nils-herrmann/clean_scirepeval huggingface dataset:
Solar-powered ventilation of African termite mounds
Venue: The Journal of Experimental Biology

How termite mounds function to facilitate climate control is still only partially understood. Recent experimental evidence in the mounds of a single species, the south Asian termite Odontotermes obesus, suggests that the daily oscillations of radiant heating associated with diurnal insolation patterns drive convective flow within them. How general this mechanism is remains unknown. To probe this, we consider the mounds of the African termite Macrotermes michaelseni, which thrives in a very different environment. By directly measuring air velocities and temperatures within the mound, we see that the overall mechanisms and patterns involved are similar to that in the south Asian species. However, there are also some notable differences between the physiology of these mounds associated with the temporal variations in radiant heating patterns and CO2 dynamics. Because of the difference between direct radiant heating driven by the position of the sun in African conditions, and the more shaded south Asian environments, we see changes in the convective flows in the two types of mounds. Furthermore, we also see that the south Asian mounds show a significant overturning of stratified gases, once a day, while the African mounds have a relatively uniform concentration of CO2. Overall, our observations show that despite these differences, termite architectures can harness periodic solar heating to drive ventilation inside them in very different environments, functioning as an external lung, with clear implications for human engineering.  Termite mounds harness oscillatory solar heating to drive internal ventilation of metabolic gases, functioning as an external lung for the colony. This passive mechanism has clear implications for human engineering.
Directional dependence of hydroxyapatite-collagen interactions on mechanics of collagen.
Venue: Journal of Biomechanics

Bone is a biological nanocomposite composed primarily of collagen and hydroxyapatite. The collagen molecules self-assemble to from a structure known as a fibril that comprises of about 85-95% of the total bone protein. In a fibril, the molecular level interactions at the interface between molecular collagen and hydroxyapatite nanocrystals have a significant role on its mechanical response. In this study, we have used molecular dynamics and steered molecular dynamics to study directional dependence of deformation response of collagen with respect to the hydroxyapatite surface. We have also studied mechanical response of collagen in the proximity of (0001) and (101 0) surfaces of hydroxyapatite. Our simulations indicate that the mechanics of collagen pulled in different directions with respect to hydroxyapatite is significantly different. Similar results were obtained for collagen pulled in the proximity of different crystallographic surfaces of hydroxyapatite.
The Ancient Chemistry of Avoiding Risks of Predation and Disease
Venue: Evolutionary Biology-new York

Illness, death, and costs of immunity and injury strongly select for avoidance of predators or contagion. Ants, cockroaches, and collembola recognize their dead using unsaturated fatty acids (e.g., oleic or linoleic acid) as “necromone” cues. Ants, bees, and termites remove dead from their nests (necrophoric behavior) whereas semi-social species seal off corpses or simply avoid their dead or injured (necrophobic behavior). Alarm and avoidance responses to exudates from injured conspecifics are widespread. This involves diverse pheromones, complex chemistry and learning. We hypothesized that necromones are a phylogenetically ancient class of related signals and predicted that terrestrial Isopoda (that strongly aggregate and lack known dispersants) would avoid body fluids and corpses using fatty acid “necromones.” Isopods were repelled by crushed conspecifics (blood), intact corpses, and alcohol extracts of bodies. As predicted, the repellent fraction contained oleic and linoleic acids and authentic standards repelled several isopod species. We further predicted a priori that social caterpillars (lacking known dispersants) would be repelled by their own body fluids and unsaturated fatty acids. Both tent caterpillars and fall webworms avoided branches treated with conspecific body fluid. Oleic and linoleic acids were also strongly avoided by both species. Necromone signaling appears widespread and likely traces to aquatic ancestors pre-dating the divergence of the Crustacea and Hexapoda at least 420 million years ago.
Degradation of alkanes by bacteria.
Venue: Environmental Microbiology

Pollution of soil and water environments by crude oil has been, and is still today, an important problem. Crude oil is a complex mixture of thousands of compounds. Among them, alkanes constitute the major fraction. Alkanes are saturated hydrocarbons of different sizes and structures. Although they are chemically very inert, most of them can be efficiently degraded by several microorganisms. This review summarizes current knowledge on how microorganisms degrade alkanes, focusing on the biochemical pathways used and on how the expression of pathway genes is regulated and integrated within cell physiology.
Reserves, Resilience and Dynamic Landscapes
Venue: AMBIO: A Journal of the Human Environment

In a world increasingly modified by human activities, the conservation of biodiversity is essential as insurance to maintain resilient ecosystems and ensure a sustainable flow of ecosystem goods and services to society. However, existing reserves and national parks are unlikely to incorporate the long-term and large-scale dynamics of ecosystems. Hence, conservation strategies have to actively incorporate the large areas of land that are managed for human use. For ecosystems to reorganize after large-scale natural and human-induced disturbances, spatial resilience in the form of ecological memory is a prerequisite. The ecological memory is composed of the species, interactions and structures that make ecosystem reorganization possible, and its components may be found within disturbed patches as well in the surrounding land-scape. Present static reserves should be complemented with dynamic reserves, such as ecological fallows and dynamic successional reserves, that are part of ecosystem management mimicking natural disturbance regimes at the landscape level.
How swifts control their glide performance with morphing wings
Venue: Nature

Gliding birds continually change the shape and size of their wings, presumably to exploit the profound effect of wing morphology on aerodynamic performance. That birds should adjust wing sweep to suit glide speed has been predicted qualitatively by analytical glide models, which extrapolated the wing’s performance envelope from aerodynamic theory. Here we describe the aerodynamic and structural performance of actual swift wings, as measured in a wind tunnel, and on this basis build a semi-empirical glide model. By measuring inside and outside swifts’ behavioural envelope, we show that choosing the most suitable sweep can halve sink speed or triple turning rate. Extended wings are superior for slow glides and turns; swept wings are superior for fast glides and turns. This superiority is due to better aerodynamic performance—with the exception of fast turns. Swept wings are less effective at generating lift while turning at high speeds, but can bear the extreme loads. Finally, our glide model predicts that cost-effective gliding occurs at speeds of 8–10 m s-1, whereas agility-related figures of merit peak at 15–25 m s-1. In fact, swifts spend the night (‘roost’) in flight at 8–10 m s-1 (ref. 11), thus our model can explain this choice for a resting behaviour. Morphing not only adjusts birds’ wing performance to the task at hand, but could also control the flight of future aircraft.
Hot bees in empty broodnest cells: heating from within
Venue: The Journal of Experimental Biology

Honeybee colonies maintain brood nest temperatures of 33–36°C. We investigated brood nest thermoregulation at the level of individual worker behaviour and the transfer of heat from workers to the brood. Worker bees contribute to the regulation of brood nest temperature by producing heat while sitting motionless on the caps of brood cells. We report here an additional, newly observed heating strategy where heating bees enter empty cells between sealed brood cells and remain there motionless for periods of up to 45 min. Individually marked worker bees on the surface of sealed brood cells maintained thorax temperatures (Tth) between 32.2±1.0°C and 38.1±2.5°C (mean ± s.d.; N=20 bees) with alternating warming and cooling periods. Most of the observed bees made one or several long-duration visits (>2 min) to empty cells within the sealed brood area. Tth at the time bees entered a cell [Tth(entry)] was 34.1–42.5°C (N=40). In 83% of these cell visits, Tth(entry) was higher (up to 5.9°C; mean 2.5±1.5°C; N=33) than the mean Tth of the same bee. High values of Tth(entry) resulted from preceding heating activity on the comb surface and from warm-ups just prior to cell visits during which Tth increased by up to +9.6°C. Bees inside empty cells had mean Tth values of 32.7±0.1°C (resting bees) to 40.6±0.7°C (heat-producing bees) during long-duration cell visits without performing any visible work. Heating behaviour inside cells resembles heating behaviour on the brood cap surface in that the bees appear to be inactive, but repeated warmings and coolings occur and Tth does not fall below the optimum brood temperature. Bees staying still inside empty cells for several minutes have previously been considered to be `resting bees'. We find, however, that the heating bees can be distinguished from the resting bees not only by their higher body temperatures but also by the continuous, rapid respiratory movements of their abdomens. By contrast, abdominal pumping movements in resting bees are discontinuous and interrupted by long pauses. Heat transfer to the brood from individual bees on the comb surface and from bees inside empty cells was simulated under controlled conditions. Heating on the comb surface causes a strong superficial warming of the brood cap by up to 3°C within 30 min. Heat transfer is 1.9–2.6 times more efficient when the thorax is in touch with the brood cap than when it is not. Heating inside empty cells raises the brood temperature of adjacent cells by up to 2.5°C within 30 min. Heat flow through the comb was detectable up to three brood cells away from the heated thorax.
Bat wing sensors support flight control
Venue: Proceedings of the National Academy of Sciences of the United States of America

Bats are the only mammals capable of powered flight, and they perform impressive aerial maneuvers like tight turns, hovering, and perching upside down. The bat wing contains five digits, and its specialized membrane is covered with stiff, microscopically small, domed hairs. We provide here unique empirical evidence that the tactile receptors associated with these hairs are involved in sensorimotor flight control by providing aerodynamic feedback. We found that neurons in bat primary somatosensory cortex respond with directional sensitivity to stimulation of the wing hairs with low-speed airflow. Wing hairs mostly preferred reversed airflow, which occurs under flight conditions when the airflow separates and vortices form. This finding suggests that the hairs act as an array of sensors to monitor flight speed and/or airflow conditions that indicate stall. Depilation of different functional regions of the bats’ wing membrane altered the flight behavior in obstacle avoidance tasks by reducing aerial maneuverability, as indicated by decreased turning angles and increased flight speed.
Cross-linking by protein oxidation in the rapidly setting gel-based glues of slugs
Venue: The Journal of Experimental Biology

The terrestrial slug Arion subfuscus secretes a glue that is a dilute gel with remarkable adhesive and cohesive strength. The function of this glue depends on metals, raising the possibility that metal-catalyzed oxidation plays a role. The extent and time course of protein oxidation was measured by immunoblotting to detect the resulting carbonyl groups. Several proteins, particularly one with a relative molecular mass (Mr) of 165×103, were heavily oxidized. Of the proteins known to distinguish the glue from non-adhesive mucus, only specific size variants were oxidized. The oxidation appears to occur within the first few seconds of secretion. Although carbonyls were detected by 2,4-dinitrophenylhydrazine (DNPH) in denatured proteins, they were not easily detected in the native state. The presence of reversible cross-links derived from carbonyls was tested for by treatment with sodium borohydride, which would reduce uncross-linked carbonyls to alcohols, but stabilize imine bonds formed by carbonyls and thus lead to less soluble complexes. Consistent with imine bond formation, sodium borohydride led to a 20–35% decrease in the amount of soluble protein with a Mr of 40–165 (×103) without changing the carbonyl content per protein. In contrast, the nucleophile hydroxylamine, which would competitively disrupt imine bonds, increased protein solubility in the glue. Finally, the primary amine groups on a protein with a Mr of 15×103 were not accessible to acid anhydrides. The results suggest that cross-links between aldehydes and primary amines contribute to the cohesive strength of the glue.
Blood Flow to Appendages and the Control of Heat Exchange in American Alligators
Venue: Physiological and Biochemical Zoology

Small American alligators (200-400 g) were heated and cooled from 20 to 35 to 20 C in a temperature-controlled wind tunnel. Blood flow to the limbs and tail was periodically occluded, using remotely controlled occlusion cuffs. When blood flow in all appendages was occluded, the rate of heating was significantly reduced from that when blood flow was unrestricted. The rate of cooling was not significantly affected by occlusion of blood flow in all appendages, however. Blood flow to appendages, rather than a generalized perfusion of the skin, appears to be primarily responsible for the differences in the rates of heating and cooling in alligators.
Desert geophytes under dew and fog: The “curly-whirlies” of Namaqualand (South Africa)
Venue: Flora

In the semidesert of Namaqualand and adjacent regions of the former Cape Province, South Africa, there occurs an assemblage of geophytes belonging to eight monocot families and some Oxalis species that exhibit special morphological adaptations of their aerial parts to harvest and absorb water from dew and fog, the main source of moisture in this region. Most of them pass their vegetative phase in winter. Leaves and in some cases axes, display a circinate, helical, tortuose, or serpentine shape and/or their margins are undulate or crispate, or (and) are provided with a ciliate or fimbriate pilosity of uncommon appearance. These morphomes, rare elsewhere among monocotyledons, promote an increased deposit of dew and fog by enlargement of surfaces and edges, keeping at the same time the overall size of the leaves restricted. They improve the water budget of these plants in three ways: (1) remnant water on the aerial parts retards the transpiration stress at day-time; (2) although special organs for direct absorption seem to be absent, field and laboratory tests show, that considerable uptake of water occurs but in quantities not exceeding that capacity found in many non-desert plants; (3) the water harvest of the leaves dripping to the soil and reaching the root zone, where it is stored in tubers, bulbs, corms and rhizomes, appears to be the main contribution. Experiments using artificial, directional fog and metal models imitating the natural profiles demonstrate that a surplus of water in efficiency rates of 0.1–66% is collected by the various surface types compared to a standard model with a non-sculptured (plain) frontal surface of the same size. The higher rates are sufficient to moisten the underlying soil down to the rhizosphere. The circumference of roots and storage organs probably does not exceed the area shadowed by the foliage. Namaqualand geophytes with such morphologies apparently form a novel desert biotype: as mesophytes they represent a distinguished strategy besides that of succulents and other xerophytes.
Biomechanics on the half shell: functional performance influences patterns of morphological variation in the emydid turtle carapace.
Venue: Zoology

This study uses the carapace of emydid turtles to address hypothesized differences between terrestrial and aquatic species. Geometric morphometrics are used to quantify shell shape, and performance is estimated for two shell functions: shell strength and hydrodynamics. Aquatic turtle shells differ in shape from terrestrial turtle shells and are characterized by lower frontal areas and presumably lower drag. Terrestrial turtle shells are stronger than those of aquatic turtles; many-to-one mapping of morphology to function does not entirely mitigate a functional trade-off between mechanical strength and hydrodynamic performance. Furthermore, areas of morphospace characterized by exceptionally poor performance in either of the functions are not occupied by any emydid species. Though aquatic and terrestrial species show no significant differences in the rate of morphological evolution, aquatic species show a higher lineage density, indicative of a greater amount of convergence in their evolutionary history. The techniques employed in this study, including the modeling of theoretical shapes to assess performance in unoccupied areas of morphospace, suggest a framework for future studies of morphological variation.
New materials for solar thermal storage—solid/liquid transitions in fatty acid esters
Venue: Solar Energy Materials and Solar Cells

Solid/liquid transitions were studied by DSC measurements in the following fatty acid esters: methyl stearate, methyl palmitate, cetyl stearate, cetyl palmitate and their binary mixtures. Four systems, with phase transition temperature close to room temperature and with high enthalpy of transition and low hysteresis, were selected for further studies relevant to passive solar thermal storage. The selected systems were: methyl palmitate and the eutectic mixtures of methyl stearate–methyl palmitate, methyl stearte–cetyl palmitate and methyl stearate–cetyl stearate. The samples, studied in 50 thermal cycles with programmed heating/cooling in the temperature range −10–60°C remained stable. The studies of the samples, having been stored at room temperature, were repeated after an interval of 18 months. The results showed that the relevant thermophysical properties did not change. The commercial building materials (gypsum, bricks) were impregnated homogeneously with the selected molten esters by simple immersion. DSC studies showed that up to ≈30 mass% of esters can be adsorbed in the building materials. The thermal energy available for storage as latent heat of melting amounts to 60 kJ/kg of the composite material.
Baobab trees (Adansonia) in Madagascar use stored water to flush new leaves but not to support stomatal opening before the rainy season.
Venue: New Phytologist

Baobab trees (Adansonia, Bombacaceae) are widely thought to store water in their stems for use when water availability is low. We tested this hypothesis by assessing the role of stored water during the dry season in three baobab species in Madagascar. In the dry season, leaves are present only during and after leaf flush. We quantified the relative contributions of stem and soil water during this period through measures of stem water content, sap flow and stomatal conductance. Rates of sap flow at the base of the trunk were near zero, indicating that leaf flushing was almost entirely dependent on stem water. Stem water content declined by up to 12% during this period, yet stomatal conductance and branch sap flow rates remained very low. Stem water reserves were used to support new leaf growth and cuticular transpiration, but not to support stomatal opening before the rainy season. Stomatal opening coincided with the onset of sap flow at the base of the trunk and occurred only after significant rainfall.
Leaves in the lowest and highest winds: temperature, force and shape.
Venue: New Phytologist

Climatic extremes can be as significant as averages in setting the conditions for successful organismal function and in determining the distribution of different forms. For lightweight, flexible structures such as leaves, even extremes lasting a few seconds can matter. The present review considers two extreme situations that may pose existential risks. Broad leaves heat rapidly when ambient air flows drop below c. 0.5 m s(-1). Devices implicated in minimizing heating include: reduction in size, lobing, and adjustments of orientation to improve convective cooling; low near-infrared absorptivity; and thickening for short-term heat storage. Different features become relevant when storm gusts threaten to tear leaves and uproot trees with leaf-level winds of 20 m s(-1) or more. Both individual leaves and clusters may curl into low-drag, stable cones and cylinders, facilitated by particular blade shapes, petioles that twist readily, and sufficient low-speed instability to initiate reconfiguration. While such factors may have implications in many areas, remarkably little relevant experimental work has addressed them.
Home Ranges, Movement, and Den Use in Long-Beaked Echidnas, Zaglossus Bartoni, from Papua New Guinea
Venue: Journal of Mammalogy

Long-beaked echidnas (Zaglossus), which are endemic to New Guinea, are the largest and least-studied of the 3 extant genera of monotremes. Zaglossus is listed as endangered by the World Conservation Union and data regarding the natural history of long-beaked echidnas are critical to efforts to protect these animals. However, no detailed studies of the ecology of this genus have been published. From 2000 to 2005, I captured 22 Zaglossus bartoni in the Crater Mountain Wildlife Management Area in Simbu Province, Papua New Guinea. Mean body masses for these animals were 6.5 kg ± 1.4 SD (n = 15, range: 4.2–9.1 kg) for adults and 4.3 ± 7.4 kg (n = 6, range: 3.2–5.1 kg) for juveniles. Eleven of the adults captured were followed via radiotelemetry for 1–12 months. The home ranges for these individuals varied in size from 10 to 168 ha. Home-range size was not correlated with body mass, age, or sex. Long-beaked echidna dens were most commonly located in underground burrows, although individual echidnas favored different types of den sites. Mean burrow length was 2.7 m ± 1.8 SD (n = 5, range: 1.3–4.9 m) and mean den depth was 0.48 m ± 7.8 SD (n = 5, range: 0.42–0.57 m) below the soil surface. Animals were never found foraging in daylight. Although no animals were found with eggs or young in the pouch, 1 individual was lactating when captured in April 2002 and again in April 2005. The data generated by this study provide valuable insights into echidna biology that will facilitate efforts to conserve populations of these unusual mammals.
Fighting Bacterial Fire With Bacterial Fire
Venue: Science

MICROBIOLOGYWork presented last week at the annual meeting of the American Society for Cell Biology in San Francisco suggests that applying a harmless bacterium or its products to surgical wounds may thwart infections by the dangerous pathogen Staphylococcus aureus , a major cause of hospital-acquired infections. Although physicians have previously pitted one bacterium against another to prevent infections of the intestinal and genitourinary tracts, this is the first attempt to use a friendly microbe to prevent infection of surgical wounds, say experts. The findings also point to a possible mechanism for this "bacterial interference." They suggest that a protein secreted by the harmless bacterium prevents the pathogen from getting a foothold in injured tissue.