Automation of clip localization in Digital Tomosynthesis for setup of breast cancer patients

The objective of this study is to develop an automatic clip localization procedure for breast cancer patient setup based on Digital Tomosynthesis (DTS) and to characterize its performance with respect to the overall registration accuracy and robustness. The study was performed under an IRB-approved protocol for 12 breast cancer patients with surgical clips implanted around the tumor cavity. The registration of DTS images to planning CTs was performed using an automatic algorithm developed to overcome specific challenges of localization and registration of clips in the breast setup images. The automatic method consisted of auto-segmentation (intensity-based thresholding with a priori knowledge about clip size and location to distinguish clips from bony features) and auto-registration of the segmented clip clusters. To determine the inherent accuracy and robustness of the registration algorithm, additional simulated DTS data was analyzed. The developed algorithm is efficient in removing false positives and negatives and provides an accuracy of better than 2.3 mm for 60° and 3.3 mm for 40° DTS. When incorporated in clinical software, this algorithm helps to facilitate fast and accurate setup evaluation with minimal dose delivered to patients.     

A Four Dimensional Spatio-Temporal Analysis of an Agricultural Dataset

While a variety of statistical models now exist for the spatio-temporal analysis of two-dimensional (surface) data collected over time, there are few published examples of analogous models for the spatial analysis of data taken over four dimensions: latitude, longitude, height or depth, and time. When taking account of the autocorrelation of data within and between dimensions, the notion of closeness often differs for each of the dimensions. Here, we consider a number of approaches to the analysis of such a dataset, which arises from an agricultural experiment exploring the impact of different cropping systems on soil moisture. The proposed models vary in their representation of the spatial correlation in the data, the assumed temporal pattern and choice of conditional autoregressive (CAR) and other priors. In terms of the substantive question, we find that response cropping is generally more effective than long fallow cropping in reducing soil moisture at the depths considered (100 cm to 220 cm). Thus, if we wish to reduce the possibility of deep drainage and increased groundwater salinity, the recommended cropping system is response cropping.     

Evaluation of Four Commercial Multiplex Molecular Tests for the Diagnosis of Acute Respiratory Infections

Acute Respiratory Infections (ARIs) are responsible for considerable morbidity and mortality worldwide. Documentation of respiratory specimens can help for an appropriate clinical management with a significant effect on the disease progress in patient, the antimicrobial therapy used and the risk of secondary spread of infection. Here, we compared the performances of four commercial multiplex kits used in French University Hospital diagnostic microbiology laboratories for the detection of ARI pathogens (i.e., the xTAG Respiratory Viral Panel Fast, RespiFinder SMART 22, CLART PneumoVir and Fast Track Diagnostics Respiratory Pathogen 33 kits). We used a standardised nucleic acids extraction protocol and a comprehensive comparative approach that mixed reference to well established real-time PCR detection techniques and analysis of convergent positive results. We tested 166 respiratory clinical samples and identified a global high degree of correlation for at least three of the techniques (xTAG, RespiFinder and FTD33). For these techniques, the highest Youden’s index (YI), positive predictive (PPV) and specificity (Sp) values were observed for Core tests (e.g., influenza A [YI:0.86–1.00; PPV:78.95–100.00; Sp:97.32–100.00] & B [YI:0.44–1.00; PPV:100.00; Sp:100.00], hRSV [YI:0.50–0.99; PPV:85.71–100.00; Sp:99.38–100.00], hMPV [YI:0.71–1.00; PPV:83.33–100.00; Sp:99.37–100.00], EV/hRV [YI:0.62–0.82; PPV:93.33–100.00; Sp:94.48–100.00], AdV [YI:1.00; PPV:100.00; Sp:100.00] and hBoV [YI:0.20–0.80; PPV:57.14–100.00; Sp:98.14–100.00]). The present study completed an overview of the multiplex techniques available for the diagnosis of acute respiratory infections.     

利用PHI数据进行区域性植物生理信息探测与分析

本次试验研究选择两个实验区 :沼泽地和植被茂盛区。利用 2 0 0 0年 9月上旬在黑龙江省大兴安岭地区获取的推帚式超光谱成像 ,(PHI,pushbroomhyperspectralimager)数据进行区域性植物生理量 (主要是叶绿素 )的探测与生态分析。在叶绿素含量探测中 ,结合所获取的成像光谱PHI数据的特点 ,在比较不同技术方法的基础之上 ,选用了有效而简单可靠的RARS(Ratioanalysisofreflectancespectra)指数。该色素指数与植物叶绿素a、b含量拟合的相关系数 (R)达 0 .8以上。利用PHI数据和野外实测植物光谱分别建立沼泽地和植被茂盛区的RARS指数模式 ,分别得到具有指示两试验区的叶绿素a (Chla)、叶绿素b (Chlb)以及类胡萝卜素 (Cars)的参数图像。更进一步地利用Blackburn(1998)所建立的RARS指数与叶绿素浓度之间的强拟合方程 ,相对定量估算了叶绿素a、b浓度的区域性分布 ,清晰地反映出植被生态状况和差异。这与野外实地考察较为一致。     

Motion Tracker: Camera-Based Monitoring of Bodily Movements Using Motion Silhouettes

Researchers in the cognitive and affective sciences investigate how thoughts and feelings are reflected in the bodily response systems including peripheral physiology, facial features, and body movements. One specific question along this line of research is how cognition and affect are manifested in the dynamics of general body movements. Progress in this area can be accelerated by inexpensive, non-intrusive, portable, scalable, and easy to calibrate movement tracking systems. Towards this end, this paper presents and validates Motion Tracker, a simple yet effective software program that uses established computer vision techniques to estimate the amount a person moves from a video of the person engaged in a task (available for download from http://jakory.com/motion-tracker/). The system works with any commercially available camera and with existing videos, thereby affording inexpensive, non-intrusive, and potentially portable and scalable estimation of body movement. Strong between-subject correlations were obtained between Motion Tracker’s estimates of movement and body movements recorded from the seat (r =.720) and back (r = .695 for participants with higher back movement) of a chair affixed with pressure-sensors while completing a 32-minute computerized task (Study 1). Within-subject cross-correlations were also strong for both the seat (r =.606) and back (r = .507). In Study 2, between-subject correlations between Motion Tracker’s movement estimates and movements recorded from an accelerometer worn on the wrist were also strong (rs = .801, .679, and .681) while people performed three brief actions (e.g., waving). Finally, in Study 3 the within-subject cross-correlation was high (r = .855) when Motion Tracker’s estimates were correlated with the movement of a person’s head as tracked with a Kinect while the person was seated at a desk (Study 3). Best-practice recommendations, limitations, and planned extensions of the system are discussed.     

Visualisation of Respiratory Tumour Motion and Co-Moving Isodose Lines in the Context of Respiratory Gating,IMRT and Flattening-Filter-Free Beams

Respiratory motion during percutaneous radiotherapy can be considered based on respiration-correlated computed tomography (4DCT). However, most treatment planning systems perform the dose calculation based on a single primary CT data set, even though cine mode displays may allow for a visualisation of the complete breathing cycle. This might create the mistaken impression that the dose distribution were independent of tumour motion. We present a movie visualisation technique with the aim to direct attention to the fact that the dose distribution migrates to some degree with the tumour and discuss consequences for gated treatment, IMRT plans and flattening-filter-free beams. This is a feasibility test for a visualisation of tumour and isodose motion. Ten respiratory phases are distinguished on the CT, and the dose distribution from a stationary IMRT plan is calculated on each phase, to be integrated into a movie of tumour and dose motion during breathing. For one example patient out of the sample of five lesions, the plan is compared with a gated treatment plan with respect to tumour coverage and lung sparing. The interplay-effect for small segments in the IMRT plan is estimated. While the high dose rate, together with the cone-shaped beam profile, makes the use of flattening-filter-free beams more problematic for conformal and IMRT treatment, it can be the option of choice if gated treatment is preferred. The different effects of respiratory motion, dose build-up and beam properties (segments and flatness) for gated vs. un-gated treatment can best be considered if planning is performed on the full 4DCT data set, which may be an incentive for future developments of treatment planning systems.     

Improved and Robust Detection of Cell Nuclei from Four Dimensional Fluorescence Images

Segmentation-free direct methods are quite efficient for automated nuclei extraction from high dimensional images. A few such methods do exist but most of them do not ensure algorithmic robustness to parameter and noise variations. In this research, we propose a method based on multiscale adaptive filtering for efficient and robust detection of nuclei centroids from four dimensional (4D) fluorescence images. A temporal feedback mechanism is employed between the enhancement and the initial detection steps of a typical direct method. We estimate the minimum and maximum nuclei diameters from the previous frame and feed back them as filter lengths for multiscale enhancement of the current frame. A radial intensity-gradient function is optimized at positions of initial centroids to estimate all nuclei diameters. This procedure continues for processing subsequent images in the sequence. Above mechanism thus ensures proper enhancement by automated estimation of major parameters. This brings robustness and safeguards the system against additive noises and effects from wrong parameters. Later, the method and its single-scale variant are simplified for further reduction of parameters. The proposed method is then extended for nuclei volume segmentation. The same optimization technique is applied to final centroid positions of the enhanced image and the estimated diameters are projected onto the binary candidate regions to segment nuclei volumes.Our method is finally integrated with a simple sequential tracking approach to establish nuclear trajectories in the 4D space. Experimental evaluations with five image-sequences (each having 271 3D sequential images) corresponding to five different mouse embryos show promising performances of our methods in terms of nuclear detection, segmentation, and tracking. A detail analysis with a sub-sequence of 101 3D images from an embryo reveals that the proposed method can improve the nuclei detection accuracy by 9 over the previous methods, which used inappropriate large valued parameters. Results also confirm that the proposed method and its variants achieve high detection accuracies ( 98 mean F-measure) irrespective of the large variations of filter parameters and noise levels.     

机械通气救治4例银环蛇咬伤急性呼吸衰竭

目的 探讨机械通气救治银环蛇咬伤致急性呼吸衰竭的治疗效果。方法 院前正确清创急救处理,及时行机械通气救治4例银环蛇咬伤致急性呼吸衰竭患者。结果 气管内插管是最佳的气道开放方法,气管插管者辅助通气4～6h后撤机及拔管可获得成功。结论 正确急救和清创,气管内插管及机械通气是救治银环蛇咬伤致急性呼吸衰竭的最有效的方法。     

碱裂解法提取重组质粒DNA及PCR验证

目的:筛选获得高质量质粒,为进一步克隆、测序奠定基础.方法:采用常规的碱裂解法从大肠杆菌重组质粒中提取质粒DNA,核酸检测仪测定提取质粒DNA产量和纯度,并用前期DDRT-PCR时采用的引物进行PCR验证性实验,琼脂糖凝胶电泳检测,并对电泳图谱加以分析和鉴定.结果:利用常规的碱裂解法提取重组质粒,通过酚和氯仿的抽提,可以有效地去除蛋白质杂质,用含有Rnase抑制剂的无菌水溶解质粒提取效果最好,得到的质粒DNA无RNA污染,纯度比较高,OD260/OD280比值介于1.8～2.0之间,OD260/OD230比值大于2.0,经PCR反应验证后与预计相符.结论:通过该方法获得的重组质粒纯度和浓度都比较高,且PCR验证与预计相一致,可以满足后续分子生物学实验的要求.     

Evaluation of Exploration and Monitoring Methods for Verification of Natural Attenuation Using the Virtual Aquifer Approach

Though natural attenuation (NA) is increasingly considered as a remediation technology, the methods for proper identification and quantification of NA are still under discussion. Here the "Virtual Aquifer" approach is used to demonstrate problems which may arise during measurement of concentrations in observation wells and for interpolation of locally measured concentrations in contaminated heterogeneous aquifers. The misinterpretation of measured concentrations complicates the identification and quantification of natural attenuation processes. The "Virtual Aquifer" approach accepts the plume simulated with a numerical model for a heterogeneous aquifer as "virtual reality". This virtual plume is investigated in the model with conventional methods like observations wells. The results of the investigation can be compared to the virtual "reality", evaluating the monitoring method. Locally determined concentrations are interpolated using various interpolation methods and different monitoring set-ups. The interpolation results are compared to the simulated plume to evaluate the quality of interpolation. This evaluation is not possible in nature, since concentrations in a heterogeneous aquifer are never known in detail.     

Evaluation of Breathing Pattern: Comparison of a Manual Assessment of Respiratory Motion (MARM) and Respiratory Induction Plethysmography

Altered breathing pattern is an aspect of dysfunctional breathing but few standardised techniques exist to evaluate it. This study investigates a technique for evaluating and quantifying breathing pattern, called the Manual Assessment of Respiratory Motion (MARM) and compares it to measures performed with Respiratory Induction Plethysmography (RIP). About 12 subjects altered their breathing and posture while 2 examiners assessed their breathing using the MARM. Simultaneous measurements with RIP were taken. Inter-examiner agreement and agreement between MARM and RIP were assessed. The ability of the measurement methods to differentiate between diverse breathing and postural patterns was compared. High levels of agreement between examiners were found with the MARM for measures of the upper rib cage relative to lower rib cage/abdomen motion during breathing but not for measures of volume. The measures of upper rib cage dominance during breathing correlated with similar measures obtained from RIP. Both RIP and MARM measures methods were able to differentiate between abdominal and thoracic breathing patterns, but only MARM was able to differentiate between breathing changes occurring as result of slumped versus erect sitting posture. This study suggests that the MARM is a reliable clinical tool for assessing breathing pattern.     

Dosimetric Verification by Using the ArcCHECK System and 3DVH Software for Various Target Sizes

Objective

To investigate the usefulness of the 3DVH software with an ArcCHECK 3D diode array detector in newly designed plans with various target sizes.

Methods

The isocenter dose was measured with an ion-chamber and was compared with the planned and 3DVH predicted doses. The 2D gamma passing rates were evaluated at the diode level by using the ArcCHECK detector. The 3D gamma passing rates for specific regions of interest (ROIs) were also evaluated by using the 3DVH software. Several dose-volume histograms (DVH)-based predicted metrics for all structures were also obtained by using the 3DVH software.

Results

The isocenter dose deviation was <1% in all plans except in the case of a 1 cm target. Besides the gamma passing rate at the diode level, the 3D gamma passing rate for specific ROIs tended to decrease with increasing target size; this was more noticeable when a more stringent gamma criterion was applied. No correlation was found with the gamma passing rates and the DVH-based metrics especially in the ROI with high-dose gradients.

Conclusions

Delivery quality assurance by using 3DVH and ArcCHECK can provide substantial information through a simple and easy approach, although the accuracy of this system should be judged cautiously.     

Modelling Adaptation to Directional Motion Using the Adelson-Bergen Energy Sensor

The motion energy sensor has been shown to account for a wide range of physiological and psychophysical results in motion detection and discrimination studies. It has become established as the standard computational model for retinal movement sensing in the human visual system. Adaptation effects have been extensively studied in the psychophysical literature on motion perception, and play a crucial role in theoretical debates, but the current implementation of the energy sensor does not provide directly for modelling adaptation-induced changes in output. We describe an extension of the model to incorporate changes in output due to adaptation. The extended model first computes a space-time representation of the output to a given stimulus, and then a RC gain-control circuit (“leaky integrator”) is applied to the time-dependent output. The output of the extended model shows effects which mirror those observed in psychophysical studies of motion adaptation: a decline in sensor output during stimulation, and changes in the relative of outputs of different sensors following this adaptation.     

Effective Treatment of Respiratory Alphaherpesvirus Infection Using RNA Interference

Background

Equine herpesvirus type 1 (EHV-1), a member of the Alphaherpesvirinae, is spread via nasal secretions and causes respiratory disease, neurological disorders and abortions. The virus is a significant equine pathogen, but current EHV-1 vaccines are only partially protective and effective metaphylactic and therapeutic agents are not available. Small interfering RNAs (siRNA''s), delivered intranasally, could prove a valuable alternative for infection control. siRNA''s against two essential EHV-1 genes, encoding the viral helicase (Ori) and glycoprotein B, were evaluated for their potential to decrease EHV-1 infection in a mouse model.

Methodology/Principal Fndings

siRNA therapy in vitro significantly reduced virus production and plaque size. Viral titers were reduced 80-fold with 37.5 pmol of a single siRNA or with as little as 6.25 pmol of each siRNA when used in combination. siRNA therapy in vivo significantly reduced viral replication and clinical signs. Intranasal treatment did not require a transport vehicle and proved effective when given up to 12 h before or after infection.

Conclusions/Significance

siRNA treatment has potential for both prevention and early treatment of EHV-1 infections.     

Regularized Sandwich Estimators for Analysis of High‐Dimensional Data Using Generalized Estimating Equations

Summary A modification of generalized estimating equations (GEEs) methodology is proposed for hypothesis testing of high‐dimensional data, with particular interest in multivariate abundance data in ecology, an important application of interest in thousands of environmental science studies. Such data are typically counts characterized by high dimensionality (in the sense that cluster size exceeds number of clusters, n>K) and over‐dispersion relative to the Poisson distribution. Usual GEE methods cannot be applied in this setting primarily because sandwich estimators become numerically unstable as n increases. We propose instead using a regularized sandwich estimator that assumes a common correlation matrix R , and shrinks the sample estimate of R toward the working correlation matrix to improve its numerical stability. It is shown via theory and simulation that this substantially improves the power of Wald statistics when cluster size is not small. We apply the proposed approach to study the effects of nutrient addition on nematode communities, and in doing so discuss important issues in implementation, such as using statistics that have good properties when parameter estimates approach the boundary (), and using resampling to enable valid inference that is robust to high dimensionality and to possible model misspecification.     

Digital Computer Simulation of Respiratory Response to Cerebrospinal Fluid PCO2 in the Cat

The respiratory control system is treated as linear with a transmission delay between ventilation and sensing points (chemoreceptors). To the accepted variables involving body gas stores, ventilatory effects, transmission effects, and steady state pH, P(CO2), P(O2) chemoreceptor response, certain detailed analysis of the central receptors have been added. By construction of a model for medullary CO(2) receptor utilizing expected values of CNS (central nervous system) circulation, CO(2) production, and tissue-buffering effects, results of experimental observation of the effects of alteration of CSF were simulated. The inclusion of CSF effects also allowed simulation of the response to alteration in inspired CO(2), hyperventilation, and the periodic breathing with prolongation of circulation time.     

Characterization of Respiratory and Cardiac Motion from Electro-Anatomical Mapping Data for Improved Fusion of MRI to Left Ventricular Electrograms

Accurate fusion of late gadolinium enhancement magnetic resonance imaging (MRI) and electro-anatomical voltage mapping (EAM) is required to evaluate the potential of MRI to identify the substrate of ventricular tachycardia. However, both datasets are not acquired at the same cardiac phase and EAM data is corrupted with respiratory motion limiting the accuracy of current rigid fusion techniques. Knowledge of cardiac and respiratory motion during EAM is thus required to enhance the fusion process. In this study, we propose a novel approach to characterize both cardiac and respiratory motion from EAM data using the temporal evolution of the 3D catheter location recorded from clinical EAM systems. Cardiac and respiratory motion components are extracted from the recorded catheter location using multi-band filters. Filters are calibrated for each EAM point using estimates of heart rate and respiratory rate. The method was first evaluated in numerical simulations using 3D models of cardiac and respiratory motions of the heart generated from real time MRI data acquired in 5 healthy subjects. An accuracy of 0.6–0.7 mm was found for both cardiac and respiratory motion estimates in numerical simulations. Cardiac and respiratory motions were then characterized in 27 patients who underwent LV mapping for treatment of ventricular tachycardia. Mean maximum amplitude of cardiac and respiratory motion was 10.2±2.7 mm (min = 5.5, max = 16.9) and 8.8±2.3 mm (min = 4.3, max = 14.8), respectively. 3D Cardiac and respiratory motions could be estimated from the recorded catheter location and the method does not rely on additional imaging modality such as X-ray fluoroscopy and can be used in conventional electrophysiology laboratory setting.