Statistical process control for electron beam monitoring

PurposeTo assess the electron beam monitoring statistical process control (SPC) in linear accelerator (linac) daily quality control. We present a long-term record of our measurements and evaluate which SPC-led conditions are feasible for maintaining control.MethodsWe retrieved our linac beam calibration, symmetry, and flatness daily records for all electron beam energies from January 2008 to December 2013, and retrospectively studied how SPC could have been applied and which of its features could be used in the future. A set of adjustment interventions designed to maintain these parameters under control was also simulated.ResultsAll phase I data was under control. The dose plots were characterized by rising trends followed by steep drops caused by our attempts to re-center the linac beam calibration. Where flatness and symmetry trends were detected they were less-well defined. The process capability ratios ranged from 1.6 to 9.3 at a 2% specification level. Simulated interventions ranged from 2% to 34% of the total number of measurement sessions. We also noted that if prospective SPC had been applied it would have met quality control specifications.ConclusionsSPC can be used to assess the inherent variability of our electron beam monitoring system. It can also indicate whether a process is capable of maintaining electron parameters under control with respect to established specifications by using a daily checking device, but this is not practical unless a method to establish direct feedback from the device to the linac can be devised.     

Immunocytochemical staining of effusions; an external quality control study in The Netherlands

Immunocytochemical staining of effusions; an external quality control study in The Netherlands
In The Netherlands an external quality control study of immunocytochemical (IC) staining of effusions was initiated, consisting of three test rounds. The 12 participating laboratories received samples of malignant effusions (runs 1, 2 and 3), and five unstained control specimens prepared from the same material in runs 2 and 3. The laboratories used their own protocols to prepare and stain the samples ('in‐house' specimens). Two persons viewed and scored the slides following preset criteria concerning number and morphology of diagnostic cells, background staining and staining specificity. Better scoring results were found for control specimens, compared with 'in‐house' specimens, primarily caused by cell loss in the latter. This finding underlines the view that high quality IC needs well organized processing and staining procedures, and warrants external quality control systems.     

Adaptive data collection for intraindividual studies affected by adherence

Recently, the use of mobile technologies in ecological momentary assessments (EMAs) and interventions has made it easier to collect data suitable for intraindividual variability studies in the medical field. Nevertheless, especially when self-reports are used during the data collection process, there are difficulties in balancing data quality and the burden placed on the subject. In this paper, we address this problem for a specific EMA setting that aims to submit a demanding task to subjects at high/low values of a self-reported variable. We adopt a dynamic approach inspired by control chart methods and design optimization techniques to obtain an EMA triggering mechanism for data collection that considers both the individual variability of the self-reported variable and of the adherence. We test the algorithm in both a simulation setting and with real, large-scale data from a tinnitus longitudinal study. A Wilcoxon signed rank test shows that the algorithm tends to have both a higher F₁ score and utility than a random schedule and a rule-based algorithm with static thresholds, which are the current state-of-the-art approaches. In conclusion, the algorithm is proven effective in balancing data quality and the burden placed on the participants, especially in studies where data collection is impacted by adherence.     

Prediction bands and intervals for the scapulo-humeral coordination based on the Bootstrap and two Gaussian methods

Quantitative motion analysis protocols have been developed to assess the coordination between scapula and humerus. However, the application of these protocols to test whether a subject's scapula resting position or pattern of coordination is “normal”, is precluded by the unavailability of reference prediction intervals and bands, respectively. The aim of this study was to present such references for the “ISEO” protocol, by using the non-parametric Bootstrap approach and two parametric Gaussian methods (based on Student's T and Normal distributions).     

Raman spectroscopy and chemometrics for on‐line control of glucose fermentation by Saccharomyces cerevisiae

This work presents the use of Raman spectroscopy and chemometrics for on‐line control of the fermentation process of glucose by Saccharomyces cerevisiae. In a first approach, an on‐line determination of glucose, ethanol, glycerol, and cells was accomplished using multivariate calibration based on partial least squares (PLS). The PLS models presented values of root mean square error of prediction (RMSEP) of 0.53, 0.25, and 0.02% for glucose, ethanol and glycerol, respectively, and RMSEP of 1.02 g L^?1 for cells. In a second approach, multivariate control charts based on multiway principal component analysis (MPCA) were developed for detection of fermentation fault‐batch. Two multivariate control charts were developed, based on the squared prediction error (Q) and Hotelling's T². The use of the Q control chart in on‐line monitoring was efficient for detection of the faults caused by temperature, type of substrate and contamination, but the T² control chart was not able to monitor these faults. On‐line monitoring by Raman spectroscopy in conjunction with chemometric procedures allows control of the fermentative process with advantages in relation to reference methods, which require pretreatment, manipulation of samples and are time consuming. Also, the use of multivariate control charts made possible the detection of faults in a simple way, based only on the spectra of the system. © 2012 American Institute of Chemical Engineers Biotechnol. Prog., 2012     

Predictive feedback in human simulated pendulum balancing

In studies of human balance, it is common to fit stimulus-response data by tuning the time-delay and gain parameters of a simple delayed feedback model. Many interpret this fitted model, a simple delayed feedback model, as evidence that predictive processes are not required to explain existing data on standing balance. However, two questions lead us to doubt this approach. First, does fitting a delayed feedback model lead to reliable estimates of the time-delay? Second, can a non-predictive controller provide an explanation compatible with the independently estimated time delay? For methodological and experimental clarity, we study human balancing of a simulated inverted pendulum via joystick and screen. A two-step approach to data analysis is used: firstly a non-parametric model—the closed-loop impulse response—is estimated from the experimental data; second, a parametric model is fitted to the non-parametric impulse-response by adjusting time-delay and controller parameters. To support the second step, a new explicit formula relating controller parameters to closed-loop impulse response is derived. Two classes of controller are investigated within a common state-space context: non-predictive and predictive. It is found that the time-delay estimate arising from the second step is strongly dependent on which controller class is assumed; in particular, the non-predictive control assumption leads to time-delay estimates that are smaller than those arising from the predictive assumption. Moreover, the time-delays estimated using the non-predictive control assumption are not consistent with a lower-bound on the time-delay of the non-parametric model whereas the corresponding predictive result is consistent. Thus while the goodness of fit only marginally favoured predictive over non-predictive control, if we add the additional constraint that the model must reproduce the non-parametric time delay, then the non-predictive control model fails. We conclude (1) the time-delay should be estimated independently of fitting a low order parametric model, (2) that balance of the simulated inverted pendulum could not be explained by the non-predictive control model and (3) that predictive control provided a better explanation than non-predictive control.     

Advanced control of dissolved oxygen concentration in fed batch cultures during recombinant protein production

Design and experimental validation of advanced pO₂ controllers for fermentation processes operated in the fed-batch mode are described. In most situations, the presented controllers are able to keep the pO₂ in fermentations for recombinant protein productions exactly on the desired value. The controllers are based on the gain-scheduling approach to parameter-adaptive proportional-integral controllers. In order to cope with the most often appearing distortions, the basic gain-scheduling feedback controller was complemented with a feedforward control component. This feedforward/feedback controller significantly improved pO₂ control. By means of numerical simulations, the controller behavior was tested and its parameters were determined. Validation runs were performed with three Escherichia coli strains producing different recombinant proteins. It is finally shown that the new controller leads to significant improvements in the signal-to-noise ratio of other key process variables and, thus, to a higher process quality.     

Investigation of Design Space for Freeze-Drying: Use of Modeling for Primary Drying Segment of a Freeze-Drying Cycle

In this work, we explore the idea of using mathematical models to build design space for the primary drying portion of freeze-drying process. We start by defining design space for freeze-drying, followed by defining critical quality attributes and critical process parameters. Then using mathematical model, we build an insilico design space. Input parameters to the model (heat transfer coefficient and mass transfer resistance) were obtained from separate experimental runs. Two lyophilization runs are conducted to verify the model predictions. This confirmation of the model predictions with experimental results added to the confidence in the insilico design space. This simple step-by-step approach allowed us to minimize the number of experimental runs (preliminary runs to calculate heat transfer coefficient and mass transfer resistance plus two additional experimental runs to verify model predictions) required to define the design space. The established design space can then be used to understand the influence of critical process parameters on the critical quality attributes for all future cycles.     

Hypothesis testing in high-throughput screening for drug discovery

Following the success of small-molecule high-throughput screening (HTS) in drug discovery, other large-scale screening techniques are currently revolutionizing the biological sciences. Powerful new statistical tools have been developed to analyze the vast amounts of data in DNA chip studies, but have not yet found their way into compound screening. In HTS, characterization of single-point hit lists is often done only in retrospect after the results of confirmation experiments are available. However, for prioritization, for optimal use of resources, for quality control, and for comparison of screens it would be extremely valuable to predict the rates of false positives and false negatives directly from the primary screening results. Making full use of the available information about compounds and controls contained in HTS results and replicated pilot runs, the Z score and from it the p value can be estimated for each measurement. Based on this consideration, we have applied the concept of p-value distribution analysis (PVDA), which was originally developed for gene expression studies, to HTS data. PVDA allowed prediction of all relevant error rates as well as the rate of true inactives, and excellent agreement with confirmation experiments was found.     

一种自优化RBF神经网络的叶绿素a浓度时序预测模型

藻类水华发生过程具有复杂性、非线性、时变性等特点,其准确预测一直是一个国际性难题.以天津市于桥水库为研究对象,根据2000年1月至2003年12月常规监测的水生生态数据(采样周期为10 d),提出了一种结合时序方法的可自优化RBF神经网络智能预测模型,对判断藻类水华的重要指标叶绿素a浓度进行预测.研究了训练样本量及RBF神经网络扩展速度SPREAD值的可自优化性能,以及该模型用于于桥水库叶绿素a浓度的短期变化趋势预测的可行性.结果表明,预测性能指标随SPREAD值及样本量不同发生变化,该预测模型能自动寻到最优SPREAD值,并发现至少需要约两年的训练样本量才能达到较好预测效果.当样本量为105,SPREAD值为10时,预测效果最好,精度较高,预测值与实测值的相关系数R达到0.982.该方法对水库的藻类水华预警有一定的参考价值.     

Identifying and Seeing beyond Multiple Sequence Alignment Errors Using Intra-Molecular Protein Covariation

Background

There is currently no way to verify the quality of a multiple sequence alignment that is independent of the assumptions used to build it. Sequence alignments are typically evaluated by a number of established criteria: sequence conservation, the number of aligned residues, the frequency of gaps, and the probable correct gap placement. Covariation analysis is used to find putatively important residue pairs in a sequence alignment. Different alignments of the same protein family give different results demonstrating that covariation depends on the quality of the sequence alignment. We thus hypothesized that current criteria are insufficient to build alignments for use with covariation analyses.

Methodology/Principal Findings

We show that current criteria are insufficient to build alignments for use with covariation analyses as systematic sequence alignment errors are present even in hand-curated structure-based alignment datasets like those from the Conserved Domain Database. We show that current non-parametric covariation statistics are sensitive to sequence misalignments and that this sensitivity can be used to identify systematic alignment errors. We demonstrate that removing alignment errors due to 1) improper structure alignment, 2) the presence of paralogous sequences, and 3) partial or otherwise erroneous sequences, improves contact prediction by covariation analysis. Finally we describe two non-parametric covariation statistics that are less sensitive to sequence alignment errors than those described previously in the literature.

Conclusions/Significance

Protein alignments with errors lead to false positive and false negative conclusions (incorrect assignment of covariation and conservation, respectively). Covariation analysis can provide a verification step, independent of traditional criteria, to identify systematic misalignments in protein alignments. Two non-parametric statistics are shown to be somewhat insensitive to misalignment errors, providing increased confidence in contact prediction when analyzing alignments with erroneous regions because of an emphasis on they emphasize pairwise covariation over group covariation.     

Model-based clustering of binary longitudinal atopic dermatitis disease histories by latent class mixture models

Atopic dermatitis is a skin disease which affects mainly children, has a very strong genetical component, and manifests itself clinically as flexural excema in connection with torturing itching. The course of disease is notoriously changeable and runs in phases, therefore it is difficult to predict the future course of disease. To improve prediction it would be interesting to identify clusters of children with different disease histories because this would shed light on common genetic and environmental risk factors. We use, relying on previous work of Nagin, a Latent class mixture model to estimate, in a data-dependent and model-based fashion, a clustering of typical binary atopic dermatitis disease histories in children. The data were collected from 1990 to 1997 in the so called MAS-study, a prospective cohort study of 1314 children in five German cities. The original method of Nagin is extended in two different aspects, first we use bootstrap confidence intervals to account for uncertainty in curve fitting, and second, we propose to model covariates for cluster membership by Anderson's Stereotype regression model. We feel that the Latent class mixture model is a valuable tool for assessing the course of atopic dermatitis, yielding a wealth of communicable and graphically displayable results.     

Real‐time product attribute control to manufacture antibodies with defined N‐linked glycan levels

Pressures for cost‐effective new therapies and an increased emphasis on emerging markets require technological advancements and a flexible future manufacturing network for the production of biologic medicines. The safety and efficacy of a product is crucial, and consistent product quality is an essential feature of any therapeutic manufacturing process. The active control of product quality in a typical biologic process is challenging because of measurement lags and nonlinearities present in the system. The current study uses nonlinear model predictive control to maintain a critical product quality attribute at a predetermined value during pilot scale manufacturing operations. This approach to product quality control ensures a more consistent product for patients, enables greater manufacturing efficiency, and eliminates the need for extensive process characterization by providing direct measures of critical product quality attributes for real time release of drug product. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:1433–1441, 2015     

Intervals for the assessment of measurement agreement: Similarities,differences, and consequences of incorrect interpretations

Several intervals have been proposed to quantify the agreement of two methods intended to measure the same quantity in the situation where only one measurement per method and subject is available. The limits of agreement are probably the most well‐known among these intervals, which are all based on the differences between the two measurement methods. The different meanings of the intervals are not always properly recognized in applications. However, at least for small‐to‐moderate sample sizes, the differences will be substantial. This is illustrated both using the width of the intervals and on probabilistic scales related to the definitions of the intervals. In particular, for small‐to‐moderate sample sizes, it is shown that limits of agreement and prediction intervals should not be used to make statements about the distribution of the differences between the two measurement methods or about a plausible range for all future differences. Care should therefore be taken to ensure the correct choice of the interval for the intended interpretation.     

The Effect of an Experimental Brood Reduction on Male Desertion in the Panamanian Blue Acara Cichlid Aequidens coeruleopunctatus

Investment in present vs. future reproduction is a life-history trade-off faced by many animals. Because males generally pay a higher cost from lost mating opportunities than females, males are expected to react more strongly to changes in brood value. We examined the effect of an experimental brood reduction on male desertion in the substrate-brooding biparental cichlid Aequidens coeruleopunctatus under field conditions. We tested the prediction that brood reduction should decrease the duration of male care and examined the effect of brood reduction on the quality of male and female parental care. Our results show that males with reduced broods stopped providing parental care earlier than males with control broods. Males with reduced broods, however, also stayed longer with their broods as the season progressed. Brood reduction did not decrease daily investment in male or female parental care. We conclude that males trade off present and future reproduction by changing the duration but not the quality of parental care. The longer duration of male care in the experimental group later in the season suggests that the trade-off between present and future reproduction changes as the season progresses because the payoffs of desertion progressively decrease.     

Prediction Intervals in Nonlinear Regression

By treating the nonlinear model as if it were linear in the parameterization θ in the neighbourhood of the least squares estimate θ, we construct two-sided nominally-q-prediction intervals by applying the usual linear model theory. The derivation of the truncated series expansion of the expected coverage of the prediction intervals at a feasible value of the parameter vector is described. The quadratic approximation of the expected coverage is then obtained for a two-parameter nonlinear model. Finally we show how we may construct the prediction intervals when a certain type of nonlinear transformation of the parameter vector has been applied.     

Parametric and non-parametric modeling of short-term synaptic plasticity. Part II: Experimental study

This paper presents a synergistic parametric and non-parametric modeling study of short-term plasticity (STP) in the Schaffer collateral to hippocampal CA1 pyramidal neuron (SC) synapse. Parametric models in the form of sets of differential and algebraic equations have been proposed on the basis of the current understanding of biological mechanisms active within the system. Non-parametric Poisson–Volterra models are obtained herein from broadband experimental input–output data. The non-parametric model is shown to provide better prediction of the experimental output than a parametric model with a single set of facilitation/depression (FD) process. The parametric model is then validated in terms of its input–output transformational properties using the non-parametric model since the latter constitutes a canonical and more complete representation of the synaptic nonlinear dynamics. Furthermore, discrepancies between the experimentally-derived non-parametric model and the equivalent non-parametric model of the parametric model suggest the presence of multiple FD processes in the SC synapses. Inclusion of an additional set of FD process in the parametric model makes it replicate better the characteristics of the experimentally-derived non-parametric model. This improved parametric model in turn provides the requisite biological interpretability that the non-parametric model lacks.     

Detection and Prediction of Tooth Mobility During the Periodontitis Healing Process

The focus of the article is on a generic approach to prediction of a healing process based on automatic measurement and modelling of mechanical disease indicators. As a specific example the healing process after treatment of advanced periodontitis is characterised and predicted based on measurement of tooth mobility (TM). For the measurement a new mechatronic instrument was developed that includes a pneumatically driven probe with incorporated sensors of tooth displacement and loading force. TM is measured by a computer controlled data acquisition system and predicted by a non-parametric regression. Similarly as in the characterisation of technical processes, a measured sample is described by TM time series detected on a particular patient, while the regression is determined by a set of samples obtained from a group of patients following periodontal therapy. The influence of surgical access therapy and systemic administration of metronidazole as an adjunct to the mechanical treatment is demonstrated. For this purpose the average changes of tooth mobility are determined on variously treated subgroups. A new method of healing process prediction is demonstrated and its performance is described by a prediction quality.     

Detection and prediction of tooth mobility during the periodontitis healing process

The focus of the article is on a generic approach to prediction of a healing process based on automatic measurement and modelling of mechanical disease indicators. As a specific example the healing process after treatment of advanced periodontitis is characterised and predicted based on measurement of tooth mobility (TM). For the measurement a new mechatronic instrument was developed that includes a pneumatically driven probe with incorporated sensors of tooth displacement and loading force. TM is measured by a computer controlled data acquisition system and predicted by a non-parametric regression. Similarly as in the characterisation of technical processes, a measured sample is described by TM time series detected on a particular patient, while the regression is determined by a set of samples obtained from a group of patients following periodontal therapy. The influence of surgical access therapy and systemic administration of metronidazole as an adjunct to the mechanical treatment is demonstrated. For this purpose the average changes of tooth mobility are determined on variously treated subgroups. A new method of healing process prediction is demonstrated and its performance is described by a prediction quality.     

No Longer Confidential: Estimating the Confidence of Individual Regression Predictions

Quantitative predictions in computational life sciences are often based on regression models. The advent of machine learning has led to highly accurate regression models that have gained widespread acceptance. While there are statistical methods available to estimate the global performance of regression models on a test or training dataset, it is often not clear how well this performance transfers to other datasets or how reliable an individual prediction is–a fact that often reduces a user’s trust into a computational method. In analogy to the concept of an experimental error, we sketch how estimators for individual prediction errors can be used to provide confidence intervals for individual predictions. Two novel statistical methods, named CONFINE and CONFIVE, can estimate the reliability of an individual prediction based on the local properties of nearby training data. The methods can be applied equally to linear and non-linear regression methods with very little computational overhead. We compare our confidence estimators with other existing confidence and applicability domain estimators on two biologically relevant problems (MHC–peptide binding prediction and quantitative structure-activity relationship (QSAR)). Our results suggest that the proposed confidence estimators perform comparable to or better than previously proposed estimation methods. Given a sufficient amount of training data, the estimators exhibit error estimates of high quality. In addition, we observed that the quality of estimated confidence intervals is predictable. We discuss how confidence estimation is influenced by noise, the number of features, and the dataset size. Estimating the confidence in individual prediction in terms of error intervals represents an important step from plain, non-informative predictions towards transparent and interpretable predictions that will help to improve the acceptance of computational methods in the biological community.