nils-herrmann/clean_scirepeval huggingface dataset:
Epoxide-Opening Cascades Promoted by Water
Venue: Science

Selectivity rules in organic chemistry have been inferred largely from nonaqueous environments. In contrast, enzymes operate in water, and the chemical effect of the medium change remains only partially understood. Structural characterization of the “ladder” polyether marine natural products raised a puzzle that persisted for 20 years: Although the stereochemistry of adjacent tetrahydropyran (THP) cycles would seem to arise from a biosynthetic cascade of epoxide-opening reactions, experience in organic solvents argued consistently that such a pathway would be kinetically disfavored. We report that neutral water acts as an optimal promoter for the requisite ring-opening selectivity, once a single templating THP is appended to a chain of epoxides. This strategy offers a high-yielding route to the naturally occurring ladder core and highlights the likely importance of aqueous-medium effects in underpinning certain noteworthy enzymatic selectivities.
Propulsive force calculations in swimming frogs II. Application of a vortex ring model to DPIV data
Venue: The Journal of Experimental Biology

Frogs propel themselves by kicking water backwards using a synchronised extension of their hind limbs and webbed feet. To understand this propulsion process, we quantified the water movements and displacements resulting from swimming in the green frog Rana esculenta, applying digital particle image velocimetry (DPIV) to the frog's wake. The wake showed two vortex rings left behind by the two feet. The rings appeared to be elliptic in planform, urging for correction of the observed ring radii. The rings' long and short axes (average ratio 1.75:1) were about the same size as the length and width of the propelling frog foot and the ellipsoid mass of water accelerated with it. Average thrust forces were derived from the vortex rings, assuming all propulsive energy to be compiled in the rings. The calculated average forces (Fav=0.10±0.04 N) were in close agreement with our parallel study applying a momentum–impulse approach to water displacements during the leg extension phase. We did not find any support for previously assumed propulsion enhancement mechanisms. The feet do not clap together at the end of the power stroke and no `wedge-action' jetting is observed. Each foot accelerates its own water mantle, ending up in a separate vortex ring without interference by the other leg.
Adaptations to in situ feeding: novel nutrient acquisition pathways in an ancient vertebrate
Venue: Proceedings of The Royal Society B: Biological Sciences

During feeding, hagfish may immerse themselves in the body cavities of decaying carcasses, encountering high levels of dissolved organic nutrients. We hypothesized that this feeding environment might promote nutrient acquisition by the branchial and epidermal epithelia. The potential for Pacific hagfish, Eptatretus stoutii, to absorb amino acids from the environment across the skin and gill was thus investigated. l-alanine and glycine were absorbed via specific transport pathways across both gill and skin surfaces, the first such documentation of direct organic nutrient acquisition in a vertebrate animal. Uptake occurred via distinct mechanisms with respect to concentration dependence, sodium dependence and effects of putative transport inhibitors across each epithelium. Significant differences in the absorbed amino acid distribution between the skin of juveniles and adults were noted. The ability to absorb dissolved organic matter across the skin and gill may be an adaptation to a scavenging lifestyle, allowing hagfish to maximize sporadic opportunities for organic nutrient acquisition. From an evolutionary perspective, hagfish represent a transitory state between the generalized nutrient absorption pathways of aquatic invertebrates and the more specialized digestive systems of aquatic vertebrates.
Influence of season of fire on flowering of wet prairie grasses in south Florida, USA
Venue: Wetlands

We measured the effects of prescribed fire during January (dormant season) and May (growing season) on flowering of three perennial grasses, muhly (Muhlenbergia capillaris), gulfdune paspalum (Paspalum monostachyum), and south Florida bluestem (Schizachyrium rhizomatum), which are dominant grasses in wet prairies of south Florida, USA. Flowering was promoted by growing season fire but not by dormant season fire. Flowering was significantly greater for all species following prescribed fire conducted during May compared with areas burned during January of the same calendar year. The strong positive effect of growing season fire on flowering of all three species decreased after the first growing season. We rejected the hypothesis that season of fire did not influence flowering. Our results indicated that flowering by these dominant, wet prairie grasses is promoted by early growing season fire, which corresponds to historical patterns of lightning-ignited fire in south Florida.
The Anatomy and Histology of Caudal Autotomy and Regeneration in Lizards*
Venue: Physiological and Biochemical Zoology

Caudal autotomy—the ability to self-detach the tail—is a dramatic adaptation common to many structural-grade lizards. For most species, tail loss is followed by the equally dramatic phenomenon of tail regeneration. Here we review the anatomy and histology of caudal autotomy and regeneration in lizards, drawing heavily from research published over the past 2 decades. The autotomous tail is characterized by various structural adaptations, which act to minimize blood loss and trauma to adjacent tissues. The early phase of wound healing involves a leukocytic response but limited inflammation. Reepithelialization via a specialized wound epithelium is not only critical for scar-free healing but also necessary for subsequent tissue patterning and regenerative outgrowth. Regeneration begins with the formation of the blastema, a mass of proliferating mesenchymal-like cells. As the blastema expands, it is invaded by blood vessels and the spinal cord. Whereas the replacement tail outwardly resembles the original appendage, it differs in several notable respects, including the tissue composition and organization of the skeleton, muscular system, and spinal cord. Increasingly, the lizard tail is being recognized among biomedical scientists as an important model for the study of wound healing and multitissue restoration.
Do anemonefishes use molecular mimicry to avoid being stung by host anemones
Venue: Journal of Experimental Marine Biology and Ecology

Anemonefishes are known to have a protective mucous coat that allows them to contact the tentacles of their host anemone without being stung. There are two conflicting hypotheses as to the source and biochemical properties of this mucous coating. One hypothesis proposes that anemonefishes acquire anemone substances from their hosts during the behavioral process of acclimation, that protect the fish from being stung. Anemonefishes are considered to use anemone mucus as “chemical camouflage” or “macromolecular mimicry” to avoid recognition as “not-self” by the anemone, and possible subsequent stinging. Another hypothesis is that anemonefishes produce their own protective mucus coat, which lacks substances that elicit cnida (nematocyst and spirocyst) discharge by their hosts. 
 
The present study used immunological techniques to test whether the anemonefish Amphiprion clarkii (Bennett) (which was innately protected from two of the anemones used in the present study) has a mucous coat that resembles the external mucus of anemones. Polyclonal antibodies were prepared to the mucus of four species of anemones [Heteractis crispa, (Ehrenberg) Stichodactyla haddoni (Saville-Kent), Macrodactyla doreenensis (Quoy and Gaimard), and Condylactis gigantea (Weinland)]. Ouchterlony (double immunodiffusion) tests showed that different antigens were present in the mucus of the four anemone species. Anemone antigens were not detected in the mucous coating of either naive (fish that had never before encountered sea anemones) or associated (those living with sea anemones) anemonefishes in Ouchterlony tests. However, more sensitive ELISA (enzyme-linked immunosorbent assay) tests showed that anemone mucus antigens were present in the mucous coating of associated anemonefish, but not naive fish. This showed that an innately protected A. clarkii does not produce a mucus coat that is biochemically similar to that of anemones, but that the same fish does acquire anemone substances in its mucus coat when it associates with anemones in aquaria. It remains to be shown whether these anemone substances actually provide the initial protection for those anemonefishes that must undergo acclimation behavior in order to keep from being stung by their host sea anemones, or additional protection for innately protected fishes.
The Role of Seed Banks in the Vegetation Dynamics of Prairie Glacial Marshes
Venue: Ecology

The presence of viable seed in 24 substrate samples from Eagle Lake, a marsh in north- central Iowa, was tested by placing subsamples of each sample under 2 environmental conditions. One set of subsamples was placed underwater (submersed treatment). Seeds of 20 species germinated and grew in this treatment. On the average, there were 8.3 species/sample. The 2nd set of subsamples was kept moist, simulating conditions on an exposed mud flat (drawdown treatment). In the drawdown treatment, on the average, seeds of 12.9 species germinated/sample. Altogether seeds of 40 species germinated in this treatment of which only 24% were also found in the submersed treatment. By combining the results from the 2 treatments, the seed banks in the 6 vegetation types studied were estimated to range from 21,445 to 42,615 seeds/m2 on the average in the upper 5 cm of soil. Field studies at Eagle Lake (1974) and Goose Lake (1976), when these marshes had no standing water, revealed that the most abundant species whose seeds germinated on exposed mud flats were the same as the most abundant species in the experimental drawdown samples from Eagle Lake. In 1975, when Eagle Lake had standing water again, the submersed and floating species that were found were the same as those found in the experimental submersed samples from Eagle Lake. The seed-bank results and vegetation sampling reveal that there are 3 types of species present in prairie marsh seed banks: emergent species (Typha, Scirpus, Sparganium, Sagittaria) germinate on exposed mud flats or in very shallow water; submersed and free-floating species (Lemna, Spirodela, Ceratophyllum, Naias, Potamogeton) whose dormant seeds or turions can survive on exposed mud flats for a year and which germinate when there is standing water; and mud-flat species (Bidens, Cyperus, Polygonum and Rumex) which are ephemerals whose seeds can only germinate on exposed mud flats during periods when no standing water exists in the marsh because of drought or water level manipulation. When the marsh refloods, these species are eliminated from the visible marsh flora. Primarily because of fluctuating water levels and muskrat damage, prairie marshes have cyclical changes in their vegetation during which mud-flat, emergent, or submersed and free-floating species replace each other as the dominant type of species in a marsh.
Directional water collection on wetted spider silk
Venue: Nature

Many biological surfaces in both the plant and animal kingdom possess unusual structural features at the micro- and nanometre-scale that control their interaction with water and hence wettability. An intriguing example is provided by desert beetles, which use micrometre-sized patterns of hydrophobic and hydrophilic regions on their backs to capture water from humid air. As anyone who has admired spider webs adorned with dew drops will appreciate, spider silk is also capable of efficiently collecting water from air. Here we show that the water-collecting ability of the capture silk of the cribellate spider Uloborus walckenaerius is the result of a unique fibre structure that forms after wetting, with the ‘wet-rebuilt’ fibres characterized by periodic spindle-knots made of random nanofibrils and separated by joints made of aligned nanofibrils. These structural features result in a surface energy gradient between the spindle-knots and the joints and also in a difference in Laplace pressure, with both factors acting together to achieve continuous condensation and directional collection of water drops around spindle-knots. Submillimetre-sized liquid drops have been driven by surface energy gradients or a difference in Laplace pressure, but until now neither force on its own has been used to overcome the larger hysteresis effects that make the movement of micrometre-sized drops more difficult. By tapping into both driving forces, spider silk achieves this task. Inspired by this finding, we designed artificial fibres that mimic the structural features of silk and exhibit its directional water-collecting ability.
Domes, arches and urchins: The skeletal architecture of echinoids (Echinodermata)
Venue: Zoomorphology

SummaryA combination of simple membrane theory and statical analysis has been used to determine how stresses are carried in echinoid skeletons. Sutures oriented circumferentially are subject principally to compression. Those forming radial zig-zags are subject to compression near the apex and tension near the ambitus. Radial and circumferential sutures in Eucidaris are equally bound with collagen fibers but in Diadema, Tripneustes, Psammechinus, Arbacia and other regular echinoids, most radial sutures are more heavily bound, and thus stronger in tension. Psammechinus, Tripneustes and several other echinoids have radial sutures thickened by ribs which increase the area of interlocking trabeculae. Ribs also increase flexural stiffness and carry a greater proportion of the stress. Further, ribs effectively draw stress from weaker areas pierced by podial pores, and increase the total load which can be sustained.Allometry indicates that regular echinoids become relatively higher at the apex as size increases, thus reducing ambital stresses. Some spatangoids with very high domes (eg Agassizia) maintain isometry, but others (eg Meoma) become flatter with size. Both holectypoids (Echinoneus) and cassiduloids (Apatopygus) maintain a constant height to diameter relationship. Flattening, and consequently ambital tensile stress, is greatest in the clypeasteroids. In this group the formation of internal buttresses which preferentially carry stress, reaches maximum development. A notable exception, however, is the high domed Clypeaster rosaceus.In this analysis it was assumed that local buckling or bending does not occur. The test of some echinoids (e.g. Diadematoida) have relatively wide sutures swathed in collagen, which allows local deformation. Others (e.g. Arbacia) have rigid sutures with reduced collagen. In Psammechinus and other members of the Order Echinoida, in addition to rib formation, inner and outer surface trabeculae are thickened so that the individual plates are stiffened. Some spatangoids (Meoma, Paleopneustes) have extensive sutural collagen, but the cassiduloid Apatopygus has collagen confined to junctions of sutures, and elsewhere the joints are strengthened and stiffened by fusion of trabeculae. Fusion of surface trabeculae is almost complete in the holectypoid, Echinoneus, and the sutures are obscured.
Lobster Sniffing: Antennule Design and Hydrodynamic Filtering of Information in an Odor Plume
Venue: Science

The first step in processing olfactory information, before neural filtering, is the physical capture of odor molecules from the surrounding fluid. Many animals capture odors from turbulent water currents or wind using antennae that bear chemosensory hairs. We used planar laser–induced fluorescence to reveal how lobster olfactory antennules hydrodynamically alter the spatiotemporal patterns of concentration in turbulent odor plumes. As antennules flick, water penetrates their chemosensory hair array during the fast downstroke, carrying fine-scale patterns of concentration into the receptor area. This spatial pattern, blurred by flow along the antennule during the downstroke, is retained during the slower return stroke and is not shed until the next flick.
Directional hearing in a silicon cricket
Venue: BioSystems

Phonotaxis is the ability to orient towards or away from sound sources. Crickets can locate conspecifics by phonotaxis to the calling (mating) song they produce, and can evade bats by negative phonotaxis from echolocation calls. The behaviour and underlying physiology have been studied in some depth, and the auditory system solves this complex problem in a unique manner. Experiments conducted on a simulation model of the system indicated that the mechanism output a directional signal to sounds ahead at calling song frequency and to sounds behind at echolocation frequencies. We suggest that this combination of responses helps simplify later processing in the cricket. To further explore this result, an analogue, very large scale integrated (aVLSI) circuit model of the mechanism was designed and built; results from testing this agreed with the simulation. The aVLSI circuit was used to test a further hypothesis about the potential advantages of the positioning of the acoustic inputs for sound localisation during walking. There was no clear advantage to the directionality of the system in their location. The aVLSI circuitry is now being extended to use on a robot along with previously modelled neural circuitry to better understand the complete sensorimotor pathway.
Natural Polyesters: Dufour's Gland Macrocyclic Lactones Form Brood Cell Laminesters in Colletes Bees
Venue: Science

Bees in the genus Colletes make their brood cells in the ground and coat them with a highly resistant, waterproof, transparent membrane. This membrane is a polyester constructed mainly from 18-hydroxyoctadecanoic acid and 20-hydroxy-eicosanoic acid, which are stored as their corresponding lactones in the Dufour's gland of the bee. When lining the cells, the bee secretes its glandular content, and the membrane is apparently a product of polycondensation reaction of its contents. This appears to be the first report of a naturally occurring linear polyester. The term laminester (lamina ≃ layer + ester) for this class of compounds is proposed.
Sacred lotus, the long-living fruits of China Antique
Venue: Seed Science Research

In the West, lotus (Nelumbo nucifera Gaertn.) is relatively little known. However, for more than 3000 years, lotus plants have been cultivated as a crop in Far-East Asia, where they are used for food, medicine and play a significant role in religious and cultural activities. Holder of the world’s record for long-term seed viability (1300 years) is a lotus fruit (China Antique) from Xipaozi, Liaoning Province, China. Five offspring of this variety, from 200–500-year-old fruits (14C dates) collected at Xipaozi, have recently been germinated, and are the first such seedlings to be raised from directly dated fruits. The fruits at Xipaozi, preserved in a dry ancient lakebed, have been exposed to low-dose γ-radiation for hundreds of years (having an accumulated soil irradiation of 0.1–1.0 Gy). Offspring from these old fruits show abnormalities that resemble those in various modern seedlings irradiated at much higher doses. Although these lotus offspring are phenotypically abnormal, the viability of old seeds was evidently not affected by accumulated doses of up to 3 Gy. Growth characteristics of first- and second-year lotus offspring of these fruits, products of the longest-term radiobiological experiment on record, are summarized here (rapid early growth, phenotypic abnormalities, lack of vigour, poor rhizome development and low photosynthetic activity during second-year growth). Aspects of their chromosomal organization, phenotype and physiology (rapid recovery from stress, heat-stable proteins, protein-repair enzyme) are discussed. Important unsolved problems are suggested to elicit interest among members of the seed science community to the study of old fruits recently collected at Xipaozi, with particular emphasis on aspects of ageing and repair.
Kingfisher feathers – colouration by pigments, spongy nanostructures and thin films
Venue: The Journal of Experimental Biology

The colours of the common kingfisher, Alcedo atthis, reside in the barbs of the three main types of feather: the orange breast feathers, the cyan back feathers and the blue tail feathers. Scanning electron microscopy showed that the orange barbs contain small pigment granules. The cyan and blue barbs contain spongy nanostructures with slightly different dimensions, causing different reflectance spectra. Imaging scatterometry showed that the pigmented barbs create a diffuse orange scattering and the spongy barb structures create iridescence. The extent of the angle-dependent light scattering increases with decreasing wavelength. All barbs have a cortical envelope with a thickness of a few micrometres. The reflectance spectra of the cortex of the barbs show oscillations when measured from small areas, but when measured from larger areas the spectra become wavelength independent. This can be directly understood with thin film modelling, assuming a somewhat variable cortex thickness. The cortex reflectance appears to be small but not negligible with respect to the pigmentary and structural barb reflectance.
Exopolymer alteration of physical properties of sea ice and implications for ice habitability and biogeochemistry in a warmer Arctic
Venue: Proceedings of the National Academy of Sciences of the United States of America

The physical properties of Arctic sea ice determine its habitability. Whether ice-dwelling organisms can change those properties has rarely been addressed. Following discovery that sea ice contains an abundance of gelatinous extracellular polymeric substances (EPS), we examined the effects of algal EPS on the microstructure and salt retention of ice grown from saline solutions containing EPS from a culture of the sea-ice diatom, Melosira arctica. We also experimented with xanthan gum and with EPS from a culture of the cold-adapted bacterium Colwellia psychrerythraea strain 34H. Quantitative microscopic analyses of the artificial ice containing Melosira EPS revealed convoluted ice-pore morphologies of high fractal dimension, mimicking features found in EPS-rich coastal sea ice, whereas EPS-free (control) ice featured much simpler pore geometries. A heat-sensitive glycoprotein fraction of Melosira EPS accounted for complex pore morphologies. Although all tested forms of EPS increased bulk ice salinity (by 11–59%) above the controls, ice containing native Melosira EPS retained the most salt. EPS effects on ice and pore microstructure improve sea ice habitability, survivability, and potential for increased primary productivity, even as they may alter the persistence and biogeochemical imprint of sea ice on the surface ocean in a warming climate.
Self-burial behaviour of Erodium cicutarium seeds.
Venue: Journal of Ecology

(1) The self-planting mechanism of the hygroscopic 'seeds' of Erodium cicutarium was examined. (2) Burial depended first on the location of crevices by the seeds. (3) The seeds were more likely to establish themselves in large crevices, even when their awn-tails, awn-hairs and carpel-tips had been removed experimentally. (4) Once in a crevice, the probability of a seed remaining there and the depth attained were greater when the crevices were small. In small crevices, seeds with intact awns and carpels attained greater depths than that of those without these structures. (5) When crevices were small and common, the seeds became established after five uncoiling-recoiling cycles. In large crevices, eight cycles were required for establishment; when crevices were small and infrequent, forty cycles were required.