Finite element simulation of skeletal muscular structures obtained from images of histological serial sections

In this study, we present a method for the three-dimensional reconstruction of objects obtained from histological serial sections (exemplified by those of a pennate striated skeletal muscle) and its application to the finite element method. A hyperelastic material model is used for modeling biological soft tissue. The reconstruction process relies on the direct construction of a volumetric mesh using an octree approach which leads to a stable finite element method. Stability can be expressed in the spectral matrix condition number. To visualize stress patterns within the underlying anatomy the simulation results are projected onto images of the histological scenario.     

A neural network model of semantic memory linking feature-based object representation and words

Recent theories in cognitive neuroscience suggest that semantic memory is a distributed process, which involves many cortical areas and is based on a multimodal representation of objects. The aim of this work is to extend a previous model of object representation to realize a semantic memory, in which sensory-motor representations of objects are linked with words. The model assumes that each object is described as a collection of features, coded in different cortical areas via a topological organization. Features in different objects are segmented via γ-band synchronization of neural oscillators. The feature areas are further connected with a lexical area, devoted to the representation of words. Synapses among the feature areas, and among the lexical area and the feature areas are trained via a time-dependent Hebbian rule, during a period in which individual objects are presented together with the corresponding words. Simulation results demonstrate that, during the retrieval phase, the network can deal with the simultaneous presence of objects (from sensory-motor inputs) and words (from acoustic inputs), can correctly associate objects with words and segment objects even in the presence of incomplete information. Moreover, the network can realize some semantic links among words representing objects with shared features. These results support the idea that semantic memory can be described as an integrated process, whose content is retrieved by the co-activation of different multimodal regions. In perspective, extended versions of this model may be used to test conceptual theories, and to provide a quantitative assessment of existing data (for instance concerning patients with neural deficits).     

Prediction of protein structural class with Rough Sets

Background  

A new method for the prediction of protein structural classes is constructed based on Rough Sets algorithm, which is a rule-based data mining method. Amino acid compositions and 8 physicochemical properties data are used as conditional attributes for the construction of decision system. After reducing the decision system, decision rules are generated, which can be used to classify new objects.     

The fractal structure of glycogen: A clever solution to optimize cell metabolism.

Fractal objects are complex structures built with a simple procedure involving very little information. This has an obvious interest for living beings, because they are splendid examples of optimization to achieve the most efficient structure for a number of goals by means of the most economic way. The lung alveolar structure, the capillary network, and the structure of several parts of higher plant organization, such as ears, spikes, umbels, etc., are supposed to be fractals, and, in fact, mathematical functions based on fractal geometry algorithms can be developed to simulate them. However, the statement that a given biological structure is fractal should imply that the iterative process of its construction has a real biological meaning, i.e., that its construction in nature is achieved by means of a single genetic, enzymatic, or biophysical mechanism successively repeated; thus, such an iterative process should not be just an abstract mathematical tool to reproduce that object. This property has not been proven at present for any biological structure, because the mechanisms that build the objects mentioned above are unknown in detail. In this work, we present results that show that the glycogen molecule could be the first known real biological fractal structure.     

Dynamics of target selection in multiple object tracking (MOT)

In four experiments we address the question whether several visual objects can be selected voluntarily (exogenously) and then tracked in a Multiple Object Tracking paradigm and, if so, whether the selection involves a different process. Experiment 1 showed that items can indeed be selected based on their labels. Experiment 2 showed that to select the complement set to a set that is automatically (exogenously) selected--e.g. to select all objects not flashed--observers require additional time and that given 1080 ms they were able to select and track them as well as those selected automatically. Experiment 3 showed that the additional time needed in the previous experiment cannot be attributed solely to time required to disengage attention from the initially automatic selections. Experiment 4 showed that the added time provides a monotonically greater benefit when there are more targets, suggesting a serial process. These results are discussed in relation to the Visual Index (FINST) theory which assumes that visual indexes are captured by a data-driven process. It is suggested that voluntarily allocated attention can be used to facilitate the automatic attention capture by objects of interest.     

Recursive construction of perfect DNA molecules from imperfect oligonucleotides

Making faultless complex objects from potentially faulty building blocks is a fundamental challenge in computer engineering, nanotechnology and synthetic biology. Here, we show for the first time how recursion can be used to address this challenge and demonstrate a recursive procedure that constructs error‐free DNA molecules and their libraries from error‐prone oligonucleotides. Divide and Conquer (D&C), the quintessential recursive problem‐solving technique, is applied in silico to divide the target DNA sequence into overlapping oligonucleotides short enough to be synthesized directly, albeit with errors; error‐prone oligonucleotides are recursively combined in vitro, forming error‐prone DNA molecules; error‐free fragments of these molecules are then identified, extracted and used as new, typically longer and more accurate, inputs to another iteration of the recursive construction procedure; the entire process repeats until an error‐free target molecule is formed. Our recursive construction procedure surpasses existing methods for de novo DNA synthesis in speed, precision, amenability to automation, ease of combining synthetic and natural DNA fragments, and ability to construct designer DNA libraries. It thus provides a novel and robust foundation for the design and construction of synthetic biological molecules and organisms.     

Infrared thermal imaging in studies of wild animals

Thermography is an imaging method which registers infrared waves in the electromagnetic spectrum that are emitted by all objects on the Earth. The state and properties of the studied objects and organisms can be evaluated by analyzing images of temperature distribution on their surface. Thermography has numerous practical applications, including in construction, industry, and the military and civil services. In natural sciences, thermal imaging techniques support safe and non-invasive measurements and the acquisition of results that cannot be obtained by any other method. Infrared thermography also creates a wide range of applications for human and veterinary medicine, ecology, zoology, and other natural sciences. Thermal imaging equipment is used to detect injuries, inflammations, and infectious diseases to control reproduction (detection of estrus and pregnancy, determination of male fertility) and lactation processes. The discussed method is applied to investigate thermoregulation in animals, to analyze the effect of environmental factors on animal behavior, to localize individuals and their habitats, and to determine the size of wildlife populations. Despite a wide range of practical applications, thermal imaging has a number of limitations which should be taken into account in studies that rely on infrared thermography techniques.     

Dating furniture and coopered vessels without waney edge – Reconstructing historical wood-working in Austria with the help of dendrochronology

In the present study, 208 furniture and 168 coopered vessels from three Austrian museums were examined. Dendrochronology was used to date objects and to extract further information such as the necessary time for seasoning, wood loss through wood-working and methods of construction. In most cases sampling was done by sanding the cross section and making digital photographs using a picture frame and measuring digitally.The dendrochronological dates of the sampled furniture range between 1524 and 1937. The group of furniture includes cupboards, chests, tables, benches, commodes and beds. In many cases furniture was artfully painted and sometimes even shows a painted year. With the help of dendrochronology it was proved that some objects had been painted for some time after construction, or had been over-painted. Most furniture, however, was painted immediately after completion. In this case, the seasoning and storage time of the boards and the wood loss due to shaping can be verified. As an average value, 14 years have passed between the dendrochronological date of the outermost ring and the painting. The time span includes time of seasoning and storage and the rings lost by wood-working. This leads, on the one hand to a short storage time of less than 10 years and on the other hand to very little wood loss due to manufacturing. Those boards being less shaped turned out to be back panels of cupboards, therefore they are recommended to be sampled for dating.Coopered vessels were dated between 1612 and 1940. There was evidence that staves were split and not sawn in many cases. The staves were often split out of the outermost part of the tree and hardly any wood was worked away which was proved by the close dendrochronological dates of the single staves of a vessel.Since there is a short time of storage and only little wood loss through wood-working, dating of objects without a waney edge becomes reasonable.     

Mastering the complexity of DNA nanostructures

The self-assembly of oligodeoxynucleotides is a versatile and powerful tool for the construction of objects in the nanoscale. The strictly information-driven pairing of DNA fragments can be used to rationally design and build nanostructures with planned topologies and geometries. Taking advantage of the steadily expanding library of well-characterized DNA motifs, several examples of structures with different dimensionalities have appeared in the literature in the past few years, laying the foundations for a promising DNA-mediated, bottom-up approach to nanotechnology. This article focuses on recent developments in this area of research and proposes a classification of DNA nanostructures based on topological considerations in addition to describing strategies for tackling the inherent complexities of such an endeavor.     

Feature binding,attention and object perception.

The seemingly effortless ability to perceive meaningful objects in an integrated scene actually depends on complex visual processes. The ''binding problem'' concerns the way in which we select and integrate the separate features of objects in the correct combinations. Experiments suggest that attention plays a central role in solving this problem. Some neurological patients show a dramatic breakdown in the ability to see several objects; their deficits suggest a role for the parietal cortex in the binding process. However, indirect measures of priming and interference suggest that more information may be implicitly available than we can consciously access.     

The transfer of motor functional strategies via action observation

When someone is choosing one piece from a bowl full of fruit, many pieces are within reach and visible. Although the desired piece seems to govern the particular pattern and direction of that person's reaching movement, the selection process is not impervious to the presence of task-irrelevant information (i.e. the other fruits). Evidence suggests that the kinematics of reach-to-grasp actions for a desired object integrates the motor features of all the objects which might become potential targets. Transcranial magnetic stimulation (TMS) and motor-evoked potentials (MEPs) were used by us to establish if that motor integration process can be transferred to an onlooker. Our results indicate that observation of hybrid reach-to-grasp movement kinematics is reflected in the observer's pattern of MEP amplitudes. This effect can be defined as a form of motor resonance which operates by 'reading' the kinematics of an observed action. The brain's ability to mirror motor integration processes while observing someone else's action helps an onlooker to understand what the other person is doing and to predict his/her motor alternatives.     

Multispectral/hyperspectral image enhancement for biological cell analysis.

BACKGROUND: Microscopes form projected images from illuminated objects, such as cellular tissue, which are recorded at a distance through the optical system's field of view. A telescope on a satellite or airplane also forms images with a similar optical projection of objects on the ground. Typical visible illuminations form a displayed set of three-color channels (Red Green Blue [RGB]) that are combined from three image sensor arrays (e.g., focal plane arrays) into a single pixel coding for each color present in the image. Analysis of these RGB color images develops a qualitative image representation of the objects. METHODS: Independent component analysis (ICA) is used for analysis and enhancement of multispectral images, and compared with the similar and widely used principal component analysis. RESULTS: The data examples indicate that the ICA enhancement, and the resulting RGB image combination display, can be useful in processing datacubes of cellular data where isolation of unknown subtle image elements representing objects is desired. CONCLUSIONS: ICA image enhancement can aid processing of datacubes of cellular data by clarifying subtle image elements. These parallelizable algorithms can be implemented for real-time, online analysis.     

城市群生态网络协同构建场景要素与路径分析——以粤港澳大湾区为例

城市群生态网络构建是城市与区域协同发展面临的重要场景之一,合理的生态网络能加强生态源地间的连通性,提高生态系统的生态功能,有效缓解生态环境问题,对保障城市与区域生态安全,提升人类福祉具有重要意义。以粤港澳大湾区城市群为例,以场景为依托开展生态网络协同构建场景要素与协同路径分析,结合景观连通性和形态学空间格局分析方法（MSPA）获得生态源地,并基于最小累积阻力模型识别生态廊道与生态节点,构建大湾区生态网络总体格局,最后从跨区域协作角度探讨城市群生态网络协同构建的潜在路径。研究结果表明：（1）研究区生态网络由40个生态源地、780条潜在生态廊道与892个生态节点构成,生态源地面积1.88万km²,占湾区总面积比例为33%,所识别的生态源地及生态廊道与自然保护区、广东省万里碧道、珠江三角洲绿道网重合程度较高;（2）识别跨区域生态廊道552条,其中,跨越佛山与广州市的生态廊道较多,一半以上的廊道跨越三个及以上城市,跨陆海区域的生态廊道连接了湾区南部主要沿海城市,构成陆海生态网络的关键组成部分;（3）提出城市群生态网络协同构建的潜在模式,应结合生态源地、生态廊道、生态节点等构建主体,分析城市内、城市间生态网络构建过程涉及的协同需求、协同对象,探索差异化的协同路径;（4）以场景为依托识别城市群生态网络构建场景的主题、时空特征、对象、路径和价值,可为进一步开展生态网络协同构建与应用示范过程提供指导。本研究是对城市群生态网络协同建设的有益探索,基于跨区域生态廊道协同构建场景模式的探讨能够为今后进一步探索区域统筹协同机制、实现景观格局协同构建和优化、促进区域生态共建共享提供理论依据。     

Introducing an inquiry-based experiment-integrated science game for elementary students: the shadow races game

Abstract

This article introduces a science game which can be used for innovative teaching and as an assessment tool. The Shadow Races Game is designed for first and second grade students to learn the phenomenon of shadow through inquiry-based activities and questions that require the children to apply inferences from those activities. In this amusing board game, students will discover the relationship between light, objects and shadows using familiar objects.     

Stochastic models for aggregation processes

Three models are presented, which describe the aggregation of objects into groups and the distributions of groups sizes and group numbers within habitats. The processes regarded are pure accumulation processes which involve only formation and invasion of groups. Invasion represents the special case of fusion when only single objects - and not groups - join a group of certain size. The basic model is derived by a single parameter, the formation probability q, which represents the probability of an object to form a new group. A novel, discrete and finite distribution that results for the group sizes is deduced from this aggregation process and it is shown that it converges to a geometric distribution if the number of objects tends to infinity. Two extensions of this model, which both converge to the Waring distribution, are added: the model can be extended either with a beta distributed formation probability or with the assumption that the invasion probability depends on the group size. Relationships between the limiting distributions involved are discussed.     

Comparison of preferences for object properties in the rat using paired- and free-choice paradigms

A common method for testing preference for objects is to determine which of a pair of objects is approached first in a paired-choice paradigm. In comparison, many studies of preference for environmental enrichment (EE) devices have used paradigms in which total time spent with each of a pair of objects is used to determine preference. While each of these paradigms gives a specific measure of the preference for one object in comparison to another, neither method allows comparisons between multiple objects simultaneously. Since it is possible that several EE objects would be placed in a cage together to improve animal welfare, it is important to determine measures for rats’ preferences in conditions that mimic this potential home cage environment. While it would be predicted that each type of measure would produce similar rankings of objects, this has never been tested empirically. In this study, we compared two paradigms: EE objects were either presented in pairs (paired-choice comparison) or four objects were presented simultaneously (simultaneous presentation comparison). We used frequency of first interaction and time spent with each object to rank the objects in the paired-choice experiment, and time spent with each object to rank the objects in the simultaneous presentation experiment. We also considered the behaviours elicited by the objects to determine if these might be contributing to object preference. We demonstrated that object ranking based on time spent with objects from the paired-choice experiment predicted object ranking in the simultaneous presentation experiment. Additionally, we confirmed that behaviours elicited were an important determinant of time spent with an object. This provides convergent evidence that both paired choice and simultaneous comparisons provide valid measures of preference for EE objects in rats.     

4D bioinformatics: a new look at the ribosome as an example

We have adapted the Java Molecular Viewer (JMV) to virtual reality display environments, through a number of extensions to the Java 3D code. Phylogenetic information derived from multiple alignments (temporal information) can be overlaid onto molecule structures (spatial information). The number of sequences included in the underlying multiple alignment can be changed instantaneously, resulting in dynamical updates of the displayed information. JMV was also extended to handle an infinite number of objects (molecules) in the same display. The objects can be manipulated in six degrees of freedom simultaneously or independently. We have used the small subunit ribosomal RNA to demonstrate the system (http:// cave.ucalgary.ca), which can be used for any molecule with a resolved structure.     

Distance and shape: perception of the 3-dimensional world by weakly electric fish.

Weakly electric fish orient at night in complete darkness by employing their active electrolocation system. They emit short electric signals and perceive the consequences of these emissions with epidermal electroreceptors. Objects are detected by analyzing the electric images which they project onto the animal's electroreceptive skin surface. This process corresponds to similar processes during vision, where visual images are cast onto the retinas of eyes. Behavioral experiments have shown that electric fish can measure the distance of objects during active electrolocation, thus possessing three-dimensional depth perception of their surroundings. The fundamental mechanism for distance determination differs from stereopsis used during vision by two-eyed animals, but resembles some supplementary mechanisms for distance deduction in humans. Weakly electric fish can also perceive the three-dimensional shape of objects. The fish can learn to identify certain objects and discriminate them from all other objects. In addition, they spontaneously categorize objects according to their shapes and not according to object size or material properties. There is good evidence that some fundamental types of perceptional invariances during visual object recognition in humans are also found in electric fish during active electrolocation. These include size invariance (maybe including size constancy), rotational invariance, and translational invariance. The mechanisms of shape detection during electrolocation are still unknown, and their discoveries require additional experiments.     

浙江省森林信息提取及其变化的空间分布

如何利用遥感技术提取森林信息是遥感应用的重要领域之一。以不同时相的Landsat TM/ETM+为数据源,采用面向对象和基于多级决策树的分类方法得到浙江省2000年、2005年以及2010年的森林植被覆被图。经实地采样点验证,2010年分类精度达到92.76%,精度满足要求。介绍了浙江森林信息的快速提取方法,即统计不同森林类型的Landsat TM影像原始波段和LBV变换值以及各种植被指数在各时相上的差异,经过C5决策树训练,选取合适的规则和阈值实现森林信息的提取。结果表明,面向对象分割与决策树算法结合可以作为森林信息提取的有效方法。最后,通过对3期森林专题图进行空间叠加分析,得到了森林资源动态变化的空间分布,并以此为基础对林地变化的类型及原因进行分析,结果显示浙江省森林资源变化主要分布在浙西北山区、浙中南山区以及沿海地带,这一结果可以为有关部门的决策提供依据。     

Consensusn-trees

It is not unusual for several classifications to be given for the same collection of objects. We present a method, called majority rule, which can be used to define a consensus of these classifications. We also discuss some mathematical properties of this consensus tree.