nils-herrmann/clean_scirepeval huggingface dataset:
Biological characterization of the skin of shortfin mako shark Isurus oxyrinchus and preliminary study of the hydrodynamic behaviour through computational fluid dynamics.
Venue: Journal of Fish Biology

This study characterized the morphology, density and orientation of the dermal denticles along the body of a shortfin mako shark Isurus oxyrinchus and identified the hydrodynamic parameters of its body through a computational fluid-dynamics model. The study showed a great variability in the morphology, size, shape, orientation and density of dermal denticles along the body of I. oxyrinchus. There was a significant higher density in dorsal and ventral areas of the body and their highest angular deviations were found in the lower part of the mouth and in the areas between the pre-caudal pit and the second dorsal and pelvic fins. A detailed three-dimensional geometry from a scanned body of a shark was carried out to evaluate the hydrodynamic properties such as drag coefficient, lift coefficient and superficial (skin) friction coefficient of the skin together with flow velocity field, according to different roughness coefficients simulating the effect of the dermal denticles. This preliminary approach contributed to detailed information of the denticle interactions. As the height of the denticles was increased, flow velocity and the effect of lift decreased whereas drag increased. The highest peaks of skin friction coefficient were observed around the pectoral fins.
Skin barrier structure and function: the single gel phase model.
Venue: Journal of Investigative Dermatology

A new model for the structure and function of the mammalian skin barrier is postulated. It is proposed that the skin barrier, i.e., the intercellular lipid within the stratum corneum, exists as a single and coherent lamellar gel phase. This membrane structure is stabilized by the very particular lipid composition and lipid chain length distributions of the stratum corneum intercellular space and has virtually no phase boundaries. The intact, i.e., unperturbed, single and coherent lamellar gel phase is proposed to be mainly located at the lower half of stratum corneum. Further up, crystalline segregation and phase separation may occur as a result of the desquamation process. The single gel phase model differs significantly from earlier models in that it predicts that no phase separation, neither between liquid crystalline and gel phases nor between different crystalline phases with hexagonal and orthorhombic chain packing, respectively, is present in the unperturbed barrier structure. The new skin barrier model may explain: (i) the measured water permeability of stratum corneum; (ii) the particular lipid composition of the stratum corneum intercellular space; (iii) the absence of swelling of the stratum corneum intercellular lipid matrix upon hydration; and (iv) the simultaneous presence of hexagonal and orthorhombic hydrocarbon chain packing of the stratum corneum intercellular lipid matrix at physiologic temperatures. Further, the new model is consistent with skin barrier formation according to the membrane folding model of Norlén (2001). This new theoretical model could fully account for the extraordinary barrier capacity of mammalian skin and is hereafter referred to as the single gel phase model.
Competition for Space, Disturbance, and the Structure of a Benthic Stream Community
Venue: Ecology

Interspecific competition for space limits the distribution and abundance of many ben- thic insects on stones in a western Montana stream. The sessile caddisfly larva Leucotrichia pictipes is territorial and aggressively eliminates conspecifics and other species from its foraging territories. Territoriality produces an intraspecific pattern of regular spacing and negative spatial associations between Leucotrichia and several other sessile insects: Parargyractis confusalis, Rheotanytarsus sp. and Eukiefferiella sp. Experimental removals of Leucotrichia resulted in higher densities of other sessile species and several mobile insects, including Baetis, Glossosoma, and Simulium. These insects show broad microhabitat overlap with Leucotrichia; competition with Leucotrichia limits their dis- tributions and abundances within otherwise suitable microhabitats. Leucotrichia is the only species that monopolizes large areas of space. Physical disturbances interrupt the formation of competitive monopolies by Leucotrichia. During seasonal reduced flows, Leucotrichia is eliminated from stones and boulders in shallow water. Greater densities of a short-lived sessile species with multiple annual generations occupy this ephemeral spatial resource. On permanently submerged stones, Leucotrichia competitively affects a large part of the benthic fauna. On small stones that overturn with higher frequencies during flooding, Leucotrichia densities are reduced and species' abundances are highly equitable. Large, more stable substrates with greater densities of Leucotrichia are characterized by lower species evenness.
On the Use of the Sucking-Fish for Catching Fish and Turtles: Studies in Echeneis or Remora, II
Venue: The American Naturalist

In 1507, there was published at Venice by Franconzio another collection of travels, entitled "Paesi Nouamente Retrouati Et Nous Mondo da Alberico Vesputio Florentino Intitulato" [Countries Newly Found and the New World of Albericus Vesputius Called the Florentine]. Chapters LXXXIIII to CXIIII faithfully reproduce the Libretto of 1504, are in fact a second edition of the Libretto, and need not detain us.14 All this however simply pushes the question back one step further and it now becomes "What or who is the source of Peter Martyr's information?" The answer is that these sources are identical with those for the "Life of Christopher Columbus " by his son Ferdinand, for Las Casas's history of the West Indies, and for Bernaldez's "Reyes Catalicos." In addition Dr. Eastman has skilfully worked out certain internal evidence which points directly to the one person who gave to Peter Martyr the data incorporated in Chapter XV of the Libretto. Let us first of all consider the account which Ferdinand gives of the fisherinan-fish incident, which seems to
The basics and underlying mechanisms of mucoadhesion.
Venue: Advanced Drug Delivery Reviews

Mucoadhesion is where two surfaces, one of which is a mucous membrane, adhere to each other. This has been of interest in the pharmaceutical sciences in order to enhance localised drug delivery, or to deliver 'difficult' molecules (proteins and oligonucleotides) into the systemic circulation. Mucoadhesive materials are hydrophilic macromolecules containing numerous hydrogen bond forming groups, the carbomers and chitosans being two well-known examples. The mechanism by which mucoadhesion takes place has been said to have two stages, the contact (wetting) stage followed by the consolidation stage (the establishment of the adhesive interactions). The relative importance of each stage will depend on the individual application. For example, adsorption is a key stage if the dosage form cannot be applied directly to the mucosa of interest, while consolidation is important if the formulation is exposed to significant dislodging stresses. Adhesive joint failure will inevitably occur as a result of overhydration of a dosage form, or as a result of epithelia or mucus turnover. New mucoadhesive materials with optimal adhesive properties are now being developed, and these should enhance the potential applications of this technology.
Anti-Erosion Function in Animals and its Biomimetic Application
Venue: Journal of Bionic Engineering

Material failure is usually caused by corrosion, wear and mechanical damage. According to previous researches, erosion wear holds about 8% of regular wear in industrial production. In the present work, a new approach, which adopted the idea of coupling bionics to improve erosion resistance of machine parts, was presented. Simulation by ANSYS/LS-DYNA finite element software was applied to predict the relative erosion severity, and experiment optimum design theory was employed to design experiment scheme. Silica sand of particle size 105 µm–830 µm was used as the erodent. The erosion tests were carried out to validate the simulation results obtained. It is shown that the simulation results are in agreement with those of the experiment. The morphologies of eroded surface were examined by scanning electron microscope, and the possible wear mechanism was discussed.
Bone density and the lightweight skeletons of birds
Venue: Proceedings of The Royal Society B: Biological Sciences

The skeletons of birds are universally described as lightweight as a result of selection for minimizing the energy required for flight. From a functional perspective, the weight (mass) of an animal relative to its lift-generating surfaces is a key determinant of the metabolic cost of flight. The evolution of birds has been characterized by many weight-saving adaptations that are reflected in bone shape, many of which strengthen and stiffen the skeleton. Although largely unstudied in birds, the material properties of bone tissue can also contribute to bone strength and stiffness. In this study, I calculated the density of the cranium, humerus and femur in passerine birds, rodents and bats by measuring bone mass and volume using helium displacement. I found that, on average, these bones are densest in birds, followed closely by bats. As bone density increases, so do bone stiffness and strength. Both of these optimization criteria are used in the design of strong and stiff, but lightweight, manmade airframes. By analogy, increased bone density in birds and bats may reflect adaptations for maximizing bone strength and stiffness while minimizing bone mass and volume. These data suggest that both bone shape and the material properties of bone tissue have played important roles in the evolution of flight. They also reconcile the conundrum of how bird skeletons can appear to be thin and delicate, yet contribute just as much to total body mass as do the skeletons of terrestrial mammals.
Evidence for trans-generational medication in nature.
Venue: Ecology Letters

Parasites pose a serious threat to host fitness, and natural selection should favour host traits that reduce infection or disease symptoms. Here, we provide the first evidence of trans-generational medication, in which animals actively use medicine to mitigate disease in their offspring. We studied monarch butterflies and their virulent protozoan parasites, and found that neither caterpillars nor adult butterflies could cure themselves of disease. Instead, adult butterflies preferentially laid their eggs on toxic plants that reduced parasite growth and disease in their offspring caterpillars. It has often been suggested that sick animals may use medication to cure themselves of disease, but evidence for the use of medication in nature has so far been scarce. Our results provide evidence that infected animals may indeed use medicine as a defence against parasites, and that such medication may target an individual's offspring rather than the individual itself.
Bacterial polymers: biosynthesis, modifications and applications
Venue: Nature Reviews Microbiology

Bacteria can synthesize a wide range of biopolymers that serve diverse biological functions and have material properties suitable for numerous industrial and medical applications. A better understanding of the fundamental processes involved in polymer biosynthesis and the regulation of these processes has created the foundation for metabolic- and protein-engineering approaches to improve economic-production efficiency and to produce tailor-made polymers with highly applicable material properties. Here, I summarize the key aspects of bacterial biopolymer production and highlight how a better understanding of polymer biosynthesis and material properties can lead to increased use of bacterial biopolymers as valuable renewable products.
Water relations of tetrapod integument
Venue: The Journal of Experimental Biology

The vertebrate integument represents an evolutionary compromise between the needs for mechanical protection and those of sensing the environment and regulating the exchange of materials and energy. Fibrous keratins evolved as a means of strengthening the integument while simultaneously providing a structural support for lipids, which comprise the principal barrier to cutaneous water efflux in terrestrial taxa. Whereas lipids are of fundamental importance to water barriers, the efficacy of these barriers depends in many cases on structural features that enhance or maintain the integrity of function. Amphibians are exceptional among tetrapods in having very little keratin and a thin stratum corneum. Thus, effective lipid barriers that are present in some specialized anurans living in xeric habitats are external to the epidermis, whereas lipid barriers of amniotes exist as a lipid-keratin complex within the stratum corneum. Amphibians prevent desiccation of the epidermis and underlying tissues either by evaporating water from a superficial aqueous film, which must be replenished, or by shielding the stratum corneum with superficial lipids. Water barrier function in vertebrates generally appears to be relatively fixed, although various species have `plasticity' to adjust the barrier effectiveness facultatively. While it is clear that both phenotypic plasticity and genetic adaptation can account for covariation between environment and skin resistance to water efflux, studies of the relative importance of these two phenomena are few. Fundamental mechanisms for adjusting the skin water barrier include changes in barrier thickness, composition and physicochemical properties of cutaneous lipids, and/or geometry of the barrier within the epidermis. While cutaneous lipids have been studied extensively in the contexts of disease and cosmetics, relatively little is known about the processes of permeability barrier ontogenesis related to adaptation and environment. Advances in such knowledge have didactic significance for understanding vertebrate evolution as well as practical application to clinical dermatology.
The function of resilin in beetle wings
Venue: Proceedings of The Royal Society B: Biological Sciences

This account shows the distribution of elastic elements in hind wings in the scarabaeid Pachnoda marginata and coccinellid Coccinella septempunctata (both Coleoptera). Occurrence of resilin, a rubber–like protein, in some mobile joints together with data on wing unfolding and flight kinematics suggest that resilin in the beetle wing has multiple functions. First, the distribution pattern of resilin in the wing correlates with the particular folding pattern of the wing. Second, our data show that resilin occurs at the places where extra elasticity is needed, for example in wing folds, to prevent material damage during repeated folding and unfolding. Third, resilin provides the wing with elasticity in order to be deformable by aerodynamic forces. This may result in elastic energy storage in the wing.
A Predator from East Africa that Chooses Malaria Vectors as Preferred Prey
Venue: PLOS ONE

All vectors of human malaria, a disease responsible for more than one million deaths per year, are female mosquitoes from the genus Anopheles. Evarcha culicivora is an East African jumping spider (Salticidae) that feeds indirectly on vertebrate blood by selecting blood-carrying female mosquitoes as preferred prey.  By testing with motionless lures made from mounting dead insects in lifelike posture on cork discs, we show that E. culicivora selects Anopheles mosquitoes in preference to other mosquitoes and that this predator can identify Anopheles by static appearance alone. Tests using active (grooming) virtual mosquitoes rendered in 3-D animation show that Anopheles' characteristic resting posture is an important prey-choice cue for E. culicivora. Expression of the spider's preference for Anopheles varies with the spider's size, varies with its prior feeding condition and is independent of the spider gaining a blood meal.  This is the first experimental study to show that a predator of any type actively chooses Anopheles as preferred prey, suggesting that specialized predators having a role in the biological control of disease vectors is a realistic possibility.
Function of the Urnulae in Protecting the Red Velvet Mite, Balaustium Sp., Against Water Loss and in Enhancing its Activity at High Temperatures
Venue: International Journal of Acarology

Features of Balaustium sp. include resistance to intense heat and desiccation, affinity for hot surfaces in bright light, abundance in semi-arid/arid biotopes, and a large pair of secretory glands called umulae with no known function (defense secretion excepted). Here we show that the urnulae secrete a waterproofing barrier that reduces the mite's cuticular permeability to water. Exposure to white light was used to stimulate release of the secretion; the urnulae protruded and exuded streams of red fluid at the tip of this structure that covered the entire body. Results showed that mites coated with urnulae secretion lost water at approximately half the rate of mites that did not secrete. Similarly, urnulae secretion coated mites demonstrated an increase in water-tightness of the cuticle reflected by a 9°C elevation in temperature threshold for water loss on an evaporation curve, increasing their optimal temperature tolerance for survival (lethal permeability temperature, LPT). Results also show a 10 kJ/mol drop in activation energy (E a) for water loss, representative of a substantial cuticular modification, and a decrease in Arrhenius frequency steric factor A, indicating an overall decrease in body water losses. The absence of a critical transition temperature (CTT), however, reveals that urnulae secretion coating functions to resist a phase change as the temperature rises, permitting the mites to cope with high temperature without succumbing to water and heat stress, by inhibiting cuticular breakdown.
A Vacuolar Arsenite Transporter Necessary for Arsenic Tolerance in the Arsenic Hyperaccumulating Fern Pteris vittata Is Missing in Flowering Plants[W][OA]
Venue: The Plant Cell

Gametophytes of the fern Pteris vittata can accumulate and tolerate more than 1% of their dry weight as arsenic. The authors provide evidence that the ACR3 arsenic transporter protein plays an important role in tolerance to high levels of arsenic by transporting arsenic into the vacuole. The fern Pteris vittata tolerates and hyperaccumulates exceptionally high levels of the toxic metalloid arsenic, and this trait appears unique to the Pteridaceae. Once taken up by the root, arsenate is reduced to arsenite as it is transported to the lamina of the frond, where it is stored in cells as free arsenite. Here, we describe the isolation and characterization of two P. vittata genes, ACR3 and ACR3;1, which encode proteins similar to the ACR3 arsenite effluxer of yeast. Pv ACR3 is able to rescue the arsenic-sensitive phenotypes of yeast deficient for ACR3. ACR3 transcripts are upregulated by arsenic in sporophyte roots and gametophytes, tissues that directly contact soil, whereas ACR3;1 expression is unaffected by arsenic. Knocking down the expression of ACR3, but not ACR3;1, in the gametophyte results in an arsenite-sensitive phenotype, indicating that ACR3 plays a necessary role in arsenic tolerance in the gametophyte. We show that ACR3 localizes to the vacuolar membrane in gametophytes, indicating that it likely effluxes arsenite into the vacuole for sequestration. Whereas single-copy ACR3 genes are present in moss, lycophytes, other ferns, and gymnosperms, none are present in angiosperms. The duplication of ACR3 in P. vittata and the loss of ACR3 in angiosperms may explain arsenic tolerance in this unusual group of ferns while precluding the same trait in angiosperms.
Freeze Tolerance and Postfreeze Recovery in the Frog Pseudacris crucifer
Venue: Copeia

This study characterizes freeze tolerance and postfreeze recovery in the frog Pseudacris crucifer. We collected frogs from Pennsylvania during the autumns of 1994 and 1995. All experiments occurred in the laboratory and employed a freezing temperature of -1.5 C. This treatment froze 45% of the body water in these frogs, and they were clearly tolerant of internal freezing. However, their survival was inversely proportional to freeze duration (3 day = 85.0%, 7 day = 52.6%, and 28 day = 0%). Cutaneous blood flow, breathing, hind-leg retraction, righting reflex, and jumping ability returned to surviving frogs within 24-48 h following the conclusion of a 3-day freeze. Complex behavioral responses (e.g., jumping) required more time to return than did basic physiological functions (e.g., cutaneous blood flow). Interestingly, rates of oxygen consumption were not altered during the recovery period with respect to the prefreeze value. This study indicates that the freezing survival of P crucifer is markedly influenced by the duration of the freeze episode, which may be an important ecological limitation during winters having few intervening thaws. Recovering frogs require 1-2 days to fully regain complex motor responses; whereas vital functions are restored quickly, and oxygen consumption is not measurably altered during this period.
Evidence that halogenated furanones from Delisea pulchra inhibit acylated homoserine lactone (AHL)-mediated gene expression by displacing the AHL signal from its receptor protein.
Venue: Microbiology

Acylated homoserine lactone (AHL)-mediated gene expression controls phenotypes involved in colonization, often specifically of higher organisms, in both marine and terrestrial environments. The marine red alga Delisea pulchra produces halogenated furanones which resemble AHLs structurally and show inhibitory activity at ecologically realistic concentrations in AHL bioassays. Evidence is presented that halogenated furanones displace tritiated OHHL [N-3-(oxohexanoyl)-L-homoserine lactone] from Escherichia coli cells overproducing LuxR with potencies corresponding to their respective inhibitory activities in an AHL-regulated bioluminescence assay, indicating that this is the mechanism by which furanones inhibit AHL-dependent phenotypes. Alternative mechanisms for this phenomenon are also addressed. General metabolic disruption was assessed with two-dimensional PAGE, revealing limited non-AHL-related effects. A direct chemical interaction between the algal compounds and AHLs, as monitored by 1H NMR spectroscopy, was shown not to occur in vitro. These results support the contention that furanones, at the concentrations produced by the alga, can control bacterial colonization of surfaces by specifically interfering with AHL-mediated gene expression at the level of the LuxR protein.