Adaptive local regularization methods for the inverse ECG problem

One of the fundamental problems in theoretical electrocardiography can be characterized by an inverse problem. We present new methods for achieving better estimates of heart surface potential distributions in terms of torso potentials through an inverse procedure. First, we outline an automatic adaptive refinement algorithm that minimizes the spatial discretization error in the transfer matrix, increasing the accuracy of the inverse solution. Second, we introduce a new local regularization procedure, which works by partitioning the global transfer matrix into sub-matrices, allowing for varying amounts of smoothing. Each submatrix represents a region within the underlying geometric model in which regularization can be specifically ‘tuned’ using an a priori scheme based on the L-curve method. This local regularization method can provide a substantial increase in accuracy compared to global regularization schemes. Within this context of local regularization, we show that a generalized version of the singular value decomposition (GSVD) can further improve the accuracy of ECG inverse solutions compared to standard SVD and Tikhonov approaches. We conclude with specific examples of these techniques using geometric models of the human thorax derived from MRI data.     

Contact-Free Palm-Vein Recognition Based on Local Invariant Features

Contact-free palm-vein recognition is one of the most challenging and promising areas in hand biometrics. In view of the existing problems in contact-free palm-vein imaging, including projection transformation, uneven illumination and difficulty in extracting exact ROIs, this paper presents a novel recognition approach for contact-free palm-vein recognition that performs feature extraction and matching on all vein textures distributed over the palm surface, including finger veins and palm veins, to minimize the loss of feature information. First, a hierarchical enhancement algorithm, which combines a DOG filter and histogram equalization, is adopted to alleviate uneven illumination and to highlight vein textures. Second, RootSIFT, a more stable local invariant feature extraction method in comparison to SIFT, is adopted to overcome the projection transformation in contact-free mode. Subsequently, a novel hierarchical mismatching removal algorithm based on neighborhood searching and LBP histograms is adopted to improve the accuracy of feature matching. Finally, we rigorously evaluated the proposed approach using two different databases and obtained 0.996% and 3.112% Equal Error Rates (EERs), respectively, which demonstrate the effectiveness of the proposed approach.     

Assessment of protein model structure accuracy estimation in CASP13: Challenges in the era of deep learning

Scoring model structure is an essential component of protein structure prediction that can affect the prediction accuracy tremendously. Users of protein structure prediction results also need to score models to select the best models for their application studies. In Critical Assessment of techniques for protein Structure Prediction (CASP), model accuracy estimation methods have been tested in a blind fashion by providing models submitted by the tertiary structure prediction servers for scoring. In CASP13, model accuracy estimation results were evaluated in terms of both global and local structure accuracy. Global structure accuracy estimation was evaluated by the quality of the models selected by the global structure scores and by the absolute estimates of the global scores. Residue-wise, local structure accuracy estimations were evaluated by three different measures. A new measure introduced in CASP13 evaluates the ability to predict inaccurately modeled regions that may be improved by refinement. An intensive comparative analysis on CASP13 and the previous CASPs revealed that the tertiary structure models generated by the CASP13 servers show very distinct features. Higher consensus toward models of higher global accuracy appeared even for free modeling targets, and many models of high global accuracy were not well optimized at the atomic level. This is related to the new technology in CASP13, deep learning for tertiary contact prediction. The tertiary model structures generated by deep learning pose a new challenge for EMA (estimation of model accuracy) method developers. Model accuracy estimation itself is also an area where deep learning can potentially have an impact, although current EMA methods have not fully explored that direction.     

Three algorithms for interpreting models consisting of ordinary differential equations: Sensitivity coefficients,sensitivity functions,global optimization

This paper reports the development and application of three powerful algorithms for the analysis and simulation of mathematical models consisting of ordinary differential equations. First, we describe an extended parameter sensitivity analysis: we measure the relative sensitivities of many dynamical behaviors of the model to perturbations of each parameter. We check sensitivities to parameter variation over both small and large ranges. These two extensions of a common technique have applications in parameter estimation and in experimental design. Second, we compute sensitivity functions, using an efficient algorithm requiring just one model simulation to obtain all sensitivities of state variables to all parameters as functions of time. We extend the analysis to a behavior which is not a state variable. Third, we present an unconstrained global optimization algorithm, and apply it in a novel way: we determine the input to the model, given an optimality criterion and typical outputs. The algorithm itself is an efficient one for high-order problems, and does not get stuck at local extrema. We apply the sensitivity analysis, sensitivity functions, and optimization algorithm to a sixth-order nonlinear ordinary differential equation model for human eye movements. This application shows that the algorithms are not only practicable for high-order models, but also useful as conceptual tools.     

Recognition method of soybean leaf diseases using residual neural network based on transfer learning

Leaf disease is an important factor restricting the high quality and high yield of the soybean plant. Insufficient control of soybean diseases will destroy the local ecological environment and break the stability of the food chain. To overcome the low accuracy in recognizing soybean leaf diseases using traditional deep learning models and complexity in chemical analysis operations, in this study, a recognition model of soybean leaf diseases was proposed based on an improved deep learning model. First, four types of soybean diseases (Septoria Glycines Hemmi, Soybean Brown Leaf Spot, Soybean Frogeye Leaf Spot, and Soybean Phyllosticta Leaf Spot) were taken as research objects. Second, image preprocessing and data expansion of original images were carried out using image registration, image segmentation, region calibration and data enhancement. The data set containing 53, 250 samples was randomly divided into the training set, verification set, and test set according to the ratio of 7:2:1. Third, the convolution layer weight of the pre-training model based on the ImageNet open data set was transferred to the convolution layer of the ResNet18 model to reconstruct the global average pooling layer and the fully connected layer for constructing recognition model of TRNet18 model. Finally, the recognition accuracy of the four leaf diseases reached 99.53%, the Macro-F1 was 99.54%, and the average recognition time was 0.047184 s. Compared with AlexNet, ResNet18, ResNet50, and TRNet50 models, the recognition accuracy and Macro-F1 of the TRNet18 model were improved by 6.03% and 5.99% respectively, and the model recognition time was saved by 16.67%, The results showed that the proposed TRNet18 model had higher classification accuracy and stronger robustness, which can not only provide a reference for accurate recognition of other crop diseases, but also be transplanted to the mobile terminal for recognition of crop leaf diseases.     

Using an Improved SIFT Algorithm and Fuzzy Closed-Loop Control Strategy for Object Recognition in Cluttered Scenes

Partial occlusions, large pose variations, and extreme ambient illumination conditions generally cause the performance degradation of object recognition systems. Therefore, this paper presents a novel approach for fast and robust object recognition in cluttered scenes based on an improved scale invariant feature transform (SIFT) algorithm and a fuzzy closed-loop control method. First, a fast SIFT algorithm is proposed by classifying SIFT features into several clusters based on several attributes computed from the sub-orientation histogram (SOH), in the feature matching phase only features that share nearly the same corresponding attributes are compared. Second, a feature matching step is performed following a prioritized order based on the scale factor, which is calculated between the object image and the target object image, guaranteeing robust feature matching. Finally, a fuzzy closed-loop control strategy is applied to increase the accuracy of the object recognition and is essential for autonomous object manipulation process. Compared to the original SIFT algorithm for object recognition, the result of the proposed method shows that the number of SIFT features extracted from an object has a significant increase, and the computing speed of the object recognition processes increases by more than 40%. The experimental results confirmed that the proposed method performs effectively and accurately in cluttered scenes.     

基于微粒群-马尔科夫复合模型的生态空间预测模拟——以长株潭城市群为例

生态空间具有重要的生态功能,对生态空间进行科学预测模拟可为保护国土空间生态安全提供决策依据。利用Arc GIS及MATLAB软件,在生态空间风险评价的基础上构建了微粒群-马尔科夫复合模型,并以长株潭城市群为研究区,基于2013年土地利用现状数据,对2020年的生态空间进行了预测模拟,最后在此基础上提出了生态空间重构的基本思路。结果表明:1)微粒群-马尔科夫复合模型(PSO-Markov)构建的基本步骤为:第一步:粒子的选择与设计,以2000 m×2000 m的正方形单元作为基本粒子。第二步:粒子的初始化设定,根据生态空间风险由低到高的原则进行选择。第三步:适应度函数的建立,用生态空间的风险值来确定生态空间的空间格局。第四步:空间位置的更新,根据自身的历史最优值及粒子群的全局最优值进行速度和位置更新。2)微粒群-马尔科夫复合模型(PSO-Markov)是一种土地利用格局预测的新途径,生态空间的数量规模可以通过改进后的马尔科夫模型进行预测,生态空间的格局可以通过微粒群模型进行预测。3)微粒群-马尔科夫复合模型具有4个特点:第一、数量预测较为合理。第二、搜索范围大、较好地考虑到局部对全局的影响。第三、受问题维数变化影响小,在求解多目标问题时具有明显优势。第四、收敛时间短、运算速度快、易于实现。4)2020年,长株潭城市群的生态空间总体数量减少,其中林地和未利用地面积变化最明显,空间变化主要集中分布在西南部地区。生态空间总面积减小的主要原因是建设用地的扩张。因此,要控制城市群的人口密度,优化城市群生产—生活—生态的数量结构及空间布局,尤其要合理规划与利用城市建设用地,充分发挥水体与未利用地的生态价值,重点保护好生态源地、廊道及关键结点,构建结构合理、功能齐全的生态网络系统,提高系统的生态服务价值功能,要在规划的指导下合理调整城市群的城乡局部空间结构,保护生态环境,提高生境质量和景观多样性。这是今后一段时期面临的主要任务。     

Natural patterns of activity and long-term synaptic plasticity

Long-term potentiation (LTP) of synaptic transmission is traditionally elicited by massively synchronous, high-frequency inputs, which rarely occur naturally. Recent in vitro experiments have revealed that both LTP and long-term depression (LTD) can arise by appropriately pairing weak synaptic inputs with action potentials in the postsynaptic cell. This discovery has generated new insights into the conditions under which synaptic modification may occur in pyramidal neurons in vivo. First, it has been shown that the temporal order of the synaptic input and the postsynaptic spike within a narrow temporal window determines whether LTP or LTD is elicited, according to a temporally asymmetric Hebbian learning rule. Second, backpropagating action potentials are able to serve as a global signal for synaptic plasticity in a neuron compared with local associative interactions between synaptic inputs on dendrites. Third, a specific temporal pattern of activity--postsynaptic bursting--accompanies synaptic potentiation in adults.     

A mechanistic approach for modeling temperature-dependent consumer-resource dynamics

Paramount to our ability to manage and protect biological communities from impending changes in the environment is an understanding of how communities will respond. General mathematical models of community dynamics are often too simplistic to accurately describe this response, partly to retain mathematical tractability and partly for the lack of biologically pleasing functions representing the model/environment interface. We address these problems of tractability and plausibility in community/environment models by incorporating the Boltzmann factor (temperature dependence) in a bioenergetic consumer-resource framework. Our analysis leads to three predictions for the response of consumer-resource systems to increasing mean temperature (warming). First, mathematical extinctions do not occur with warming; however, stable systems may transition into an unstable (cycling) state. Second, there is a decrease in the biomass density of resources with warming. The biomass density of consumers may increase or decrease depending on their proximity to the feasibility (extinction) boundary. Third, consumer biomass density is more sensitive to warming than resource biomass density (with some exceptions). These predictions are in line with many current observations and experiments. The model presented and analyzed here provides an advancement in the testing framework for global change scenarios and hypotheses of latitudinal and elevational species distributions.     

Comparative footprinting of DNA-binding proteins

MOTIVATION: Comparative modelling is a computational method used to tackle a variety of problems in molecular biology and biotechnology. Traditionally it has been applied to model the structure of proteins on their own or bound to small ligands, although more recently it has also been used to model protein-protein interfaces. This work is the first to systematically analyze whether comparative models of protein-DNA complexes could be built and be useful for predicting DNA binding sites. RESULTS: First, we describe the structural and evolutionary conservation of protein-DNA interfaces, and the limits they impose on modelling accuracy. Second, we find that side-chains from contacting residues can be reasonably modeled and therefore used to identify contacting nucleotides. Third, the DNASITE protocol is implemented and different parameters are benchmarked on a set of 85 regulators from Escherichia coli. Results show that comparative footprinting can make useful predictions based solely on structural data, depending primarily on the interface identity with respect to the template used. AVAILABILITY: DNASITE code available on request from the authors.     

High‐resolution crystal structures leverage protein binding affinity predictions

Predicting protein binding affinities from structural data has remained elusive, a difficulty owing to the variety of protein binding modes. Using the structure‐affinity‐benchmark (SAB, 144 cases with bound/unbound crystal structures and experimental affinity measurements), prediction has been undertaken either by fitting a model using a handfull of predefined variables, or by training a complex model from a large pool of parameters (typically hundreds). The former route unnecessarily restricts the model space, while the latter is prone to overfitting. We design models in a third tier, using 12 variables describing enthalpic and entropic variations upon binding, and a model selection procedure identifying the best sparse model built from a subset of these variables. Using these models, we report three main results. First, we present models yielding a marked improvement of affinity predictions. For the whole dataset, we present a model predicting K_d within 1 and 2 orders of magnitude for 48% and 79% of cases, respectively. These statistics jump to 62% and 89% respectively, for the subset of the SAB consisting of high resolution structures. Second, we show that these performances owe to a new parameter encoding interface morphology and packing properties of interface atoms. Third, we argue that interface flexibility and prediction hardness do not correlate, and that for flexible cases, a performance matching that of the whole SAB can be achieved. Overall, our work suggests that the affinity prediction problem could be partly solved using databases of high resolution complexes whose affinity is known. Proteins 2016; 84:9–20. © 2015 Wiley Periodicals, Inc.     

An approach to automated particle picking from electron micrographs based on reduced representation templates

Reduced representation templates are used in a real-space pattern matching framework to facilitate automatic particle picking from electron micrographs. The procedure consists of five parts. First, reduced templates are constructed either from models or directly from the data. Second, a real-space pattern matching algorithm is applied using the reduced representations as templates. Third, peaks are selected from the resulting score map using peak-shape characteristics. Fourth, the surviving peaks are tested for distance constraints. Fifth, a correlation-based outlier screening is applied. Test applications to a data set of keyhole limpet hemocyanin particles indicate that the method is robust and reliable.     

Scale Interactions and Regional Climate: Examples from the Susquehanna River Basin

One of the most difficult problems faced by climatologists is how to translate global climate model (GCM) output into regional- and local-scale information that health and environmental effects researchers can use. It will be decades before GCMs will be able to resolve scales small enough for most effects research, so climatologists have developed climate downscaling methods to bridge the gap between the global and local scales. There are two main streams of climate downscaling research. First, high-resolution, limited-area climate models can be embedded in the coarse-scale GCMs, producing much finer resolution climate data. Second, empirical downscaling techniques develop transfer functions linking the large-scale atmospheric circulation generated by the GCMs to surface data. Examples of both types of downscaling, aimed at improving projections of future climate in the Susquehanna River Basin (the Mid-Atlantic Region of the United States), are presented. A third case is also described in which an even higher-resolution nested atmospheric model is being developed and linked to a hydrologic model system, with the ultimate goal of simulating the environmental response to climate forcing at all time and space scales.     

Invariant recognition of feature combinations in the visual system

 The operation of a hierarchical competitive network model (VisNet) of invariance learning in the visual system is investigated to determine how this class of architecture can solve problems that require the spatial binding of features. First, we show that VisNet neurons can be trained to provide transform-invariant discriminative responses to stimuli which are composed of the same basic alphabet of features, where no single stimulus contains a unique feature not shared by any other stimulus. The investigation shows that the network can discriminate stimuli consisting of sets of features which are subsets or supersets of each other. Second, a key feature-binding issue we address is how invariant representations of low-order combinations of features in the early layers of the visual system are able to uniquely specify the correct spatial arrangement of features in the overall stimulus and ensure correct stimulus identification in the output layer. We show that output layer neurons can learn new stimuli if the lower layers are trained solely through exposure to simpler feature combinations from which the new stimuli are composed. Moreover, we show that after training on the low-order feature combinations which are common to many objects, this architecture can – after training with a whole stimulus in some locations – generalise correctly to the same stimulus when it is shown in a new location. We conclude that this type of hierarchical model can solve feature-binding problems to produce correct invariant identification of whole stimuli. Received: 4 August 1999 / Accepted in revised form: 11 October 2000     

SEGA: semiglobal graph alignment for structure-based protein comparison

Comparative analysis is a topic of utmost importance in structural bioinformatics. Recently, a structural counterpart to sequence alignment, called multiple graph alignment, was introduced as a tool for the comparison of protein structures in general and protein binding sites in particular. Using approximate graph matching techniques, this method enables the identification of approximately conserved patterns in functionally related structures. In this paper, we introduce a new method for computing graph alignments motivated by two problems of the original approach, a conceptual and a computational one. First, the existing approach is of limited usefulness for structures that only share common substructures. Second, the goal to find a globally optimal alignment leads to an optimization problem that is computationally intractable. To overcome these disadvantages, we propose a semiglobal approach to graph alignment in analogy to semiglobal sequence alignment that combines the advantages of local and global graph matching.     

The Role of L1 Stalk-tRNA Interaction in the Ribosome Elongation Cycle

The ribosomal L1 stalk is a mobile structure implicated in directing tRNA movement during translocation through the ribosome. This article investigates three aspects of L1 stalk-tRNA interaction. First, by combining data from cryo electron microscopy, X-ray crystallography, and molecular dynamics simulations through the molecular dynamics flexible fitting method, we obtained atomic models of different tRNAs occupying the hybrid P/E state interacting with the L1 stalk. These models confirm the assignment of fluorescence resonance energy transfer states from previous single-molecule investigations of L1 stalk dynamics. Second, the models reconcile how initiator tRNA^fMet interacts less strongly with the L1 stalk compared to elongator tRNA^Phe, as seen in previous single-molecule experiments. Third, results from a simulation of the entire ribosome in which the L1 stalk is moved from a half-closed conformation to its open conformation are found to support the hypothesis that L1 stalk opening is involved in tRNA release from the ribosome.     

SecProMTB: Support Vector Machine‐Based Classifier for Secretory Proteins Using Imbalanced Data Sets Applied to Mycobacterium tuberculosis

Secretory proteins of Mycobacterium tuberculosis have created more concern, given their dominant immunogenicity and role in pathogenesis. In view of expensive and time‐consuming traditional biochemical experiments, an advanced support vector machine model named SecProMTB is constructed in this study and the proteins are identified by a bioinformatic approach. First, an improved pseudo‐amino acid composition (PseAAC) algorithm is used to extract features from all entities. Second, a novel imbalanced‐data strategy is proposed and adopted to divide the original data set into train set and test set. Third, to overcome the overfitting problem, feature‐ranking algorithms are applied with an increment feature selection. Finally, the model is trained and optimized. Consequently, a model is obtained with an area under the curve of 0.862 and average accuracy of 86% in the independent test. For the convenience of users, SecProMTB and related data are openly accessible at http://server.malab.cn/SecProMTB/index.jsp .     

A two-step model for the kinetics of BTX degradation and intermediate formation by Pseudomonas putida F1

A two-step model is developed for the aerobic biodegradation of benzene,toluene, and p-xylene (BTX) by Pseudomonas putida F1. The model contains three unique features. First, an initial dioxygenation step transforms BTX into their catechol intermediates, but does not support biomassgrowth. Second, the benzene or toluene intermediates are mineralized, which supports biomass synthesis. Third, BTX exhibit competitive inhibition on each other's transformation, while toluene and benzenenoncompetitively inhibit the mineralization of their catechol intermediate. A suite of batch and chemostat experiments is used to systematically measure the kinetic parameters for the two-step transformations and the substrate interactions.     

Remote Excited Raman Optical Activity of Adenine Along Ag Plasmonic Waveguide

We report the remote excited Raman optical activity (ROA) of adenine along Ag plasmonic waveguide. First, the surface plasmons that propagate along Ag nanowire is demonstrated experimentally. Second, the Raman spectra of adenine are measured experimentally. Third, the remote exited ROA by plasmonic waveguide are measured and compared. It is found that the plasmon chirality strongly influenced the molecular ORA by the local surface plasmon and remote plasmon waveguide. The plasmon chirality of nanostructures and the chirality plasmon waveguide should be considered in the experiments for the local and remote measurement.