nils-herrmann/clean_scirepeval huggingface dataset:
Only natural local odours allow homeward orientation in homing pigeons released at unfamiliar sites
Venue: Journal of Comparative Physiology A

According to the olfactory navigation hypothesis, birds are able to exploit the spatial distribution of environmental odourants to determine the direction of displacement and navigate from non-familiar locations. The so-called “olfactory activation hypothesis” challenged the specific role of olfactory cues in navigation by suggesting that olfactory stimuli only activate a navigational system that is based on non-olfactory cues, predicting that even artificial odourants alone are sufficient to allow unimpaired navigation. In this experiment, we compared tracks of experimental birds exposed to different olfactory stimuli before being made anosmic at the release site prior to release. One group of pigeons was exposed to purified air enriched with artificial odourants, while a second group was exposed to environmental air. The birds stimulated with artificial nonsense odourants displayed several behavioural differences from both untreated controls and anosmic pigeons exposed to environmental air prior to release: nonsense odourants birds were unable to determine the home direction, they mostly flew within a space outside the homeward oriented quadrant, and they flew shorter distances on the day of release. Our data failed to support a mere activational role of olfactory stimuli in navigation, and are consistent with the olfactory navigation hypothesis.
Oxygen consumption of desert pupfish at ecologically relevant temperatures suggests a significant role for anaerobic metabolism
Venue: Journal of Comparative Physiology B

Oxygen consumption is oftentimes used as a proxy for metabolic rate. However, pupfish acclimated to ecologically relevant temperatures may employ extended periods of anaerobism despite the availability of oxygen—a process we called paradoxical anaerobism. In this study, we evaluated data from pupfish exhibiting stable oxygen consumption. Routine oxygen consumption ($${R_{V{{\text{O}}_{\text{2}}}}}$$RVO2) of a refuge population derived from Cyprinodon spp. acclimated to 28 and 33 °C was evaluated at the ecologically relevant assay temperatures of between 25 and 38 °C. Different interpretations of the data are available depending on normalization. For instance, $${R_{V{{\text{O}}_{\text{2}}}}}$$RVO2 of smaller fish, measured per fish, was remarkably stable over a wide range of assay temperatures and was not different between acclimation groups. However, when measured on a mass-specific basis, $${R_{V{{\text{O}}_{\text{2}}}}}$$RVO2 in these same smaller fish increases more predictably as temperature increased. $${R_{V{{\text{O}}_{\text{2}}}}}$$RVO2 of refuge fish and the closely related pupfish, C. nevadensis mionectes, measured near their respective acclimation temperatures, were essentially identical. However, $${R_{V{{\text{O}}_{\text{2}}}}}$$RVO2 of 28 °C acclimated fish of both species, when measured at 34 °C, was greater than that of the 33 °C acclimated fish measured at 28 °C. We suggest that this observed ‘efficiency’ may result from significant anaerobic metabolism use. Experiments investigating factorial aerobic scope ($${\text{Ma}}{{\text{x}}_{V{{\text{O}}_{\text{2}}}}}$$MaxVO2/$${R_{V{{\text{O}}_{\text{2}}}}}$$RVO2) yielded values less than 1 in 21–36% of the 33 °C acclimated fish. These values indicate a substantial contribution of anaerobic metabolism to energy utilization by these fish. However, muscle lactate levels are not elevated in exercising fish—a result that is consistent with paradoxical anaerobism use.
Muscle-specific activation of calpain system in hindlimb unloading rats and hibernating Daurian ground squirrels: a comparison between artificial and natural disuse
Venue: Journal of Comparative Physiology B

To determine whether the regulation of calpain system is involved in non-hibernators and hibernators in disused condition, the soleus (SOL) and extensor digitorum longus (EDL) muscles were used for investigating the muscle mass, the ratio of muscle wet weight/body weight (MWW/BW), fiber-type distribution, fiber cross-sectional area (CSA), and the protein expression of MuRF1, calpain-1, calpain-2, calpastatin, desmin, troponin T, and troponin C in hindlimb unloading rats and hibernating Daurian ground squirrels. The muscle mass, MWW/BW, and fiber CSA were found significantly decreased in SOL and EDL of hindlimb unloading rats, but unchanged in hibernating ground squirrels. The MuRF1 expression was increased in both SOL and EDL of unloading rats, while it was only increased in SOL, but maintained in EDL of hibernating ground squirrels. The expression levels of calpain-1 and calpain-2 were increased in different degrees in unloaded SOL and EDL in rats, while they were maintained in EDL and even reduced in SOL of hibernating ground squirrels. Besides, the expression of calpastatin was decreased in unloaded rats, but increased in hibernating ground squirrels. The desmin expression was decreased in unloaded rats, but maintained in hibernating squirrels. Interestingly, the levels of troponin T and troponin C were decreased in both SOL and EDL of unloaded rats, but increased in hibernating ground squirrels with muscle-type specificity. In conclusion, differential calpain activation and substrate-selective degradation in slow and fast muscles are involved in the mechanisms of muscle atrophy of unloaded rats and remarkable ability of muscle maintenance of hibernating ground squirrels.
The energetics of torpor in a temperate passerine endemic to New Zealand, the Rifleman (Acanthisitta chloris)
Venue: Journal of Comparative Physiology B

Compared to other birds, passerines, reflecting their small mass, have a narrow set of behavioral characteristics. One difference is that few enter torpor, especially in temperate environments. The few that do include swallows, none of which live throughout the year in cold-temperate environments, because their food, flying insects, is not available in winter and no passerine is known to hibernate. They seasonally migrate to warm-temperate and tropical environments. We present data on the energetics of the Rifleman (Acanthisitta chloris), a small, insectivorous member of the Acanthisittidae, a passerine family endemic to temperate New Zealand. This family is considered to be the sister taxon to all living passerines, which raises the question whether its physiological and behavioral characteristics reflect its evolutionary status in a manner that distinguishes it from other passerines. Only two of the eight known species in this family survive; four of the extinct species were flightless, a condition that evolved independently three times and is almost absent from other passerines. The Rifleman readily enters torpor, which is facilitated by its small mass. It enters torpor at ambient temperatures that are commonly encountered in its wet, cool-to-cold environment. As a result, its body temperature and rate of metabolism are highly variable. An estimate of the basal rate of metabolism is similar to that expected from body mass. Unlike some  torpor-prone birds, the Rifleman is a permanent resident in a temperate environment. This residency is possible, because the Rifleman gleans insect prey from surfaces, which does not require insects to have high body temperatures for activity. Its only living relative, the endangered, insectivorous Rock Wren (Xenicus gilviventris), is a permanent resident at altitudes from ca. 1000 to 2500 m in the mountains of South Island, New Zealand. There it faces severe winter conditions that are not avoided by descent to lower altitudes. Its response to these conditions may be an extended period of torpor. The repeated evolution of a flightless condition possibly reflects some distinctive property of the acanthisittids. The evolution of torpor and a flightless condition in acanthisittids may have facilitated their survival on a geographically isolated, temperate landmass, and these character states permitted by the absence of endemic mammalian predators.
Ocean acidification: effects of pH on 45Ca uptake by lobster branchiostegites
Venue: Journal of Comparative Physiology B

Gill chambers of the Atlantic lobster, Homarus americanus, possess three structures that are involved with respiration and ion regulation: gill filaments, epipodites, and branchiostegites. This paper describes ion transport mechanisms present in the plasma membranes of branchiostegite epithelial cells and the effects of pH on the uptake of 45Ca by these processes. Partially purified membrane vesicles (PPMV) of branchiostegite cells were produced by a homogenization/centrifugation method that has previously been used to define ion transport processes in both crab and lobster gill tissues. In the present study, lobster branchiostegite PPMV 45Ca uptake was highest at pH 8.5 and lowest at pH values between 6.0 and 7.0 (p < 0.02). At pH 8.0, 45Ca uptake was a biphasic process consisting of a saturable process at low [Ca] and a linear process at higher [Ca]. At pH 6.0, 45Ca uptake was only a linear process and paralleled linear uptake at pH 8.0. A valinomycin/K+-induced membrane potential (PD, inside negative) doubled 45Ca uptake at pH 7.0 above that in the absence of a PD (p < 0.05). An induced PD at pH 8.0 did not significantly (p > 0.05) affect 45Ca uptake observed in the absence of a PD, but was threefold greater than uptake at pH 7.0 in the absence of a PD (p < 0.05). Amiloride (2 mM) did not affect 45Ca uptake at pH 8.0, but 2 mM amiloride + 100 µM verapamil reduced uptake by approximately 50%. In the presence of both 2 mM amiloride + 100 µM verapamil, 15 s 45Ca influx at pH 8.5 was a hyperbolic function of [Ca] (0.1–5 mM) (Km = 4.2 ± 0.3 mM; Jmax = 9792 ± 439 pmol/mg protein × 15 s). 45Ca influxes at pH 7.5 under the same conditions were also hyperbolic with Km = 8.3 ± 1.4 mM; Jmax = 10732 ± 1250 pmol/mg protein × 15 s. Km values were significantly different (p < 0.05), but Jmax values were not (p > 0.05). These results suggest that 45Ca uptake by lobster branchiostegites may have occurred by the combination of diffusion through a verapamil-inhibited calcium channel and carrier-mediated transport by amiloride-insensitive, electroneutral, 1Ca2+/2H+ antiporters. Decreased pH, as might occur during ocean acidification, did not appear to modify calcium diffusion through the channels, but protons acted as competitive inhibitors of calcium transport by carrier-mediated antiport. Decreased calcium uptake with continued ocean acidification may significantly affect calcification processes during periodic molting, potentially influencing mortality.
Savanna elephants maintain homeothermy under African heat
Venue: Journal of Comparative Physiology B

To conserve body water, mammals may reduce evaporative water loss by storing heat, allowing core body temperature to rise more than usual during the day, and to fall more than usual during the cooler night, so demonstrating heterothermy. It has been proposed that elephants are heterothermic, but body temperature never has been measured in elephants over 24 h at environmental temperatures higher than body temperature, where elephants would have to rely on evaporative cooling to maintain homeothermy. We used ingested temperature data loggers to record core temperature of four partly free-ranging savanna elephants exposed to high solar radiation and environmental temperatures that exceeded core temperature (> 36 °C) in their natural habitat. The elephants maintained core temperature at an average 36.6 °C within narrow daily limits of about 1.3 °C. While mean 24-h core temperature increased with maximum air temperature, it did not increase with mean air temperature. Maximum and minimum daily core temperatures also did not change with maximum air temperatures. As a result, core temperature range remained constant despite large variations in daily air temperatures. Contrary to the view that elephants exhibit heterothermy to cope with heat, savanna elephants in their natural habitat with access to adequate resources of food and water, and able to use thermoregulatory behaviour, maintained homeothermy.
Species-specific low plasma glucose in fish is associated with relatively high tissue glucose content and is inversely correlated with cardiac glycogen content
Venue: Journal of Comparative Physiology B

The relationship between plasma glucose concentration and intracellular glucose (liver, heart, brain, gill, gonad, intestine, kidney, spleen, white muscle) was determined in fish species with a range in plasma glucose (Atlantic cod, 5.06 mM; cunner, 3.8 mM; rainbow trout, 3.7 mM; lumpfish, 0.9 mM; short-horned sculpin, 0.6 mM; and winter flounder, 0.6 mM). The ratio of intracellular glucose/plasma glucose was always higher than one in liver for all species consistent with a diffusion gradient from the tissue to the plasma. In all other tissues in Atlantic cod, cunner, and rainbow trout the diffusion gradient was from the plasma to the intracellular space. In short-horned sculpin, the mean ratio in heart and white muscle exceeded one and in winter flounder the ratio was significantly greater than one at 5.97 and 2.92 for heart and muscle, respectively. The presence of an active glucose 6-phosphatase in white muscle could account for elevated amounts of free glucose. The white muscle of all species displayed phosphoenolpyruvate carboxykinase and in winter flounder the activity was as high in white muscle as in liver suggesting that gluconeogenesis may be associated with a relatively high-muscle glucose content. The glycogen content was highest in liver followed by heart with lower amounts in all other tissues. There was an inverse correlation between heart glycogen content and plasma glucose concentration when all species were included. It is contended that in species with low plasma glucose, heart glycogen is accumulated at a slow rate under normoxia, to be called upon under hypoxic conditions when the gradient for inward diffusion is unfavourable for high rates of glucose metabolism.
The role of spatial texture in visual control of bumblebee learning flights
Venue: Journal of Comparative Physiology A

When leaving the nest for the first time, bees and wasps perform elaborate learning flights, during which the location of the nest is memorised. These flights are characterised by a succession of arcs or loops of increasing radius centred around the nest, with an incremental increase in ground speed, which requires precise control of the flight manoeuvres by the insect. Here, we investigated the role of optic flow cues in the control of learning flights by manipulating spatial texture in the ventral and panoramic visual field. We measured height, lateral displacement relative to the nest and ground speed during learning flights in bumblebees when ventral and panoramic optic flow cues were present or minimised, or features of the ground texture varied in size. Our observations show that ventral optic flow cues were required for the smooth execution of learning flights. We also found that bumblebees adjusted their flight height in response to variations of the visual texture on the ground. However, the presence or absence of panoramic optic flow did not have a substantial effect on flight performance. Our findings suggest that bumblebees mainly rely on optic flow information from the ventral visual field to control their learning flights.
Lateral undulation of the flexible spine of sprawling posture vertebrates
Venue: Journal of Comparative Physiology A

Sprawling posture vertebrates have a flexible spine that bends the trunk primarily in the horizontal plane during locomotion. By coordinating cyclical lateral trunk flexion and limb movements, these animals are very mobile and show extraordinary maneuverability. The dynamic and static stability displayed in complex and changing environments are highly correlated with such lateral bending patterns. The axial dynamics of their compliant body can also be critical for achieving energy-efficient locomotion at high velocities. In this paper, lateral undulation is used to characterize the bending pattern. The production of ground reaction forces (GRFs) and the related center of mass (COM) dynamics during locomotion are the fundamental mechanisms to be considered. Mainly based on research on geckos, which show unrestricted movement in three-dimensional space, we review current knowledge on the trunk flexibility and waveforms of lateral trunk movement. We investigate locomotion dynamics and mechanisms underlying the lateral undulation pattern. This paper also provides insights into the roles of this pattern in obtaining flexible and efficient walking, running, and climbing. Finally, we discuss the potential application of lateral undulation patterns to bio-inspired robotics.
Olfactory navigation versus olfactory activation: a controversy revisited
Venue: Journal of Comparative Physiology A

In the early 1970s, Floriano Papi and colleagues proposed the olfactory-navigation hypothesis, which explains the homing ability of pigeons by the existence of an odor-based map acquired through learning. This notion, although supported by some observations, has also generated considerable controversy since its inception. As an alternative, Paulo Jorge and colleagues formulated in 2009 the olfactory-activation hypothesis, which states that atmospheric odorants do not provide navigational information but, instead, activate a non-olfactory path integration system. However, this hypothesis is challenged by an investigation authored by Anna Gagliardo and colleagues and published in the current issue of the Journal of Comparative Physiology A. In this editorial, the significance of the findings of this study is assessed in the broader context of the role of olfaction in avian navigation and homing, and experiments are suggested that might help to finally resolve the olfactory-navigation versus olfactory-activation controversy.
The peregrine falcon’s rapid dive: on the adaptedness of the arm skeleton and shoulder girdle
Venue: Journal of Comparative Physiology A

During a dive, peregrine falcons (Falco peregrinus) can reach a velocity of up to 320 km h− 1. Our computational fluid dynamics simulations show that the forces that pull on the wings of a diving peregrine can reach up to three times the falcon’s body mass at a stoop velocity of 80 m s− 1 (288 km h− 1). Since the bones of the wings and the shoulder girdle of a diving peregrine falcon experience large mechanical forces, we investigated these bones. For comparison, we also investigated the corresponding bones in European kestrels (Falco tinnunculus), sparrow hawks (Accipiter nisus) and pigeons (Columba livia domestica). The normalized bone mass of the entire arm skeleton and the shoulder girdle (coracoid, scapula, furcula) was significantly higher in F. peregrinus than in the other three species investigated. The midshaft cross section of the humerus of F. peregrinus had the highest second moment of area. The mineral densities of the humerus, radius, ulna, and sternum were highest in F. peregrinus, indicating again a larger overall stability of these bones. Furthermore, the bones of the arm and shoulder girdle were strongest in peregrine falcons.
Physiological protective action of dissolved organic carbon on ion regulation and nitrogenous waste excretion of zebrafish (Danio rerio) exposed to low pH in ion-poor water
Venue: Journal of Comparative Physiology B

Dissolved organic carbon (DOC) represents a heterogeneous group of naturally-occurring molecules in aquatic environments, and recent studies have evidenced that optically dark DOCs can exert some positive effects on ionoregulatory homeostasis of aquatic organisms in acidic waters. We investigated the effects of Luther Marsh DOC, a dark allochthonous DOC, on ion regulation and N-waste excretion of zebrafish acutely exposed to either neutral or low pH in ion-poor water. In the first experiment, simultaneous exposure to pH 4.0 and DOC greatly attenuated the stimulation of Na+ diffusive losses (JoutNa), and prevented the blockade of Na+ uptake (JinNa) seen in zebrafish exposed to pH 4.0 alone, resulting in much smaller disturbances in Na+ net losses (JnetNa). DOC also attenuated the stimulation of net Cl− losses (JnetCl) and ammonia excretion (JnetAmm) during acidic challenge. In the second experiment, zebrafish acclimated to DOC displayed similar regulation of JinNa and JoutNa, and, therefore, reduced JnetNa at pH 4.0, effects which persisted even when DOC was no longer present. Protective effects of prior acclimation to DOC on JnetCl and JnetAmm at pH 4.0 also occurred, but were less marked than those on Na+ balance. Urea fluxes were unaffected by the experimental treatments. Overall, these effects were clearly beneficial to the ionoregulatory homeostasis of zebrafish at low pH, and were quite similar to those seen in a recent parallel study using darker DOC from the upper Rio Negro. This suggests that dark allochthonous DOCs share some chemical properties that render fish tolerant to ionoregulatory disturbances during acidic challenge.
Effects of ocean acidification and salinity variations on the physiology of osmoregulating and osmoconforming crustaceans
Venue: Journal of Comparative Physiology B

Survival, osmoregulatory pattern, oxygen consumption, energy spent on metabolism, ammonia excretion, type of oxidized energy substrate, and hepatosomatic index were evaluated in decapods (an osmoregulating crab, Callinectes danae, and an osmoconforming seabob shrimp, Xiphopenaeus kroyeri) exposed to carbon dioxide-induced water acidification (pH 7.3, control pH 8.0) and different salinities (20, 25, 30, 35, and 40‰) for 3 days. Compared to the animals kept at controlled pH, exposure to reduced pH resulted in the loss of osmoregulatory capacity in C. danae at all salinities, except for some hyporegulation at 40‰, and reduced oxygen consumption and ammonia excretion at 20 and 40‰. Xiphopenaeus kroyeri remained an osmoconformer in all evaluated conditions, except for some hyporegulation at 40‰, and when exposed to the reduced pH, it presented changes in oxygen consumption at all salinities and reductions in ammonia excretion at 20 and 35‰ compared to the control animals. Both species use protein as the main energy substrate and decrease the hepatosomatic index when exposed to reduced pH relative to the control. The observed changes may be associated with changes in the activity of enzymes related to osmoregulation, the use of amino acids as osmotic effectors of cell volume control and recovery, and the Bohr effect, and, because the gills are multifunctional organs related to osmoregulation, the changes may be related to acid–base control, nitrogen excretion, and respiration, with a change in one of these functions bringing about changes in the others.