Radiomics analysis of EPID measurements for patient positioning error detection in thyroid associated ophthalmopathy radiotherapy

PurposeElectronic portal imaging detector (EPID)-based patient positioning verification is an important component of safe radiotherapy treatment delivery. In computer simulation studies, learning-based approaches have proven to be superior to conventional gamma analysis in the detection of positioning errors. To approximate a clinical scenario, the detectability of positioning errors via EPID measurements was assessed using radiomics analysis for patients with thyroid-associated ophthalmopathy.MethodsTreatment plans of 40 patients with thyroid-associated ophthalmopathy were delivered to a solid anthropomorphic head phantom. To simulate positioning errors, combinations of 0-, 2-, and 4-mm translation errors in the left–right (LR), superior-inferior (SI), and anterior-posterior (AP) directions were introduced to the phantom. The positioning errors-induced dose differences between measured portal dose images were used to predict the magnitude and direction of positioning errors. The detectability of positioning errors was assessed via radiomics analysis of the dose differences. Three classification models—support vector machine (SVM), k-nearest neighbors (KNN), and XGBoost—were used for the detection of positioning errors (positioning errors larger or smaller than 3 mm in an arbitrary direction) and direction classification (positioning errors larger or smaller than 3 mm in a specific direction). The receiver operating characteristic curve and the area under the ROC curve (AUC) were used to evaluate the performance of classification models.ResultsFor the detection of positioning errors, the AUC values of SVM, KNN, and XGBoost models were all above 0.90. For LR, SI, and AP direction classification, the highest AUC values were 0.76, 0.91, and 0.80, respectively.ConclusionsCombined radiomics and machine learning approaches are capable of detecting the magnitude and direction of positioning errors from EPID measurements. This study is a further step toward machine learning-based positioning error detection during treatment delivery with EPID measurements.     

Components of error in predictions of species compositional change

Abstract. A method is given for measuring two components of error (rate and direction) in predictions of compositional change through time. Observed compositional change between two times can be represented as a vector between two points in multidimensional species space. The point at the tail of this vector is the species composition at one particular time. A vector of predicted compositional change will diverge from the vector of observed change to some degree. The error in the predicted rate of change is measured by the difference between the lengths of the two vectors. The error in the predicted direction of change is measured by the angle between the vectors. The cosine of this angle is a non-standardized correlation coefficient (r_n) between the predicted and observed species compositions. The quantity 1 - r_n² measures the error in direction of the predicted dynamics without being influenced by the overall rate of change. These measures in Euclidean space have useful counterparts in city-block space. The method is illustrated by comparing actual long-term changes in Midwestern old-growth forests with the changes predicted by a growth and yield model, TWIGS.     

On-line state recognition in a yeast fed-batch culture using error vectors

The physiological states with respect to cell growth and ethanol production in a yeast fed-batch culture expressed in linguistic form could be recognized on-line by fuzzy inferencing based on error vectors. The error vector was newly defined here in a macroscopic elemental balance equation. The physiological states for cell growth and ethanol production were characterized by error vectors using many experimental data from fed-batch cultures. Fuzzy membership functions were constructed from the frequency distributions of the error vectors and state recognition was performed by fuzzy inferencing. In particular, an unusual physiological state for a yeast cultivation, in which aerobic ethanol production was accompanied by very low cell growth, could be recognized accurately. According to the results of the state recognition, an energy parameter, the P/O ratio in the metabolic reaction model was adaptively estimated, and the cell growth was successfully evaluated with the estimated P/O. (c) 1995 John Wiley & Sons, Inc.     

Multiple protein structure alignment.

A method was developed to compare protein structures and to combine them into a multiple structure consensus. Previous methods of multiple structure comparison have only concatenated pairwise alignments or produced a consensus structure by averaging coordinate sets. The current method is a fusion of the fast structure comparison program SSAP and the multiple sequence alignment program MULTAL. As in MULTAL, structures are progressively combined, producing intermediate consensus structures that are compared directly to each other and all remaining single structures. This leads to a hierarchic "condensation," continually evaluated in the light of the emerging conserved core regions. Following the SSAP approach, all interatomic vectors were retained with well-conserved regions distinguished by coherent vector bundles (the structural equivalent of a conserved sequence position). Each bundle of vectors is summarized by a resultant, whereas vector coherence is captured in an error term, which is the only distinction between conserved and variable positions. Resultant vectors are used directly in the comparison, which is weighted by their error values, giving greater importance to the matching of conserved positions. The resultant vectors and their errors can also be used directly in molecular modeling. Applications of the method were assessed by the quality of the resulting sequence alignments, phylogenetic tree construction, and databank scanning with the consensus. Visual assessment of the structural superpositions and consensus structure for various well-characterized families confirmed that the consensus had identified a reasonable core.     

选择标记可去除的植物高效表达载体的构建

在常用的植物组成型表达载体pBI121的选择标记基因NPTII两侧插入同向的lox位点并用多克隆位点(MCS)取代了GUS基因序列,构建了NPTII基因可被去除的和可插入目的基因的通用植物表达载体pBI121-lox-MCS。替换pBI121-lox-MCS中驱动目的基因表达的35S启动子,可构建成一系列具有其他表达特性的植物表达载体,如本文描述的韧皮部特异表达载体pBdENP-lox-MCS。为方便地筛选去除选择标记基因的转基因植物,还构建了绿色荧光蛋白(GFP)表达框与NPTII表达框连锁的pBI121-gfp-lox-MCS载体。上述植物表达载体可广泛应用于培育选择标记可去除的转基因植物。     

A novel Ti-plasmid-convertible λ phage vector system suitable for gene isolation by genetic complementation of Arabidopsis thaliana mutants

A new λ phage vector system, λTI, has been constructed to facilitate genetic complementation of higher plant mutations. The λTI vectors are stable, and by using the Cre— lox site-specific recombination, are automatically convertible into Ti-plasmid binary vectors which are capable of expressing genes in higher plants. Two λTI vectors were constructed: (i) λTI1, which can generate a Ti-plasmid that contains the cauliflower mosaic virus (CaMV) 35S promoter and is suitable for the expression of cDNA in transformed plants and (ii) λTI2, which can generate a Ti-plasmid with the multicloning site (MCS). cDNA and genomic libraries, which were constructed from the cruciferous plant Arabidopsis thaliana in these λTI vectors, can be probed by large DNA fragments of more than 100 kb, such as yeast artificial chromosomes (YACs), enabling the direct screening of the clones in the chromosome region containing a specified genetic locus. These libraries will certainly become powerful tools for the genetic complementation of Arabidopsis mutant phenotypes by quickly providing transformation-competent clones.     

A set of modular plant transformation vectors allowing flexible insertion of up to six expression units

We have constructed a binary vector for Agrobacterium-mediated plant transformation, which has a multiple cloning site consisting of 13 hexanucleotide restriction sites, 6 octanucleotide restriction sites and 5 homing endonuclease sites. The homing endonuclease sites have the advantages to be extremely rare in natural sequences and to allow unidirectional cloning. We have also constructed a set of auxiliary vectors allowing the assembly of expression cassettes flanked by homing endonuclease sites. The expression cassettes assembled in these auxiliary vectors can be transferred into the binary vector with virtually no risk of cutting the vector within previously introduced sequences. This vector set is ideally suited for the construction of plant transformation vectors containing multiple expression cassettes and/or other elements such as matrix attachment regions. With this modular vector system, six different expression units were constructed in as many auxiliary vectors and assembled together in one plant transformation vector. The transgenic nature of Arabidopsis thaliana plants, transformed with this plant transformation vector, was assessed and the expression of each of the six genes was demonstrated.     

Some psychophysics of the pigeon's use of landmarks

1. Three pigeons (Columba livia) were trained to find hidden food in a sunken well (3.3 cm in diameter) at a constant place within an (160 cm x 160 cm) experimental box (Fig. 1). After learning the location, the animals were tested occasionally with the well and food absent. Landmarks in the experimental box might be transformed on such tests. 2. Changing the height or width of a nearby landmark had no systematic influence on the position of peak search. Translating a nearby landmark, however, led to a shift in peak search position. All three birds then searched most somewhere between the original goal location, as defined by the unmoved landmarks, and the goal location as defined by the shifted landmark. Within a limited range of landmark shift, the peak shift as a function of landmark shift is linear (Fig. 3). 3. To explain the data (Fig. 7), the pigeon records at the location of the goal the algebraic vectors from a number of landmarks to the goal. These vectors have both a direction and a distance component. When searching for the goal again in the experimental box, it computes independently for each landmark a navigation vector. This is arrived at by vector-adding the algebraic vector from the bird's current position to the landmark in question, supplied by perception, to the corresponding landmark-goal vector in its record. The pigeon moves in the direction and distance specified by a weighted average of the independently calculated navigation vectors. For positive vector weights, vector geometry guarantees that the bird would search somewhere between the original goal and the goal according to the shifted landmark. The extent to which it shifts toward the shifted goal reflects the vector weight given to the shifted landmark.     

Linear constrain relations in biochemical reaction systems III. Sequential application of data reconciliation for sensitive detection of systematic errors

This article presents a method to test the presence of relatively small systematic measurement errors; e.g., those caused by inaccurate calibration or sensor drift. To do this, primary measurements-flow rates and concentrations-are first translated into observed conversions, which should satisfy several constraints, like the laws of conservation of chemical elements. This study considers three objectives: 1.Modification of the commonly used balancing technique to improve error sensitivity to be able to detect small systematic errors. To this end, the balancing technique is applied sequentially in time.2.Extension of the method to enable direct diagnosis of errors in the primary measurements instead of diagnosing errors in the observed conversions. This was achieved by analyzing how individual errors in the primary measurements are expressed in the residual vector.3.Derivation of a new systematic method to quantitatively determine the sensitivity of the error, is that error size at which the expected value of the chisquare test function equals its critical value.The method is applied to industrial data demonstrating the effectiveness of the approach. It was shown that, for most possible error sources, a systematic errors of 2% to 5% could be detected. In given application, the variation of the N-content of biomass was appointed to be the cause of errors. (c) 1994 John Wiley & Sons, Inc.     

A learned neural network that simulates properties of the neuronal population vector

This paper considers steady-state and timedependent characteristics of the response of the hidden-layer neurons in a dynamic model for the neural network trained through supervised learning to perform transformation of input signals into output signals. This transformation is set up so as to correspond to variation in the directions of two-dimensional vectors and is treated as creation by the network of a movement direction in response to a stimulus direction. The input vector is encoded in the state of the input layer at the initial instant of time, and the output vector in the state of the output layer at great values of time. After the network has been trained on examples of the input-output relation, the hidden neurons turn out to be broadly tuned to direction. The corresponding dependence for their activity is approximated with a smooth function, whose maximum allows some preferred direction to be attributed to each neuron. If each hidden neuron is assigned a vector pointing in its preferred direction, then any arbitrarily chosen direction can be characterized by an imaginary neuronal population vector (Georgopoulos et al. 1986) defined as the sum of the vectors of preferred direction for the neurons, with the weights equal to their activities for the chosen direction. It is demonstrated that, although hidden neurons are broadly tuned to direction, the population vector points in a direction congruent with that of the input vector at the initial moment of time and accurately predicts the direction of the output vector at great values of time. In between, the population vector turns continuously from the one direction towards the other. The dynamic and stationary properties of the population vector of the hidden-layer neurons, as obtained within the framework of the model in question, show a close similarity to the experimentally observed (Georgopoulos et al. 1986; Georgopoulos et al. 1989) behaviour of the population vector constructed in the same manner on the ensemble of motor cortex neurons sensitive to a certain type of movement.     

Simultaneous cloning of open reading frames into several different expression vectors

Genomic sequencing has enabled the prediction of thousands of genes, most of which either cannot be assigned a function or can be only broadly categorized on the basis of sequence alone. High-throughput strategies for elucidating protein function are of high priority, and numerous approaches are being developed. Many of these approaches require the cloning of open reading frames (ORFs) into expression vectors that enable the encoded proteins to be tested for biological and biochemical activities. Typically, more than one type of vector must be employed, as different experiments require different conditions of protein production. Here we show that it is possible to simultaneously transfer a single ORF from a source vector to four target vectors using a commercially available in vitro recombination system. To test the approach, we constructed new vectors for expression of fusion proteins in yeast, including vectors for the LexA two-hybrid system. We show that individual ORFs can be efficiently transferred to four different vectors in a single in vitro reaction. The resulting expression plasmids can be separated using prototrophic markers specific to each vector. Using this system to produce multiple expression constructs simultaneously could greatly facilitate high-throughput subcloning and proteomic studies.     

Evaluation of the ability of three commercially available dosimeters to detect systematic delivery errors in step-and-shoot IMRT plans

BackgroundThere is limited data on error detectability for step-and-shoot intensity modulated radiotherapy (sIMRT) plans, despite significant work on dynamic methods. However, sIMRT treatments have an ongoing role in clinical practice. This study aimed to evaluate variations in the sensitivity of three patient-specific quality assurance (QA) devices to systematic delivery errors in sIMRT plans.Materials and methodsFour clinical sIMRT plans (prostate and head and neck) were edited to introduce errors in: Multi-Leaf Collimator (MLC) position (increasing field size, leaf pairs offset (1–3 mm) in opposite directions; and field shift, all leaves offset (1–3 mm) in one direction); collimator rotation (1–3 degrees) and gantry rotation (0.5–2 degrees). The total dose for each plan was measured using an ArcCHECK diode array. Each field, excluding those with gantry offsets, was also measured using an Electronic Portal Imager and a MatriXX Evolution 2D ionisation chamber array. 132 plans (858 fields) were delivered, producing 572 measured dose distributions. Measured doses were compared to calculated doses for the no-error plan using Gamma analysis with 3%/3 mm, 3%/2 mm, and 2%/2 mm criteria (1716 analyses).ResultsGenerally, pass rates decreased with increasing errors and/or stricter gamma criteria. Pass rate variations with detector and plan type were also observed. For a 3%/3 mm gamma criteria, none of the devices could reliably detect 1 mm MLC position errors or 1 degree collimator rotation errors.ConclusionsThis work has highlighted the need to adapt QA based on treatment plan type and the need for detector specific assessment criteria to detect clinically significant errors.     

THE DIRICHLET-MULTINOMIAL MODEL: ACCOUNTING FOR INTER-TRIAL VARIATION IN REPLICATED RATINGS

Differences in sensory acuity and hedonic reactions to products lead to latent groups in pooled ratings data. Manufacturing locations and time differences also are sources of rating heterogeneity. Intensity and hedonic ratings are ordered categorical data. Categorical responses follow a multinomial distribution and this distribution can be applied to pooled data over trials if the multinomial probabilities are constant from trial to trial. The common test statistic used for comparing vectors of proportions or frequencies is the Pearson chi-square statistic. When ratings data are obtained from repeated ratings experiments or from a cluster sampling procedure, the covariance matrix for the vector of category proportions can differ dramatically from the one assumed for the multinomial model because of inter-trial. This effect is referred to as overdispersion. The standard multinomial model does not fit overdispersed multinomial data. The practical implication of this is that an inflated Type I error can result in a seriously erroneous conclusion. Another implication is that overdispersion is a measurable quantity that may be of interest because it can be used to signal the presence of latent segments. The Dirichlet-Multinomial (DM) model is introduced in this paper to fit overdispersed intensity and hedonic ratings data. Methods for estimating the parameters of the DM model and the test statistics based on them to test against a specified vector or compare vectors of proportions are given. A novel theoretical contribution of this paper is a method for calculating the power of the tests. This method is useful both in evaluating the tests and determining sample size and the number of trials. A test for goodness of fit of the multinomial model against the DM model is also given. The DM model can be extended further to the Generalized Dirichlet-Multinomial (GDM) model, in which multiple sources of variation are considered. The GDM model and its applications are discussed in this paper. Applications of the DM and GDM models in sensory and consumer research are illustrated using numerical examples.     

2个表达单元间相互位置和转录方向对表达的影响

目的:研究质粒表达载体中2个表达单元间相互位置和转录方向关系对表达的影响,找出利于2个表达单元表达的优化的相互关系。方法:以全抗体为研究对象,构建了轻重链方向不同的2种相互关系的单质粒表达载体pIRESdhfrA和pIRESdhfrB,转染CHO-dhfr-细胞后,对瞬时表达水平进行了比较。以pIRESdhfrA和pIRESdhfrB为基础,构建了瞬时表达载体pIRESdhfrA-sv40ori和pIRESdhfrB-sv40ori,在COS-7细胞中进行了瞬时表达水平的比较。构建了基于CHO定点细胞系的稳定表达细胞株,对pIRESdhfrA和pIRESdhfrB进行稳定表达水平的比较。结果:在CHO-dhfr-的瞬时表达水平比较中,pIRESdhfrB转染的细胞表达水平是pIRESdhfrA转染细胞的2.18倍。与pIRESdhfrA-sv40ori在COS-7细胞的瞬时表达水平相比,pIRESdhfrB-sv40ori是其表达水平的2.3倍。pIRESdhfrB-FRT构建的CHO定点细胞平均表达水平是pIRESdhfrA-FRT构建的CHO定点细胞的11.6倍。结论:在构建的真核细胞质粒表达载体pIRESdhfr中,2个表达盒的启动子头-头转录方向关系比头-尾方向关系更利于重组蛋白的表达。     

Simultaneous inference for ratios of linear combinations of general linear model parameters

Consider a general linear model with p -dimensional parameter vector beta and i.i.d. normal errors. Let K(1), ..., K(k ), and L be linearly independent vectors of constants such that L(T)beta not equal 0. We describe exact simultaneous tests for hypotheses that Ki(T)beta/L(T)beta equal specified constants using one-sided and two-sided alternatives, and describe exact simultaneous confidence intervals for these ratios. In the case where the confidence set is a single bounded contiguous set, we describe what we claim are the best possible conservative simultaneous confidence intervals for these ratios - best in that they form the minimum k -dimensional hypercube enclosing the exact simultaneous confidence set. We show that in the case of k = 2, this "box" is defined by the minimum and maximum values for the two ratios in the simultaneous confidence set and that these values are obtained via one of two sources: either from the solutions to each of four systems of equations or at points along the boundary of the simultaneous confidence set where the correlation between two t variables is zero. We then verify that these intervals are narrower than those previously presented in the literature.     

A vector-sum process produces curved aiming paths under rotated visual-motor mappings

Under a 90° rotation of motor space relative to visual space, human two-dimensional aiming movements frequently take the form of smooth arcs such as spirals and semi-circles. A time-independent differential equation explains this tendency in terms of a rotation-induced vector field made up, at each point in the two-dimensional space, of two input vectors. One vector represents a visual error signal and the other represents a motor error signal. A trajectory's instantaneous direction of movement at each point can be described as the resultant of the two vectors. This mathematical formulation incorporates plausible visual-motor mechanisms and, when expressed in polar coordinates, leads to a new method for analyzing the spatial properties of movements (i.e., movement paths). Plots of the angle between the resultant and the target vector () against distance from the target (r, in the polar representation) summarize the arc-shaped movement paths as a simple relation that can be analyzed statistically with respect to properties such as monotonicity. The polar representation is a plausible representation of visually-guided movements, with the visual error vector functioning as an objective function relative to which behavior is optimized. We extend the model and ther, movement path analysis to non-90° rotations, and we find that the model predicts an observed qualitative shift in behavior for rotations greater than 90°. It also predicts qualitatively different path shapes observed under visual-motor reflections.This work was performed while the first author was under the support of Grant IST-8511589 from the National Science Foundation and Grant NCC2-307 from the National Aeronautics and Space Administration     

High efficiency single step production of expression plasmids from cDNA clones using the Flexi Vector cloning system

The success of structural genomics and proteomics initiatives is dependent on the availability of target genes in vectors suitable for protein production. Here, we compare two high-throughput methods for producing expression vectors from plasmid-derived cDNA fragments. Expression vectors were constructed for compatibility with the Gateway recombination cloning system and the Flexi Vector restriction-based cloning system. Cloning protocols for each system were conducted in parallel for 96 different target genes from PCR through the production of sequence-verified expression clones. The short nucleotide sequences required to prepare the target open reading frames for Flexi Vector cloning allowed a single-step PCR protocol, resulting in fewer mutations relative to the Gateway protocol. Furthermore, through initial cloning of the target open reading frames directly into an expression vector, the Flexi Vector system gave time and cost savings compared to the protocol required for the Gateway system. Within the Flexi Vector system, genes were transferred between four different expression vectors. The efficiency of gene transfer between Flexi Vectors depended on including a region of sequence identity adjacent to one of the restriction sites. With the proper construction in the flanking sequence of the vector, gene transfer efficiencies of 95-98% were demonstrated.     

Construction of two recombination yeast two-hybrid vectors by in vitro recombination

Recombination-based restrictionless, ligation-independent cloning has been proven to be advantageous over restriction digestion and ligation cloning. To utilize the recombination cloning and previously constructed two-hybrid cDNA libraries, a new Gateway yeast two-hybrid bait vector, pEZY202, and a new prey vector, pEZY45, were constructed. The two-hybrid vectors were generated by in vitro recombination using a protocol that can be easily adapted for the conversion of other existing vectors. The new vectors were used to assay the interaction between the WW domain of PQBP1 (PQBPww) and the WW domain binding protein WBP11. Both PQBPww and WBP11 were cloned into a Gateway donor vector by in vitro recombination. They were then subcloned into pEZY45 and pEZY202, respectively, by in vitro recombination. The binding between PQBPww and WBP11 was reported in a two-hybrid experiment using the new vectors. The results of testing the new vectors in combination with the original vectors indicated that the new bait vector could be used to screen cDNA libraries that are constructed using the original prey vectors.     

Influence of IMU position and orientation placement errors on ground reaction force estimation

Wearable inertial measurement units (IMU) have been proposed to estimate GRF outside of specialized laboratories, however the precise influence of sensor placement error on accuracy is unknown. We investigated the influence of IMU position and orientation placement errors on GRF estimation accuracy. Methods: Kinematic data from twelve healthy subjects based on marker trajectories were used to simulate 1848 combinations of sensor position placement errors (range ± 100 mm) and orientation placement errors (range ± 25°) across eight body segments (trunk, pelvis, left/right thighs, left/right shanks, and left/right feet) during normal walking trials for baseline cases when a single sensor was misplaced and for the extreme cases when all sensors were simultaneously misplaced. Three machine learning algorithms were used to estimate GRF for each placement error condition and compared with the no placement error condition to evaluate performance. Results: Position placement errors for a single misplaced IMU reduced vertical GRF (VGRF), medio-lateral GRF (MLGRF), and anterior-posterior GRF (APGRF) estimation accuracy by up to 1.1%, 2.0%, and 0.9%, respectively and for all eight simultaneously misplaced IMUs by up to 4.9%, 6.0%, and 4.3%, respectively. Orientation placement errors for a single misplaced IMU reduced VGRF, MLGRF, and APGRF estimation accuracy by up to 4.8%, 7.3%, and 1.5%, respectively and for all eight simultaneously misplaced IMUs by up to 20.8%, 23.4%, and 12.3%, respectively. Conclusion: IMU sensor misplacement, particularly orientation placement errors, can significantly reduce GRF estimation accuracy and thus measures should be taken to account for placement errors in implementations of GRF estimation via wearable IMUs.     

Vector migration and dispersal rates for sylvatic Trypanosoma cruzi transmission

The spread of vector-borne diseases are greatly increased by a vector's ability to migrate. Recent studies of sylvatic Trypanosoma cruzi transmission have motivated the study of vector migration across geographic regions. Due to the natural mechanisms in which vector-borne diseases are transmitted between vectors and hosts, vector dispersal among different host populations is a critical factor in the ability of the parasite to be spread across large regions. In this study we develop a general framework for deriving large-scale, discrete-space migration rates from small-scale, continuous-space dispersal data. We identify three defining characteristics of vector migration: distance, preferred direction of dispersal, and strength of preference for a particular direction. We consider several migration scenarios in which vectors may have no preference for dispersal in a particular direction or may disperse with a preferred direction, such as northeast. We examine what effect preferred direction has on the migration rate, as well as use the local to global framework to calculate numerical estimates for vector migration rates for the primary vectors in the southeast U.S. and northern Mexico, Triatoma sanguisuga and Triatoma gerstaeckeri, based on biological and experimental data. Results from this study can be applied to metapopulation models for species that migrate.