nils-herrmann/clean_scirepeval huggingface dataset:
Structural fiber reinforcement of keel blubber in harbor porpoise (Phocoena phocoena)
Venue: Journal of Morphology

This study investigated the functional morphology of the blubber that forms the caudal keels of the harbor porpoise (Phocoena phocoena). Blubber is a pliant biocomposite formed by adipocytes and structural fibers composed of collagen and elastic fibers. Caudal keels are dorsally and ventrally placed triangular wedges of blubber that define the hydrodynamic profile of the porpoise tailstock. Mechanical tests on carcasses demonstrate that when keels are bent, they strain nonuniformly along their lengths, with highest strains just caudal to the dorsal fin and lowest at the insertion of the flukes. Therefore, caudal keels undergo nonuniform longitudinal deformation while maintaining a stable, triangular cross‐sectional shape. Polarizing and transmitted light microscopy techniques were used to investigate blubber's 3D fiber architecture along the length of the dorsal keel. The triangular cross‐sectional shape of the keel appears to be maintained by structural fibers oriented to act as tensile stays. The construction of the blubber composite is regionally specific :structural fiber densities and diameters are higher in the relatively stiff caudal region of the keel than in the more deformable cranial keel region. The orientations of structural fibers also change along the length of the keel. Cranially, no fibers are oriented along the long axis, whereas a novel population of longitudinally oriented fibers reinforces the keel at the insertion of the flukes. Thus, differences in the distribution and orientation of structural fibers contribute to the regionally specific mechanical properties of the dorsal keel.  2004.
The ice worm, Mesenchytraeus solifugus, elevates adenylate levels at low physiological temperature.
Venue: Comparative Biochemistry and Physiology A-molecular & Integrative Physiology

The ice worm, Mesenchytraeus solifugus, is among a few metazoan species that survive exclusively in glacier ice/snow. In this study, we demonstrate that ice worm adenylate levels [i.e. adenosine 5'-triphosphate (ATP), ADP and AMP] are maintained at levels well above their mesophilic counterparts, and that their response to temperature change is distinctly opposite, namely, ice worms increase energy levels as temperatures fall. Initially, this response is characterized by a sharp spike in [ATP] and the adenylate energy charge (even at sub-zero temperatures), which is followed by corresponding increases in [ADP] and [AMP] within a few days. These results suggest that ice worms have evolved a compensatory mechanism by which gains in adenylate nucleotides off-set, at least in part, the inherent lethargy and death usually associated with cold temperature.
Cnidocyte mechanoreceptors are tuned to the movements of swimming prey by chemoreceptors.
Venue: Science

Cnidocytes, the stinging cells of cnidarians, discharge nematocysts in response to physical contact accompanied by the stimulation of specific chemoreceptors. Cnidocytes in fishing tentacles of a sea anemone are now found to discharge nematocysts preferentially into targets vibrating at 30, 55, and 65 to 75 hertz. Moreover, in the presence of submicromolar concentrations of known chemosensitizers, such as N-acetylated sugars and mucin, these optima shift to 5, 15, 30, and 40 hertz, frequencies that correspond to the movements of swimming prey. Hence, chemoreceptors for these substances tune cnidocyte mechanoreceptors to frequencies that match the movements of the prey.
Thermoregulation: What Role for UCPs in Mammals
and Birds?
Venue: Bioscience Reports

Mammals and birds are endotherms and respond to cold exposure by the means of regulatory thermogenesis, either shivering or non-shivering. In this latter case, waste of cell energy as heat can be achieved by uncoupling of mitochondrial respiration. Uncoupling proteins, which belong to the mitochondrial carrier family, are able to transport protons and thus may assume a thermogenic function. The mammalian UCP1 physiological function is now well understood and gives to the brown adipose tissue the capacity for heat generation. But is it really the case for its more recently discovered isoforms UCP2 and UCP3? Additionally, whereas more and more evidence suggests that non-shivering also exists in birds, is the avian UCP also involved in response to cold exposure? In this review, we consider the latest advances in the field of UCP biology and present putative functions for UCP1 homologues.
Heat Exchange from the Toucan Bill Reveals a Controllable Vascular Thermal Radiator
Venue: Science

Toucan Heat Exchanger Toucans are instantly recognizable by their large bills, which in the toco toucan (Ramphastos toco) accounts for about one-third of the total body length. The toucan's bill has been interpreted as a sexual ornament and as an adaptation for handling fruit. Tattersall et al. (p. 468) explore an alternative explanation in which the bill serves primarily as a thermoregulator. Infrared thermography techniques, which allow detailed observations with minimal disturbance to the birds, show that the birds alter blood flow to the bill according to ambient conditions, effectively using it as a radiator to “dump heat.” Toucans alter blood flow to their massive bills according to ambient conditions. The toco toucan (Ramphastos toco), the largest member of the toucan family, possesses the largest beak relative to body size of all birds. This exaggerated feature has received various interpretations, from serving as a sexual ornament to being a refined adaptation for feeding. However, it is also a significant surface area for heat exchange. Here we show the remarkable capacity of the toco toucan to regulate heat distribution by modifying blood flow, using the bill as a transient thermal radiator. Our results indicate that the toucan's bill is, relative to its size, one of the largest thermal windows in the animal kingdom, rivaling elephants’ ears in its ability to radiate body heat.
Revisiting a medical case of “stinging” in the human oral cavity caused by ingestion of raw squid (Cephalopoda: Teuthida): new data on the functioning of squid’s spermatophores
Venue: Zoomorphology

Male squid produce intricate spermatophores that, when transferred to the female, undergo the spermatophoric reaction, a complex process of evagination that leads to the attachment of the spermatangium, that is, the everted spermatophore containing the sperm mass. While this process is still not completely understood, the medical literature includes several reports of “oral stinging” (i.e., punctured wounds in the human oral cavity) following consumption of raw male squid, which contains undischarged spermatophores able to inflict such wounds. Here, we revisit a recent medical report of oral stinging by Shiraki et al.
An excitable gene regulatory circuit induces transient cellular differentiation
Venue: Nature

Certain types of cellular differentiation are probabilistic and transient. In such systems individual cells can switch to an alternative state and, after some time, switch back again. In Bacillus subtilis, competence is an example of such a transiently differentiated state associated with the capability for DNA uptake from the environment. Individual genes and proteins underlying differentiation into the competent state have been identified, but it has been unclear how these genes interact dynamically in individual cells to control both spontaneous entry into competence and return to vegetative growth. Here we show that this behaviour can be understood in terms of excitability in the underlying genetic circuit. Using quantitative fluorescence time-lapse microscopy, we directly observed the activities of multiple circuit components simultaneously in individual cells, and analysed the resulting data in terms of a mathematical model. We find that an excitable core module containing positive and negative feedback loops can explain both entry into, and exit from, the competent state. We further tested this model by analysing initiation in sister cells, and by re-engineering the gene circuit to specifically block exit. Excitable dynamics driven by noise naturally generate stochastic and transient responses, thereby providing an ideal mechanism for competence regulation.
The contribution of mineral to the material properties of vertebral cartilage from the smooth-hound shark Mustelus californicus
Venue: The Journal of Experimental Biology

Elasmobranch vertebral cartilage has a substantial mineral fraction (39–55%) and the arrangement of mineral varies among species. We examined vertebrae from one shark species, Mustelus californicus, to determine mineral content, the effect of mineral on material properties and the viscoelastic response of vertebral cartilage. We serially demineralized vertebrae and compressively tested them to failure at varying strain rates. Mineral in vertebral cartilage varies within individuals, intraspecifically and interspecifically; this is in contrast to bone, in which significant variation in mineral content is pathological or an interspecific effect. Within Mustelus, vertebrae with larger mineral fractions were significantly stiffer and stronger; however when variation is assessed across species, the structure has a larger effect. Shark vertebral cartilage did not show a substantial viscoelastic response at biologically relevant strain rates, validating the use of quasistatic testing for this material.
Exploiting social evolution in biofilms.
Venue: Current Opinion in Microbiology

Bacteria are highly social organisms that communicate via signaling molecules, move collectively over surfaces and make biofilm communities. Nonetheless, our main line of defense against pathogenic bacteria consists of antibiotics-drugs that target individual-level traits of bacterial cells and thus, regrettably, select for resistance against their own action. A possible solution lies in targeting the mechanisms by which bacteria interact with each other within biofilms. The emerging field of microbial social evolution combines molecular microbiology with evolutionary theory to dissect the molecular mechanisms and the evolutionary pressures underpinning bacterial sociality. This exciting new research can ultimately lead to new therapies against biofilm infections that exploit evolutionary cheating or the trade-off between biofilm formation and dispersal.
Lunar Rhythm in the Emergence of an Ephemeropteran
Venue: Nature

IN a paper published in 1927, Hora1 suggests that the swarming of some Ephemeroptera is related to the lunar cycle. Evidence has been obtained which suggests that Povilla adusta Navas, a mayfly widely distributed in Central and Southern Africa, shows such a rhythm of emergence in Uganda. The interest of this lies in the fact that very few examples are known of lunar rhythms in non-marine animals (see Gaspers2).
Starling Flock Networks Manage Uncertainty in Consensus at Low Cost
Venue: PLOS Computational Biology

Flocks of starlings exhibit a remarkable ability to maintain cohesion as a group in highly uncertain environments and with limited, noisy information. Recent work demonstrated that individual starlings within large flocks respond to a fixed number of nearest neighbors, but until now it was not understood why this number is seven. We analyze robustness to uncertainty of consensus in empirical data from multiple starling flocks and show that the flock interaction networks with six or seven neighbors optimize the trade-off between group cohesion and individual effort. We can distinguish these numbers of neighbors from fewer or greater numbers using our systems-theoretic approach to measuring robustness of interaction networks as a function of the network structure, i.e., who is sensing whom. The metric quantifies the disagreement within the network due to disturbances and noise during consensus behavior and can be evaluated over a parameterized family of hypothesized sensing strategies (here the parameter is number of neighbors). We use this approach to further show that for the range of flocks studied the optimal number of neighbors does not depend on the number of birds within a flock; rather, it depends on the shape, notably the thickness, of the flock. The results suggest that robustness to uncertainty may have been a factor in the evolution of flocking for starlings. More generally, our results elucidate the role of the interaction network on uncertainty management in collective behavior, and motivate the application of our approach to other biological networks.
Immunochemical and electrophysiological analyses of magnetically responsive neurons in the mollusc Tritonia diomedea
Venue: Journal of Comparative Physiology A-neuroethology Sensory Neural and Behavioral Physiology

Tritonia diomedea uses the Earth’s magnetic field as an orientation cue, but little is known about the neural mechanisms that underlie magnetic orientation behavior in this or other animals. Six large, individually identifiable neurons in the brain of Tritonia (left and right Pd5, Pd6, Pd7) are known to respond with altered electrical activity to changes in earth-strength magnetic fields. In this study we used immunochemical, electrophysiological, and neuroanatomical techniques to investigate the function of the Pd5 neurons, the largest magnetically responsive cells. Immunocytochemical studies localized TPeps, neuropeptides isolated from Pd5, to dense-cored vesicles within the Pd5 somata and within neurites adjacent to ciliated foot epithelial cells. Anatomical analyses revealed that neurites from Pd5 are located within nerves innervating the ipsilateral foot and body wall. These results imply that Pd5 project to the foot and regulate ciliary beating through paracrine release. Electrophysiological recordings indicated that, although both LPd5 and RPd5 responded to the same magnetic stimuli, the pattern of spiking in the two cells differed. Given that TPeps increase ciliary beating and Tritonia locomotes using pedal cilia, our results are consistent with the hypothesis that Pd5 neurons control or modulate the ciliary activity involved in crawling during orientation behavior.
Mutual Feedbacks Maintain Both Genetic and Species Diversity in a Plant Community
Venue: Science

The forces that maintain genetic diversity among individuals and diversity among species are usually studied separately. Nevertheless, diversity at one of these levels may depend on the diversity at the other. We have combined observations of natural populations, quantitative genetics, and field experiments to show that genetic variation in the concentration of an allelopathic secondary compound in Brassica nigra is necessary for the coexistence of B. nigra and its competitor species. In addition, the diversity of competing species was required for the maintenance of genetic variation in the trait within B. nigra. Thus, conservation of species diversity may also necessitate maintenance of the processes that sustain the genetic diversity of each individual species.
Moving calls: a vocal mechanism underlying quorum decisions in cohesive groups
Venue: Proceedings of The Royal Society B: Biological Sciences

Members of social groups need to coordinate their behaviour when choosing between alternative activities. Consensus decisions enable group members to maintain group cohesion and one way to reach consensus is to rely on quorums. A quorum response is where the probability of an activity change sharply increases with the number of individuals supporting the new activity. Here, we investigated how meerkats (Suricata suricatta) use vocalizations in the context of movement decisions. Moving calls emitted by meerkats increased the speed of the group, with a sharp increase in the probability of changing foraging patch when the number of group members joining the chorus increased from two up to three. These calls had no apparent effect on the group's movement direction. When dominant individuals were involved in the chorus, the group's reaction was not stronger than when only subordinates called. Groups only increased speed in response to playbacks of moving calls from one individual when other group members emitted moving calls as well. The voting mechanism linked to a quorum probably allows meerkat groups to change foraging patches cohesively with increased speed. Such vocal coordination may reflect an aggregation rule linking individual assessment of foraging patch quality to group travel route.
An exceptionally fast actomyosin reaction powers insect flight muscle
Venue: Proceedings of the National Academy of Sciences of the United States of America

Insects, as a group, have been remarkably successful in adapting to a great range of physical and biological environments, in large part because of their ability to fly. The evolution of flight in small insects was accompanied by striking adaptations of the thoracic musculature that enabled very high wing beat frequencies. At the cellular and protein filament level, a stretch activation mechanism evolved that allowed high-oscillatory work to be achieved at very high frequencies as contraction and nerve stimulus became asynchronous. At the molecular level, critical adaptations occurred within the motor protein myosin II, because its elementary interactions with actin set the speed of sarcomere contraction. Here, we show that the key myosin enzymatic adaptations required for powering the very fast flight muscles in the fruit fly Drosophila melanogaster include the highest measured detachment rate of myosin from actin (forward rate constant, 3,698 s−1), an exceptionally weak affinity of MgATP for myosin (association constant, 0.2 mM−1), and a unique rate-limiting step in the cross-bridge cycle at the point of inorganic phosphate release. The latter adaptations are constraints imposed by the overriding requirement for exceptionally fast release of the hydrolytic product MgADP. Otherwise, as in Drosophila embryonic muscle and other slow muscle types, a step associated with MgADP release limits muscle contraction speed by delaying the detachment of myosin from actin.
Cytoplasmic Free Ca2+ in Arabidopsis Roots Changes in Response to Touch but Not Gravity
Venue: Plant Physiology

Changes in cytoplasmic Ca2+ concentration ([Ca2+]i) have been proposed to be involved in signal transduction pathways in response to a number of stimuli, including gravity and touch. The current hypothesis proposes that the development of gravitropic bending is correlated with a redistribution of [Ca2+]i in gravistimulated roots. However, no study has demonstrated clearly the development of an asymmetry of this ion during root curvature. We tested this hypothesis by quantifying the temporal and spatial changes in [Ca2+]i in roots of living Arabidopsis seedlings using ultraviolet-confocal Ca2+-ratio imaging and vertical stage fluorescence microscopy to visualize root [Ca2+]i. We observed no changes in [Ca2+]i associated with the graviresponse whether monitored at the whole organ level or in individual cells in different regions of the root for up to 12 h after gravistimulation. However, touch stimulation led to transient increases in [Ca2+]i in all cell types monitored. The increases induced in the cap cells were larger and longer-lived than in cells in the meristematic or elongation zone. One millimolar La3+ and 100 [mu]M verapamil did not prevent these responses, whereas 5 mM EGTA or 50 [mu]M ruthenium red inhibited the transients, indicating an intracellular origin of the Ca2+ increase. These results suggest that, although touch responses of roots may be mediated through a Ca2+-dependent pathway, the gravitropic response is not associated with detectable changes in
Unique Structural Features Facilitate Lizard Tail Autotomy
Venue: PLOS ONE

Autotomy refers to the voluntary shedding of a body part; a renowned example is tail loss among lizards as a response to attempted predation. Although many aspects of lizard tail autotomy have been studied, the detailed morphology and mechanism remains unclear. In the present study, we showed that tail shedding by the Tokay gecko (Gekko gecko) and the associated extracellular matrix (ECM) rupture were independent of proteolysis. Instead, lizard caudal autotomy relied on biological adhesion facilitated by surface microstructures. Results based on bio-imaging techniques demonstrated that the tail of Gekko gecko was pre-severed at distinct sites and that its structural integrity depended on the adhesion between these segments.
Variation in annual and lifetime reproductive success of lance-tailed manakins: alpha experience mitigates effects of senescence on siring success
Venue: Proceedings of The Royal Society B: Biological Sciences

The causes of variation in individual reproductive success over a lifetime are not well understood. In long-lived vertebrates, reproductive output usually increases during early adulthood, but it is difficult to disentangle the roles of development and learning on this gain of reproductive success. Lekking lance-tailed manakins provide an opportunity to separate these processes, as the vast majority of male reproduction occurs after a bird obtains alpha status and maintains a display area in the lek, but the age at which males achieve alpha status varies widely. Using 11 years of longitudinal data on age, social status and genetic siring success, I assessed the factors influencing variation in siring success by individuals over their lifetimes. The data show increases in annual reproductive success with both age and alpha experience. At advanced ages, these gains were offset by senescence in fecundity. Individual ontogeny, rather than compositional change of the population, generated a nonlinear relationship of breeding tenure with lifetime success; age of assuming alpha status was unrelated to tenure as a breeder, or success in the alpha role. Importantly, these findings suggest that social experience can mitigate the negative effects of senescence in older breeders.
Resolution of experimentally induced symmetrical conflicts of interest in meerkats
Venue: Animal Behaviour

Changes in activity in animal groups are a potential source of group fragmentation if members do not coordinate themselves. This coordination can become further complicated when individuals within a group face conflicts of interest. We experimentally induced symmetrical conflicts of interest over which direction to choose in meerkat, Suricata suricatta, groups. We trained dominant and subordinate individuals to expect food at locations in opposite directions when the group was still at its sleeping burrow (i.e. before the group started foraging). Trained individuals were more likely to initiate group departure in the direction of their rewarded location and there was no difference between dominants and subordinates in initiation rate. Initiation of group departure seemed to be the most important factor determining the final direction of the group, as the direction chosen by the first initiator was rarely challenged. We did not observe any obvious signals used to enhance recruitment during this process. Over the experimental days, initiator identity changed suggesting that individual motivation to initiate group departure varies from day to day. Meerkats voluntarily avoided immediate foraging benefits to maintain cohesion with the group, which probably prevented them from incurring costs associated with becoming isolated. We conclude that individuals refrain from initiating group splits when conflicts of interest are low and any individual can take the lead, often without the use of obvious signals other than the displacement itself.