particular mutation patterns that may be detectable in sequence alignments. RESULTS: In this paper, we investigate several statistics for detecting double-coding sequences with pairwise alignments--including a new maximum-likelihood method. We also develop a model for double-coding sequence evolution. Using simulated sequences generated with the model, we characterize the distribution of each statistic as a function of sequence composition, length, divergence time and double-coding frame. Using these results, we develop several algorithms for detecting overlapping CDSs. The algorithms were tested on known overlapping CDSs and other overlapping open reading frames (ORFs) in the hepatitis B virus (HBV), Escherichia coli and Salmonella typhimurium genomes. The algorithms should prove useful for detecting novel overlapping genes--especially short coding ORFs in viruses. AVAILABILITY: Programs may be obtained from the authors. SUPPLEMENTARY INFORMATION: http://biochem.otago.ac.nz/double.html.     

Improved classification of mass spectrometry database search results using newer machine learning approaches

Manual analysis of mass spectrometry data is a current bottleneck in high throughput proteomics. In particular, the need to manually validate the results of mass spectrometry database searching algorithms can be prohibitively time-consuming. Development of software tools that attempt to quantify the confidence in the assignment of a protein or peptide identity to a mass spectrum is an area of active interest. We sought to extend work in this area by investigating the potential of recent machine learning algorithms to improve the accuracy of these approaches and as a flexible framework for accommodating new data features. Specifically we demonstrated the ability of boosting and random forest approaches to improve the discrimination of true hits from false positive identifications in the results of mass spectrometry database search engines compared with thresholding and other machine learning approaches. We accommodated additional attributes obtainable from database search results, including a factor addressing proton mobility. Performance was evaluated using publically available electrospray data and a new collection of MALDI data generated from purified human reference proteins.     

Separate attentional resources for vision and audition

Current models of attention, typically claim that vision and audition are limited by a common attentional resource which means that visual performance should be adversely affected by a concurrent auditory task and vice versa. Here, we test this implication by measuring auditory (pitch) and visual (contrast) thresholds in conjunction with cross-modal secondary tasks and find that no such interference occurs. Visual contrast discrimination thresholds were unaffected by a concurrent chord or pitch discrimination, and pitch-discrimination thresholds were virtually unaffected by a concurrent visual search or contrast discrimination task. However, if the dual tasks were presented within the same modality, thresholds were raised by a factor of between two (for visual discrimination) and four (for auditory discrimination). These results suggest that at least for low-level tasks such as discriminations of pitch and contrast, each sensory modality is under separate attentional control, rather than being limited by a supramodal attentional resource. This has implications for current theories of attention as well as for the use of multi-sensory media for efficient informational transmission.     

Magnetic Resonance Imaging Assessment of Effective Ablated Volume following High Intensity Focused Ultrasound

Under magnetic resonance (MR) guidance, high intensity focused ultrasound (HIFU) is capable of precise and accurate delivery of thermal dose to tissues. Given the excellent soft tissue imaging capabilities of MRI, but the lack of data on the correlation of MRI findings to histology following HIFU, we sought to examine tumor response to HIFU ablation to determine whether there was a correlation between histological findings and common MR imaging protocols in the assessment of the extent of thermal damage. Female FVB mice (n = 34), bearing bilateral neu deletion tumors, were unilaterally insonated under MR guidance, with the contralateral tumor as a control. Between one and five spots (focal size 0.5 × 0.5 × 2.5 mm³) were insonated per tumor with each spot receiving approximately 74.2 J of acoustic energy over a period of 7 seconds. Animals were then imaged on a 7T MR scanner with several protocols. T1 weighted images (with and without gadolinium contrast) were collected in addition to a series of T2 weighted and diffusion weighted images (for later reconstruction into T2 and apparent diffusion coefficient maps), immediately following ablation and at 6, 24, and 48 hours post treatment. Animals were sacrificed at each time point and both insonated/treated and contralateral tumors removed and stained for NADH-diaphorase, caspase 3, or with hematoxylin and eosin (H&E). We found the area of non-enhancement on contrast enhanced T1 weighted imaging immediately post ablation correlated with the region of tissue receiving a thermal dose CEM43 ≥ 240 min. Moreover, while both tumor T2 and apparent diffusion coefficient values changed from pre-ablation values, contrast enhanced T1 weighted images appeared to be more senstive to changes in tissue viability following HIFU ablation.     

3D Stationary electric current density in a spherical tumor treated with low direct current: an analytical solution

Electrotherapy with direct current delivered through implanted electrodes is used for local control of solid tumors in both preclinical and clinical studies. The aim of this research is to develop a solution method for obtaining a three-dimensional analytical expression for potential and electric current density as functions of direct electric current intensity, differences in conductivities between the tumor and the surrounding healthy tissue, and length, number and polarity of electrodes. The influence of these parameters on electric current density in both media is analyzed. The results show that the electric current density in the tumor is higher than that in the surrounding healthy tissue for any value of these parameters. The conclusion is that the solution method presented in this study is of practical interest because it provides, in a few minutes, a convenient way to visualize in 3D the electric current densities generated by a radial electrode array by means of the adequate selection of direct current intensity, length, number, and polarity of electrodes, and the difference in conductivity between the solid tumor and its surrounding healthy tissue.     

MicroCT image based simulation to design heating protocols in magnetic nanoparticle hyperthermia for cancer treatment

ObjectivesThe objective is to design heating protocols to completely damage PC3 tumors after a single magnetic nanoparticle hyperthermia session with minimal collateral thermal damage, based on microCT image generated tumor and mouse models.MethodsTumor geometries and volumetric heat generation rate distributions that are generated from microCT scans in our previous study are imported into COMSOL 4.3® multiphysics for heat transfer simulations and heating protocol design using the Arrhenius damage model. Then, parametric studies are performed to evaluate how significantly the infusion rate affects the protocol design and its resulted collateral thermal damage.ResultsThe simulated temperature field in the generated tumor geometry and volumetric heat generation rate distribution are reasonable and correlates well with the amount of the total thermal energy deposited into the tumors. The time needed for complete thermal damage is determined to be approximately 12 min or 25 min if one uses the Arrhenius integral Ω equal to 1 or 4 as the damage threshold, when the infusion rate is 3 μL/min. The heating time increases 26% or 91% in the higher infusion rate groups of 4 or 5 μL/min, respectively. Collateral thermal damage to the surrounding tissue is also assessed. Although the two larger infusion rate groups can still cause thermal damage to the entire tumor, the collateral thermal damage would have exceeded the design criterion of 5%, while the assessment criterion is acceptable only in the infusion rate group of 3 μL/min. Based on the results of this study, we identify an injection strategy and heating protocols to be implemented in future animal experiments to evaluate treatment efficacy for model validation.     

Automatic tumor-stroma separation in fluorescence TMAs enables the quantitative high-throughput analysis of multiple cancer biomarkers

The upcoming quantification and automation in biomarker based histological tumor evaluation will require computational methods capable of automatically identifying tumor areas and differentiating them from the stroma. As no single generally applicable tumor biomarker is available, pathology routinely uses morphological criteria as a spatial reference system. We here present and evaluate a method capable of performing the classification in immunofluorescence histological slides solely using a DAPI background stain. Due to the restriction to a single color channel this is inherently challenging. We formed cell graphs based on the topological distribution of the tissue cell nuclei and extracted the corresponding graph features. By using topological, morphological and intensity based features we could systematically quantify and compare the discrimination capability individual features contribute to the overall algorithm. We here show that when classifying fluorescence tissue slides in the DAPI channel, morphological and intensity based features clearly outpace topological ones which have been used exclusively in related previous approaches. We assembled the 15 best features to train a support vector machine based on Keratin stained tumor areas. On a test set of TMAs with 210 cores of triple negative breast cancers our classifier was able to distinguish between tumor and stroma tissue with a total overall accuracy of 88%. Our method yields first results on the discrimination capability of features groups which is essential for an automated tumor diagnostics. Also, it provides an objective spatial reference system for the multiplex analysis of biomarkers in fluorescence immunohistochemistry.     

Whole body diffusion for metastatic disease assessment in neuroendocrine carcinomas: comparison with OctreoScan(R) in two cases

ABSTRACT: Neuroendocrine tumor (NET) patients must be adequately staged in order to improve a multidisciplinary approach and optimal management for metastatic disease. Currently available imaging studies include somatostatin receptor scintigraphy, like OctreoScan(R), computed tomography (CT), scans and magnetic resonance imaging (MRI), which analyze vascular concentration and intravenous contrast enhancement for anatomic tumor localization. However, these techniques require high degree of expertise for interpretation and are limited by their availability, cost, reproducibility, and follow-up imaging comparisons. NETs significantly reduce water diffusion as compared to normal tissue. Diffusion-weighted imaging (DWI) in MRI has an advantageous contrast difference: the tumor is represented with high signal over a black normal surrounding background. The whole-body diffusion (WBD) technique has been suggested to be a useful test for detecting metastasis from various anatomic sites. In this article we report the use of DWI in MRI and WBD in two cases of metastatic pulmonary NET staging in comparison with OctreoScan(R) in order to illustrate the potential advantage of DWI and WBD in staging NETs.     

Theoretical temperature distributions produced by an annular phased array-type system in CT-based patient models

Theoretical calculations for the specific absorption rate (SAR) and the resulting temperature distributions produced by an annular phased array (APA)-type system are made. The finite element numerical method is used in the formulation of both the electromagnetic (EM) and thermal boundary value problems. A number of detailed two-dimensional patient models based on CT-scan data from the pelvic, visceral, and thoracic regions are generated to simulate a variety of tumor locations and surrounding normal tissues. The SAR values from the EM solution are put into the bioheat transfer equation, and steady-state temperature distributions are calculated for a wide range of blood flow rates. Based on our theoretical modeling, the APA shows no preferential heating of superficial over deep-seated tumors. However, in most cases for all three regions of the human trunk only fair thermal profiles (therapeutic area near 60%) are obtained in tumors with little or no blood flow and poor temperature patterns (therapeutic area less than 50%) are found in tumors with moderate to high perfusion rates. These theoretical calculations should aid the clinician in the evaluation of the effectiveness of APA-type devices in heating tumors located in the trunk region.     

In vivo characterization of thermal stabilities of Aeropyrum pernix cellular components by differential scanning calorimetry

Revival studies of Aeropyrum pernix show that the viability of cells and cell recovery after heat treatment depends on the temperature of treatment. Differential scanning calorimetry (DSC) is used to analyze the relative thermal stabilities of cellular components of A. pernix and to identify the cellular components responsible for the observed lag phase and reduced maximum growth following a heat treatment. DSC thermograms show 5 visible endothermic transitions with 2 major transitions. DSC analysis of isolated crude ribosomes aids the assignment of the 2 major peaks observed in whole-cell thermograms to denaturation of ribosomal structures. A comparison of partial and immediate full rescan thermograms of A. pernix whole cells indicates that both major peaks represent irreversible thermal transitions. A DNA peak is also identified in the whole-cell thermogram by comparison with the optical data of isolated pure DNA. DNA melting is shown to be irreversible in dilute solution, whereas it is partially reversible in whole cells, owing at least in part, to restricted volume effects. In contrast to mesophilic organisms, hyperthermophilic A. pernix ribosomes are more thermally stable than DNA, but in both organisms, irreversible changes leading to cell death occur owing to ribosomal denaturation.     

What makes a cell face selective? The importance of contrast

Faces are robustly detected by computer vision algorithms that search for characteristic coarse contrast features. Here, we investigated whether face-selective cells in the primate brain exploit contrast features as well. We recorded from face-selective neurons in macaque inferotemporal cortex, while presenting?a face-like collage of regions whose luminances were changed randomly. Modulating contrast combinations between regions induced activity changes ranging from no response to a response greater than that to a real face in 50% of cells. The critical stimulus factor determining response magnitude was contrast polarity, for example, nose region brighter than left eye. Contrast polarity preferences were consistent across cells, suggesting a common computational strategy across the population, and matched features used by computer vision algorithms for face detection. Furthermore, most cells were tuned both for contrast polarity and for the geometry of facial features, suggesting cells encode information useful both for detection and recognition.     

Fluorescence Detection of Free Radicals by Nitroxide Scavenging

The fluorescence quantum yield of 4-(1-napthoyloxy)-2,2,6,6-tetramethylpiperidine-l-oxyl (I) in acetonitrile and hexane is 55 and 30-fold lower, respectively, than those of diamagnetic analogs. Experiments described herein demonstrate that this property makes possible the fluorescence detection of radical scavenging reactions in which the paramagnetic nitroxide-substituted naphthalene is converted to a diamagnetic N-alkoxy derivative. 2-Cyanopropyl free radicals were generated by the thermal decomposition of azobisisobutyronitrile (AIBN) in cyclohexane or in acetonitrile containing 1. The fluorescence intensity of the sample increased proportionally to the decrease in its ESR signal intensity, indicating the conversion of the paramagnetic nitroxide to the diamagnetic product. The linear relationship between the increase in fluorescence intensity and decrease in ESR signal intensity shows that the changes in the fluorescence intensity can serve as a sensitive means for optically detecting radicals.