nils-herrmann/clean_scirepeval huggingface dataset:
Crossflow filtration in suspension-feeding fishes
Venue: Nature

Rows of comb-like or tufted gill rakers in the oral cavity of suspension-feeding fishes (for example, herring, anchovies and tilapia) have been thought to serve as (1) non-porous barriers that direct particle-laden water to the sticky oral roof, where particles are retained as water exits from the oral cavity, (2) conventional dead-end filters that sieve particles from water exiting between rakers, or (3) sticky filters that retain particles encountered by a hydrosol filtration mechanism. Here we present data from computational fluid dynamics and video endoscopy in suspension-feeding fish indicating that the rakers of three distantly related species function instead as a crossflow filter. Particles are concentrated inside the oral cavity as filtrate exits between the rakers, but particles are not retained on the rakers. Instead, the high-velocity crossflow along the rakers carries particles away from the raker surfaces and transports the particles towards the oesophagus. This crossflow prevents particles from clogging the gaps between the rakers, and solves the mystery of particle transport from the rakers to the oesophagus.
Cytokeratins mediate epithelial innate defense through their antimicrobial properties.
Venue: Journal of Clinical Investigation

Epithelial cells express antimicrobial proteins in response to invading pathogens, although little is known regarding epithelial defense mechanisms during healthy conditions. Here we report that epithelial cytokeratins have innate defense properties because they constitutively produce cytoprotective antimicrobial peptides. Glycine-rich C-terminal fragments derived from human cytokeratin 6A were identified in bactericidal lysate fractions of human corneal epithelial cells. Structural analysis revealed that these keratin-derived antimicrobial peptides (KDAMPs) exhibited coil structures with low α-helical content. Synthetic analogs of these KDAMPS showed rapid bactericidal activity against multiple pathogens and protected epithelial cells against bacterial virulence mechanisms, while a scrambled peptide showed no bactericidal activity. However, the bactericidal activity of a specific KDAMP was somewhat reduced by glycine-alanine substitutions. KDAMP activity involved bacterial binding and permeabilization, but the activity was unaffected by peptide charge or physiological salt concentration. Knockdown of cytokeratin 6A markedly reduced the bactericidal activity of epithelial cell lysates in vitro and increased the susceptibility of murine corneas to bacterial adherence in vivo. These data suggest that epithelial cytokeratins function as endogenous antimicrobial peptides in the host defense against infection and that keratin-derived antimicrobials may serve as effective therapeutic agents.
Material properties of the skin of the Kenyan sand boa Gongylophis colubrinus (Squamata, Boidae)
Venue: Journal of Comparative Physiology A-neuroethology Sensory Neural and Behavioral Physiology

On the basis of structural data, it has been previously assumed that the integument of snakes consists of a hard, robust, inflexible outer surface (Oberhäutchen and β-layer) and soft, flexible inner layers (α-layers). The aim of this study was to compare material properties of the outer and inner scale layers of the exuvium of Gongylophis colubrinus, to relate the structure of the snake integument to its mechanical properties. The nanoindentation experiments have demonstrated that the outer scale layers are harder, and have a higher effective elastic modulus than the inner scale layers. The results obtained provide strong evidence about the presence of a gradient in the material properties of the snake integument. The possible functional significance of this gradient is discussed here as a feature minimizing damage to the integument during sliding locomotion on an abrasive surface, such as sand.
Calcitic microlenses as part of the photoreceptor system in brittlestars
Venue: Nature

Photosensitivity in most echinoderms has been attributed to ‘diffuse’ dermal receptors. Here we report that certain single calcite crystals used by brittlestars for skeletal construction are also a component of specialized photosensory organs, conceivably with the function of a compound eye. The analysis of arm ossicles in Ophiocoma showed that in light-sensitive species, the periphery of the labyrinthic calcitic skeleton extends into a regular array of spherical microstructures that have a characteristic double-lens design. These structures are absent in light-indifferent species. Photolithographic experiments in which a photoresist film was illuminated through the lens array showed selective exposure of the photoresist under the lens centres. These results provide experimental evidence that the microlenses are optical elements that guide and focus the light inside the tissue. The estimated focal distance (4–7 µm below the lenses) coincides with the location of nerve bundles—the presumed primary photoreceptors. The lens array is designed to minimize spherical aberration and birefringence and to detect light from a particular direction. The optical performance is further optimized by phototropic chromatophores that regulate the dose of illumination reaching the receptors. These structures represent an example of a multifunctional biomaterial that fulfills both mechanical and optical functions.
Photoperiodic Adjustments in Immune Function Protect Siberian Hamsters from Lethal Endotoxemia
Venue: Journal of Biological Rhythms

Seasonal changes in day length enhance or suppress components of immune function in individuals of several mammalian species. Siberian hamsters (Phodopus sungorus) exhibit multiple changes in neuroendocrine, reproductive, and immune function after exposure to short days. The manner in which these changes are integrated into the host response to pathogens is not well understood. The present experiments tested the hypothesis that short-day changes in immune function alter the pathogenesis of septic shock and survival after challenge with endotoxin. Male and female Siberian hamsters raised in long-day photoperiods were transferred as adults to short days or remained in their natal photoperiod. Six to 8 weeks later, hamsters were injected i.p. with 0, 1, 2.5, 10, 25, or 50 mg/kg bacterial lipopolysaccharide (LPS) (the biologically active constituent of endotoxin), and survival was monitored for 96 h. Short days significantly improved survival of male hamsters treated with 10 or 25 mg/kg LPS and improved survival in females treated with 50 mg/kg LPS. Transfer from long to short days shifted the LD5 0 in males by approximately 90%, from 5.3 to 9.9 mg/kg, and in females from 11.1 to 15.0 mg/kg ([#002B]35%). Long-day females were more resistant than were males to lethal endotoxemia. In vitro production of the proinflammatory cytokine TNFα in response to LPS stimulation was significantly lower in macrophages extracted from short-day relative to long-day hamsters, as were circulating concentrations of TNFα in vivo after i.p. administration of LPS, suggesting that diminished cytokine responses to LPS in short days may mitigate the lethality of endotoxemia. Adaptation to short days induces changes in immune parameters that affect survival in the face of immune challenges.
FM echolocating bats shift frequencies to avoid broadcast–echo ambiguity in clutter
Venue: Proceedings of the National Academy of Sciences of the United States of America

Sonar broadcasts are followed by echoes at different delays from objects at different distances. When broadcasts are emitted rapidly in cluttered surroundings, echo streams from successive broadcasts overlap and cause ambiguity in matching echoes to corresponding broadcasts. To identify reactions to ambiguity in clutter, echolocating bats that emit multiple-harmonic FM sounds were trained to fly into a dense, extended array of obstacles (multiple rows of vertically hanging chains) while the sonar sounds the bat emitted were recorded with a miniature radio microphone carried by the bat. Flight paths were reconstructed from thermal-infrared video recordings. Successive rows of chains extended more than 6 m in depth, so each broadcast was followed by a series of echoes from multiple rows of chains that lasted up to 40 ms. Bats emitted sounds in pairs (“strobe groups”) at short (20–40 ms) interpulse intervals (IPIs) alternating with longer IPIs (>50 ms). For many short IPIs, the stream of echoes from the first broadcast was still arriving when the second broadcast was emitted. This overlap caused ambiguity about matching echoes with broadcasts. Bats shifted frequencies of the first sound in each strobe group upward and the second sound downward by 3–6 kHz. When overlap and ambiguity ceased, frequency shifts ceased also. Frequency differences were small compared with the total broadcast band, which was 75–80 kHz wide, but the harmonic structure of echoes enhances the differences in spectrograms. Bats could use time–frequency comparisons of echoes with broadcasts to assign echoes to the corresponding broadcasts and thus avoid ambiguity.
Always on the bright side of life: anti-adhesive properties of insect ommatidia grating
Venue: The Journal of Experimental Biology

The surface of some insect eyes consists of arrays of cuticular protuberances, which are 50–300 nm in diameter, and are termed corneal nipples or ommatidia gratings. They were widely reported to reduce the reflectance for normally incident light, contributing to camouflage by reducing glare to predators, while furthermore enhancing the intake of light, which is especially important for nocturnal insects. Our preliminary observations suggest a third function: in contrast to the rest of the body, ommatidia of various insects remain clean, even in a heavy contaminated environment. In order to prove such an anti-contamination hypothesis of these structures, we measured the adhesive properties of polymer moulds of insect ommatidia, and compared these data with control surfaces having the same curvature radii but lacking such a nanostructure. A scanning electron microscope (SEM) study and force measurements using an atomic force microscope (AFM) on the eye surfaces of three different insect species, dragonfly Aeshna mixta (Odonata), moth Laothoe populi (Lepidoptera) and fly Volucella pellucens (Diptera), were undertaken. We revealed that adhesion is greatly reduced by corneal grating in L. populi and V. pellucens when compared with their smooth controls. The smooth cornea of A. mixta showed no statistically significant difference to its control. We assume that this anti-adhesive phenomenon is due to a decrease in the real contact area between contaminating particles and the eye's surface. Such a combination of three functions in one nanostructure can be interesting for the development of industrial multifunctional surfaces capable of enhancing light harvesting while reducing light reflection and adhesion.
Contribution of the Alternative Pathway to Respiration during Thermogenesis in Flowers of the Sacred Lotus1
Venue: Plant Physiology

We report results from in vivo measurements, using oxygen isotope discrimination techniques, of fluxes through the alternative and cytochrome respiratory pathways in thermogenic plant tissue, the floral receptacle of the sacred lotus (Nelumbo nucifera). Fluxes through both pathways were measured in thermoregulating flowers undergoing varying degrees of thermogenesis in response to ambient temperature. Significant increases in alternative pathway flux were found in lotus receptacles with temperatures 16°C to 20°C above ambient, but not in those with lesser amounts of heating. Alternative pathway flux in the hottest receptacles was 75% of the total respiratory flux. In contrast, fluxes through the cytochrome pathway did not change significantly during thermogenesis. These data support the hypothesis that increased flux through the alternative pathway is responsible for heating in the lotus and that it is unlikely that uncoupling proteins, which would have produced increased fluxes through the cytochrome pathway, contribute significantly to heating in this tissue. Comparisons of actual flux, with capacity determined using inhibitors, suggested that the alternative pathway was operating at close to maximum capacity in heating tissues of lotus. However, in nonheating tissues the inhibitor data significantly overestimated the alternative pathway flux. This confirms that isotopic measurements are necessary for accurate determination of fluxes through the two pathways.
Catapulting Tentacles in a Sticky Carnivorous Plant
Venue: PLOS ONE

Among trapping mechanisms in carnivorous plants, those termed ‘active’ have especially fascinated scientists since Charles Darwin’s early works because trap movements are involved. Fast snap-trapping and suction of prey are two of the most spectacular examples for how these plants actively catch animals, mainly arthropods, for a substantial nutrient supply. We show that Drosera glanduligera, a sundew from southern Australia, features a sophisticated catapult mechanism: Prey animals walking near the edge of the sundew trigger a touch-sensitive snap-tentacle, which swiftly catapults them onto adjacent sticky glue-tentacles; the insects are then slowly drawn within the concave trap leaf by sticky tentacles. This is the first detailed documentation and analysis of such catapult-flypaper traps in action and highlights a unique and surprisingly complex mechanical adaptation to carnivory.
Chameleons have independent eye movements but synchronise both eyes during saccadic prey tracking
Venue: Experimental Brain Research

The movements of both eyes and the head were recorded with search coils in unrestrained, freely moving chameleons. As a main result I found that the generation of saccades in the left and the right eye was either independent from each other or was highly correlated according to the behavioural situation. When no prey item was fixated, disconjugate saccades were observed which was in accordance with earlier observations in chameleons. During prey tracking the chameleons switched to a different oculomotor behaviour and pursued the moving prey with synchronous saccades. At higher target velocities, the tracking movement of the head was also saccadic and was synchronised with the two eyes. Binocular coupling affected only the timing of the saccades but not the metrics: the amplitudes of the synchronous saccades were usually different in the two eyes. These observations suggest the existence of two independent premotor neuronal circuits for left and right eye saccadic motor control in the chameleon. Binocular coupling in prey-tracking chameleons is probably achieved by neuronal coupling of these premotor circuits during eye–head coordination. The ability to switch between synchronous and uncoupled saccadic eye movements has not been described for any other vertebrate. This unique ability of the chameleon may help to understand the organisation of the oculomotor system of other vertebrates since evidence for separate left eye and right eye saccade generation and position control has recently also been reported in primates.
Extracellular Proteins Limit the Dispersal of Biogenic Nanoparticles
Venue: Science

High–spatial-resolution secondary ion microprobe spectrometry, synchrotron radiation–based Fourier-transform infrared spectroscopy, and polyacrylamide gel analysis demonstrated the intimate association of proteins with spheroidal aggregates of biogenic zinc sulfide nanocrystals, an example of extracellular biomineralization. Experiments involving synthetic zinc sulfide nanoparticles and representative amino acids indicated a driving role for cysteine in rapid nanoparticle aggregation. These findings suggest that microbially derived extracellular proteins can limit the dispersal of nanoparticulate metal-bearing phases, such as the mineral products of bioremediation, that may otherwise be transported away from their source by subsurface fluid flow.
Physicochemical characterization of the microhabitat of the epibionts associated with Alvinella pompejana, a hydrothermal vent annelid
Venue: Geochimica et Cosmochimica Acta

Alvinella pompejana is a polychaetous annelid that inhabits narrow tubes along the walls of high-temperature hydrothermal vent chimneys. The worm hosts a rich community of epibiotic bacteria that coats its dorsal surface. Although the worm tube microhabitat is a challenging environment to sample, characterizing the thermal and geochemical regime is important for understanding the ecology of the worm and its bacteria, as the worm spends most of its time inside the tube. We characterized the physicochemical conditions of diffuse hydrothermal flow inside inhabited worm tubes using in situ analysis and wet chemical analysis of discrete water samples. Thermistor probes deployed inside worm tubes measured temperatures ranging from 28.6°C to 84.0°C, while temperatures at tube orifices ranged from 7.5°C to 40.0°C. In situ electrochemical analysis of tube fluids revealed undetectable oxygen (
Spray aiming in the bombardier beetle: photographic evidence.
Venue: Proceedings of the National Academy of Sciences of the United States of America

Bombardier beetles, when physically assaulted, eject a hot quinonoid spray from the tip of the abdomen. Photographic evidence is presented demonstrating that the African bombardier beetle, Stenaptinus insignis, can aim its spray in virtually any direction. It can target its individual legs, and even the individual segments of its legs. Moreover, in aiming at a leg, it takes into account the postural orientation of that leg. The beetle is able even to target sites on its back. It is postulated that the ability to aim helps the beetle mainly in defense against ants.
Characterization of an electron conduit between bacteria and the extracellular environment
Venue: Proceedings of the National Academy of Sciences of the United States of America

A number of species of Gram-negative bacteria can use insoluble minerals of Fe(III) and Mn(IV) as extracellular respiratory electron acceptors. In some species of Shewanella, deca-heme electron transfer proteins lie at the extracellular face of the outer membrane (OM), where they can interact with insoluble substrates. To reduce extracellular substrates, these redox proteins must be charged by the inner membrane/periplasmic electron transfer system. Here, we present a spectro-potentiometric characterization of a trans-OM icosa-heme complex, MtrCAB, and demonstrate its capacity to move electrons across a lipid bilayer after incorporation into proteoliposomes. We also show that a stable MtrAB subcomplex can assemble in the absence of MtrC; an MtrBC subcomplex is not assembled in the absence of MtrA; and MtrA is only associated to the membrane in cells when MtrB is present. We propose a model for the modular organization of the MtrCAB complex in which MtrC is an extracellular element that mediates electron transfer to extracellular substrates and MtrB is a trans-OM spanning β-barrel protein that serves as a sheath, within which MtrA and MtrC exchange electrons. We have identified the MtrAB module in a range of bacterial phyla, suggesting that it is widely used in electron exchange with the extracellular environment.
A branched material based on biomimetic design: Synthesis and electrochemical properties
Venue: Materials Science and Engineering: C

Based on the biomimetic route the metal material with tree-like fractal structure was prepared, which showed a rough surface observed by scanning electron microscopy. According to the electrochemical experiments, the formed material exhibited the strong catalytic capability as an electrode in hydrogen evolution reaction, comparing with other conventional structure materials under comparable scales. We suggested this promotion of property arose from the contribution of the great surface area and the excellent connectivity offered from the fractal structure.
A functional interpretation of cilia and mucocyte distributions on the abfrontal surface of bivalve gills
Venue: Marine Biology

The lack of fundamental data on the abfrontal surface of bivalve gills has prompted a comparative study of cilia and mucocytes on this surface, using scanning electron microscopy and histology on eight species of bivalves, representing seven families and the four major gill types: Mytilus edulis, Modiolus modiolus, Arca zebra, Placopecten magellanicus, Crassostrea virginica, Spisula solidissima, Mercenaria mercenaria, and Mya arenaria. Abfrontal cilia and mucocytes were found in all species studied, with types and densities differing within and between gill types. The three species of homorhabdic filibranchs presented different densities of abfrontal cilia and mucocytes, from very dense in M. edulis to sparse in A. zebra. The heterorhabdic gills had intermediate cilia and mucocyte densities, with highest concentrations of both abfrontal cilia and mucocytes on the principal filaments. The eulamellibranchs showed low ciliary densities together with high mucocyte densities, especially in S. solidissima, where the abfrontal mucocytes were glandular. These results indicate that: (1) the abfrontal surface is a vestigial mucociliary surface; (2) the abfrontal surface cannot participate in water pumping in most species, due to low ciliary densities; and (3) species with high densities of abfrontal mucocytes could utilize abfrontal mucus to reduce drag, especially in the highly fused gills, such as those of the eulamellibranchs. The differing distributions of abfrontal cilia and mucocytes may reflect different selective pressures acting on the gills within the various taxa.
FT Protein Movement Contributes to Long-Distance Signaling in Floral Induction of Arabidopsis
Venue: Science

In plants, seasonal changes in day length are perceived in leaves, which initiate long-distance signaling that induces flowering at the shoot apex. The identity of the long-distance signal has yet to be determined. In Arabidopsis, activation of FLOWERING LOCUS T (FT) transcription in leaf vascular tissue (phloem) induces flowering. We found that FT messenger RNA is required only transiently in the leaf. In addition, FT fusion proteins expressed specifically in phloem cells move to the apex and move long distances between grafted plants. Finally, we provide evidence that FT does not activate an intermediate messenger in leaves. We conclude that FT protein acts as a long-distance signal that induces Arabidopsis flowering.