nils-herrmann/clean_scirepeval huggingface dataset:
Shell growth and chamber formation of aquarium-reared Nautilus pompilius (Mollusca, Cephalopoda) by X-ray analysis.
Venue: Journal of Experimental Zoology Part A: Comparative Experimental Biology

Observations on the growth rate of aquarium maintained Nautilus pompilius in different developmental stages, i.e. juveniles (shell length about 8.75 cm), late juveniles (approximately 10 cm), and early adolescent (approximately 13.5 cm), indicate that this species is fully grown at an age of 7.3-8 years. The age calculations are based on two different computations: (1) the measurement of the increase of the shell length per day and (2) the formation of new septa in time intervals of 150+/-5 days, as demonstrated by X-ray analyses. After N. pompilius hatches, its shell grows about 139 mm to reach full growth and approximately 28 septa are formed. With an increase of the shell length of 0.052 mm per day, it takes about 2,673 days (7.3 years) to reach maturity. Provided that the process of chamber formation follows an exponential function, these computations result in approximately 2,925 days (8 years) to reach full maturity. Supposing that N. pompilius may live for several years after onset of maturity like Nautilus belauensis, the total life span for this species may exceed 11-12 years.
Dehydration-induced expression of a 31-kDa dehydrin in Polypodium polypodioides (Polypodiaceae) may enable large, reversible deformation of cell walls.
Venue: American Journal of Botany

Current and predicted climate changes caused by global warming compel greater understanding of the molecular mechanisms that plants use to survive drought. The desiccation-tolerant fern Polypodium polypodioides exhibits extensive cell wall folding when dried to less than 15% relative water content (RWC) and rapidly (within 24 h) rehydrates when exposed to water and high humidity. A 31-kDa putative dehydrin polypeptide expressed in partially and fully dry tissues detected via western blotting was present only during drying and rapidly dissipated (within 24 h) upon tissue rehydration. Immunostaining indicates the presence of dehydrin near the cell wall of partially and fully dried tissues. Atomic force microscopy of tracheal scalariform perforations indicates that dry vascular tissue does not undergo significant strain. Additionally, environmental scanning electron microscopy reveals differential hydrophilicity between the abaxial and adaxial leaf surfaces as well as large, reversible deformation. The ability to avoid cell wall damage in some desiccation-tolerant species may be partially attributed to cell wall localization of dehydrins enabling reversible, large cell-wall deformation. Thus, the de novo synthesis of dehydrin proteins and potential localization to the cell walls of these desiccation-tolerant species may play a role in avoiding mechanical failure during drought.
Halogenated DOPA in a Marine Adhesive Protein
Venue: Journal of Adhesion

The sandcastle worm Phragmatopoma californica, a marine polychaete, constructs a tube-like shelter by cementing together sand grains using a glue secreted from the building organ in its thorax. The glue is a mixture of post-translationally modified proteins, notably the cement proteins Pc-1 and Pc-2 with the amino acid, 3,4-dihydroxyphenyl-L-alanine (DOPA). Significant amounts of a halogenated derivative of DOPA were isolated from the worm cement following partial acid hydrolysis and capture of catecholic amino acids by phenylboronate affinity chromatography. Analysis by tandem mass spectrometry and 1H NMR indicates the DOPA derivative to be 2-chloro-4, 5-dihydroxyphenyl-L-alanine. The potential roles of 2-chloro-DOPA in chemical defense and underwater adhesion are considered.
Fracture toughness of locust cuticle
Venue: The Journal of Experimental Biology

Insect cuticle is one of the most common biological materials, yet very little is known about its mechanical properties. Many parts of the insect exoskeleton, such as the jumping legs of locusts, have to withstand high and repeated loading without failure. This paper presents the first measurements of fracture toughness for insect cuticle using a standard engineering approach. Our results show that the fracture toughness of cuticle in locust hind legs is 4.12 MPa m1/2 and decreases with desiccation of the cuticle. Stiffness and strength of the tibia cuticle were measured using buckling and cantilever bending and increased with desiccation. A combination of the cuticle’s high toughness with a relatively low stiffness of 3.05 GPa results in a work of fracture of 5.56 kJ m–2, which is amongst the highest of any biological material, giving the insect leg an exceptional ability to tolerate defects such as cracks and damage. Interestingly, insect cuticle achieves these unique properties without using reinforcement by a mineral phase, which is often found in other biological composite materials. These findings thus might inspire the development of new biomimetic composite materials.
Avoidance of Catastrophic Structural Failure as an Evolutionary Constraint: Biomechanics of the Acorn Weevil Rostrum.
Venue: Advanced Materials

The acorn weevil (Curculio Linnaeus, 1758) rostrum (snout) exhibits remarkable flexibility and toughness derived from the microarchitecture of its exoskeleton. Modifications to the composite profile of the rostral cuticle that simultaneously enhance the flexibility and toughness of the distal portion of the snout are characterized. Using classical laminate plate theory, the effect of these modifications on the elastic behavior of the exoskeleton is estimated. It is shown that the tensile behavior of the rostrum across six Curculio species with high morphological variation correlates with changes in the relative layer thicknesses and orientation angles of layers in the exoskeleton. Accordingly, increased endocuticle thickness is strongly correlated with increased tensile strength. Rostrum stiffness is shown to be inversely correlated with work of fracture; thus allowing a highly curved rostrum to completely straighten without structural damage. Finally, exocuticle rich invaginations of the occipital sutures are identified both as a likely site of crack initiation in tensile failure and as a source of morphological constraint on the evolution of the rostrum in Curculio weevils. It is concluded that avoidance of catastrophic structural failure, as initiated in these sutures under tension, is the driving selective pressure in the evolution of the female Curculio rostrum.
Induced niche shift as an anti-predator response for an endoparasitoid
Venue: Proceedings of The Royal Society B: Biological Sciences

When two developmental stages do not share the same ecological niche, the control of the niche shift through a change in developmental timing, referred to as ‘heterokairy’, can provide an adaptive advantage for the individual (e.g. if mortality risk is higher in the first niche). For endoparasitic species that develop inside another (host) species, mortality of the host may directly induce mortality risk for the parasite. Thus, endoparasitoid larvae should be selected for response to host predation. In this study, aphids previously parasitized by the endoparasitoid Endaphis fugitiva, Gagné and Muratori (Diptera: Cecidomyiidae), were experimentally exposed to increased mortality risks. Both simulated attack and actual predator attacks against aphid hosts induced early emergence of the parasitoid larvae. Parasitoid emergence from the aphids occurred several minutes before the predator finished feeding on the aphid, allowing enough time for the parasitoid larvae to avoid direct predation. Predator-induced emergence produced significantly smaller parasitoid larvae than controls, but, interestingly, no effect on Endaphis adult size was found. To our knowledge, this is the first evidence of induced emergence in an insect parasitoid, but we suggest that this mechanism might be at work in many other species where plasticity in development time allows the individual to perform an adaptive niche shift.
Collenchyma: a versatile mechanical tissue with dynamic cell walls.
Venue: Annals of Botany

Collenchyma has remained in the shadow of commercially exploited mechanical tissues such as wood and fibres, and therefore has received little attention since it was first described. However, collenchyma is highly dynamic, especially compared with sclerenchyma. It is the main supporting tissue of growing organs with walls thickening during and after elongation. In older organs, collenchyma may become more rigid due to changes in cell wall composition or may undergo sclerification through lignification of newly deposited cell wall material. While much is known about the systematic and organographic distribution of collenchyma, there is rather less information regarding the molecular architecture and properties of its cell walls.



This review summarizes several aspects that have not previously been extensively discussed including the origin of the term 'collenchyma' and the history of its typology. As the cell walls of collenchyma largely determine the dynamic characteristics of this tissue, I summarize the current state of knowledge regarding their structure and molecular composition. Unfortunately, to date, detailed studies specifically focusing on collenchyma cell walls have not been undertaken. However, generating a more detailed understanding of the structural and compositional modifications associated with the transition from plastic to elastic collenchyma cell wall properties is likely to provide significant insights into how specific configurations of cell wall polymers result in specific functional properties. This approach, focusing on architecture and functional properties, is likely to provide improved clarity on the controversial definition of collenchyma.
Aerodynamics of the hovering hummingbird
Venue: Nature

Despite profound musculoskeletal differences, hummingbirds (Trochilidae) are widely thought to employ aerodynamic mechanisms similar to those used by insects. The kinematic symmetry of the hummingbird upstroke and downstroke has led to the assumption that these halves of the wingbeat cycle contribute equally to weight support during hovering, as exhibited by insects of similar size. This assumption has been applied, either explicitly or implicitly, in widely used aerodynamic models and in a variety of empirical tests. Here we provide measurements of the wake of hovering rufous hummingbirds (Selasphorus rufus) obtained with digital particle image velocimetry that show force asymmetry: hummingbirds produce 75% of their weight support during the downstroke and only 25% during the upstroke. Some of this asymmetry is probably due to inversion of their cambered wings during upstroke. The wake of hummingbird wings also reveals evidence of leading-edge vortices created during the downstroke, indicating that they may operate at Reynolds numbers sufficiently low to exploit a key mechanism typical of insect hovering. Hummingbird hovering approaches that of insects, yet remains distinct because of effects resulting from an inherently dissimilar—avian—body plan.
The tubercles on humpback whales' flippers: application of bio-inspired technology.
Venue: Integrative and Comparative Biology

The humpback whale (Megaptera novaeangliae) is exceptional among the large baleen whales in its ability to undertake aquabatic maneuvers to catch prey. Humpback whales utilize extremely mobile, wing-like flippers for banking and turning. Large rounded tubercles along the leading edge of the flipper are morphological structures that are unique in nature. The tubercles on the leading edge act as passive-flow control devices that improve performance and maneuverability of the flipper. Experimental analysis of finite wing models has demonstrated that the presence of tubercles produces a delay in the angle of attack until stall, thereby increasing maximum lift and decreasing drag. Possible fluid-dynamic mechanisms for improved performance include delay of stall through generation of a vortex and modification of the boundary layer, and increase in effective span by reduction of both spanwise flow and strength of the tip vortex. The tubercles provide a bio-inspired design that has commercial viability for wing-like structures. Control of passive flow has the advantages of eliminating complex, costly, high-maintenance, and heavy control mechanisms, while improving performance for lifting bodies in air and water. The tubercles on the leading edge can be applied to the design of watercraft, aircraft, ventilation fans, and windmills.
Biomechanics of climbing palms and how they climb
Venue: Plant Signaling & Behavior

Climbing plants have fascinated botanists since the pioneering works of Darwin and his contemporaries in the 19th century. Diverse plants have evolved different ways of climbing and a wide range of attachment devices and stem biomechanics to cope with the particular physical demands of life as a climber. We investigated the biomechanics of attachment in a range of climbing palms, including true rattans from Southeast Asia and the genus Desmoncus from South America. We found that hook strength and orientation is coordinated with rachis geometry and rigidity. These findings support the notion of a ratchet-type attachment mechanism and partly explain why these spiny plants are so catchy and efficient at attaching to supports.
Mechanical adaptations of a giant kelp
Venue: Limnology and Oceanography

Unusually high extensibility of the kelp Nereocystis luetkeana minimizes breakage by waves and tidal currents. Cellulose fibrils in cortical cell walls have a preferred angle of 60° to the stipe axis; this may be the structural basis of stipe extensibility. Although undamaged plants can sustain drag due to most waves and tides, breakage of single plants occurs most often at flaws in the stipes caused by sea urchin grazing or by abrasion.
Intertidal “trees”: consequences of aggregation on the mechanical and photosynthetic properties of sea-palms Postelsia palmaeformis Ruprecht
Venue: Journal of Experimental Marine Biology and Ecology

Sea-palms Postelsia palmaeformis Ruprecht are annual brown algae that grow on wave-swept rocky shores, oRen forming dense stands. Unlike most macroalgae, Postelsia stands upright in air- like trees. The stipe flexibility that permits Postelsia to withstand waves is provided by the low elastic modulus (5-10 MPa) of stipe tissue; in spite of the weakness (low breaking stress, ~ 1 MPa) of this tissue, a large amount of energy ( ~ 100 kJ/m 3) is required to break a stipe because they can be extended by 20-25 % before breaking. Although made of such easily deformed tissue, Postelsia can stand upright in air due to the width (high second moment of area) and resilience of their stipes, but the brittleness (low work of fracture, 400-900 J/m 2) that accompanies this resilience renders them susceptible to bre~age if they sustain deep scratches. Although wave-induced stresses experienced by individuals in aggregations are not lower than those experienced by isolated sea-palms, photon flux densities of photosynthetically active radiation within these dense groves are less than 10% of those above Postelsia canopies. A number of morphological features differ between canopy, understory, and isolated individuals. Canopy plants in dense aggregations are taller than isolated individuals and may exceed limiting proportions for elastic stability. Postelsia shows photo- synthetic characteristics of"shade-adapted" plants, understory individuals being especially effective at using low light. Despite this, blade growth rates of understory plants are lower than those of either canopy or isolated individuals.
Are chickadees good listeners? Antipredator responses to raptor vocalizations
Venue: Animal Behaviour

Many animals gather information about predators with a variety of cues, such as visual, acoustic, and olfactory. Several species of birds, including chickadees, are good at discriminating between species of raptors using visual cues, and they can encode information about the threat level in their alarm calls. Much less is known about how birds discriminate between the calls of different species of predators. We played back the calls of three species of raptors to black-capped chickadees, Poecile atricapillus, mountain chickadees, Poecile gambeli, and chestnut-backed chickadees, Poecile rufescens, to determine whether they can discriminate between them using acoustic cues. We played the calls of two species of small, high-threat raptors, northern pygmy-owl, Glaucidium gnoma, and sharp-shinned hawk, Accipiter striatus, which have very different hunting strategies (mainly sit-and-wait ambush predator versus very fast surprise attack flights). We also played a larger, lower-threat northern goshawk, Accipiter gentilis. Black-capped and mountain chickadees responded much more to the calls of the two small, more dangerous raptors than to the northern goshawk; they also responded very differently to the calls of the two small raptors. Chestnut-backed chickadees did not respond differently to the calls of the three raptors. These results indicate that black-capped and mountain chickadees can make specific discriminations between the calls of these three raptors and that they encode information in their alarm calls in sophisticated ways.
Fog Catchment Sand Trenches Constructed by Tenebrionid Beetles, Lepidochora, from the Namib Desert
Venue: Science

Three species of coastal Namib Desert tenebrionid beetles (Lepidochora) build trenches on desert sand dunes. Trenches are constructed perpendicular to fog winds and concentrate moisture during fogs. The beetles return along the ridges of the trenches extracting water from them. The water content of a population of these beetles increased by 13.9 percent during one fog
Mechanical properties and structure of Strombus gigas, Tridacna gigas, and Haliotis rufescens sea shells: A comparative study
Venue: Materials Science and Engineering: C

Sea shells are composed of calcium carbonate crystals interleaved with layers of viscoelastic proteins, having dense, tailored structures that yield excellent mechanical properties. Shells such as conch (Strombus gigas), giant clam (Tridacna gigas), and red abalone (Haliotis rufescens) have hierarchical architectures that differ depending on growth requirements and shell formation of the particular mollusk. Mechanical tests have been carried out on these shells for a comparison of strength with respect to the microstructural architecture and sample orientation. The mechanical response is found to vary significantly from specimen to specimen and requires the application of Weibull statistics in order to be quantitatively evaluated. The complex micro-laminate structure of these biocomposite materials is characterized and related to their mechanical properties. The red abalone has the highest compressive (233–540 MPa) and flexure strengths of the three shells. The giant clam has the lowest strength (87–123 MPa) and the conch has an intermediate value (166–218 MPa) in compression. The high compressive strength observed in the abalone is attributed to an optimization of microstructural architecture in the form of 2-D laminates, enhancing the fracture toughness of this shell material and enabling higher stresses to develop before fracture. D 2005 Elsevier B.V. All rights reserved.
Alkaliphiles: Some Applications of Their Products for Biotechnology
Venue: Microbiology and Molecular Biology Reviews

The term “alkaliphile” is used for microorganisms that grow optimally or very well at pH values above 9 but cannot grow or grow only slowly at the near-neutral pH value of 6.5. Alkaliphiles include prokaryotes, eukaryotes, and archaea. Many different taxa are represented among the alkaliphiles, and some of these have been proposed as new taxa. Alkaliphiles can be isolated from normal environments such as garden soil, although viable counts of alkaliphiles are higher in samples from alkaline environments. The cell surface may play a key role in keeping the intracellular pH value in the range between 7 and 8.5, allowing alkaliphiles to thrive in alkaline environments, although adaptation mechanisms have not yet been clarified. Alkaliphiles have made a great impact in industrial applications. Biological detergents contain alkaline enzymes, such as alkaline cellulases and/or alkaline proteases, that have been produced from alkaliphiles. The current proportion of total world enzyme production destined for the laundry detergent market exceeds 60%. Another important application is the industrial production of cyclodextrin by alkaline cyclomaltodextrin glucanotransferase. This enzyme has reduced the production cost and paved the way for cyclodextrin use in large quantities in foodstuffs, chemicals, and pharmaceuticals. It has also been reported that alkali-treated wood pulp could be biologically bleached by xylanases produced by alkaliphiles. Other applications of various aspects of alkaliphiles are also discussed.
Epithelial sodium channels (ENaC) are uniformly distributed on motile cilia in the oviduct and the respiratory airways
Venue: Histochemistry and Cell Biology

Epithelial sodium channels (ENaCs) are located on the apical surface of cells and funnel Na+ ions from the lumen into the cell. ENaC function also regulates extracellular fluid volume as water flows across membranes accompanying Na+ ions to maintain osmolarity. To examine the sites of expression and intracellular localization of ENaC, we generated polyclonal antibodies against the extracellular domain of human α-ENaC subunit that we expressed in E. coli. Three-dimensional (3D) confocal microscopy of immunofluorescence using these antibodies for the first time revealed that ENaCs are uniformly distributed on the ciliary surface in all epithelial cells with motile cilia lining the bronchus in human lung and female reproductive tract, all along the fimbrial end of the fallopian tube, the ampulla and rare cells in the uterine glands. Quantitative analysis indicated that cilia increase cell surface area >70-fold and the amount of ENaC on cilia is >1,000-fold higher than on non-ciliated cell surface. These findings indicate that ENaC functions as a regulator of the osmolarity of the periciliary fluid bathing the cilia. In contrast to ENaC, cystic fibrosis transmembrane conductance regulator (CFTR) that channels chloride ions from the cytoplasm to the lumen is located mainly on the apical side, but not on cilia. The cilial localization of ENaC requires reevaluation of the mechanisms of action of CFTR and other modulators of ENaC function. ENaC on motile cilia should be essential for diverse functions of motile cilia, such as germ cell transport, fertilization, implantation, clearance of respiratory airways and cell migration.