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.

     

Behavior underpins the predictive power of a trait‐based model of butterfly movement

1. Dispersal ability is key to species persistence in times of environmental change. Assessing a species' vulnerability and response to anthropogenic changes is often performed using one of two methods: correlative approaches that infer dispersal potential based on traits, such as wingspan or an index of mobility derived from expert opinion, or a mechanistic modeling approach that extrapolates displacement rates from empirical data on short‐term movements.
2. Here, we compare and evaluate the success of the correlative and mechanistic approaches using a mechanistic random‐walk model of butterfly movement that incorporates relationships between wingspan and sex‐specific movement behaviors.
3. The model was parameterized with new data collected on four species of butterfly in the south of England, and we observe how wingspan relates to flight speeds, turning angles, flight durations, and displacement rates.
4. We show that flight speeds and turning angles correlate with wingspan but that to achieve good prediction of displacement even over 10 min the model must also include details of sex‐ and species‐specific movement behaviors.
5. We discuss what factors are likely to differentially motivate the sexes and how these could be included in mechanistic models of dispersal to improve their use in ecological forecasting.

     

Accounting for space and uncertainty in real‐time location system‐derived contact networks

1. Point data obtained from real‐time location systems (RTLSs) can be processed into animal contact networks, describing instances of interaction between tracked individuals. Proximity‐based definitions of interanimal “contact,” however, may be inadequate for describing epidemiologically and sociologically relevant interactions involving body parts or other physical spaces relatively far from tracking devices. This weakness can be overcome by using polygons, rather than points, to represent tracked individuals and defining “contact” as polygon intersections.
2. We present novel procedures for deriving polygons from RTLS point data while maintaining distances and orientations associated with individuals' relocation events. We demonstrate the versatility of this methodology for network modeling using two contact network creation examples, wherein we use this procedure to create (a) interanimal physical contact networks and (b) a visual contact network. Additionally, in creating our networks, we establish another procedure to adjust definitions of “contact” to account for RTLS positional accuracy, ensuring all true contacts are likely captured and represented in our networks.
3. Using the methods described herein and the associated R package we have developed, called contact, researchers can derive polygons from RTLS points. Furthermore, we show that these polygons are highly versatile for contact network creation and can be used to answer a wide variety of epidemiological, ethological, and sociological research questions.
4. By introducing these methodologies and providing the means to easily apply them through the contact R package, we hope to vastly improve network‐model realism and researchers' ability to draw inferences from RTLS data.

     

Rethinking trophic niches: Speed and body mass colimit prey space of mammalian predators

1. Realized trophic niches of predators are often characterized along a one‐dimensional range in predator–prey body mass ratios. This prey range is constrained by an “energy limit” and a “subdue limit” toward small and large prey, respectively. Besides these body mass ratios, maximum speed is an additional key component in most predator–prey interactions.
2. Here, we extend the concept of a one‐dimensional prey range to a two‐dimensional prey space by incorporating a hump‐shaped speed‐body mass relation. This new “speed limit” additionally constrains trophic niches of predators toward fast prey.
3. To test this concept of two‐dimensional prey spaces for different hunting strategies (pursuit, group, and ambush predation), we synthesized data on 63 terrestrial mammalian predator–prey interactions, their body masses, and maximum speeds.
4. We found that pursuit predators hunt smaller and slower prey, whereas group hunters focus on larger but mostly slower prey and ambushers are more flexible. Group hunters and ambushers have evolved different strategies to occupy a similar trophic niche that avoids competition with pursuit predators. Moreover, our concept suggests energetic optima of these hunting strategies along a body mass axis and thereby provides mechanistic explanations for why there are no small group hunters (referred to as “micro‐lions”) or mega‐carnivores (referred to as “mega‐cheetahs”).
5. Our results demonstrate that advancing the concept of prey ranges to prey spaces by adding the new dimension of speed will foster a new and mechanistic understanding of predator trophic niches and improve our predictions of predator–prey interactions, food web structure, and ecosystem functions.

     

Scale dependence of sex‐specific movement in a small‐bodied stream fish

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State‐space modeling reveals habitat perception of a small terrestrial mammal in a fragmented landscape

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Autoimmunity and the microbiome: T‐cell receptor mimicry of “self” and microbial antigens mediates self tolerance in holobionts

I propose a T‐cell receptor (TcR)‐based mechanism by which immunity mediates both “genetic self” and “microbial self” thereby, connecting microbiome disease with autoimmunity. The hypothesis is based on simple principles. First, TcR are selected to avoid strong cross‐reactivity with “self,” resulting in selection for a TcR repertoire mimicking “genetic self.” Second, evolution has selected for a “microbial self” that mimics “genetic self” so as to share tolerance. In consequence, our TcR repertoire also mimics microbiome antigenicity, providing a novel mechanism for modulating tolerance to it. Also, the microbiome mimics the TcR repertoire, acting as a secondary immune system. I call this TcR‐microbiome mimicry “holoimmunity” to denote immune tolerance to the “holobiont self.” Logically, microbiome‐host mimicry means that autoimmunity directed at host antigens will also attack components of the microbiome, and conversely, an immunological attack on the microbiome may cross‐react with host antigens producing “holoautoimmunity.”

     

Dietary Restraint and Control Over “Wanting” Following Consumption of “Forbidden” Food

Eating behavior can be influenced by the rewarding value of food, i.e., “liking” and “wanting.” The objective of this study was to assess in normal‐weight dietary restrained (NR) vs. unrestrained (NU) eaters how rewarding value of food is affected by satiety, and by eating a nonhealthy perceived, dessert‐specific food vs. a healthy perceived, neutral food (chocolate mousse vs. cottage cheese). Subjects (24NR age = 25.0 ± 8.2 years, BMI = 22.3 ± 2.1 kg/m²; 26NU age = 24.8 ± 8.0 years, BMI = 22.1 ± 1.7 kg/m²) came to the university twice, fasted (randomized crossover design). Per test‐session “liking” and “wanting” for 72 items divided in six categories (bread, filling, drinks, dessert, sweets, stationery (placebo)) was measured, before and after consumption of chocolate mousse/cottage cheese, matched for energy content (5.6 kJ/g) and individual daily energy requirements (10%). Chocolate mousse was liked more than cottage cheese (P < 0.05). After consumption of chocolate mousse or cottage cheese, appetite and “liking” vs. placebo were decreased in NR and NU (P < 0.03), whereas “wanting” was only decreased in NR vs. NU (P ≤ 0.01). In NR vs. NU “wanting” was specifically decreased after chocolate mousse vs. cottage cheese; this decrease concerned especially “wanting” for bread and filling (P < 0.05). To conclude, despite similar decreases in appetite and “liking” after a meal in NR and NU, NR decrease “wanting” in contrast to NU. NR decrease “wanting” specifically for a nonhealthy perceived, “delicious,” dessert‐specific food vs. a nutritional identical, yet healthy perceived, slightly less “delicious,” “neutral” food. A healthy perceived food may thus impose greater risk for control of energy intake in NR.     

Resolving the heading‐direction ambiguity in vertical‐beam radar observations of migrating insects

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Patterns on a parr: Drivers of long‐term salmon parr length in U.K. and French rivers depend on geographical scale

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Formation and function of the “Xestoleberis‐spot” in Xestoleberis hanaii (Crustacea: Ostracoda)

The crescent sculpture of the so‐called “Xestoleberis‐spot” develops inside the calcified valve of the family Xestoleberididae. Electron microscopic observations on both, intermoult and postmoult stages of Xestoleberis species reveal that the “Xestoleberis‐spot” system consists of three elements; two calcified chambers, a vesicle of electron‐dense material and an uncalcified procuticle. The formation and function of the “Xestoleberis‐spot” system are discussed. In conclusion, the “Xestoleberis‐spot” system functions as the muscle attachment site for several antennal muscles, and provides the material for chitinous fibers in the exocuticle of outer lamella. The unique cuticular structures of the family Xestoleberididae are due to the “Xestoleberis‐spot” system.     

Weak relationships of parasite infection with sexual and life‐history traits in wild‐caught Texas field crickets (Gryllus texensis)

1. Sex differences in immune investment and infection rate are predicted due to the divergent life histories of males and females, where females invest more toward immunity due to the fitness consequences of a reduced lifespan and males allocate less toward immunity due to increased resource investment in traits critical to sexual selection. Consequently, males are expected to fight infection less adeptly, resulting in higher parasite loads relative to females across all taxa.
2. Wild animals rarely face a single parasite within their given environment, yet nearly all studies on sex‐biased infection rates have focused on a single host–parasite relationship. Here, we investigate how simultaneous natural infections of ecto‐ and endosymbionts (i.e. both parasitic and phoretic taxa) correlate with sex biases in host immune response and reproductive investment in a field‐caught cricket, Gryllus texensis.
3. Our comprehensive analysis found no significant sex differences in two measures of immune response (melanization and nodulation), and found no strong evidence of a sex bias in the prevalence or intensity of parasitism by the three most common parasites infecting wild G. texensis field crickets (Eutrombidiidae, gregarines, and nematodes).
4. Two traits related to female fitness, egg number and egg size, showed no relation to parasitic infection; however, males having wider heads and poorer body condition were significantly more infected by eutrombidiid mites, gregarines, and nematodes.
5. Despite frequent predictions of male‐biased parasitism in the literature, our results concur with many other studies indicating that the divergent life histories of males and females alone are not sufficient to explain natural infection rates in wild insects.

     

“Active” and “passive” ecological restoration strategies in meta‐analysis

One of the means of creating a more robust methodology for ecological restoration involves reducing the gap between ecological theory and restoration practices. A common strategy to do so is using meta‐analysis to understand key drivers of restoration outcomes. “Active” and “passive” is a dichotomy often used to separate restoration strategies in such meta‐analyses. We investigate previously raised concerns about selection bias and subjective categorization of strategies. We promote a paired experimental design in future empirical research and propose the use of three categories of restoration strategy in lieu of “passive” and “active” to alleviate inconsistency in definitions and categorization.     

Long‐term sound and movement recording tags to study natural behavior and reaction to ship noise of seals

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“Capacity”, “best interests”, “will and preferences” and the UN Convention on the Rights of Persons with Disabilities

The United Nations (UN) Convention on the Rights of Persons with Disabilities (CRPD) is the most up‐to‐date international legal instrument concerning the rights of persons with disabilities. Such persons are taken to include those with serious mental disorders. According to an authoritative interpretation of a crucial Article (Article 12 ‐ Equal recognition before the law) by the UN CRPD Committee, involuntary detention and treatment of people with mental health disabilities are prohibited under the Convention. Both conventional mental health law and “capacity‐based” law are deemed to violate the Convention. However, some other UN bodies are not in full agreement (for example, the UN Human Rights Committee and the Subcommittee on Prevention of Torture and Other Cruel, Inhuman or Degrading Treatment or Punishment), while others are less explicitly absolutist (for example, the Human Rights Council). Furthermore, strong criticisms of the position of the CRPD Committee have been mounted from a number of academic quarters. These criticisms center on whether the role of a person's ability to make a decision can be ignored, no matter the circumstances. Much of the above debate turns on the concept of “legal capacity” and the now often‐repeated precept that one must always respect the “will and preferences” of the person with a disability. However, “will and preferences” remains undefined. In this paper, I offer an analysis of “will and preferences” that can clarify interventions that may be acceptable or non‐acceptable under the terms of the UN Convention.     

“Reverse” sexual dichromatism in a Neotropical frog

Sexual dichromatism is widespread among animals, but examples of “reverse” sexual dichromatism, in which females are more brightly colored than males, are extremely rare. We discovered a unique case of reverse sexual dichromatism in the golden rocket frog (Anomaloglossus beebei), a diurnal Neotropical frog. Females are bright “golden” in color, and males are drab tan with brown pigmentation that darkens when they are calling. Here, we document this color variation with calibrated digital photography and further show that there is no evidence for sex‐specific habitat matching; both sexes live in the same well‐lit habitat on green bromeliad leaves. Our results suggest that color variation in this species is an intraspecific signal and provide an important exception to the general expectation that males are more visually conspicuous in species with conventional sex roles.     

Automatic detection of fish and tracking of movement for ecology

1. Animal movement studies are conducted to monitor ecosystem health, understand ecological dynamics, and address management and conservation questions. In marine environments, traditional sampling and monitoring methods to measure animal movement are invasive, labor intensive, costly, and limited in the number of individuals that can be feasibly tracked. Automated detection and tracking of small‐scale movements of many animals through cameras are possible but are largely untested in field conditions, hampering applications to ecological questions.
2. Here, we aimed to test the ability of an automated object detection and object tracking pipeline to track small‐scale movement of many individuals in videos. We applied the pipeline to track fish movement in the field and characterize movement behavior. We automated the detection of a common fisheries species (yellowfin bream, Acanthopagrus australis) along a known movement passageway from underwater videos. We then tracked fish movement with three types of tracking algorithms (MOSSE, Seq‐NMS, and SiamMask) and evaluated their accuracy at characterizing movement.
3. We successfully detected yellowfin bream in a multispecies assemblage (F1 score =91%). At least 120 of the 169 individual bream present in videos were correctly identified and tracked. The accuracies among the three tracking architectures varied, with MOSSE and SiamMask achieving an accuracy of 78% and Seq‐NMS 84%.
4. By employing this integrated object detection and tracking pipeline, we demonstrated a noninvasive and reliable approach to studying fish behavior by tracking their movement under field conditions. These cost‐effective technologies provide a means for future studies to scale‐up the analysis of movement across many visual monitoring systems.

     

Accurate geometries for “Mountain pass” regions of the Ramachandran plot using quantum chemical calculations

Unusual local arrangements of protein in Ramachandran space are not well represented by standard geometry tools used in either protein structure refinement using simple harmonic geometry restraints or in protein simulations using molecular mechanics force fields. In contrast, quantum chemical computations using small poly‐peptide molecular models can predict accurate geometries for any well‐defined backbone Ramachandran orientation. For conformations along transition regions—ϕ from −60 to 60°—a very good agreement with representative high‐resolution experimental X‐ray (≤1.5 Å) protein structures is obtained for both backbone C⁻¹‐N‐C_α angle and the nonbonded O⁻¹…C distance, while “standard geometry” leads to the “clashing” of O…C atoms and Amber FF99SB predicts distances too large by about 0.15 Å. These results confirm that quantum chemistry computations add valuable support for detailed analysis of local structural arrangements in proteins, providing improved or missing data for less understood high‐energy or unusual regions.     

Carrier Transport and Recombination in Efficient “All‐Small‐Molecule” Solar Cells with the Nonfullerene Acceptor IDTBR

Reaching device efficiencies that can rival those of polymer‐fullerene Bulk Heterojunction (BHJ) solar cells (>10%) remains challenging with the “All‐Small‐Molecule” (All‐SM) approach, in part because of (i) the morphological limitations that prevail in the absence of polymer and (ii) the difficulty to raise and balance out carrier mobilities across the active layer. In this report, the authors show that blends of the SM donor DR3TBDTT (DR3) and the nonfullerene SM acceptor O‐IDTBR are conducive to “All‐SM” BHJ solar cells with high open‐circuit voltages (V_OC) >1.1 V and PCEs as high as 6.4% (avg. 6.1%) when the active layers are subjected to a post‐processing solvent vapor‐annealing (SVA) step with dimethyl disulfide (DMDS). Combining electron energy loss spectroscopy (EELS) analyses and systematic carrier recombination examinations, the authors show that SVA treatments with DMDS play a determining role in improving charge transport and reducing non‐geminate recombination for the DR3:O‐IDTBR system. Correlating the experimental results and device simulations, it is found that substantially higher BHJ solar cell efficiencies of >12% can be achieved if the IQE and carrier mobilities of the active layer are increased to >85% and >10^?4 cm² V^?1 s^?1, respectively, while suppressing the recombination rate constant k to <10^?12 cm³ s^?1.     

Encapsulated fusion protein confers “sense and respond” activity to chitosan–alginate capsules to manipulate bacterial quorum sensing

We demonstrate that “nanofactory”‐loaded biopolymer capsules placed in the midst of a bacterial population can direct bacterial communication. Quorum sensing (QS) is a process by which bacteria communicate through small‐molecules, such as autoinducer‐2 (AI‐2), leading to collective behaviors such as virulence and biofilm formation. In our approach, a “nanofactory” construct is created, which comprises an antibody complexed with a fusion protein that produces AI‐2. These nanofactories are entrapped within capsules formed by electrostatic complexation of cationic (chitosan) and anionic (sodium alginate) biopolymers. The chitosan capsule shell is crosslinked by tripolyphosphate (TPP) to confer structural integrity. The capsule shell is impermeable to the encapsulated nanofactories, but freely permeable to small molecules. In turn, the capsules are able to take in substrates from the external medium via diffusion, and convert these via the nanofactories into AI‐2, which then diffuses out. The exported AI‐2 is shown to stimulate QS responses in vicinal Escherichia coli. Directing bacterial population behavior has potential applications in next‐generation antimicrobial therapy and pathogen detection. We also envision such capsules to be akin to artificial “cells” that can participate in native biological signaling and communicate in real‐time with the human microbiome. Through such interaction capabilities, these “cells” may sense the health of the microbiome, and direct its function in a desired, host‐friendly manner. Biotechnol. Bioeng. 2013; 110: 552–562. © 2012 Wiley Periodicals, Inc.