nils-herrmann/clean_scirepeval huggingface dataset:
Landscape‐scale carbon storage associated with beaver dams
Venue: Geophysical Research Letters

Beaver meadows form when beaver dams promote prolonged overbank flooding and floodplain retention of sediment and organic matter. Extensive beaver meadows form in broad, low-gradient valley segments upstream from glacial terminal moraines. Surveyed sediment volume and total organic carbon content in beaver meadows on the eastern side of Rocky Mountain National Park are extrapolated to create a first-order approximation of landscape-scale carbon storage in these meadows relative to adjacent uplands. Differences in total organic carbon between abandoned and active beaver meadows suggest that valley-bottom carbon storage has declined substantially as beaver have disappeared and meadows have dried. Relict beaver meadows represent ~8% of total carbon storage within the landscape, but the value was closer to 23% when beaver actively maintained wet meadows. These changes reflect the general magnitude of cumulative effects in heterotrophic respiration and organic matter oxidation associated with historical declines in beaver populations across the continent.
Oxygen mass transfer in a model three-dimensional artery
Venue: Journal of the Royal Society Interface

Arterial geometry is commonly non-planar and associated with swirling blood flow. In this study, we examine the effect of arterial three-dimensionality on the distribution of wall shear stress (WSS) and the mass transfer of oxygen from the blood to the vessel wall in a U-bend, by modelling the blood vessels as either cylindrical or helical conduits. The results show that under physiological flow conditions, three-dimensionality can reduce both the range and extent of low WSS regions and substantially increase oxygen flux through the walls. The Sherwood number and WSS distributions between the three-dimensional helical model and a human coronary artery show remarkable qualitative agreement, implying that coronary arteries may potentially be described with a relatively simple idealized three-dimensional model, characterized by a small number of well-defined geometric parameters. The flow pattern downstream of a planar bend results in separation of the Sh number and WSS effects, a finding that implies means of investigating them individually.
Improved light extraction in the bioluminescent lantern of a Photuris firefly (Lampyridae).
Venue: arXiv: Optics

A common problem of light sources emitting from an homogeneous high-refractive index medium into air is the loss of photons by total internal reflection. Bioluminescent organisms, as well as artificial devices, have to face this problem. It is expected that life, with its mechanisms for evolution, would have selected appropriate optical structures to get around this problem, at least partially. The morphology of the lantern of a specific firefly in the genus Photuris has been examined. The optical properties of the different parts of this lantern have been modelled, in order to determine their positive or adverse effect with regard to the global light extraction. We conclude that the most efficient pieces of the lantern structure are the misfit of the external scales (which produce abrupt roughness in air) and the lowering of the refractive index at the level of the cluster of photocytes, where the bioluminescent production takes place.
Salt tolerance mechanisms in mangroves: a review
Venue: Trees-structure and Function

Mangroves are woody plants which form the dominant vegetation in tidal, saline wetlands along tropical and subtropical coasts. The current knowledge concerning the most striking feature of mangroves i.e., their unique ability to tolerate high salinity is summarized in the present review. In this review, we shall discuss recent studies that have focused on morphological, anatomical, physiological, biochemical, molecular and genetic attributes associated with the response to salinity, some of which presumably function to mediate salt tolerance in the mangroves. Here we shall also review the major advances recently made at both the genetic and the genomic levels in mangroves. Salinity tolerance in mangroves depends on a range of adaptations, including ion compartmentation, osmoregulation, selective transport and uptake of ions, maintenance of a balance between the supply of ions to the shoot, and capacity to accommodate the salt influx. The tolerance of mangroves to a high saline environment is also tightly linked to the regulation of gene expression. By integrating the information from mangroves and performing comparisons among species of mangroves and non-mangroves, we could give a general picture of salt tolerance mechanisms of mangroves, thus providing a new avenue for development of salt tolerance in crop plants through effective breeding strategies and genetic engineering techniques.
Desiccation resistance of adhesive secretion in the protocarnivorous plant Roridula gorgonias as an adaptation to periodically dry environment
Venue: Planta

To analyse the change of mass in the resinous secretion of Roridula gorgonias, we carried out long-term measurements using a computerised ultra microbalance. In contrast to the aqueous mucilage of other carnivorous flypaper traps, this water-insoluble secretion does not desiccate even in dead and formalin-preserved plants. We found no significant desiccation of secretory drops within 10 h of continuous weighing. After 100 days of the secretion exposure to dry conditions, only about 8% of the mass was lost. Interestingly, returning these samples to humid conditions resulted in a mass recovery to the initial amount. This property of the secretion is discussed as an ecological adaptation to the periodically dry Fynbos habitat of the plant.
Physiological colour change in the elytra of the hercules beetle, Dynastes hercules
Venue: Journal of Insect Physiology

The male of the hercules beetle, Dynastes hercules, is able to change the colour of its elytra from yellowish to black and back again to yellowish within a few minutes. The epicuticle of the elytra is transparent and about 3 μm thick. Below it is a yellow spongy layer that is usually about 5 μm thick. The cuticle below the yellow sponge is black. When the layer of yellow sponge is air filled it becomes optically heterogeneous, and the light reflected from the elytra is yellow. When the yellow sponge is liquid filled it becomes optically homogeneous, and the black cuticle below is seen. If a beetle that has yellowish elytra is placed in a saturated atmosphere, the elytra become black. When the relative humidity is appreciably reduced, yellow patches begin to appear on the elytra, usually within 30 sec to 2 min. However, if the beetle is kept at a constant relative humidity that previously caused yellowing, it will become black given enough time. Most colour changes observed were clearly in response to changes in the ambient humidity and were not affected when the beetles were kept in the light or in total darkness nor by blackening their eyes or prodding them or exposing them to sounds of different intensities or frequencies. If an elytron is removed from a live beetle, it changes colour in response to changes in relative humidity exactly like the elytron left attached. When a restricted area of the elytra is subjected to a humidity that normally causes blackening and an adjacent area to a humidity that normally causes yellowing, both change colour in the expected way. This local control of colour change seems to preclude hormonal control. It is suggested that the epidermal cells or both the epidermal and blood cells in the elytra are responsible for the hydration and dehydration of the layer of yellow sponge.
Photosynthetic adaptation of two semi-arid species of Gethyllis (Kukumakranka) to drought-and-shade stress
Venue: South African Journal of Botany

Gethyllis multifolia and Gethyllis villosa are winter-growing, summer-blooming, deciduous and bulbous geophytes that grow naturally in the semi-arid ‘Succulent Karoo Biome’ of South Africa. G. multifolia is threatened in its natural habitat and resides in the ‘Vulnerable’ category of the ‘Red Data List of Southern African Plants’. Previous investigations suggested that G. multifolia is more sensitive to drought stress than G. villosa and that both species adopted certain morphological changes in their leaves during shade stress. Current models indicate that this biome is being exposed to increasingly drier conditions and shading from encroaching indigenous plant species. In this study, the photosynthetic gas exchange responses of both species to drought and shade stresses were investigated and the ‘Vulnerable’ conservation status of G. multifolia. This investigation found that during drought stress G. villosa had a more enhanced photosynthetic performance than G. multifolia which appears not to be related to foliar adaptations such as specific leaf mass (SLM), but to the G. villosa's leaves maintaining their stomatal conductance (Gs), photosynthetic light compensation (LCP) and photon yields. Furthermore, during shade stress G. villosa also had an improved photosynthetic performance by not altering its photosynthetic LCP during reduced light conditions. It can be concluded that G. multifolia has a lower capacity than G. villosa to adapt its photosynthetic apparatus to changing environments such as increasing drought and shaded conditions. This may be a contributing factor to the threatened conservation status of G. multifolia.
Designing efficient microlens arrays: lessons from Nature
Venue: Journal of Materials Chemistry

provides a whole host of superior multifunctional structures that can be used as inspirational systems for the design and synthesis of new, technologically important materials and devices. We review here the exceptional optical performance of microlens arrays formed by light-sensitive brittlestars, their structural and compositional features, and advantageous properties. We show that brittlestars form a nearly perfect optical device with micron-scale, lightweight, mechanically strong, aberration-free, birefringence-free, individually-addressed lenses, which offer a unique focusing effect, signal enhancement, intensity adjustment, angular selectivity, and photochromic activity. We discuss first materials fabrication strategies that were inspired by the principles involved in the formation of echinoderm calcitic structures. The biomimetic synthetic microlens arrays could be potentially used as highly tunable optical elements for a wide variety of applications.
A conserved spider silk domain acts as a molecular switch that controls fibre assembly
Venue: Nature

A huge variety of proteins are able to form fibrillar structures, especially at high protein concentrations. Hence, it is surprising that spider silk proteins can be stored in a soluble form at high concentrations and transformed into extremely stable fibres on demand. Silk proteins are reminiscent of amphiphilic block copolymers containing stretches of polyalanine and glycine-rich polar elements forming a repetitive core flanked by highly conserved non-repetitive amino-terminal and carboxy-terminal domains. The N-terminal domain comprises a secretion signal, but further functions remain unassigned. The C-terminal domain was implicated in the control of solubility and fibre formation initiated by changes in ionic composition and mechanical stimuli known to align the repetitive sequence elements and promote β-sheet formation. However, despite recent structural data, little is known about this remarkable behaviour in molecular detail. Here we present the solution structure of the C-terminal domain of a spider dragline silk protein and provide evidence that the structural state of this domain is essential for controlled switching between the storage and assembly forms of silk proteins. In addition, the C-terminal domain also has a role in the alignment of secondary structural features formed by the repetitive elements in the backbone of spider silk proteins, which is known to be important for the mechanical properties of the fibre.
Vortex wake and flight kinematics of a swift in cruising flight in a wind tunnel
Venue: The Journal of Experimental Biology

In this paper we describe the flight characteristics of a swift (Apus apus) in cruising flight at three different flight speeds (8.0, 8.4 and 9.2 m s–1) in a low turbulence wind tunnel. The wingbeat kinematics were recorded by high-speed filming and the wake of the bird was visualized by digital particle image velocimetry (DPIV). Certain flight characteristics of the swift differ from those of previously studied species. As the flight speed increases, the angular velocity of the wingbeat remains constant, and so as the wingbeat amplitude increases, the frequency decreases accordingly, as though the flight muscles were contracting at a fixed rate. The wings are also comparatively inflexible and are flexed or retracted rather little during the upstroke. The upstroke is always aerodynamically active and this is reflected in the wake, where shedding of spanwise vorticity occurs throughout the wingbeat. Although the wake superficially resembles those of other birds in cruising flight, with a pair of trailing wingtip vortices connected by spanwise vortices, the continuous shedding of first positive vorticity during the downstroke and then negative vorticity during the upstroke suggests a wing whose circulation is gradually increasing and then decreasing during the wingbeat cycle. The wake (and implied wing aerodynamics) are not well described by discrete vortex loop models, but a new wake-based model, where incremental spanwise and streamwise variations of the wake impulse are integrated over the wingbeat, shows good agreement of the vertical momentum flux with the required weight support. The total drag was also estimated from the wake alone, and the calculated lift:drag ratio of approximately 13 for flapping flight is the highest measured yet for birds.
The geometry of the forisome-sieve element-sieve plate complex in the phloem of Vicia faba L. leaflets.
Venue: Journal of Experimental Botany

Forisomes are contractile protein bodies that appear to control flux rates in the phloem of faboid legumes by reversibly plugging the sieve tubes. Plugging is triggered by Ca(2+) which induces an anisotropic deformation of forisomes, consisting of a longitudinal contraction and a radial expansion. By conventional light microscopy and confocal laser-scanning microscopy, the three-dimensional geometry of the forisome-sieve element-sieve plate complex in intact sieve tubes of leaflets of Vicia faba L. was reconstructed. Forisomes were mostly located close to sieve plates, and occasionally were observed drifting unrestrainedly along the sieve element, suggesting that they might be utilized as internal markers of flow direction. The diameter of forisomes in the resting state correlated with the diameter of their sieve elements, supporting the idea that radial expansion of forisomes is the geometric basis of reversible sieve tube plugging. Comparison of the present results regarding forisome geometry in situ with previously published data on forisome reactivity in vitro makes it questionable, however, whether forisomes are capable of completely sealing sieve tubes in V. faba leaves.
A biological sub-micron thickness optical broadband reflector characterized using both light and microwaves
Venue: Journal of the Royal Society Interface

Broadband optical reflectors generally function through coherent scattering from systems comprising one of three designs: overlapped; chirped; or chaotic multilayer reflectors. For each, the requirement to scatter a broad band of wavelengths is met through the presence of a variation in nanostructural periodicity running perpendicular to the systems' outer surfaces. Consequently, the requisite total thickness of the multilayer can often be in excess of 50 μm. Here, we report the discovery and the microwave-assisted characterization of a natural system that achieves excellent optical broadband reflectivity but that is less than 1 μm thick. This system, found on the wing scales of the butterfly Argyrophorus argenteus, comprises a distinctive variation in periodicity that runs parallel to the reflecting surface, rather than perpendicular to it. In this way, the requirement for an extensively thick system is removed.
Visible light reflection spectra from cuticle layered materials
Venue: Optical Materials Express

The brilliant metallic appearance of two kinds of beetles, the Chrysina aurigans and the Chrysina limbata, is displayed visually as well as from normalized reflection measurements of non polarized visible light under normal incidence. The C. limbata is reflective over the visible spectral wavelength range, with a silver-like aspect, while the golden-like C. aurigans is reflective for wavelengths larger than 525 nm, and with a well defined sequence of minima and maxima depicted in the reflection spectra. Both specimens show selective reflection of circular polarized light with the effect being significantly weaker for the C. limbata. A transfer matrix formalism is applied to approach the main features displayed in the measured reflection spectra, by assuming a chirped multilayer structure with decreasing thicknesses of successive layers through the cuticle of the beetles.
Sympodial construction of Fibonacci-type leaf rosettes in Pinguicula moranensis (Lentibulariaceae).
Venue: Annals of Botany

The leaf rosettes of the carnivorous Pinguicula moranensis follow a spiral phyllotaxis approaching a Fibonacci pattern while the stalked flowers arise from extra-axillary sites between the leaves. The organization of this rosette has been discussed by various authors, with various results. The aim of the present study was to clarify the development of the flowering rosettes of this species.



The formation of the rosettes is shown with the aid of scanning electron microscopy.



The scanning electron micrographs show that each flower terminates an article (sympodial unit). The leaves of consecutive articles of such sympodially constructed rosettes are arranged along a spiral Fibonacci pattern (with divergence angles around 137 degrees). This results from homodromy of leaf initiation in consecutive articles with the first leaf (prophyll) of a new article inserted in an obliquely transverse position next to the floral scape that terminates the former article. Sympodial construction of flowering shoots and leaf rosettes is also known from Aloe, Gunnera and Philodendron. As a by-product of this study, the unidirectional development of the Pinguicula flower is confirmed and discussed.
Peptide tag forming a rapid covalent bond to a protein, through engineering a bacterial adhesin
Venue: Proceedings of the National Academy of Sciences of the United States of America

Protein interactions with peptides generally have low thermodynamic and mechanical stability. Streptococcus pyogenes fibronectin-binding protein FbaB contains a domain with a spontaneous isopeptide bond between Lys and Asp. By splitting this domain and rational engineering of the fragments, we obtained a peptide (SpyTag) which formed an amide bond to its protein partner (SpyCatcher) in minutes. Reaction occurred in high yield simply upon mixing and amidst diverse conditions of pH, temperature, and buffer. SpyTag could be fused at either terminus or internally and reacted specifically at the mammalian cell surface. Peptide binding was not reversed by boiling or competing peptide. Single-molecule dynamic force spectroscopy showed that SpyTag did not separate from SpyCatcher until the force exceeded 1 nN, where covalent bonds snap. The robust reaction conditions and irreversible linkage of SpyTag shed light on spontaneous isopeptide bond formation and should provide a targetable lock in cells and a stable module for new protein architectures.
Radular teeth as models for the improvement of industrial cutting devices
Venue: Materials Science and Engineering: C

Limpets (Gastropoda) and chitons (Polyplacophora) feed on epi- and endolithic organisms by means of the radula, a specialized feeding apparatus located in the mouth cavity. The radula owes most of its abrasive capability to the presence of numerous mineralized teeth. Here we report on the shape, internal structure, wearing pattern, feeding position, and distribution of hardness and elastic properties of these teeth in an attempt to generate ideas for the innovation of industrial cutting devices. The teeth remain sharp during their entire working-life mainly due to the fact that wearing preferentially occurs along surfaces formed by the internal structure of the tooth. It is shown that shape, internal structure, positioning and material characteristics concertedly function in minimizing the rate at which the teeth wear down and in maintaining optimal cutting behaviour. Implementation of these self-sharpening characteristics into industrial cutting devices is discussed.
Hydrogen is an energy source for hydrothermal vent symbioses
Venue: Nature

The discovery of deep-sea hydrothermal vents in 1977 revolutionized our understanding of the energy sources that fuel primary productivity on Earth. Hydrothermal vent ecosystems are dominated by animals that live in symbiosis with chemosynthetic bacteria. So far, only two energy sources have been shown to power chemosynthetic symbioses: reduced sulphur compounds and methane. Using metagenome sequencing, single-gene fluorescence in situ hybridization, immunohistochemistry, shipboard incubations and in situ mass spectrometry, we show here that the symbionts of the hydrothermal vent mussel Bathymodiolus from the Mid-Atlantic Ridge use hydrogen to power primary production. In addition, we show that the symbionts of Bathymodiolus mussels from Pacific vents have hupL, the key gene for hydrogen oxidation. Furthermore, the symbionts of other vent animals such as the tubeworm Riftia pachyptila and the shrimp Rimicaris exoculata also have hupL. We propose that the ability to use hydrogen as an energy source is widespread in hydrothermal vent symbioses, particularly at sites where hydrogen is abundant.
Biodegradation of volatile organic compounds by five fungal species
Venue: Applied Microbiology and Biotechnology

Five fungal species, Cladosporium resinae (ATCC 34066), Cladosporium sphaerospermum (ATCC 200384), Exophiala lecanii-corni (CBS 102400), Mucor rouxii (ATCC 44260), and Phanerochaete chrysosporium (ATCC 24725), were tested for their ability to degrade nine compounds commonly found in industrial off-gas emissions. Fungal cultures inoculated on ceramic support media were provided with volatile organic compounds (VOCs) via the vapor phase as their sole carbon and energy sources. Compounds tested included aromatic hydrocarbons (benzene, ethylbenzene, toluene, and styrene), ketones (methyl ethyl ketone, methyl isobutyl ketone, and methyl propyl ketone), and organic acids (n-butyl acetate, ethyl 3-ethoxypropionate). Experiments were conducted using three pH values ranging from 3.5 to 6.5. Fungal ability to degrade each VOC was determined by observing the presence or absence of visible growth on the ceramic support medium during a 30-day test period. Results indicate that E. lecanii-corni and C. sphaerospermum can readily utilize each of the nine VOCs as a sole carbon and energy source. P. chrysosporium was able to degrade all VOCs tested except for styrene under the conditions imposed. C. resinae was able to degrade both organic acids, all of the ketones, and some of the aromatic compounds (ethylbenzene and toluene); however, it was not able to grow utilizing benzene or styrene under the conditions tested. With the VOCs tested, M. rouxii produced visible growth only when supplied with n-butyl acetate or ethyl 3-ethoxypropionate. Maximum growth for most fungi was observed at a pH of approximately 5.0. The experimental protocol utilized in these studies is a useful tool for assessing the ability of different fungal species to degrade gas-phase VOCs under conditions expected in a biofilter application.