nils-herrmann/clean_scirepeval huggingface dataset:
Building a home from foam—túngara frog foam nest architecture and three-phase construction process
Venue: Biology Letters

Frogs that build foam nests floating on water face the problems of over-dispersion of the secretions used and eggs being dangerously exposed at the foam : air interface. Nest construction behaviour of túngara frogs, Engystomops pustulosus, has features that may circumvent these problems. Pairs build nests in periodic bursts of foam production and egg deposition, three discrete phases being discernible. The first is characterized by a bubble raft without egg deposition and an approximately linear increase in duration of mixing events with time. This phase may reduce initial over-dispersion of foam precursor materials until a critical concentration is achieved. The main building phase is marked by mixing events and start-to-start intervals being nearly constant in duration. During the final phase, mixing events do not change in duration but intervals between them increase in an exponential-like fashion. Pairs joining a colonial nesting abbreviate their initial phase, presumably by exploiting a pioneer pair's bubble raft, thereby reducing energy and material expenditure, and time exposed to predators. Finally, eggs are deposited only in the centre of nests with a continuously produced, approximately 1 cm deep egg-free cortex that protectively encloses hatched larvae in stranded nests.
A nocturnal mammal, the greater mouse-eared bat, calibrates a magnetic compass by the sun
Venue: Proceedings of the National Academy of Sciences of the United States of America

Recent evidence suggests that bats can detect the geomagnetic field, but the way in which this is used by them for navigation to a home roost remains unresolved. The geomagnetic field may be used by animals both to indicate direction and to locate position. In birds, directional information appears to be derived from an interaction of the magnetic field with either the sun or the stars, with some evidence suggesting that sunset/sunrise provides the primary directional reference by which a magnetic compass is calibrated daily. We demonstrate that homing greater mouse-eared bats (Myotis myotis) calibrate a magnetic compass with sunset cues by testing their homing response after exposure to an altered magnetic field at and after sunset. Magnetic manipulation at sunset resulted in a counterclockwise shift in orientation compared with controls, consistent with sunset calibration of the magnetic field, whereas magnetic manipulation after sunset resulted in no change in orientation. Unlike in birds, however, the pattern of polarization was not necessary for the calibration. For animals that occupy ecological niches where the sunset is rarely observed, this is a surprising finding. Yet it may indicate the primacy of the sun as an absolute geographical reference not only for birds but also within other vertebrate taxa.
Polarization sensitivity in two species of cuttlefish – Sepia plangon (Gray 1849) and Sepia mestus (Gray 1849) – demonstrated with polarized optomotor stimuli
Venue: The Journal of Experimental Biology

The existence of polarization sensitivity (PS), most likely resulting from the orthogonal arrangement of microvilli in photoreceptors, has been proposed in cephalopods for some time, although it has rarely been examined behaviourally. Here, we tested the mourning cuttlefish, Sepia plangon, and the reaper cuttlefish, Sepia mestus, for polarization sensitivity using a large-field optomotor stimulus containing polarization contrast. Polaroid filter drums with stripes producing alternating e-vectors were rotated around free-moving animals. Polarized optomotor responses were displayed, and these responses were similar to those performed in response to a black-and-white, vertically-striped drum, whereas no responses were displayed to a plain polarizing control drum producing just a vertical e-vector. This indicates that the animals are able to see the contrast between adjacent stripes in the polarizing drum. To our knowledge, this is the first demonstration of functional polarization sensitivity in cuttlefish.
Identification and characterization of a multidomain hyperthermophilic cellulase from an archaeal enrichment.
Venue: Nature Communications

Despite extensive studies on microbial and enzymatic lignocellulose degradation, relatively few Archaea are known to deconstruct crystalline cellulose. Here we describe a consortium of three hyperthermophilic archaea enriched from a continental geothermal source by growth at 90 °C on crystalline cellulose, representing the first instance of Archaea able to deconstruct lignocellulose optimally above 90 °C. Following metagenomic studies on the consortium, a 90 kDa, multidomain cellulase, annotated as a member of the TIM barrel glycosyl hydrolase superfamily, was characterized. The multidomain architecture of this protein is uncommon for hyperthermophilic endoglucanases, and two of the four domains of the enzyme have no characterized homologues. The recombinant enzyme has optimal activity at 109 °C, a half-life of 5 h at 100 °C, and resists denaturation in strong detergents, high-salt concentrations, and ionic liquids. Cellulases active above 100 °C may assist in biofuel production from lignocellulosic feedstocks by hydrolysing cellulose under conditions typically employed in biomass pretreatment.
DIFFERENCES IN POLYSACCHARIDE STRUCTURE BETWEEN CALCIFIED AND UNCALCIFIED SEGMENTS IN THE CORALLINE CALLIARTHRON CHEILOSPORIOIDES (CORALLINALES, RHODOPHYTA) 1
Venue: Journal of Phycology

The articulated coralline Calliarthron cheilosporioides Manza produces segmented fronds composed of calcified segments (intergenicula) separated by uncalcified joints (genicula), which allow fronds to bend and reorient under breaking waves in the wave‐swept intertidal zone. Genicula are formed when calcified cells decalcify and restructure to create flexible tissue. The present study has identified important differences in the main agaran disaccharidic repeating units [→3)‐β‐d‐Galp (1→ 4)‐α‐l‐Galp(1→] synthesized by genicular and intergenicular segments. Based on chemical and spectroscopical analyses, we report that genicular cells from C. cheilosporioides biosynthesize a highly methoxylated galactan at C‐6 position with low levels of branching with xylose side stubs on C‐6 of the [→3)‐β‐d‐Galp (1→] units, whereas intergenicular segments produce xylogalactans with high levels of xylose and low levels of 6‐O‐methyl β‐d‐Gal units. These data suggest that, during genicular development, xylosyl branched, 3‐linked β‐d‐Galp units present in the xylogalactan backbones from intergenicular walls are mostly replaced by 6‐O‐methyl‐d‐galactose units. We speculate that this structural shift is a consequence of a putative and specific methoxyl transferase that blocks the xylosylation on C‐6 of the 3‐linked β‐d‐Galp units. Changes in galactan substitutions may contribute to the distinct mechanical properties of genicula and may lend insight into the calcification process in coralline algae.
Foam nest components of the túngara frog: a cocktail of proteins conferring physical and biological resilience
Venue: Proceedings of The Royal Society B: Biological Sciences

The foam nests of the túngara frog (Engystomops pustulosus) form a biocompatible incubation medium for eggs and sperm while resisting considerable environmental and microbiological assault. We have shown that much of this behaviour can be attributed to a cocktail of six proteins, designated ranaspumins (Rsn-1 to Rsn-6), which predominate in the foam. These fall into two discernable classes based on sequence analysis and biophysical properties. Rsn-2, with an amphiphilic amino acid sequence unlike any hitherto reported, exhibits substantial detergent-like surfactant activity necessary for production of foam, yet is harmless to the membranes of eggs and spermatozoa. A further four (Rsn-3 to Rsn-6) are lectins, three of which are similar to fucolectins found in teleosts but not previously identified in a land vertebrate, though with a carbohydrate binding specificity different from previously described fucolectins. The sixth, Rsn-1, is structurally similar to proteinase inhibitors of the cystatin class, but does not itself appear to exhibit any such activity. The nest foam itself, however, does exhibit potent cystatin activity. Rsn-encoding genes are transcribed in many tissues of the adult frogs, but the full cocktail is present only in oviduct glands. Combinations of lectins and cystatins have known roles in plants and animals for defence against microbial colonization and insect attack. Túngara nest foam displays a novel synergy of selected elements of innate defence plus a specialized surfactant protein, comprising a previously unreported strategy for protection of unattended reproductive stages of animals.
The suctorial organ of the Solifugae (Arachnida, Solifugae)
Venue: Arthropod Structure & Development

The ability of members of the arachnid order Solifugae to climb smooth, vertical surfaces and the organs involved in this behavior are investigated. Macroscopic, microscopic, and scanning electron microscopic observations are made of a palpal organ called the suctorial organ. Observations of the behavior but not the microstructure have been made in the past. Histological examination illustrates the internal gross anatomy of this structure and scanning electron microscopy demonstrates the fine structure in adults of four genera: Eremobates (Eremobatidae), Eremochelis (Eremobatidae), Eremorhax (Eremobatidae), Ammotrechula (Ammotrechidae), as well as an unidentified late stage immature and third stage instar. The suctorial organ is most likely primarily used for prey capture in the wild.
On the Mound of Macrotermes michaelseni as an Organ of Respiratory Gas Exchange
Venue: Physiological and Biochemical Zoology

Patterns and rates of air movements in the mounds and nests of Macrotermes michaelseni were studied using tracer methods. Wind is a significant source of energy for powering nest ventilation, despite the mound being a completely enclosed structure. Nests are ventilated by a tidal movement of air driven by temporal variation in wind speed and wind direction. Density gradients sufficiently steep to drive bulk flow by natural convection will be rare. However, metabolism‐induced buoyant forces may interact with wind energy in a way that promotes homeostasis of the mound atmosphere.
The diversity of hydrostatic skeletons
Venue: The Journal of Experimental Biology

A remarkably diverse group of organisms rely on a hydrostatic skeleton for support, movement, muscular antagonism and the amplification of the force and displacement of muscle contraction. In hydrostatic skeletons, force is transmitted not through rigid skeletal elements but instead by internal pressure. Functioning of these systems depends on the fact that they are essentially constant in volume as they consist of relatively incompressible fluids and tissue. Contraction of muscle and the resulting decrease in one of the dimensions thus results in an increase in another dimension. By actively (with muscle) or passively (with connective tissue) controlling the various dimensions, a wide array of deformations, movements and changes in stiffness can be created. An amazing range of animals and animal structures rely on this form of skeletal support, including anemones and other polyps, the extremely diverse wormlike invertebrates, the tube feet of echinoderms, mammalian and turtle penises, the feet of burrowing bivalves and snails, and the legs of spiders. In addition, there are structures such as the arms and tentacles of cephalopods, the tongue of mammals and the trunk of the elephant that also rely on hydrostatic skeletal support but lack the fluid-filled cavities that characterize this skeletal type. Although we normally consider arthropods to rely on a rigid exoskeleton, a hydrostatic skeleton provides skeletal support immediately following molting and also during the larval stage for many insects. Thus, the majority of animals on earth rely on hydrostatic skeletons.
On the buoyancy of the pearly nautilus
Venue: Journal of the Marine Biological Association of the United Kingdom

Nautilus macromphalus Sowerby when freshly caught was close to neutral buoyancy having a weight in sea water of about 0–2% of its weight in air. The animals without their shells varied considerably in density but the volume of the shell was an approximately constant fraction of the total volume of the whole animal and whole animals were brought approximately to the same density by havingmore or less liquid inside the chambers of the shell. About 80 % of the gas space in the shell was used to support the weight of the shell itself in sea water.In an adult animal the centre of buoyancy was found to be about 6 mm above the centre of gravity, which made the animal very stable in its natural swimming position, a couple of about 350 g. cm being required to turn it through 90°. The pearly partsof the chamber walls were impermeable to sea water but the chalky and horny siphuncular tubes joining the septal necks were very porous. The most newly formed tenor so chambers were the only ones to contain liquids in appreciable volume and theydid this in diminishing amounts from the newest to the oldest. The watery liquids found within the chambers were always hypotonic to sea water and sometimes markedly so; they contained principally sodium and chloride ions. One animal was in the process of forming a new chamber, this incomplete chamber was completely full of liquidwith an osmolarity close to that of sea water but differing in composition from seawater.
How strong is intracanopy leaf plasticity in temperate deciduous trees?
Venue: American Journal of Botany

Intracanopy plasticity in tree leaf form is a major determinant of whole-plant function and potentially of forest understory ecology. However, there exists little systematic information for the full extent of intracanopy plasticity, whether it is linked with height and exposure, or its variation across species. For arboretum-grown trees of six temperate deciduous species averaging 13-18 m in height, we quantified intracanopy plasticity for 11 leaf traits across three canopy locations (basal-interior, basal-exterior, and top). Plasticity was pronounced across the canopy, and maximum likelihood analyses indicated that plasticity was primarily linked with irradiance, regardless of height. Intracanopy plasticity (the quotient of values for top and basal-interior leaves) was often similar across species and statistically indistinguishable across species for several key traits. At canopy tops, the area of individual leaves was on average 0.5-0.6 times that at basal-interior, stomatal density 1.1-1.5 times higher, sapwood cross-sectional area up to 1.7 times higher, and leaf mass per area 1.5-2.2 times higher; guard cell and stomatal pore lengths were invariant across the canopy. Species differed in intracanopy plasticity for the mass of individual leaves, leaf margin dissection, ratio of leaf to sapwood areas, and stomatal pore area per leaf area; plasticity quotients ranged only up to ≈2. Across the six species, trait plasticities were uncorrelated and independent of the magnitude of the canopy gradient in irradiance or height and of the species' light requirements for regeneration. This convergence across species indicates general optimization or constraints in development, resulting in a bounded plasticity that improves canopy performance.
A biomechanical perspective on the role of large stem volume and high water content in baobab trees (Adansonia spp.; Bombacaceae).
Venue: American Journal of Botany

The stems of large trees serve in transport, storage, and support; however, the degree to which these roles are reflected in their morphology is not always apparent. The large, water-filled stems of baobab trees (Adansonia spp.) are generally assumed to serve a water storage function, yet recent studies indicate limited use of stored water. Through an analysis of wood structure and composition, we examined whether baobab morphology reflects biomechanical constraints rather than water storage capacity in the six Madagascar baobab species. Baobab wood has a high water content (up to 79%), low wood density (0.09-0.17 g · cm(-3)), high parenchyma content (69-88%), and living cells beyond 35 cm into the xylem from the cambium. Volumetric construction cost of the wood is several times lower than in more typical trees, and the elastic modulus approaches that of parenchyma tissue. Safety factors calculated from estimated elastic buckling heights were low, indicating that baobabs are not more overbuilt than other temperate and tropical trees, yet the energy investment in stem material is comparable to that in temperate deciduous trees. Furthermore, the elastic modulus of the wood decreases with water content, such that excessive water withdrawal from the stem could affect mechanical stability.
Hydrophobic trichome layers and epicuticular wax powders in Bromeliaceae.
Venue: American Journal of Botany

The distinctive foliar trichome of Bromeliaceae has promoted the evolution of an epiphytic habit in certain taxa by allowing the shoot to assume a significant role in the uptake of water and mineral nutrients. Despite the profound ecophysiological and taxonomic importance of this epidermal structure, the functions of nonabsorbent trichomes in remaining Bromeliaceae are not fully understood. The hypothesis that light reflection from these trichome layers provides photoprotection was not supported by spectroradiometry and fluorimetry in the present study; the mean reflectance of visible light from trichome layers did not exceed 6.4% on the adaxial surfaces of species representing a range of ecophysiological types nor was significant photoprotection provided by their presence. Several reports suggesting water repellency in some terrestrial Bromeliaceae were investigated. Scanning electron microscopy (SEM) and a new technique-fluorographic dimensional imaging (FDI)-were used to assess the interaction between aqueous droplets and the leaf surfaces of 86 species from 25 genera. In the majority of cases a dense layer of overlapping, stellate or peltate trichomes held water off the leaf epidermis proper. In the case of hydrophobic tank-forming tillandsioideae, a powdery epicuticular wax layer provided water repellency. The irregular architecture of these indumenta resulted in relatively little contact with water droplets. Most mesic terrestrial Pitcairnioideae examined either possessed glabrous leaf blades or hydrophobic layers of confluent trichomes on the abaxial surface. Thus, the present study indicates that an important ancestral function of the foliar trichome in Bromeliaceae was water repellency. The ecophysiological consequences of hydrophobia are discussed.
The incidence and implications of clouds for cloud forest plant water relations.
Venue: Ecology Letters

Although clouds are the most recognisable and defining feature of tropical montane cloud forests, little research has focussed on how clouds affect plant functioning. We used satellite and ground-based observations to study cloud and leaf wetting patterns in contrasting tropical montane and pre-montane cloud forests. We then studied the consequences of leaf wetting for the direct uptake of water accumulated on leaf surfaces into the leaves themselves. During the dry season, the montane forest experienced higher precipitation, cloud cover and leaf wetting events of longer duration than the pre-montane forest. Leaf wetting events resulted in foliar water uptake in all species studied. The capacity for foliar water uptake differed significantly between the montane and pre-montane forest plant communities, as well as among species within a forest. Our results indicate that foliar water uptake is common in these forest plants and improves plant water status during the dry season.
Functional morphology of scale hinges used to transport water: convergent drinking adaptations in desert lizards (Moloch horridus and Phrynosoma cornutum)
Venue: Zoomorphology

The Australian thorny devil, Moloch horridus Gray, 1841, and the Texas horned lizard, Phrynosoma cornutum Harlan, 1825, have the remarkable ability to rapidly move water through interscalar spaces on their skin’s surface to their mouth for drinking. The morphology of these scale hinges has not been studied. We used histological and SEM techniques to examine and compare the scale hinges of both species. Additional taxa in their respective lineages were examined in order to evaluate the potential that convergent evolution has occurred. In the two species that transport water, each scale hinge has a basally expanded and semi-enclosed channel formed by the hinge joint that is interconnected with all scale hinges on the body. We hypothesize that it is within this semi-tubular channel system of hinge joints, where the β-layer keratin of the integument is very thin, that water is transported. Hinge joint walls are covered by a complex topography of fractured surfaces that greatly expand the channel’s surface area and probably enhance capillary transport of water. In addition, we note differing morphology of scale surfaces at the rear of the jaws of both species. We hypothesize that capillary forces fill the scale-hinge system and additional forces, generated within the mouth by observed motions during drinking, depress local water-pressure to pull water through the channels of the hinge-joint system. We conclude that the combined features in the two species, semi-tubular hinge-joint channels with convoluted walls and a jaw-buccal cavity pumping-mechanism, have convergently evolved for capture, transport, and drinking of water from sporadic rainfall.
Function of spiral grain in trees
Venue: Trees-structure and Function

SummaryThrough spiral grain, conduits for sap lead from each root to all branches. This uniform distribution of sap is indicated by the paths of vessels and tracheids, and has been proven experimentally by means of dyed sap injected into the base of stems or taken up by roots. Trees receiving water only from roots at one side of the root collar nevertheless stay green and continue growing. Spiral grain in bark distributes food from each branch to other flanks of the stem and to most roots. Experimental interruptions of the sap and food conduits caused the cambial zone to reorient new conduit cells in new directions, bypassing the interruption. In particular, spiral grooves cut into the stem surface caused spiral grain. The new cells reorient through division and growth. Although spiral grain is largely under genetic control, trees appear to have a spiral grain especially where needed for distribution of water when root spheres are dry at one side. Compared with straight-grained trees, spiral-grained stems and branches bend and twist more when exposed to strong wind, in this way offering less wind resistance and being less likely to break. Through the bending and twisting, snow slides down from branches rather than breaking them, but the main function of spiral grain is the uniform distribution of supplies from each root to all branches, and from each branch to many roots.