Joint kinematics estimation using a multi-body kinematics optimisation and an extended Kalman filter,and embedding a soft tissue artefact model

To reduce the impact of the soft tissue artefact (STA) on the estimate of skeletal movement using stereophotogrammetric and skin-marker data, multi-body kinematics optimisation (MKO) and extended Kalman filters (EKF) have been proposed. This paper assessed the feasibility and efficiency of these methods when they embed a mathematical model of the STA and simultaneously estimate the ankle, knee and hip joint kinematics and the model parameters. A STA model was used that provides an estimate of the STA affecting the marker-cluster located on a body segment as a function of the kinematics of the adjacent joints. The MKO and the EKF were implemented with and without the STA model. To assess these methods, intra-cortical pin and skin markers located on the thigh, shank, and foot of three subjects and tracked during the stance phase of running were used. Embedding the STA model in MKO and EKF reduced the average RMS of marker tracking from 12.6 to 1.6 mm and from 4.3 to 1.9 mm, respectively, showing that a STA model trial-specific calibration is feasible. Nevertheless, with the STA model embedded in MKO, the RMS difference between the estimated and the reference joint kinematics determined from the pin markers slightly increased (from 2.0 to 2.1 deg) On the contrary, when the STA model was embedded in the EKF, this RMS difference was slightly reduced (from 2.0 to 1.7 deg) thus showing a better potentiality of this method to attenuate STA effects and improve the accuracy of joint kinematics estimate.     

Kalman smoothing improves the estimation of joint kinematics and kinetics in marker-based human gait analysis

We developed a Kalman smoothing algorithm to improve estimates of joint kinematics from measured marker trajectories during motion analysis. Kalman smoothing estimates are based on complete marker trajectories. This is an improvement over other techniques, such as the global optimisation method (GOM), Kalman filtering, and local marker estimation (LME), where the estimate at each time instant is only based on part of the marker trajectories. We applied GOM, Kalman filtering, LME, and Kalman smoothing to marker trajectories from both simulated and experimental gait motion, to estimate the joint kinematics of a ten segment biomechanical model, with 21 degrees of freedom. Three simulated marker trajectories were studied: without errors, with instrumental errors, and with soft tissue artefacts (STA). Two modelling errors were studied: increased thigh length and hip centre dislocation. We calculated estimation errors from the known joint kinematics in the simulation study. Compared with other techniques, Kalman smoothing reduced the estimation errors for the joint positions, by more than 50% for the simulated marker trajectories without errors and with instrumental errors. Compared with GOM, Kalman smoothing reduced the estimation errors for the joint moments by more than 35%. Compared with Kalman filtering and LME, Kalman smoothing reduced the estimation errors for the joint accelerations by at least 50%. Our simulation results show that the use of Kalman smoothing substantially improves the estimates of joint kinematics and kinetics compared with previously proposed techniques (GOM, Kalman filtering, and LME) for both simulated, with and without modelling errors, and experimentally measured gait motion.     

Hybrid-EKF: Hybrid model coupled with extended Kalman filter for real-time monitoring and control of mammalian cell culture

In a decade when Industry 4.0 and quality by design are major technology drivers of biopharma, automated and adaptive process monitoring and control are inevitable requirements and model-based solutions are key enablers in fulfilling these goals. Despite strong advancement in process digitalization, in most cases, the generated datasets are not sufficient for relying on purely data-driven methods, whereas the underlying complex bioprocesses are still not completely understood. In this regard, hybrid models are emerging as a timely pragmatic solution to synergistically combine available process data and mechanistic understanding. In this study, we show a novel application of the hybrid-EKF framework, that is, hybrid models coupled with an extended Kalman filter for real-time monitoring, control, and automated decision-making in mammalian cell culture processing. We show that, in the considered application, the predictive monitoring accuracy of such a framework improves by at least 35% when developed with hybrid models with respect to industrial benchmark tools based on PLS models. In addition, we also highlight the advantages of this approach in industrial applications related to conditional process feeding and process monitoring. With regard to the latter, for an industrial use case, we demonstrate that the application of hybrid-EKF as a soft sensor for titer shows a 50% improvement in prediction accuracy compared with state-of-the-art soft sensor tools.     

On the development and application of a continuous-discrete recursive prediction error algorithm

Recursive state and parameter reconstruction is a well-established field in control theory. In the current paper we derive a continuous-discrete version of recursive prediction error algorithm and apply the filter in an environmental and biological setting as a possible alternative to the well-known extended Kalman filter. The framework from which the derivation is started is the so-called 'innovations-format' of the (continuous time) system model, including (discrete time) measurements. After the algorithm has been motivated and derived, it is subsequently applied to hypothetical and 'real-life' case studies including reconstruction of biokinetic parameters and parameters characterizing the dynamics of a river in the United Kingdom. Advantages and characteristics of the method are discussed.     

基于集合卡尔曼滤波的南雄烟草LAI数据同化研究

叶面积指数(LAI)是表征烟草生长健康状态的重要指标之一,获取准确的LAI数据是监测烟草生长走势的重要步骤。以广东省南雄地区为试验区开展了集合卡尔曼滤波同化方法在烟草LAI的应用研究。通过野外实测得到南雄烟草生长期内的高光谱数据,并计算每个生长期的归一化植被指数(NDVI),依据NDVI值获得LAI测量数据;通过积温数据和实测LAI数据构建了符合南雄地区烟草LAI变化规律的LOGISTIC模型;并以LAI为研究变量,利用集合卡尔曼滤波数据同化技术融合NDVI数据计算得到的LAI和简化LOGSITIC模型拟合得到的LAI这两种不同的数据信息,获取实验区烟草生长期时间序列上的连续LAI数据。最后,进一步对比了数据同化方法、NDVI计算LAI方法和LOGISTIC模型拟合这3种方法获取烟草LAI的效果。结果显示:数据同化方法、NDVI计算LAI方法和LOGISTIC模型拟合3种方法均可一定程度上表征烟草LAI的变化状态,其中数据同化方法拟合效果最优。实验发现NDVI计算LAI方法在烟草生长前后期LAI值出现偏大或偏小的异常情况;LOGISTIC模型拟合则不能有效的描述烟草LAI的突发性变化;同化方法综合作物生长模型和遥感监测的优势,能够动态调节参数得到LAI优化结果,同化后LAI结果和真实值吻合,变化曲线更符合烟草的实际生长状况。     

A biomechanical study of the relationship between running velocity and three-dimensional lumbosacral kinetics

Faster running is not performed with proportional increase in all joint torque/work exertions. Although previous studies have investigated lumbopelvic kinetics for a single velocity, it is unclear whether each lumbopelvic torque should increase for faster running. We examined the relationship between running velocity and lumbopelvic kinetics. We calculated the three-dimensional lumbosacral kinetics of 10 male sprinters during steady-state running on a temporary indoor running track at five target velocities: 3.0 (3.20 ± 0.16), 4.5 (4.38 ± 0.18), 6.0 (5.69 ± 0.47), 7.5 (7.30 ± 0.41), and maximal sprinting (9.27 ± 0.36 m/s). The lumbosacral axial rotation torque increased more markedly (from 0.37 ± 0.06 to 1.99 ± 0.46 Nm/kg) than the extension and lateral flexion torques. The increase in the axial rotation torque was larger above 7.30 m/s. Conversely, the extension and lateral flexion torques plateaued when running velocity increased above 7.30 m/s. Similar results were observed for mechanical work. The results indicate that faster running required larger lumbosacral axial rotation torque. Conversely, the extension and lateral flexion torques were relatively invariant to running velocity above 7 m/s, implying that faster running below 7 m/s might increase the biomechanical loads causing excessive pelvic posterior tilt and excessive pelvic drop which has the potential to cause pain/injury related to lumbopelvic extensors and lateral flexors, whereas these biomechanical loads might not relate with running velocity above 7 m/s.     

Use of an Extended Kalman Filter and development of an automated system for xylose fermentation by a recombinantEscherichia coli

Summary An automated system was developed for on-line monitoring and control of xylose fermentation by a recombinantEscherichia coli. A 7-L fermenter was interfaced with a personal computer. Control circuits were constructed and a software was developed to estimate the states of the fermentation using an Extended Kalman Filter. The automated system combined with the Extended Kalman Filter provided a satisfactory way to obtain on-line information regarding estimation of fermentation parameters.     

The development and concurrent validity of a real-time algorithm for temporal gait analysis using inertial measurement units

The use of inertial measurement units (IMUs) for gait analysis has emerged as a tool for clinical applications. Shank gyroscope signals have been utilized to identify heel-strike and toe-off, which serve as the foundation for calculating temporal parameters of gait such as single and double limb support time. Recent publications have shown that toe-off occurs later than predicted by the dual minima method (DMM), which has been adopted as an IMU-based gait event detection algorithm. In this study, a real-time algorithm, Noise-Zero Crossing (NZC), was developed to accurately compute temporal gait parameters. Our objective was to determine the concurrent validity of temporal gait parameters derived from the NZC algorithm against parameters measured by an instrumented walkway. The accuracy and precision of temporal gait parameters derived using NZC were compared to those derived using the DMM. The results from Bland-Altman Analysis showed that the NZC algorithm had excellent agreement with the instrumented walkway for identifying the temporal gait parameters of Gait Cycle Time (GCT), Single Limb Support (SLS) time, and Double Limb Support (DLS) time. By utilizing the moment of zero shank angular velocity to identify toe-off, the NZC algorithm performed better than the DMM algorithm in measuring SLS and DLS times. Utilizing the NZC algorithm’s gait event detection preserves DLS time, which has significant clinical implications for pathologic gait assessment.     

Life-cycle greenhouse gas emissions assessment and extended exergy accounting of a horizontal-flow constructed wetland for municipal wastewater treatment: A case study in Chile

The life-cycle greenhouse gaseous emissions and primary exergy resources consumption associated with a horizontal subsurface flow constructed wetland (HSSF) were investigated. The subject of study was a wetland for municipal wastewater treatment with a 700-person-equivalent capacity. The effects of two types of emergent aquatic macrophytes (Phragmites australis and Schoenoplectus californicus) and seasonality on greenhouse gas (GHG) gas emissions, the environmental remediation cost (ERC) and the specific environmental remediation cost (SERC) were assessed. The results indicate that GHG emissions per capita (12–22 kgCO2eq/p.e/yr) and primary exergy resources consumed (24–27 MJ/m³) for the HSSF are lower than those of a conventional wastewater treatment plant (67.9 kgCO2eq/p.e/yr and 96 MJ/m³). The SERC varied between 176 and 216 MJ/kg biological oxygen demand (BOD₅) removal, which should be further reduced by 20% for an improved BOD₅ removal efficiency above 90%. The low organic matter removal efficiency is associated with a high organic load and low bacterial development. Seasonality has a marked effect on the organic removal efficiency and the SERC, but the macrophyte species does not.     

A general solution for optimal egg size during external fertilization, extended scope for intermediate optimal egg size and the introduction of Don Ottavio 'tango'

Egg sizes of marine invertebrates vary greatly, both within and between species. Among the proposed causes of this are a trade-off between egg size, egg number and survival probability of offspring, and a selection pressure exerted by sperm limitation during external fertilization. Although larger eggs are indeed a larger target for sperm, producing larger eggs also implies making fewer of them. There has been discussion about whether sperm limitation can (theoretically) and does (in nature) select for larger egg size than under ad libitum sperm. In one specific model, based on a particular fertilization kinetics model and an empirically derived mortality function, the theoretical possibility of a negative shift in optimal egg size with sperm concentration was demonstrated. Here we present a generalized analytical model to explore the effects of survival and fertilization probabilities on optimal egg size. It is demonstrated that incorporating fertilization kinetics greatly increases the scope for intermediate optimal egg size, as opposed to eggs of minimal or maximal size. Second, we present a general analytical qualitative solution to the question whether optimal egg size depends on sperm concentration. It is shown that, under the condition that an intermediate optimal egg size exists, this qualitative outcome of the model (positive, negative or no relation between optimal egg size and sperm limitation) depends on the structure of the fertilization kinetics part of the model. Finally, we evaluate fertilization kinetics models with respect to the general solution, using two previously published kinetics models ('Don Giovanni' and 'Don Ottavio') and a novel alteration of one of them in which sperm concentration covaries with egg concentration (Don Ottavio 'tango'). For all three models the relationship between optimal egg size and sperm concentration is shown to be always negative. This paper thus shows how biologically realistic relationships between egg size on the one hand and survival and fertilization probability on the other hand predict optimal egg size to be intermediate, and that this optimum is in general expected to increase when sperm become more limiting.     

农业害虫发生动态的Fuzzy优选识别模式及其应用

本文对山东省曲阜市１９８２－１９９４年二代棉铃虫发生动态的虫情与相应年份的气象资料进行了数量分析,应用Ｆｕｚｚｙ优选识别原理,建立了二代棉铃虫发生动态的Ｆｕｚｚｙ优选识别模式·对历史资料进行回代验证,其历史拟合率为 １００％．书 １９９５,１９９６ 两年的观测数据资料作为独立样本进行试报,预测结果与实际一致．本研究为农业害虫发生动态的预测预报提供了一种新的研究方法．     

Performance and microbial analysis of defined and non-defined inocula for the removal of dimethyl sulfide in a biotrickling filter

The performance and microbial communities of three differently inoculated biotrickling filters removing dimethyl sulfide (DMS) were compared. The biotrickling filters were inoculated with Thiobacillus thioparus TK-m (THIO), sludge (HANDS) and sludge + T. thioparus TK-m + Hyphomicrobium VS (HANDS++), respectively. The criteria investigated were length of the start-up period, the maximum elimination capacity, and the effects of intermittent loading rates, low pH, peak loading and very low loading rate on the DMS removal efficiency. The HANDS++ reactor exhibited the best performance considering all treatments. HANDS performed almost equally well as HANDS++, except during the determination of the EC(max), while THIO was generally the least efficient. During stable DMS loading at concentrations of 20 ppmv or lower, all reactors exhibited similar and high removal efficiencies (>99%). Denaturing gradient gel electrophoresis (DGGE) analysis showed the establishment of T. thioparus in the biofilm of all reactors, but not of Hyphomicrobium VS. Quantitative monitoring of the introduced bacterial strains was performed with a newly developed real-time PCR protocol. Initially, the inoculated strains were exclusively found in the reactors in which they were added. Afterwards, however, both strains developed in the biofilm of all three reactors, although T. thioparus attained higher cell densities than Hyphomicrobium. The presence of T. thioparus in THIO was related with the DMS loading rates that were applied, in the sense that intermittent DMS loading and very low DMS loading rates (0.5 ppmv) induced a decrease in gene copy numbers. Real-time PCR and DGGE both gave consistent results regarding the presence of Hyphomicrobium VS and Thiobacillus thioparus TK-m in the reactors. Only real-time PCR could be used to detect bacteria comprising of less than 1.4% of the total bacterial community ( approximately 10(5) copies ring(-1)).     

Evaluation of filter paper as a means of transporting inactivated Gram-negative non-fermentative bacteria and Haemophilus spp. for identification using the MALDI-TOF MS system

This study aimed to evaluate the filter paper as a means to transport inactivated Gram-negative non-fermentative (GNNF) bacteria and Haemophilus spp. for analysis using MALDI-TOF MS. A total of 133 isolates were evaluated and the analysis of each isolate was performed directly from original bacterial colony and in filter paper after the processing. To evaluate the agreement between the identification performed directly from the colony and after impregnation in filter paper, we assign the scores: >2·3 as excellent (E); 2·0 to 2·3 as very good (VG); 1·7–1·99 as good (G); <1·7 as unidentified (U). The divergences were classified as: Minor Divergence, Intermediate Divergence and Major Divergence. A total of 80 isolates transported in the filter paper disks presented full category concordance; 39 isolates presented Minor Divergence; 4 isolates present Intermediate Divergence; 4 isolates present Major Divergence and 6 isolates present better results after impregnation in filter paper. The proposed methodology of bacteria transportation presented a sensitivity of 96·9% and a specificity of 100%. The filter paper as a means to transport and storage of inactivated GNNF and Haemophilus spp. may be considered a potential tool for faster, more accurate, biosafe and less-expensive identification.     

An exception to the matched filter hypothesis: A mismatch of male call frequency and female best hearing frequency in a torrent frog

The matched filter hypothesis proposes that the tuning of auditory sensitivity and the spectral character of calls will match in order to maximize auditory processing efficiency during courtship. In this study, we analyzed the acoustic structure of male calls and both male and female hearing sensitivities in the little torrent frog (Amolops torrentis), an anuran species who transmits acoustic signals across streams. The results were in striking contradiction to the matched filter hypothesis. Auditory brainstem response results showed that the best hearing range was 1.6–2 kHz consistent with the best sensitive frequency of most terrestrial lentic taxa, yet completely mismatched with the dominant frequency of conspecific calls (4.3 kHz). Moreover, phonotaxis tests show that females strongly prefer high‐frequency (4.3 kHz) over low‐frequency calls (1.6 kHz) regardless of ambient noise levels, although peripheral auditory sensitivity is highest in the 1.6–2 kHz range. These results are consistent with the idea that A. torrentis evolved from nonstreamside species and that high‐frequency calls evolved under the pressure of stream noise. Our results also suggest that female preferences based on central auditory system characteristics may evolve independently of peripheral auditory system sensitivity in order to maximize communication effectiveness in noisy environments.     

Conformational and helicoidal analysis of the molecular dynamics of proteins: "curves," dials and windows for a 50 psec dynamic trajectory of BPTI

A new procedure for the graphic analysis of molecular dynamics (MD) simulations on proteins is introduced, in which comprehensive visualization of results and pattern recognition is greatly facilitated. The method involves determining the conformational and helicoidal parameters for each structure entering the analysis via the method "Curves," developed for proteins by Sklenar, Etchebest, and Lavery (Proteins: Structure, Function Genet. 6:46-60, 1989) followed by a novel computer graphic display of the results. The graphic display is organized systematically using conformation wheels ("dials") for each torsional parameter and "windows" on the range values assumed by the linear and angular helicoidal parameters, and is present in a form isomorphous with the primary structure per se. The complete time evolution of dynamic structure can then be depicted in a set of four composite figures. Dynamic aspects of secondary and tertiary structure are also provided. The procedure is illustrated with an analysis of a 50 psec in vacuo simulation on the 58 residue protein, bovine pancreatic trypsin inhibitor (BPTI), in the vicinity of the local minimum on the energy surface corresponding to a high resolution crystal structure. The time evolution of 272 conformational and 788 helicoidal parameters for BPTI is analyzed. A number of interesting features can be discerned in the analysis, including the dynamic range of conformational and helicoidal motions, the dynamic extent of 2 degrees structure motifs, and the calculated fluctuations in the helix axis. This approach is expected to be useful for a critical analysis of the effects of various assumptions about force field parameters, truncation of potentials, solvation, and electrostatic effects, and can thus contribute to the development of more reliable simulation protocols for proteins. Extensions of the analysis to present differential changes in conformational and helicoidal parameters is expected to be valuable in MD studies of protein complexes with substrates, inhibitors, and effectors and in determining the nature of structural changes in protein-protein interactions.     

A repetitive and species-specific sequence as a tool for detecting the genome contribution in somatic hybrids of the genus Medicago

 A highly repeated sequence (C300) was cloned from Medicago coerulea and its organization in the M. sativa-coerulea-falcata complex, M. arborea, and three somatic hybrids involving M. sativa, was investigated. Southern-blot analysis revealed a tandemly repeated array and a species-specificity of the sequence to those species belonging to the complex. Various degrees of amplification of C300 were detected among the species of the complex and the outcome in the somatic hybrids was dependent on parental composition. Sequence analysis revealed strong homology (96%) of C300 with a clone (E180) previously isolated from M. sativa. As FISH analysis showed that C300 was dispersed along the chromosomes of Medicago spp., it should prove a valid tool for establishing the chromosome origin of somatic hybrids. Received: 14 April 1997 / Accepted: 18 April 1997     

A note on the incidence of reverse complementary fungal ITS sequences in the public sequence databases and a software tool for their detection and reorientation

Reverse complementary DNA sequences––sequences that are inadvertently cast backward and in which all purines and pyrimidines are transposed––are not uncommon in sequence databases, where they may introduce noise into sequence-based research. We show that about 1% of the public fungal ITS sequences, the most commonly sequenced genetic marker in mycology, are reverse complementary, and we introduce an open source software solution to automate their detection and reorientation. The MacOSX/Linux/UNIX software operates on public or private datasets of any size, although some 50 base pairs of the 5.8S gene of the ITS region are needed for the analysis.     

A mixed strategy model for the emergence and intensification of social learning in a periodically changing natural environment

Based on a population genetic model of mixed strategies determined by alleles of small effect, we derive conditions for the evolution of social learning in an infinite-state environment that changes periodically over time. Each mixed strategy is defined by the probabilities that an organism will commit itself to individual learning, social learning, or innate behavior. We identify the convergent stable strategies (CSS) by a numerical adaptive dynamics method and then check the evolutionary stability (ESS) of these strategies. A strategy that is simultaneously a CSS and an ESS is called an attractive ESS (AESS). For certain parameter sets, a bifurcation diagram shows that the pure individual learning strategy is the unique AESS for short periods of environmental change, a mixed learning strategy is the unique AESS for intermediate periods, and a mixed learning strategy (with a relatively large social learning component) and the pure innate strategy are both AESS's for long periods. This result entails that, once social learning emerges during a transient era of intermediate environmental periodicity, a subsequent elongation of the period may result in the intensification of social learning, rather than a return to innate behavior.     

A combinatorial approach of structure-based virtual screening and molecular dynamics simulation towards the discovery of a highly selective inhibitor for VP9 coat protein of Banna virus

Structure based virtual screening of two libraries containing 27,628 numbers of antiviral compounds was used to discover a few of the potent inhibitor molecules against Banna virus (BAV). Cross-docking studies with many common interfering proteins provided five of the highly selective inhibitor for BAV. Analyses of the leading molecules with ADME-Tox filtering tool and atomistic molecular dynamics simulation studies finally discovered a benzoxazolone derivative as one of the most promising molecules towards the highly selective inhibition of BAV. The theoretical calculations are also supported by the experimental evidences where the interactions between the hit ligand and a model peptide sequence, mimicking the VP9 protein of BAV, were studied. Overall the development of a personalized therapeutic towards the highly selective inhibition of BAV is discussed herein for the first time in literature.