nils-herrmann/clean_scirepeval huggingface dataset:
Passive propulsion in vortex wakes
Venue: Journal of Fluid Mechanics

A dead fish is propelled upstream when its flexible body resonates with oncoming vortices formed in the wake of a bluff cylinder, despite being well outside the suction region of the cylinder. Within this passive propulsion mode, the body of the fish extracts sufficient energy from the oncoming vortices to develop thrust to overcome its own drag. In a similar turbulent wake and at roughly the same distance behind a bluff cylinder, a passively mounted high-aspect-ratio foil is also shown to propel itself upstream employing a similar flow energy extraction mechanism. In this case, mechanical energy is extracted from the flow at the same time that thrust is produced. These results prove experimentally that, under proper conditions, a body can follow at a distance or even catch up to another upstream body without expending any energy of its own. This observation is also significant in the development of low-drag energy harvesting devices, and in the energetics of fish dwelling in flowing water and swimming behind wake-forming obstacles.
Biologically inspired humidity sensor based on three-dimensional photonic crystals
Venue: Applied Physics Letters

This letter presents a biomimetic humidity sensor inspired by the humidity-dependent color change observed in the cuticle of the Hercules beetle. A thin-film-type humidity sensor with nanoporous structures (three-dimensional photonic crystals) mimicking the spongy multilayer in the beetles was designed and fabricated using the colloidal templating method and a hydrophilic surface treatment. The visible color of the fabricated humidity sensor changes from blue-green to red as the environmental humidity increases. The wavelength of reflected light that is predicted by Bragg’s equation considering the effect of water absorption shows a good agreement with experimental results.
Enhanced visual fields in hammerhead sharks
Venue: The Journal of Experimental Biology

Several factors that influence the evolution of the unusual head morphology of hammerhead sharks (family Sphyrnidae) are proposed but few are empirically tested. In this study we tested the ‘enhanced binocular field’ hypothesis (that proposes enhanced frontal binocularity) by comparison of the visual fields of three hammerhead species: the bonnethead shark, Sphyrna tiburo, the scalloped hammerhead shark, Sphyrna lewini, and the winghead shark, Eusphyra blochii, with that of two carcharhinid species: the lemon shark, Negaprion brevirostris, and the blacknose shark, Carcharhinus acronotus. Additionally, eye rotation and head yaw were quantified to determine if species compensate for large blind areas anterior to the head. The winghead shark possessed the largest anterior binocular overlap (48 deg.) and was nearly four times larger than that of the lemon (10 deg.) and blacknose (11 deg.) sharks. The binocular overlap in the scalloped hammerhead sharks (34 deg.) was greater than the bonnethead sharks (13 deg.) and carcharhinid species; however, the bonnethead shark did not differ from the carcharhinids. These results indicate that binocular overlap has increased with lateral head expansion in hammerhead sharks. The hammerhead species did not demonstrate greater eye rotation in the anterior or posterior direction. However, both the scalloped hammerhead and bonnethead sharks exhibited greater head yaw during swimming (16.9 deg. and 15.6 deg., respectively) than the lemon (15.1 deg.) and blacknose (15.0 deg.) sharks, indicating a behavioral compensation for the anterior blind area. This study illustrates the larger binocular overlap in hammerhead species relative to their carcharhinid sister taxa and is consistent with the ‘enhanced binocular field’ hypothesis.
Food and Feeding Behavior of the Black-faced Spoonbill
Venue: Waterbirds

Feeding Black-faced Spoonbills (Platalea minor) were studied in four main areas along the coasts of South Korea, Taiwan, China and Vietnam. They fed on nekton, mainly fish and shrimps, varying in length between 2-21 cm that were caught by sweeping the bill in the water. The feeding behavior of a spoonbill is a chain of feeding and inter-feeding bouts. Each feeding bout started by putting the bill into the water and ended when the bill was taken out and any prey captured was swallowed. The times between feeding bouts were short and no or few steps were made. In a complete feeding bout, up to three functional phases were distinguished. These were successively (1) the attempt to locate a prey, (2) the attempt to catch the located prey, (3) the handling and swallowing of the prey. A feeding bout could end in any phase. A total of 1,684 feeding bouts were recorded of which 65% ended with swallowing prey. The mean outcome was 45.4 small (<5 cm long) and 1.3 large (>5 cm long) prey per 10 min. Tentative measurements indicated that a feeding spoonbill walked on average 3.87 m per 10 s, during which time the bill made 15.7 sweeps with a bill velocity of 5.8 km.h-1, meanwhile testing about 17% of the area within reach of their bill for the presence of food. Feeding by Black-faced Spoonbills often looked chaotic because they usually walk all over the feeding site at a variable speed, while showing a large variety of actions especially when large prey is present. However, analyses of the observations show that they behave efficiently and reduce time and energy spent in feeding in several ways, including giving-up times not much longer than the duration of bouts with success, pursuing only large prey, ceasing feeding and starting to rest or going to another site when no prey is caught in 5-10 min. With their tactile way of feeding on invisible prey, they also behaved efficiently by consuming all detected prey that could be caught and swallowed.
Filtration of submicrometer particles by pelagic tunicates
Venue: Proceedings of the National Academy of Sciences of the United States of America

Salps are common in oceanic waters and have higher per-individual filtration rates than any other zooplankton filter feeder. Although salps are centimeters in length, feeding via particle capture occurs on a fine, mucous mesh (fiber diameter d ∼0.1 μm) at low velocity (U = 1.6 ± 0.6 cm·s−1, mean ± SD) and is thus a low Reynolds-number (Re ∼10−3) process. In contrast to the current view that particle encounter is dictated by simple sieving of particles larger than the mesh spacing, a low-Re mathematical model of encounter rates by the salp feeding apparatus for realistic oceanic particle-size distributions shows that submicron particles, due to their higher abundances, are encountered at higher rates (particles per time) than larger particles. Data from feeding experiments with 0.5-, 1-, and 3-μm diameter polystyrene spheres corroborate these findings. Although particles larger than 1 μm (e.g., flagellates, small diatoms) represent a larger carbon pool, smaller particles in the 0.1- to 1-μm range (e.g., bacteria, Prochlorococcus) may be more quickly digestible because they present more surface area, and we find that particles smaller than the mesh size (1.4 μm) can fully satisfy salp energetic needs. Furthermore, by packaging submicrometer particles into rapidly sinking fecal pellets, pelagic tunicates can substantially change particle-size spectra and increase downward fluxes in the ocean.
Grass roots chemistry: meta-Tyrosine, an herbicidal nonprotein amino acid
Venue: Proceedings of the National Academy of Sciences of the United States of America

Fine fescue grasses displace neighboring plants by depositing large quantities of an aqueous phytotoxic root exudate in the soil rhizosphere. Via activity-guided fractionation, we have isolated and identified the nonprotein amino acid m-tyrosine as the major active component. m-Tyrosine is significantly more phytotoxic than its structural isomers o- and p-tyrosine. We show that m-tyrosine exposure results in growth inhibition for a wide range of plant species and propose that the release of this nonprotein amino acid interferes with root development of competing plants. Acid hydrolysis of total root protein from Arabidopsis thaliana showed incorporation of m-tyrosine, suggesting this as a possible mechanism of phytotoxicity. m-Tyrosine inhibition of A. thaliana root growth is counteracted by exogenous addition of protein amino acids, with phenylalanine having the most significant effect. The discovery of m-tyrosine, as well as a further understanding of its mode(s) of action, could lead to the development of biorational approaches to weed control.
Biogeochemistry and microbial ecology of methane oxidation in anoxic environments: a review
Venue: Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology

Evidence supporting a key role for anaerobic methane oxidation in the global methane cycle is reviewed. Emphasis is on recent microbiological advances. The driving force for research on this process continues to be the fact that microbial communities intercept and consume methane from anoxic environments, methane that would otherwise enter the atmosphere. Anaerobic methane oxidation is biogeochemically important because methane is a potent greenhouse gas in the atmosphere and is abundant in anoxic environments. Geochemical evidence for this process has been observed in numerous marine sediments along the continental margins, in methane seeps and vents, around methane hydrate deposits, and in anoxic waters. The anaerobic oxidation of methane is performed by at least two phylogenetically distinct groups of archaea, the ANME-1 and ANME-2. These archaea are frequently observed as consortia with sulfate-reducing bacteria, and the metabolism of these consortia presumably involves a syntrophic association based on interspecies electron transfer. The archaeal member of a consortium apparently oxidizes methane and shuttles reduced compounds to the sulfate-reducing bacteria. Despite recent advances in understanding anaerobic methane oxidation, uncertainties still remain regarding the nature and necessity of the syntrophic association, the biochemical pathway of methane oxidation, and the interaction of the process with the local chemical and physical environment. This review will consider the microbial ecology and biogeochemistry of anaerobic methane oxidation with a special emphasis on the interactions between the responsible organisms and their environment.
Interaction between temperature and hypoxia in the alligator.
Venue: American Journal of Physiology-regulatory Integrative and Comparative Physiology

Hypoxia elicits behavioral hypothermia in alligators. Under normoxic conditions, the selected body temperature is 27.8 +/- 1.2 degrees C. However, when inspired O2 is lowered to 4%, selected body temperature decreases to 15.4 +/- 1.0 degrees C. The threshold for the behavioral hypothermia is between 4 and 5% inspired O2, the lowest threshold measured so far in terrestrial vertebrates. This study assessed the physiological significance of the behavioral hypothermia. The body temperature was clamped at 15, 25, and 35 degrees C for measurements of ventilation, blood gases, metabolic rate, plasma lactate, and acid-base status. Hypoxia-induced changes in ventilation, acid-base status, oxygen consumption, and lactate were proportional to body temperature, being pronounced at 35 degrees C, less at 25 degrees C, and absent at 15 degrees C. The correlation between selected body temperature under severe hypoxia and the measured parameters show that behavioral hypothermia is a beneficial response to hypoxia in alligators.
Ladder polyether synthesis via epoxide-opening cascades using a disappearing directing group.
Venue: Journal of the American Chemical Society

The combination of a trimethylsilyl group, a Brønsted base, a fluoride source, and a hydroxylic solvent enables the first construction of the tetrad of tetrahydropyran rings found in the majority of the ladder polyether natural products by way of a cascade of epoxide-opening events that emulates the final step of Nakanishi's proposed biosynthetic pathway. The trimethylsilyl group disappears during the course of the cascade, and thus these are the first epoxide ring-opening cascades that afford ladder polyether subunits containing no directing groups at the end of the cascade.
Nanocellulose, a Versatile Green Platform: From Biosources to Materials and Their Applications.
Venue: Chemical Reviews

With increasing environmental and ecological concerns due to the use of petroleum-based chemicals and products, the synthesis of fine chemicals and functional materials from natural resources is of great public value. Nanocellulose may prove to be one of the most promising green materials of modern times due to its intrinsic properties, renewability, and abundance. In this review, we present nanocellulose-based materials from sourcing, synthesis, and surface modification of nanocellulose, to materials formation and applications. Nanocellulose can be sourced from biomass, plants, or bacteria, relying on fairly simple, scalable, and efficient isolation techniques. Mechanical, chemical, and enzymatic treatments, or a combination of these, can be used to extract nanocellulose from natural sources. The properties of nanocellulose are dependent on the source, the isolation technique, and potential subsequent surface transformations. Nanocellulose surface modification techniques are typically used to introduce either charged or hydrophobic moieties, and include amidation, esterification, etherification, silylation, polymerization, urethanization, sulfonation, and phosphorylation. Nanocellulose has excellent strength, high Young's modulus, biocompatibility, and tunable self-assembly, thixotropic, and photonic properties, which are essential for the applications of this material. Nanocellulose participates in the fabrication of a large range of nanomaterials and nanocomposites, including those based on polymers, metals, metal oxides, and carbon. In particular, nanocellulose complements organic-based materials, where it imparts its mechanical properties to the composite. Nanocellulose is a promising material whenever material strength, flexibility, and/or specific nanostructuration are required. Applications include functional paper, optoelectronics, and antibacterial coatings, packaging, mechanically reinforced polymer composites, tissue scaffolds, drug delivery, biosensors, energy storage, catalysis, environmental remediation, and electrochemically controlled separation. Phosphorylated nanocellulose is a particularly interesting material, spanning a surprising set of applications in various dimensions including bone scaffolds, adsorbents, and flame retardants and as a support for the heterogenization of homogeneous catalysts.
Hydrophobins: multipurpose proteins.
Venue: Annual Review of Microbiology

Class I and class II hydrophobins are small secreted fungal proteins that play a role in a broad range of processes in the growth and development of filamentous fungi. For instance, they are involved in the formation of aerial structures and in the attachment of hyphae to hydrophobic surfaces. The mechanisms by which hydrophobins fulfill these functions are based on their property to self-assemble at hydrophilic-hydrophobic interfaces into a 10 nm-thin highly amphipathic film. Complementation studies have shown that class I hydrophobins belong to a closely related group of morphogenetic proteins, but that they have evolved to function at specific interfaces. Recent evidence indicates that hydrophobins do not only function by self-assembly. Monomeric hydrophobin has been implicated in cell-wall assembly, but the underlying mechanism is not yet clear. In addition, hydrophobin monomers could act as toxins and elicitors.
Micromechanics of plant tissues beyond the linear-elastic range
Venue: Planta

We investigated the relation between cell wall structure and the resulting mechanical characteristics of different plant tissues. Special attention was paid to the mechanical behaviour beyond the linear-elastic range, the underlying micromechanical processes and the fracture characteristics. The previously proposed model of reorientation and slippage of the cellulose microfibrils in the cell wall [H.-CH. Spatz et al. (1999)  was supported and is here refined, using measurements of the changes in microfibrillar angle during straining. Our model explains the widespread phenomenon of stress-strain curves with two linear portions of different slope and sheds light on the micromechanical processes involved in viscoelasticity and plastic yield. We also analysed the velocity dependence of viscoelasticity under the perspective of the Kelvin model, resolving the measured viscoelasticity into functions of a velocity-dependent and a velocity-independent friction. The influence of lignin on the above-mentioned mechanical properties was examined by chemical lignin extraction from tissues of Aristolochia macrophylla Lam. and by the use of transgenic plants of Arabidopsis thaliana (L.) Heynh. with reduced lignin content. Additionally, the influence of extraction of hemicelluloses on the mechanical properties was investigated as well as a cell wall mutant of Arabidopsis with an altered configuration of the cellulose microfibrils.
Finite element modeling of shell shape in the freshwater turtle Pseudemys concinna reveals a trade‐off between mechanical strength and hydrodynamic efficiency
Venue: Journal of Morphology

Aquatic species can experience different selective pressures on morphology in different flow regimes. Species inhabiting lotic regimes often adapt to these conditions by evolving low‐drag (i.e., streamlined) morphologies that reduce the likelihood of dislodgment or displacement. However, hydrodynamic factors are not the only selective pressures influencing organismal morphology and shapes well suited to flow conditions may compromise performance in other roles. We investigated the possibility of morphological trade‐offs in the turtle Pseudemys concinna. Individuals living in lotic environments have flatter, more streamlined shells than those living in lentic environments; however, this flatter shape may also make the shells less capable of resisting predator‐induced loads. We tested the idea that “lotic” shell shapes are weaker than “lentic” shell shapes, concomitantly examining effects of sex. Geometric morphometric data were used to transform an existing finite element shell model into a series of models corresponding to the shapes of individual turtles. Models were assigned identical material properties and loaded under identical conditions, and the stresses produced by a series of eight loads were extracted to describe the strength of the shells. “Lotic” shell shapes produced significantly higher stresses than “lentic” shell shapes, indicating that the former is weaker than the latter. Females had significantly stronger shell shapes than males, although these differences were less consistent than differences between flow regimes. We conclude that, despite the potential for many‐to‐one mapping of shell shape onto strength, P. concinna experiences a trade‐off in shell shape between hydrodynamic and mechanical performance. This trade‐off may be evident in many other turtle species or any other aquatic species that also depend on a shell for defense. However, evolution of body size may provide an avenue of escape from this trade‐off in some cases, as changes in size can drastically affect mechanical performance while having little effect on hydrodynamic performance.
Why Do Woodpeckers Resist Head Impact Injury: A Biomechanical Investigation
Venue: PLOS ONE

Head injury is a leading cause of morbidity and death in both industrialized and developing countries. It is estimated that brain injuries account for 15% of the burden of fatalities and disabilities, and represent the leading cause of death in young adults. Brain injury may be caused by an impact or a sudden change in the linear and/or angular velocity of the head. However, the woodpecker does not experience any head injury at the high speed of 6–7 m/s with a deceleration of 1000 g when it drums a tree trunk. It is still not known how woodpeckers protect their brain from impact injury. In order to investigate this, two synchronous high-speed video systems were used to observe the pecking process, and the force sensor was used to measure the peck force. The mechanical properties and macro/micro morphological structure in woodpecker's head were investigated using a mechanical testing system and micro-CT scanning. Finite element (FE) models of the woodpecker's head were established to study the dynamic intracranial responses. The result showed that macro/micro morphology of cranial bone and beak can be recognized as a major contributor to non-impact-injuries. This biomechanical analysis makes it possible to visualize events during woodpecker pecking and may inspire new approaches to prevention and treatment of human head injury.
Chaperonin-mediated protein folding: fate of substrate polypeptide
Venue: Quarterly Reviews of Biophysics

1. Chaperonin action – an overview 230 2. Polypeptide binding – an essential action 235 3. Recognition of non-native polypeptide – role of hydrophobicity 236 4. Crystallographic analyses of peptide binding 237 5. Topology and secondary and tertiary structure of bound substrate polypeptide – fluorescence, hydrogen exchange and NMR studies 239 6. Binding by GroEL associated with a putative unfolding action 242 7. A potential action of substrate unfolding driven by ATP/GroES binding 245 8. Folding in theciscavity 247 9. GroEL–GroES-mediated folding of larger substrate proteins by atransmechanism 249 10. Prospects for resolving the conformations and fate of polypeptide in the chaperonin reaction 251 11. References 252 Chaperonins are megadalton ring assemblies that mediate essential ATP-dependent assistance of protein folding to the native state in a variety of cellular compartments, including the mitochondrial matrix, the eukaryotic cytosol, and the bacterial cytoplasm. Structural studies of the bacterial chaperonin, GroEL, both alone and in complex with its co-chaperonin, GroES, have resolved the states of chaperonin that bind and fold non-native polypeptides. Functional studies have resolved the action of ATP binding and hydrolysis in driving the GroEL–GroES machine through its folding-active and binding-active states, respectively. Yet the exact fate of substrate polypeptide during these steps is only poorly understood. For example, while binding involves multivalent interactions between hydrophobic side-chains facing the central cavity of GroEL and exposed hydrophobic surfaces of the non-native protein, the structure of any polypeptide substrate while bound to GroEL remains unknown. It is also unclear whether binding to an open GroEL ring is accompanied by structural changes in the non-native substrate, in particular whether there is an unfolding action. As a polypeptide-bound ring becomes associated with GroES, do the large rigid-body movements of the GroEL apical domains serve as another source of a potential unfolding action? Regarding the encapsulated folding-active state, how does the central cavity itself influence the folding trajectory of a substrate? Finally, how do GroEL and GroES serve, as recently recognized, to assist the folding of substrates too large to be encapsulated inside the machine? Here, such questions are addressed with the findings available to date, and means of further resolving the states of chaperonin-associated polypeptide are discussed.