nils-herrmann/clean_scirepeval huggingface dataset:
Spiderweb deformation induced by electrostatically charged insects
Venue: Scientific Reports

Capture success of spider webs has been associated with their microstructure, ornamentation, and wind-induced vibrations. Indirect evidence suggests that statically charged objects can attract silk thread, but web deformations induced by charged insects have not yet been described. Here, we show under laboratory conditions that electrostatically charged honeybees, green bottle flies, fruit flies, aphids, and also water drops falling near webs of cross-spiders (Araneus diadematus) induce rapid thread deformation that enhances the likelihood of physical contact, and thus of prey capture.
Comparison of surface microfouling and bacterial attachment on the egg capsules of two molluscan species representing Cephalopoda and Neogastropoda
Venue: Aquatic Microbial Ecology

Many organisms naturally defend themselves against microbial attachment and biofoul- ing in the marine environment. In this study, we investigated microbial fouling on 2 molluscan egg capsules using scanning electron microscopy (SEM), two-photon laser scanning microscopy (TPLSM) with bacterial viability staining and bacterial attachment experiments with the biofilm-forming Pseudoalteromonas sp. S91 in flow chambers. Results indicated that early stage egg capsules of Dicathais orbita (Neogastropoda) are relatively free of surface microorganisms. Egg capsules during the trocophore stage had a regularly ridged microtexture, but as capsules matured, shedding of the outer wall was observed, followed by the extrusion of unidentified droplets, which then accumulated on the capsule surface in association with bacteria. By comparison, the egg capsules of Sepioteuthis australis (Cephalopoda) were found to have an irregular surface with many hills and valleys that accommodate colonization by a variety of microorganisms. At the later stages of development these squid egg capsules become heavily colonized by algal spores. Cross sections of egg capsules revealed that S. australis capsule walls were about 12 times thicker than D. orbita egg capsules. Staining the egg capsules with BacLight™ also revealed a significantly thicker biofilm, with more live and dead bacteria on S. australis capsules than on those of D. orbita (p < 0.05). Flow chamber exper- iments indicated that the surface of S. australis capsules provided a suitable substrate for colonization by Pseudoalteromonas sp. S91, whereas colonization was significantly less on D. orbita egg capsules after 24 and 72 h (p < 0.01). These experiments indicated that D. orbita egg capsules are better defended against fouling microbes than are the eggs of S. australis. D. orbita appears to use a combi- nation of physical, mechanical and possibly chemical defense mechanisms to reduce fouling on their egg capsules.
Insect metabolism: Preventing cyanide release from leaves
Venue: Nature

Organisms that produce hydrogen cyanide gas to protect themselves against predators can do so by the enzymatic breakdown of a class of compounds known as cyanogens (such as cyanogenic glycosides). Here we show how a neotropical butterfly, Heliconius sara, can avoid the harmful effects of the cyanogenic leaves of Passiflora auriculata (passion vine), on which its larvae feed exclusively. To our knowledge this is the first example of an insect that is able to metabolize cyanogens and thereby prevent the release of cyanide. The mechanistic details of this pathway might suggest new ways to make cyanogenic crops more useful as a food source.
Underwater components of humpback whale bubble-net feeding behaviour
Venue: Behaviour

Humpback whales (Megaptera novaeangliae) employ a unique and complex foraging behaviour — bubble-netting — that involves expelling air underwater to form a vertical cylinder-ring of bubbles around prey. We used digital suction cup tags (DTAGs) that concurrently measure pitch, roll, heading, depth and sound (96 kHz sampling rate), to provide the first depiction of the underwater behaviours in which humpback whales engage during bubble-net feeding. Body mechanics and swim paths were analysed using custom visualization software that animates the underwater track of the whale and quantifies tag sensor values. Bubble production was identified aurally and through spectrographic analysis of tag audio records. We identified two classes of behaviour (upward-spiral; 6 animals, 118 events and double-loop; 3 animals, 182 events) that whales used to create bubble nets. Specifically, we show the actual swim path of the whales (e.g., number of revolutions, turning rate, depth interval of spiral), when and where in the process bubbles were expelled and the pattern of bubble expulsion used by the animals. Relative to other baleanopterids, bubble-netting humpbacks demonstrate increased manoeuvrability probably aided by a unique hydrodynamicly enhanced body form. We identified an approximately 20 m depth or depth interval limit to the use of bubble nets and suggest that this limit is due to the physics of bubble dispersal to which humpback whales have behaviourally adapted. All animals were feeding with at
Collective decision making and social interaction rules in mixed-species flocks of songbirds
Venue: Animal Behaviour

Associations in mixed-species foraging groups are common in animals, yet have rarely been explored in the context of collective behaviour. Despite many investigations into the social and ecological conditions under which individuals should form groups, we still know little about the specific behavioural rules that individuals adopt in these contexts, or whether these can be generalized to heterospecifics. Here, we studied collective behaviour in flocks in a community of five species of woodland passerine birds. We adopted an automated data collection protocol, involving visits by RFID-tagged birds to feeding stations equipped with antennae, over two winters, recording 91 576 feeding events by 1904 individuals. We demonstrated highly synchronized feeding behaviour within patches, with birds moving towards areas of the patch with the largest proportion of the flock. Using a model of collective decision making, we then explored the underlying decision rule birds may be using when foraging in mixed-species flocks. The model tested whether birds used a different decision rule for conspecifics and heterospecifics, and whether the rules used by individuals of different species varied. We found that species differed in their response to the distribution of conspecifics and heterospecifics across foraging patches. However, simulating decisions using the different rules, which reproduced our data well, suggested that the outcome of using different decision rules by each species resulted in qualitatively similar overall patterns of movement. It is possible that the decision rules each species uses may be adjusted to variation in mean species abundance in order for individuals to maintain the same overall flock-level response. This is likely to be important for maintaining coordinated behaviour across species, and to result in quick and adaptive flock responses to food resources that are patchily distributed in space and time.
A Passionate Free Climber: Structural Development and Functional Morphology of the Adhesive Tendrils in Passiflora discophora
Venue: International Journal of Plant Sciences

Premise of research. Passiflora discophora is exceptional among passion flowers for its climbing strategy, using branched tendrils with terminal adhesive pads instead of coiling tendrils as typical within this family. This article investigates the structural development and morphology of these adhesive pads and aims to understand the underlying structure-function relationship of the attachment process. Based on our results, we discuss possible mechanical consequences of the tendril structure and compare our findings with similar attachment systems in unrelated species in order to identify general strategies of this mode of attachment. We investigated the temporal development of the attachment process, including detailed studies of the morphology and anatomy of the adhesive pads, using LM with different staining procedures and SEM. Pivotal results. Young tendrils establish initial contact with a supporting substrate by interlocking with their hook-shaped tips. Touch stimuli induce the tips to develop into adhesive pads by callus-like growth of papillate epidermal cells. Fully grown pads are hemispherical on flat substrates or completely fill out larger cavities of the substrate. By apical cell division, the pad tissue perfectly mimics the microtopography of the substrate and also grows into minute gaps and fissures, establishing firm anchorage by optimal form closure. Additionally, an extracellular substance is visible at the interface between pad and substrate surface, which might act as adhesive. The opportunistic growth and cellular structure make the tendrils and adhesive pads of P. discophora a highly adaptive attachment system. Comparison with other not closely related taxa reveals general principles of this climbing mode, namely, (1) branched tendrils with multiple adhesive pads, (2) papillate cells establishing optimal form closure with the substrate and in some species additionally secreting adhesive substances, (3) free coiling of axes, and (4) persisting anchorage after senescence.
Microenvironmental Role of a Secreted Aqueous Solution in the Afro-Alpine Plant Lobelia keniensis
Venue: Biotropica

On montre que la solution aqueuse et mucilagineuse secretee par L. kiniensis sert a preserver du froid les bourgeons vegetatifs. La substance mucilagineuse identifiee a la pectine servirait a proteger la reserve d'eau de l'evaporation
Life on the rocks.
Venue: Environmental Microbiology

Biofilms are interface micro-habitats formed by microbes that differ markedly from those of the ambient environment. The term 'subaerial biofilm' (SAB) was coined for microbial communities that develop on solid mineral surfaces exposed to the atmosphere. Subaerial biofilms are ubiquitous, self-sufficient, miniature microbial ecosystems that are found on buildings, bare rocks in deserts, mountains, and at all latitudes where direct contact with the atmosphere and solar radiation occurs. Subaerial biofilms on exposed terrestrial surfaces are characterized by patchy growth that is dominated by associations of fungi, algae, cyanobacteria and heterotrophic bacteria. Inherent subaerial settlers include specialized actinobacteria (e.g. Geodermatophilus), cyanobacteria and microcolonial fungi. Individuals within SAB communities avoid sexual reproduction, but cooperate extensively with one another especially to avoid loss of energy and nutrients. Subaerial biofilm metabolic activity centres on retention of water, protecting the cells from fluctuating environmental conditions and solar radiation as well as prolonging their vegetative life. Atmospheric aerosols, gases and propagatory particles serve as sources of nutrients and inoculum for these open communities. Subaerial biofilms induce chemical and physical changes to rock materials, and they penetrate the mineral substrate contributing to rock and mineral decay, which manifests itself as bio-weathering of rock surfaces. Given their characteristic slow and sensitive growth, SAB may also serve as bioindicators of atmospheric and/or climate change.
The position of lysine controls the catechol-mediated surface adhesion and cohesion in underwater mussel adhesion.
Venue: Joint International Conference on Information Sciences

Intensive studies have found that 3,4-dihydroxyphenylalanine (Dopa) is one of the key molecules for underwater mussel adhesion. Although basic mechanisms of mussel adhesion have been elucidated, little is known about how mussels control the balance between surface adhesion and cohesion, which is critical for successful adhesion without peeling and/or tearing. In this work, we focused on lysine (Lys) molecules which are frequently flanked to Dopa residues in interfacial adhesive proteins, specifically their synergy and anti-synergy on surface adhesion and cohesion. Three model peptides were designed to characterize flanking Lys effects. Through nano-mechanistic analyses, we found that flanking Lys enhanced surface adhesion but disrupted Fe3+-mediated cohesion. Through nuclear magnetic resonance analyses and density functional theory calculations, we corroborated the synergetic effect on surface adhesion and anti-synergetic effect on cohesion. We also confirmed the consistency of flanking Lys effects in the actual protein system. Thus, we, for the first time, discovered that each Dopa molecule in interfacial adhesive proteins is participated in surface adhesion and cohesion differently through controlling the existence of flanking Lys. Our discovery enlightens how nature designs adhesive proteins through according roles of Dopa.
Reversed deep-sea carbonate ion basin gradient during Paleocene-Eocene thermal maximum
Venue: Paleoceanography

The Paleocene-Eocene thermal maximum (PETM, ∼55 Ma ago) was marked by widespread CaCO3 dissolution in deep-sea sediments, a process that has been attributed to massive release of carbon into the ocean-atmosphere system. The pattern of carbonate dissolution is key to reconstructing changes in deep sea carbonate chemistry and, ultimately, the rate, magnitude, and location of carbon input. Here we show that during the PETM, the deep-sea undersaturation was not homogeneous among the different ocean basins. Application of a sediment model to a suite of data records from different sites and ocean basins shows that a globally uniform decrease in deep-sea carbonate ion concentration ([CO32−]) is inconsistent with the data. Rather, we demonstrate that deep-sea [CO32−] increased from the Atlantic through the Southern Ocean into the Pacific. Our results show that the PETM deep-sea [CO32−] basin gradient during dissolution was reversed relative to the modern.
Pinna Temperature in Exercising Jackrabbits, Lepus californicus
Venue: Journal of Mammalogy

Pinna surface temperatures of Lepus californicus were examined radiographically before and after forced exercise (e.g., running at about 6 km/h for 6 min) in an outdoor enclosure. Air temperatures were from −1.6 to +19.4°C, and radiant sky temperatures were from —27 to +22°C. In resting animals, average pinna surface temperature was only 0.3 to 2.5°C above air temperature, and pinna arteries were not evident radiographically. Immediately after exercise, average pinna temperature was often near 30°C and pinna arteries were evident, indicating vasodilation. Cooling of the pinnae to resting temperatures after exercise generally took 15 to 25 min. Calculations indicate that the pinnae can dissipate most of the excess metabolic heat generated during the exercise examined, and it is suggested that the role of the pinnae as dissipators of exercise-induced heat loads should be considered as a factor in the evolution of pinna size.
Propagation and Perception of Bioluminescence: Factors Affecting Counterillumination as a Cryptic Strategy
Venue: The Biological Bulletin

Many deep-sea species, particularly crustaceans, cephalopods, and fish, use photophores to illuminate their ventral surfaces and thus disguise their silhouettes from predators viewing them from below. This strategy has several potential limitations, two of which are examined here. First, a predator with acute vision may be able to detect the individual photophores on the ventral surface. Second, a predator may be able to detect any mismatch between the spectrum of the bioluminescence and that of the background light. The first limitation was examined by modeling the perceived images of the counterillumination of the squid Abralia veranyi and the myctophid fish Ceratoscopelus maderensis as a function of the distance and visual acuity of the viewer. The second limitation was addressed by measuring downwelling irradiance under moonlight and starlight and then modeling underwater spectra. Four water types were examined: coastal water at a depth of 5 m and oceanic water at 5, 210, and 800 m. The appearance of the counterillumination was more affected by the visual acuity of the viewer than by the clarity of the water, even at relatively large distances. Species with high visual acuity (0.11° resolution) were able to distinguish the individual photophores of some counterilluminating signals at distances of several meters, thus breaking the camouflage. Depth and the presence or absence of moonlight strongly affected the spectrum of the background light, particularly near the surface. The increased variability near the surface was partially offset by the higher contrast attenuation at shallow depths, which reduced the sighting distance of mismatches. This research has implications for the study of spatial resolution, contrast sensitivity, and color discrimination in deep-sea visual systems.
On Nonexistence of any λ0-invariand positive harmonic function, a counter example to stroock' conjecture
Venue: Communications in Partial Differential Equations

Consider a sub-Markovian semigroup such that λ0, the border number between recrrence and transience, equals zero. In 1982, D. W. Stroock conjectured that under general hypotheses on the semi-group the corresponding process always admits an invariant measure. In this paper we present an example of a second order elliptic operator P with a generalized principal eigenvalue λ0 which equals zero such that the parabolic equation does not admit any positive invariant P—harmonic function and also any invariant measure. This gives a counter example to Stroock's conjecture for diffusion processes. We also present an example of a complete Riemannian manifold M which does not admit any positive invariant harmonic function while λ0, the bottom of the spectrum of M, is zero. This gives a partial answer to a question of Stroock and Sullivan.
Remora fish suction pad attachment is enhanced by spinule friction
Venue: The Journal of Experimental Biology

The remora fishes are capable of adhering to a wide variety of natural and artificial marine substrates using a dorsal suction pad. The pad is made of serial parallel pectinated lamellae, which are homologous to the dorsal fin elements of other fishes. Small tooth-like projections of mineralized tissue from the dorsal pad lamella, known as spinules, are thought to increase the remora's resistance to slippage and thereby enhance friction to maintain attachment to a moving host. In this work, the geometry of the spinules and host topology as determined by micro-computed tomography and confocal microscope data, respectively, are combined in a friction model to estimate the spinule contribution to shear resistance. Model results are validated with natural and artificially created spinules and compared with previous remora pull-off experiments. It was found that spinule geometry plays an essential role in friction enhancement, especially at short spatial wavelengths in the host surface, and that spinule tip geometry is not correlated with lamellar position. Furthermore, comparisons with pull-off experiments suggest that spinules are primarily responsible for friction enhancement on rough host topologies such as shark skin.  The geometry of remora fish suction disc spinules increases passive friction on rough host surfaces such as shark skin.
Inter-plant communication through mycorrhizal networks mediates complex adaptive behaviour in plant communities
Venue: Aob Plants

Trees can communicate with each other through networks in soil. Much like social networks or neural networks, the fungal mycelia of mycorrhizas allow signals to be sent between trees in a forest. These mycorrhizal networks are effectively an information highway, with recent studies demonstrating the exchange of nutritional resources, defence signals and allelochemicals. Sensing and responding to networked signals elicits complex behavioural responses in plants. This ability to communicate ('tree talk') is a foundational process in forest ecosystems.
Assembly mechanism of recombinant spider silk proteins
Venue: Proceedings of the National Academy of Sciences of the United States of America

Spider silk threads are formed by the irreversible aggregation of silk proteins in a spinning duct with dimensions of only a few micrometers. Here, we present a microfluidic device in which engineered and recombinantly produced spider dragline silk proteins eADF3 (engineered Araneus diadematus fibroin) and eADF4 are assembled into fibers. Our approach allows the direct observation and identification of the essential parameters of dragline silk assembly. Changes in ionic conditions and pH result in aggregation of the two proteins. Assembly of eADF3 fibers was induced only in the presence of an elongational flow component. Strikingly, eADF4 formed fibers only in combination with eADF3. On the basis of these results, we propose a model for dragline silk aggregation and early steps of fiber assembly in the microscopic regime.
Nitrogen Fixation by Symbiotic and Free-Living Spirochetes
Venue: Science

Spirochetes from termite hindguts and freshwater sediments possessed homologs of a nitrogenase gene (nifH) and exhibited nitrogenase activity, a previously unrecognized metabolic capability in spirochetes. Fixation of 15-dinitrogen was demonstrated with termite gut Treponema ZAS-9 and free-livingSpirochaeta aurantia. Homologs of nifH were also present in human oral and bovine ruminal treponemes. Results implicate spirochetes in the nitrogen nutrition of termites, whose food is typically low in nitrogen, and in global nitrogen cycling. These results also proffer spirochetes as a likely origin of certainnifHs observed in termite guts and other environments that were not previously attributable to known microbes.
The Long and Short of Hearing in the Mosquito Aedes aegypti
Venue: Current Biology

Mating behavior in Aedes aegypti mosquitoes occurs mid-air and involves the exchange of auditory signals at close range (millimeters to centimeters) [1-6]. It is widely assumed that this intimate signaling distance reflects short-range auditory sensitivity of their antennal hearing organs to faint flight tones [7, 8]. To the contrary, we show here that male mosquitoes can hear the female's flight tone at surprisingly long distances-from several meters to up to 10 m-and that unrestrained, resting Ae. aegypti males leap off their perches and take flight when they hear female flight tones. Moreover, auditory sensitivity tests of Ae. aegypti's hearing organ, made from neurophysiological recordings of the auditory nerve in response to pure-tone stimuli played from a loudspeaker, support the behavioral experiments. This demonstration of long-range hearing in mosquitoes overturns the common assumption that the thread-like antennal hearing organs of tiny insects are strictly close-range ears. The effective range of a hearing organ depends ultimately on its sensitivity [9-13]. Here, a mosquito's antennal ear is shown to be sensitive to sound levels down to 31 dB sound pressure level (SPL), translating to air particle velocity at nanometer dimensions. We note that the peak of energy of the first formant of the vowels of the human speech spectrum range from about 200-1,000 Hz and is typically spoken at 45-70 dB SPL; together, they lie in the sweet spot of mosquito hearing.