nils-herrmann/clean_scirepeval huggingface dataset:
Mechanical Design in Sea Anemones
Venue: Coelenterate Ecology and Behavior; The Journal of Experimental Biology

By applying principles of fluid and solid mechanics to biological structures, I have studied the morphological adaptations of two species of sea anemones to the mechanical activities they perform and the environmental forces they encounter. The two species of anemones I used represent different extremes in mechanical behavior: Metridium senile, a calm-water species noted for the great range of shapes and sizes it can assume (Batham and Pantin, 1950), and Anthopleura xanthogrammica, a species occurring in areas exposed to extreme wave action (Hand, 1956; Dayton, 1971). I chose anemones because they are simple in structure, thus differences in morphology and function between species are easier to recognize and characterize than they would be for more complex animals.
Prolyl hydroxylase activity in tissue homogenates of annelids from deep sea hydrothermal vents.
Venue: Matrix Biology

Tissue homogenates of the deep sea annelids Alvinella caudata and Alvinella pompejana were found to contain enzyme activity resembling vertebrate prolyl 4-hydroxylase. The release of 3H2O from [3,4-(3)H]proline labeled, under-hydroxylated chicken protocollagen type I depended on the presence of the cofactors 2-oxoglutarate, ascorbate, Fe2+ and O2. The release of 3H2O could be inhibited by the prolyl 4-hydroxylase inhibitors zinc, 2,2'-dipyridyl, 3,4-dihydroxybenzoic acid and pyridine-2,4-dicarboxylate, as well as by the synthetic peptide (Pro-Pro-Gly)10. This synthetic peptide could also serve as substrate, because it enhanced the decarboxylation of 2-oxo[5-(14)C]glutarate. Alvinella prolyl hydroxylase appeared to be related to type II vertebrate enzyme because of its lack of affinity for poly (L-proline) and resistance to inactivation by an irreversible peptide inhibitor of chicken prolyl 4-hydroxylase. Maximal enzyme activity was observed in solutions with less than 10% oxygen saturation. By contrast, chicken enzyme was most active at saturating oxygen concentrations. Further data suggest that the Alvinella enzymes are able to accept the 2-oxo acids pyruvate, oxaloacetate and 2-oxoadipinate as substitutes of the cosubstarate 2-oxoglutarate. The data explain the high hydroxylation of Alvinella collagens despite the low oxygen concentrations around hydrothermal vents.
Diet effects on honeybee immunocompetence
Venue: Biology Letters

The maintenance of the immune system can be costly, and a lack of dietary protein can increase the susceptibility of organisms to disease. However, few studies have investigated the relationship between protein nutrition and immunity in insects. Here, we tested in honeybees (Apis mellifera) whether dietary protein quantity (monofloral pollen) and diet diversity (polyfloral pollen) can shape baseline immunocompetence (IC) by measuring parameters of individual immunity (haemocyte concentration, fat body content and phenoloxidase activity) and glucose oxidase (GOX) activity, which enables bees to sterilize colony and brood food, as a parameter of social immunity. Protein feeding modified both individual and social IC but increases in dietary protein quantity did not enhance IC. However, diet diversity increased IC levels. In particular, polyfloral diets induced higher GOX activity compared with monofloral diets, including protein-richer diets. These results suggest a link between protein nutrition and immunity in honeybees and underscore the critical role of resource availability on pollinator health.
On the strength, stiffness and stability of tubular plant stems and leaves
Venue: Journal of Theoretical Biology

thin walled tubes of circular cross-section are efficient structural elements and thus, as would be expected, are not uncommon in plants, especially those which belong to the Monocotyledonae. Traditional analyses of the strength of these tubular members utilize formulae which were developed for isotropic materials. The present paper deals with the great influence of the high elastic anisotropy of the plant tissue on the mechanical behavior of such tubular stems and leaves in bending. It will be seen that under these circumstances the propensity of the tube to fail due to non-linear effects (deformation of the cross-section) is greatly increased.
Pollination Efficiency and the Evolution of Specialized Deceptive Pollination Systems
Venue: The American Naturalist

The ultimate causes of evolution of highly specialized pollination systems are little understood. We investigated the relationship between specialization and pollination efficiency, defined as the proportion of pollinated flowers relative to those that experienced pollen removal, using orchids with different pollination strategies as a model system. Rewarding orchids showed the highest pollination efficiency. Sexually deceptive orchids had comparably high pollination efficiency, but food‐deceptive orchids had significantly lower efficiency. Values for pollinator sharing (a measure of the degree of generalization in pollination systems) showed the reverse pattern, in that groups with high pollination efficiency had low values of pollinator sharing. Low pollinator sharing may thus be the basis for efficient pollination. Population genetic data indicated that both food‐ and sexually deceptive species have higher degrees of among‐population gene flow than do rewarding orchids. Thus, the shift from food to sexual deception may be driven by selection for more efficient pollination, without compromising the high levels of gene flow that are characteristic of deceptive species.
Egg attachment of the asparagus beetle Crioceris asparagi to the crystalline waxy surface of Asparagus officinalis
Venue: Proceedings of The Royal Society B: Biological Sciences

Plant surfaces covered with crystalline epicuticular waxes are known to be anti-adhesive, hardly wettable and preventing insect attachment. But there are insects that are capable of gluing their eggs to these surfaces by means of proteinaceous secretions. In this study, we analysed the bonding region between the eggs of Crioceris asparagi and the plant surface of Asparagus officinalis using light and cryo-scanning electron microscopy. The wettability of the plant surface by egg secretion was compared with that by Aqua Millipore water, aqueous sugar solution and chicken egg white. Furthermore, the force required to remove C. asparagi eggs from the plant surface was measured, in order to evaluate the egg's bonding strength. Mean pull-off force was 14.7 mN, which is about 8650 times higher than the egg weight. Egg glue was observed spreading over the wax crystal arrays on the plant cladophyll and wetting them. Similar wetting behaviour on the A. officinalis surface was observed for chicken egg white. Our results support the hypothesis that the mechanism of insect egg adhesion on micro- and nanostructured hydrophobic plant surfaces is related to the proteinaceous nature of adhesive secretions of insect eggs. The secretion wets superhydrophobic surfaces and after solidifying builds up a composite, consisting of the solidified glue and wax crystals, at the interface between the egg and plant cuticle.
STRUCTURAL, BEHAVIORAL, AND PHYSIOLOGICAL ADAPTATIONS OF BEES (APOIDEA) FOR COLLECTING POLLEN'
Venue: Annals of the Missouri Botanical Garden

Bees, like their wasp relatives, forage for and transport food to a nest as provisions for their offspring. Unlike female Sphecoidea which transport arthropods one at a time as prey, bees transport pollen requiring specialized scopal (brush) or corbicular (fringed plate) structures to transport the dustlike material externally. Scopae often exhibit further modifications in density and amount of plumosity in relation to the size and ornamentation of the pollen grains they transport. Bees also differ from sphecid wasps by possessing branched body hairs that are relatively densely packed. These hairs, the electrostatic surface potential, and specialized hair groups for extraction of hidden pollen are important in the acquisition of pollen from flowers. Structures for grooming (brushes, combs, and scrapers) and grooming behavior patterns are modified to permit manipulation and packing of pollen in the specialized transport structures. The addition of nectar, so that pollen is packed moist, is a behavior that permits the carrying of pollen of a great variety of sizes and ornamentations in relatively simplified scopae or in corbiculae. The addition of oils to the diet of some bees has resulted in a modified type of scopal structure that has a wooly area basally and stiff guard hairs extending distally and that can transport a mixture of oil and pollen. Special hairs on the fore and mid basitarsi and teeth of hind tibial spurs are modified as oil scraper and manipulation structures. The use of corbiculae in Apidae to transport nesting materials and the hind tibiae in male orchid bees (Euglossini: Apidae) for transporting aromatic compounds involves behavior patterns similar to those for pollen transport in grooming, manipulating, and packing the materials. Other behavioral and physiological adaptations important in the location and acquisition of pollen by bees include individual constancy, oligolecty, seasonal synchrony, preimaginal conditioning, daily synchrony, buzz pollination, and other responses to specific modes of pollen presentation. Most of the behavioral patterns involve learning. They may be modified by extrinsic factors, and they may modify intrinsic structural and physiological characters.
A sticky situation: solifugids (Arachnida, Solifugae) use adhesive organs on their pedipalps for prey capture
Venue: Journal of Ethology

Solifugids (Arachnida, Solifugae) have unique evertable adhesive organs on the tips of their pedipalps, named ‘suctorial’ or ‘palpal’ organs. Previous studies have shown that these organs enable solifugids to climb smooth glass-like surfaces and have hypothesized that these structures facilitate prey capture. Here, we use high-speed videography to demonstrate that the suctorial organs of Eremochelis bilobatus are its primary means of capturing insect prey. We also present calculations of the adhesive pressure exerted by these suctorial organs during real prey capture events.
Mutualism as reciprocal exploitation: African plant-ants defend foliar but not reproductive structures.
Venue: Ecology

The foundation of many plant-ant mutualisms is ant protection of plants from herbivores in exchange for food and/or shelter. While the role of symbiotic ants in protecting plants from stem- and leaf-feeding herbivores has been intensively studied, the relationship between ant defense and measures of plant fitness has seldom been quantified. We studied ant aggression, damage by herbivores and seed predators, and fruit production among Acacia drepanolobium trees occupied by four different acacia-ant species in an East African savanna. Levels of ant aggression in response to experimental disturbance differed strongly among the four species. All four ant species recruited more strongly to new leaf growth on host plants following disturbance, while recruitment to developing fruits was on average an order of magnitude lower. Host plants occupied by more aggressive ant species suffered significantly less vegetative damage from leaf-feeding insects, stem-boring beetles, and vertebrate browsers than host plants occupied by less aggressive ant species. However, there were no differences among fruiting host plants occupied by different ant species in levels of seed predation by bruchid seed predators. Fruit production on host trees was significantly correlated with tree stem diameter but not with the identity of resident ants. Our results demonstrate that defense of host plants may differ substantially among ant species and between vegetative and reproductive structures and that fruit production is not necessarily correlated with high levels of aggression by resident ants.
Evolution of color and vision of butterflies.
Venue: Arthropod Structure & Development

Butterfly eyes consist of three types of ommatidia, which are more or less randomly arranged in a spatially regular lattice. The corneal nipple array and the tapetum, optical structures that many but not all butterflies share with moths, suggest that moths are ancestral to butterflies, in agreement with molecular phylogeny. A basic set of ultraviolet-, blue- and green-sensitive receptors, encountered among nymphalid butterflies, forms the basis for trichromatic vision. Screening pigments surrounding the light-receiving rhabdoms can modify the spectral sensitivity of the photoreceptors so that the sensitivity peak is in the violet, yellow, red, or even deep-red, specifically in swallowtails (Papilionidae) and whites (Pieridae), thus enhancing color discriminability. The photoreceptor sensitivity spectra are presumably tuned to the wing colors of conspecific butterflies.
Temperatures of Desert Plants: Another Perspective on the Adaptability of Leaf Size
Venue: Science

Surface temperatures of perennial plants in the Sonoran Desert of California ranged from 20�C above air temperature to over 18�C below air temperature during rapid growth periods following rain. Desert cactus with large photosynthetic stem surfaces had the highest temperatures and lowest transpiration rates. Perennial plants with relatively small leaves had moderate transpiration rates and leaf temperatures close to air temperature. Desert perennials with relatively large leaves had leaf temperatures well below air temperature along with the greatest accompanying transpiration rates of over 20 micrograms per square centimeter per second, but also had correspondingly low temperatures for maximum photosynthesis. The low leaf temperatures measured for these large-leafed species are an exception to the more common pattern for desert plants whereby a smaller leaf size prevents overheating and leads to reductions in transpiration and increased water-use efficiency. The contribution of a larger leaf size to a lower leaf temperature, and thus higher rate of photosynthesis for these large-leafed species, may represent an adaptive pattern previously unrecognized for desert plants.
Hagfish predatory behaviour and slime defence mechanism
Venue: Scientific Reports

Hagfishes (Myxinidae), a family of jawless marine pre-vertebrates, hold a unique evolutionary position, sharing a joint ancestor with the entire vertebrate lineage. They are thought to fulfil primarily the ecological niche of scavengers in the deep ocean. However, we present new footage from baited video cameras that captured images of hagfishes actively preying on other fish. Video images also revealed that hagfishes are able to choke their would-be predators with gill-clogging slime. This is the first time that predatory behaviour has been witnessed in this family, and also demonstrates the instantaneous effectiveness of hagfish slime to deter fish predators. These observations suggest that the functional adaptations and ecological role of hagfishes, past and present, might be far more diverse than previously assumed. We propose that the enduring success of this oldest extant family of fishes over 300 million years could largely be due to their unique combination of functional traits.
Gait selection in the ostrich: mechanical and metabolic characteristics of walking and running with and without an aerial phase
Venue: Proceedings of The Royal Society B: Biological Sciences

It has been argued that minimization of metabolic–energy costs is a primary determinant of gait selection in terrestrial animals. This view is based predominantly on data from humans and horses, which have been shown to choose the most economical gait (walking, running, galloping) for any given speed. It is not certain whether a minimization of metabolic costs is associated with the selection of other prevalent forms of terrestrial gaits, such as grounded running (a widespread gait in birds). Using biomechanical and metabolic measurements of four ostriches moving on a treadmill over a range of speeds from 0.8 to 6.7 m s−1, we reveal here that the selection of walking or grounded running at intermediate speeds also favours a reduction in the metabolic cost of locomotion. This gait transition is characterized by a shift in locomotor kinetics from an inverted–pendulum gait to a bouncing gait that lacks an aerial phase. By contrast, when the ostrich adopts an aerial–running gait at faster speeds, there are no abrupt transitions in mechanical parameters or in the metabolic cost of locomotion. These data suggest a continuum between grounded and aerial running, indicating that they belong to the same locomotor paradigm.
Ionizing Radiation Changes the Electronic Properties of Melanin and Enhances the Growth of Melanized Fungi
Venue: PLOS ONE

Melanin pigments are ubiquitous in nature. Melanized microorganisms are often the dominating species in certain extreme environments, such as soils contaminated with radionuclides, suggesting that the presence of melanin is beneficial in their life cycle. We hypothesized that ionizing radiation could change the electronic properties of melanin and might enhance the growth of melanized microorganisms.  Ionizing irradiation changed the electron spin resonance (ESR) signal of melanin, consistent with changes in electronic structure. Irradiated melanin manifested a 4-fold increase in its capacity to reduce NADH relative to non-irradiated melanin. HPLC analysis of melanin from fungi grown on different substrates revealed chemical complexity, dependence of melanin composition on the growth substrate and possible influence of melanin composition on its interaction with ionizing radiation. XTT/MTT assays showed increased metabolic activity of melanized C. neoformans cells relative to non-melanized cells, and exposure to ionizing radiation enhanced the electron-transfer properties of melanin in melanized cells. Melanized Wangiella dermatitidis and Cryptococcus neoformans cells exposed to ionizing radiation approximately 500 times higher than background grew significantly faster as indicated by higher CFUs, more dry weight biomass and 3-fold greater incorporation of 14C-acetate than non-irradiated melanized cells or irradiated albino mutants. In addition, radiation enhanced the growth of melanized Cladosporium sphaerospermum cells under limited nutrients conditions.  Exposure of melanin to ionizing radiation, and possibly other forms of electromagnetic radiation, changes its electronic properties. Melanized fungal cells manifested increased growth relative to non-melanized cells after exposure to ionizing radiation, raising intriguing questions about a potential role for melanin in energy capture and utilization.
Enzymatic conversion of CO(2) to bicarbonate in functionalized mesoporous silica.
Venue: Microporous and Mesoporous Materials

We report here a concept converting carbon dioxide to biocarbonate in a biomimetic nanoconfiguration. Carbonic anhydrase (CA), the fastest enzyme that can covert carbon dioxide to bicarbonate, can be spontaneously entrapped in carboxylic acid group-functionalized mesoporous silica (HOOC-FMS) with super-high loading density (up to 0.5 mg of protein/mg of FMS) in sharp contrast to normal porous silica. The binding of CA to HOOC-FMS resulted in a partial conformational change comparing to the enzyme free in solution, but it can be overcome with increased protein loading density. The higher the protein loading density, the less conformational change, hence the higher enzymatic activity and the higher enzyme immobilization efficiency (up to >60%). The released enzyme still displayed the native conformational structure and the same high enzymatic activity as that prior to the enzyme entrapment, indicating that the conformational change resulted from the electrostatic interaction of CA with HOOC-FMS was not permanent. This work may provide a new approach converting carbon dioxide to biocarbonate that can be integrated with the other part of biosynthesis process for the assimilation of carbon dioxide.
The role of biota in the initiation and growth of islands on the floodplain of the Okavango alluvial fan, Botswana
Venue: Earth Surface Processes and Landforms

A group of islands of varying size on the floodplain of the Okavango alluvial fan, were studied to establish the processes which lead to the initiation and growth of islands. It was found that islands are initiated by the mound-building activities of the termite Macrotermes michaelseni. These termites import fine grained materials to use as a mortar for the construction of epigeal mounds. Their activities create a topographic feature, raised above the level of seasonal flooding, and also change the physical properties and nutrient status of the mound soil. Shrubs and trees are able to colonize these mounds, which results in increased transpiration. As a result, precipitation of calcite and silica from the shallow ground water occurs preferentially beneath the mounds, resulting in vertical and especially lateral growth, causing island expansion.
Functional Changes with Feeding in the Gastro-Intestinal Epithelia of the Burmese Python (Python molurus)
Venue: Zoological Science

The morphology of the digestive system in fasting and refed Burmese pythons was determined, as well as the localization of the proton (H+, K+-ATPase) and sodium (Na+, K+-ATPase) pumps. In fasting pythons, oxyntopeptic cells located within the fundic glands are typically non-active, with a thick apical tubulovesicular system and numerous zymogen granules. They become active immediately after feeding but return to a non-active state 3 days after the ingestion of the prey. The proton pump, expressed throughout the different fasting/feeding states, is either sequestered in the tubulovesicular system in non-active cells or located along the apical digitations extending within the crypt lumen in active cells. The sodium pump is rapidly upregulated in fed animals and is classically located along the baso-lateral membranes of the gastric oxyntopeptic cells. In the intestine, it is only expressed along the lateral membranes of the enterocytes, i.e., above the lateral spaces and not along the basal side of the cells. Thus, solute transport within the intestinal lining is mainly achieved through the apical part of the cells and across the lateral spaces while absorbed fat massively crosses the entire height of the cells and flows into the intercellular spaces. Therefore, in the Burmese python, the gastrointestinal cellular system quickly upregulates after feeding, due to inexpensive cellular changes, passive mechanisms, and the progressive activation and synthesis of key enzymes such as the sodium pump. This cell plasticity also allows anticipation of the next fasting and feeding periods.
Biomimetic strain-sensing microstructure for improved strain sensor: fabrication results and optical characterization
Venue: Journal of Micromechanics and Microengineering

This paper describes the fabrication, and early optical characterization results of a new biomimetic strain-sensing microstructure. The microstructures were inspired from the campaniform sensillum, a highly sensitive strain sensor found in the exocuticle layer of insects. We investigate the natural strain-sensor characteristics by mimicking some of its simplest structural features. Blind-hole- and membrane-structural features were combined and fabricated as membrane-in-recess microstructure. To investigate the strain-sensing (or strain-amplifying) property of the microstructure, an optical characterization setup was devised based on the interference pattern formed by reflected laser beams from different surfaces of the microstructures. Preliminary qualitative analysis of the results obtained shows unsimilar intensity level changes as a function of spatial location on the membrane, thus indicated the biomimetic microstructure's strain-amplifying property. This property could be utilized for future improvement of currently available planar-based conventional strain sensors.