trajr: An R package for characterisation of animal trajectories

Quantitative characterisation of the trajectories of moving animals is an important component of many behavioural and ecological studies, however methods are complicated and varied, and sometimes require well‐developed programming skills to implement. Here, we introduce trajr, an R package that serves to analyse animal paths, from unicellular organisms, through insects to whales. It makes a variety of statistical characterisations of trajectories, such as tortuosity, speed and changes in direction, available to biologists who may not have a background in programming. We discuss a range of indices that have been used by researchers, describe the package in detail, then use movement observations of whales and clearwing moths to demonstrate some of the capabilities of trajr. As an open‐source R package, trajr encourages open and reproducible research. It supports the implementation of additional methods by providing access to trajectory analysis “building blocks,” allows the full suite of R statistical analysis tools to be applied to trajectory analysis, and the source code can be independently validated.     

Variation in the Trajectories of Depressive Symptoms: Results from the Americans' Changing Lives Study

This study examines the association between race and depressive symptoms over a 16‐year study period. The analysis is based on the responses of 3,485 African-American and White respondents from four waves of the Americans' Changing Lives Panel Study. Growth mixture modeling was used to identify latent trajectory classes based on the reported levels of depressive symptoms over 16 years. Four latent trajectory classes were identified: two “high-risk” groups and two “low-risk” groups. Findings show the heterogeneity among and within racial groups in their trajectories of depressive symptoms and the distinct demographic and social relationship predictors for symptom trajectories.     

A new direction for differentiating animal activity based on measuring angular velocity about the yaw axis

1. The use of animal‐attached data loggers to quantify animal movement has increased in popularity and application in recent years. High‐resolution tri‐axial acceleration and magnetometry measurements have been fundamental in elucidating fine‐scale animal movements, providing information on posture, traveling speed, energy expenditure, and associated behavioral patterns. Heading is a key variable obtained from the tandem use of magnetometers and accelerometers, although few field investigations have explored fine‐scale changes in heading to elucidate differences in animal activity (beyond the notable exceptions of dead‐reckoning).
2. This paper provides an overview of the value and use of animal heading and a prime derivative, angular velocity about the yaw axis, as an important element for assessing activity extent with potential to allude to behaviors, using “free‐ranging” Loggerhead turtles (Caretta caretta) as a model species.
3. We also demonstrate the value of yaw rotation for assessing activity extent, which varies over the time scales considered and show that various scales of body rotation, particularly rate of change of yaw, can help resolve differences between fine‐scale behavior‐specific movements. For example, oscillating yaw movements about a central point of the body's arc implies bouts of foraging, while unusual circling behavior, indicative of conspecific interactions, could be identified from complete revolutions of the longitudinal axis.
4. We believe this approach should help identification of behaviors and “space‐state” approaches to enhance our interpretation of behavior‐based movements, particularly in scenarios where acceleration metrics have limited value, such as for slow‐moving animals.

     

Dynamic properties of the native free antithrombin from molecular dynamics simulations: computational evidence for solvent- exposed Arg393 side chain

While antithrombin (AT) has small basal inhibitory activity, it reaches its full inhibitory potential against activated blood coagulation factors, FXa, FIXa, and FIIa (thrombin), via an allosteric and/or template (bridging) mechanism by the action of heparin, heparan sulfate, or heparin-mimetic pentasaccharides (PS). From the numerous X-ray structures available for different conformational states of AT, only indirect and incomplete conclusions can be drawn on the inherently dynamic properties of AT. As a typical example, the basal inhibitory activity of AT cannot be interpreted on the basis of “non-activated” free antithrombin X-ray structures since the Arg393 side chain, playing crucial role in antithrombin-proteinase interaction, is not exposed. In order to reveal the intrinsic dynamic properties and the reason of basal inhibitory activity of antithrombin, 2 μs molecular dynamics simulations were carried out on its native free-forms. It was shown from the simulation trajectories that the reactive center loop which is functioning as “bait” for proteases, even without any biasing potential can populate conformational state in which the Arg393 side chain is solvent exposed. It is revealed from the trajectory analysis that the peptide sequences correspond to the helix D extension, and new helix P formation can be featured with especially large root-mean-square fluctuations. Mutual information analyses of the trajectory showed remarkable (generalized) correlation between those regions of antithrombin which changed their conformations as the consequence of AT–PS complex formation. This suggests that allosteric information propagation pathways are present even in the non-activated native form of AT.     

New method of three-dimensional analysis of bipedal locomotion for the study of displacements of the body and body-parts centers of mass in man and non-human primates: Evolutionary framework

The current biomechanical interpretation of the chimpanzee's bipedal walking argues that larger lateral and vertical displacements of the body center of mass occur in the chimpanzee's “side-to-side” gait than in the human striding gait. The evolutionary hypothesis underlying this study is the following: during the evolution of human bipedalism one of the necessary changes could have been the progressive reduction of these displacements of the body center of mass. In order to quantitatively test this hypothesis, it is necessary to obtain simultaneously the trajectories of the centers of mass of the whole body and of the different body parts. To solve this problem, a new method of three-dimensional analysis of walking, associated with a volumetric modelling of the body, has been developed based on finite-element modelling. An orthogonal synchrophotographic device yielding four synchronous pictures of the walking subject allows a qualitative analysis of the photographic sequences together with the results of their quantitative analysis. This method was applied to an adult man, a 3-year-old girl and a 9-year-old male chimpanzee. Our results suggest that the trajectory of the body center of mass of the human is distinguished from that of the chimpanzee not by a lower movement amplitude but by the synchronization of the transverse and vertical displacements into two periodic curves in phase with one another. The non-human primate uses its repertoire of arboreal movements in its bipedal terrestrial gait, provisionally referred to as a “rope-walker” gait. We show that the interpretation of a “side-to-side” gait is not applicable to the chimpanzee. We argue that similarly this interpretation and the initial hypothesis presuppose a basic symmetric structure of the gait, in relation to the sagittal plane of progression, similar to the human one. This lateral symmetry of the right and left displacements of the center of gravity, in phase with the right and left single supports of walking, is probably a very derived feature of the human gait. We suggest that low lateral and vertical displacements of the body center of mass are not indicative of a progressive bipedal gait and we discuss the new evolutionary implications of our results. © 1993 Wiley-Liss, Inc.     

Formation and control of optimal trajectory in human multijoint arm movement

In this paper, we study trajectory planning and control in voluntary, human arm movements. When a hand is moved to a target, the central nervous system must select one specific trajectory among an infinite number of possible trajectories that lead to the target position. First, we discuss what criterion is adopted for trajectory determination. Several researchers measured the hand trajectories of skilled movements and found common invariant features. For example, when moving the hand between a pair of targets, subjects tended to generate roughly straight hand paths with bell-shaped speed profiles. On the basis of these observations and dynamic optimization theory, we propose a mathematical model which accounts for formation of hand trajectories. This model is formulated by defining an objective function, a measure of performance for any possible movement: square of the rate of change of torque integrated over the entire movement. That is, the objective function CT is defined as follows: (formula; see text) We overcome this difficult by developing an iterative scheme, with which the optimal trajectory and the associated motor command are simultaneously computed. To evaluate our model, human hand trajectories were experimentally measured under various behavioral situations. These results supported the idea that the human hand trajectory is planned and controlled in accordance with the minimum torque-change criterion.     

Integrating Concern for Animals into Personal Values

Recent scholarship in human–animal relationships demonstrates that new theoretical insights emerge when these relationships are seriously considered. We suggest that the most prominent measures of values in the environmental decision-making research literature, the Schwartz approach, may not adequately capture key aspects of how individuals value animals. Our research used confirmatory factor analysis and ordinary least squares regression techniques on data collected from an Amazon Mechanical Turk online survey. It expands on the values commonly used in the environmental decision-making literature to consider whether there is a distinct value dimension focused on animals. Our suggestion that a “concern for animals” value orientation constitutes a motivation that is separate from the other values commonly used in research on environmental decision-making finds support in our data. Traditional scaling methods indicate that the items we created have high reliability when used to form an unweighted additive scale. The results of confirmatory factor analysis are consistent with the argument that this “concern for animals” value orientation is distinct from biospheric altruism, humanistic altruism, self-interest, traditionalism, openness to change, and hedonism. Finally, our regressions using values and demographic, social, and political characteristics as controls show that an animal-focused value orientation and biospheric altruism have different relationships with identification with the animal rights movement than with identification with the environmental movement.     

Local knowledge held by farmers in Eastern Tyrol (Austria) about the use of plants to maintain and improve animal health and welfare

Background

The sustainable management of animal health and welfare is of increasing importance to consumers and a key topic in the organic farming movement. Few systematic studies have been undertaken investigating farmers’ local knowledge related to this issue. Ethnoveterinary medicine (EVM) is a discipline focusing on local knowledge and folk methods in veterinary medicine, however most ethnoveterinarian studies primarily address the treatment of animal diseases. Very few studies have explored prophylactic methods.

Methods

An ethnoveterinary research project in Eastern Tyrol (Austria) was conducted in 2004 and 2005 to gather information about local knowledge of animal husbandry from 144 informants, with the emphasis on plants that maintain livestock health and welfare.

Results

Informants mentioned a total of 87 plants and 22 plant-based generic terms in the context of maintaining and improving livestock health and welfare. The most important preventive measures for maintaining and improving animal health and welfare were practices related to “fodder” and “feeding”. In this category the plants mentioned could be grouped according to three different perceptions about their effect on animals: “Good or bad fodder”, “Functional fodder” and “Fodder medicine”. In addition to fodder, environmental management, the human-animal relationship, household remedies and cultural/religious activities were also mentioned. When asked about practices in the past that maintained animal health and well-being, interviewees mentioned, for example, the importance of the diversity of sources that used to be available to obtain feed and fodder.

Conclusions

The informants’ approach that feeding is central to livestock welfare is in line with the standard scientific literature on animal health, including in organic farming. Various scientific studies into common fodder evaluate the nutritive and dietary value, efficiency and safety of fodder. Future studies also have to consider the evaluation of traditional, local fodder resources. In fact, the value of ‘food as medicine’ for humans in the context of local knowledge has been widely assessed, but the potential health benefits of fodder and nutraceuticals in local and traditional ethnoveterinary methods require further attention.

     

Bestial Wisdom and Human Tragedy: The Genesis of the Animal Epic

ABSTRACT

A radical redefinition or blurring of the boundaries between the human and animal realms, between “us” and “them,” can sometimes open dramatic new aesthetic and cultural possibilities. This paper discusses the earliest example of this, an ancient Akkadian fragment known, a bit deceptively, as “The Fable of the Fox.” Set against the background of a terrible drought which may well have destroyed the Akkadian Empire, it records the exchanges of a fox or jackal, a wolf, a lion and a dog. The last of these animals, especially, seems to bear a tragic destiny, of a sort that traditional literature tends to identify exclusively with the “human condition.” The essay goes on to trace how the story may have been the origin of a tradition which includes such important literary works as the Hindu Panchatantra, the Arab Kalila wa Dimna and even Shakespeare's “Othello.” Finally, it concludes with suggestions as to how recognition of tragedy not simply as part of “the human condition” but also as a bond with animals and the environment may open new aesthetic possibilities in the years to come.     

Kinematic construction of the trajectory of sequential arm movements

A kinematic construction rule determining the trajectory of human sequential movements is formulated using minimum-jerk and minimum-angular-jerk trajectories. The kinematic construction rule states that the observed trajectory of sequential movements coincides with a weighted average of the minimum-jerk trajectory and the segmented minimum-angular-jerk trajectory. This rule covers not only point-to-point movements but also simple sequential movements. Five kinds of experiments that measure the trajectories in planar, multijoint sequential arm movements were conducted. The measured trajectories coincide with the predictions made on the basis of the kinematic construction rule presented here. Moreover, predictions of previous models such as the minimum-jerk, the equilibrium-trajectory, and the minimum-torque-change models are shown to be incompatible with our observations of sequential movements. Received: 31 October 1997 /Accepted in revised form: 18 November 1998     

Bearbeitergesteuerte Analyse von Verhaltenszeitreihen am Digitalrechner

1. Both the organization of behaviour and communicative interactions can be established by analyzing behavioural time series. By means of an analysis of this kind, conclusions about the control of behaviour and the principles of interindividual communication can be reached. An analysis may be based on simultaneous and successive behavioural events. In these multi-channel time series the temporal arrangement of patterns (“Strukturierung”), the organization and the conditions determining the occurrence of behavioural events can be specified.
2. Data-analysis by digital computer permits rapid processing of a large quantity of material in regard to several respects. “Sets of data” can be stored, thus enabling the user to correct, alter, combine and finally analyze them with respect to various questions. For this purpose, a program system for the digital processing of behavioural time series (title “PROVED”) was developed.
3. The course of behavioural events is composed of temporal patterns which are ordered in a definite hierarchy (Fig. 1). Several quantitative and qualitative characteristics (“Muster-Merkmale”) can be attributed to each pattern (Figs. 2,4). With the PROVED-System, the temporal arrangement of behavioural patterns is reestablished by the computer according to the control orders of the user. These orders must take into consideration the physiological relevance that is to be confirmed by an analysis of time serics (Fig. 3). The orders controlling the temporal arragement as well as the asignment of pattern characteristics to sets of data are available for further evaluation.
4. The PROVED-System includes several procedures involving input, output, storage, administration, correction, assignment of characteristics, temporal arrangement and analysis of data. The examiner can select and combine these procedures at will using statements of a particular control language.
5. During the first step of data analysis, a fixed number of parameters for each pattern is determined, the number of parameters varying with the complexity of the problem. Any measured value which is related to the pattern under investigation can be regarded as a parameter. During the second step, multidimensional frequency distributions of crossclassified parameters are established which can be examined by means of statistical tests (third step) (Figs. 5,6).
6. Determination of the parameters by the examiner decisively influences the further course of the analysis. The control statements for one parameter consist of two parts: 1. quality of the parameter (type of pattern, temporal distance, etc.), 2. position of the parameter in the behavioural time series (pattern under investigation, immediately subsequent pattern, next pattern with the same characteristics, etc.). The latter is determined by a series of shifts of indices controlled by the user (Fig. 7,8).
7. The PROVED-System can be applied to the analysis of various behavioural time series (succession of sounds, recordings of movements, observations of behavioural acts, etc.). Depending upon the aim of the analysis (temporal arrangement, organization, control of behaviour or communication), spontaneous behavioural events, input-output experiments (stimulus-reaction) and social interaction can be evaluated.

     

“野生动物”的概念框架和术语定义

“野生动物”(wild animal)一词不止在我国, 在全球的英语使用者中也有不同的含义。通过梳理相关研究、国内法和国际法背景下的定义和适用范围, 结合人类对动物繁殖和生活条件的控制情况, 本文提出了“野生动物”的二维概念框架, 梳理了动物从“野生”到“驯化”的12个连续状态。以下状态即未经中长期人工选择的动物类群应被视为野生动物: (1)其在荒野自然或人工环境(如城市或乡村)中自由生存繁殖, 无论是否存在人工投喂、经救护或辅助生殖后被放归的个体; (2)被捕捉圈养在人工环境中生活, 或源自野外但在圈养条件下出生的个体; (3)直系血亲(《濒危野生动植物种国际贸易公约》解释为世系前四代)仍有野外来源的人工繁育后代; (4)放生、逃逸或引入到自然环境中的人工繁育个体。在野生动物物种保护的目标和语境之下, 经过长期人工选择的驯化动物, 无论其是否在人类控制下生活, 如家养猫狗、家禽家畜或模式实验动物, 以及流浪猫狗、放生禽畜和野化家养动物等都不是“野生动物”。但对于一些经过一定程度的人工选择, 所处人类控制情况和对野外种群的影响各异(如经过多代人工繁育的驯养动物、因人类活动导致的外来动物等), 其是否需被作为野生动物管理, 则需要根据生态安全、物种管理、立法目标等特别设定监管范围。《中华人民共和国野生动物保护法》的保护对象可以考虑为: 受到人类威胁濒临灭绝的, 或者具有重要生态作用的野生动物物种, 其状态可不限于是在野外还是人工控制条件下。其他动物的管理, 可根据遗传资源保护、疫病防控、动物福利和生态安全等需要, 另外设立《动物福利法》《生物安全法》等, 并和已有的法律法规如《动物防疫法》《渔业法》等做好衔接。本文还就《野生动物保护法》可能采用的“野生动物”定义提出建议。     

Virtual trajectory and stiffness ellipse during multijoint arm movement predicted by neural inverse models

We predict the virtual trajectories and stiffness ellipses during multijoint arm movements by computer simulations. A two-link manipulator with four single-joint muscles and two double-joint muscles is used as a model of the human arm. Physical parameters of the model are derived from several experimental data. Among them, special emphasis is put on low values of the dynamic hand stiffness recently measured during single joint and multijoint movements. The feedback-error-learning scheme to acquire the inverse dynamics model and the inverse statics model is utilized for this prediction. The virtual trajectories are much more complex than the actual trajectories. This indicates that planning the virtual trajectory is as difficult as solving the inverse dynamics problem for medium and fast movements, and simply falsifies the advocated computational advantage of the virtual trajectory control hypothesis. Thus, we conclude that learning inverse models is essential even in the virtual trajectory control framework. Finally, we propose a new computational model to learn the complicated shape of the virtual trajectories by integrating the virtual trajectory control and the feedback-error-learning scheme.     

Plastic,inquisitive roots and intelligent plants in the light of some new vistas in plant biology

Abstract

Metaphors, such as those used in the title of this article, are often useful for the comprehension of specialised topics in plant biology. A brief attempt is made to elucidate one of these metaphors, plant “intelligence”, as it relates to the plastic responses of roots and root systems to their environment. Tropisms and nastic movements of root apices are two expressions of an inherent plasticity of form exhibited by roots. In soil, roots are exposed to multiple stimuli, many of which can potentially elicit such movements. Hence, a key question is how roots respond to and process the different stimuli which simultaneously reach their surfaces. Assuming that roots always use the same site along their length to express their movement responses, and that they also use an auxin‐based information‐transduction pathway, the most evident choices for the processing of stimuli are that roots either prioritise the various incoming stimuli and respond only to the strongest or they amalgamate stimuli and mount an averaged compromise response to all of them. The proposal that plants may be “intelligent”, especially in respect to their plastic growth responses, is one that draws upon knowledge of this faculty from animal biology. Also implied is that plants and animals are sufficiently similar to share usage of this term “intelligence”. But an alternative view is that plants and animals are sufficiently different and so intelligence is an unfitting term. Following the line of enquiry into creative evolution initiated by Henri Bergson, plants can be viewed differently to animals. The tendency of plants is towards instinctive behaviour rather than intelligent behaviour.     

Animal morality: What is the debate about?

Empirical studies of the social lives of non-human primates, cetaceans, and other social animals have prompted scientists and philosophers to debate the question of whether morality and moral cognition exists in non-human animals. Some researchers have argued that morality does exist in several animal species, others that these species may possess various evolutionary building blocks or precursors to morality, but not quite the genuine article, while some have argued that nothing remotely resembling morality can be found in any non-human species. However, these different positions on animal morality generally appear to be motivated more by different conceptions of how the term “morality” is to be defined than by empirical disagreements about animal social behaviour and psychology. After delving deeper into the goals and methodologies of various of the protagonists, I argue that, despite appearances, there are actually two importantly distinct debates over animal morality going on, corresponding to two quite different ways of thinking about what it is to define “morality”, “moral cognition”, and associated notions. Several apparent skirmishes in the literature are thus cases of researchers simply talking past each other. I then focus on what I take to be the core debate over animal morality, which is concerned with understanding the nature and phylogenetic distribution of morality conceived as a psychological natural kind. I argue that this debate is in fact largely terminological and non-substantive. Finally, I reflect on how this core debate might best be re-framed.     

Kinematic description of variability of fast movements: analytical and experimental approaches

Analysis of variability of fast aimed movements predicts the properties of trajectory variance. The analysis is based on a kinematic model with nonlinear changes in “internal time”. The purpose of the work was to identify different sources of variability and their influence on the trajectory variance. An analytical expression for the speed-accuracy trade-off is introduced. Experiments were performed with subjects making single-joint elbow flexion movements over different distances as fast as possible with their eyes closed to memorized targets. Standard deviation of movement trajectory increased during the first part of the movement and subsequently decreased. The variance peaked after the time of peak velocity, close to the time of peak deceleration. A dependence of the trajectory variance on movement distance (speed-accuracy trade-off) was seen during the movement (at times of peak velocity and peak deceleration) but not after the movement termination. We conclude that the previously reported drop in the variability of movement trajectory during the deceleration phase does not necessarily mean a compensation by the control system but may result from purely kinematic properties of the movement. The importance of the time of measurement for analysis of the speed-accuracy trade-offs is emphasized.