nils-herrmann/clean_scirepeval huggingface dataset:
Alternative fire resistance strategies in savanna trees
Venue: Oecologia

Bark properties (mainly thickness) are usually presented as the main explanation for tree survival in intense fires. Savanna fires are mild, frequent, and supposed to affect tree recruitment rather than adult survival: trunk profile and growth rate of young trees between two successive fires can also affect survival. These factors and fire severity were measured on a sample of 20 trees near the recruitment stage of two savanna species chosen for their contrasted fire resistance strategies (Crossopteryx febrifuga and Piliostigma thonningii). Crossopteryx has a higher intrinsic resistance to fire (bark properties) than Piliostigma: a 20-mm-diameter stem of Crossopteryx survives exposure to 650°C, while Piliostigma needs a diameter of at least 40 mm to survive. Crossopteryx has a thicker trunk than Piliostigma: for two trees of the same height, the basal diameter of Crossopteryx will be 1.6 times greater. Piliostigma grows 2.26 times faster than Crossopteryx between two successive fires. The two species have different fire resistance strategies: one relies on resistance of aboveground structures to fire, while the other relies on its ability to quickly re-build aboveground structures. Crossopteryx is able to recruit in almost any fire conditions while Piliostigma needs locally or temporarily milder fire conditions. In savannas, fire resistance is a complex property which cannot be assessed simply by measuring only one of its components, such as bark thickness. Bark properties, trunk profile and growth rate define strategies of fire resistance. Fire resistance may interact with competition: we suggest that differences in fire resistance strategies have important effects on the structure and dynamics of savanna ecosystems.
The activity of a selected extract of Drimys winteri bark and polygodial on settling and probing behavior of the lettuce aphid Nasonovia ribisnigri
Venue: Phytoparasitica

An n-hexane extract and the sesquiterpene polygodial isolated from the bark of Drimys winteri J.R. Forster & G. Forster (Winteraceae) were tested to assess their ability to inhibit settling of the aphid Nasonovia ribisnigri Mosley on lettuce leaves; assessments were made using a choice and no-choice leaf-disk assay. The n-hexane extract and the polygodial both significantly inhibited settling in the choice and no-choice tests, but their application on lettuce leaves did not result in any aphid mortality. Probing behavior of N. ribisnigri on polygodial-treated plants was assessed by means of the electrical penetration graph technique. Polygodial interfered with aphid probing behavior by reducing the total probing time, the number of probes, and the number of intracellular punctures. Aphids did not reach the sieve elements of polygodial-treated plants during the 2-h access period. Both tested compounds have the potential to be used in the development of lettuce aphid control agents to reduce the risk of virus transmission.
Bionic photovoltaic panels bio-inspired by green leaves
Venue: Journal of Bionic Engineering

In strong solar light, silicon solar panels can heat up by 70°C and, thereby, loose approximately one third of their efficiency for electricity generation. Leaf structures of plants on the other hand, have developed a series of technological adaptations, which allow them to limit their temperature to 40–45°C in full sunlight, even if water evaporation is suppressed. This is accomplished by several strategies such as limitation of leaf size, optimization of aerodynamics in wind, limitation of absorbed solar energy only to the useful fraction of radiation and by efficient thermal emission. Optical and infrared thermographic measurements under a solar simulator and in a streaming channel were used to investigate the corresponding properties of leaves and to identify suitable bionic model systems. Experiments started with the serrated structure of ordinary green leaves distributed over typical twig structures and finally identified the Australian palm tree Licuala ramsayi as a more useful bionic model. It combines a large area for solar energy harvesting with optimized aerodynamic properties for cooling and is able to restructure itself as a protection against strong winds. The bionic models, which were constructed and built, are analyzed and discussed.
Epicormic strand structure in Angophora, Eucalyptus and Lophostemon (Myrtaceae): implications for fire resistance and recovery
Venue: New Phytologist

• Epicormic bud producing structures in the eucalypts, a large group of woody plants of considerable ecological, horticultural and silvicultural importance, are described here. 
• The outer portion of epicormic strands excised from the bark of large diameter stems of 18 Eucalyptus species, two Angophora species and Lophostemon confertus was examined anatomically in semithin sections. 
• In the inner bark each eucalypt strand usually possessed 5–12 radially orientated strips of tissue of meristematic appearance. The meristem strips were c. 30–50 µm high, 70–110 µm wide and 2000–10 000 µm long, with a lacuna above the meristem surface. Few buds or bud primordia were associated with the strands and the strands appeared to have a reduced regenerative potential in the outer bark. 
• In most angiosperm trees dormant epicormic buds are present in the outer bark, a position where they could be killed by fire. By contrast, in eucalypts the greatest epicormic bud initiation potential is at the level of the vascular cambium, which is protected by the maximum bark thickness. This might explain the pronounced ability of eucalypts to produce bole and branch epicormic shoots after moderate to intense fire.
Ultrastructural architecture of the microtrichia of the insect cuticle
Venue: Journal of Morphology

The ultrastructure of the microtrichia (MT) of the insect cuticle was studied using scanning electron microscopy (SEM). After dissolving the protein matrix of chitin‐protein microfibrils with NaOH, the orientation of the axial chitin fibers was three‐dimensionally demonstrated. Microfibrils of the outermost exocuticular lamella lie parallel to the slope of the cone surface of the MT and rotate slightly on the top of the MT. Microfibrils of the external lamella of the transitional area between planar cuticle and conical cuticle of the MT corresponded to the shape of the surface within one lamella and preferred directions of MT's microfibrils in the successive lamella rotated. In the deeper layers of the cuticle, the rotation of both the microfibrils and successive lamella results in the twisted straw architecture of the microfibrils' composition within the MT. The deepest microfibrils that are located close to the axis of the MT form compact clusters of fibrils (1.0–1.5 μm length). The twisted‐straw architecture of microfibrils in the MT is derived from principles of development of extracellular fibrous composites. It is suggested, however, that this architecture has an additional functional significance as a strategic design with particular mechanical properties.
Pummelos as Concept Generators for Biomimetically Inspired Low Weight Structures with Excellent Damping Properties
Venue: Advanced Engineering Materials

Natural materials often exhibit excellent mechanical properties. An example of outstanding impact resistance is the pummelo fruit (Citrus maxima) which can drop from heights of 10 m and more without showing significant outer damage. Our data suggest that this impact resistance is due to the hierarchical organization of the fruit peel, called pericarp. The project presented in the current paper aims at transferring structural features from the pummelo pericarp to engineering materials, in our case metal foams, produced by the investment casting process. The transfer necessitates a detailed structural and mechanical analysis of the biological model on the one hand, and the identification and development of adequate materials and processes on the other hand. Based on this analysis, engineering composite foam structures are developed and processed which show enhanced damping and impact properties. The modified investment casting process and the model alloy Bi57Sn43 proved to be excellent candidates to make these bio-inspired structures. Mechanical testing of both the natural and the engineering structures has to consider the necessity to evaluate the impact of the different hierarchical features. Therefore, specimens of largely varying sizes have to be tested and size effects cannot be ignored, especially as the engineering structures might be upscaled in comparison with the natural role model. All in all, the present results are very promising: the basis for a transfer of bio-inspired structural hierarchical levels has been set.
Antibacterial properties of larval secretions of the blowfly, Lucilia sericata
Venue: Medical and Veterinary Entomology

The antibacterial properties of secretions aseptically collected from larvae of the greenbottle fly Lucilia sericata (Meigen) (Diptera: Calliphoridae) were examined. These investigations revealed the presence of small (<1 kDa) antibacterial factor(s) within the larval secretions, active against a range of bacteria. These include the Gram‐positive Staphylococcus aureus, both methicillin‐resistant Staphylococcus aureus (MRSA) and methicillin‐sensitive Staphylococcus aureus (MSSA), Streptococcus pyogenes and to a lesser extent the Gram‐negative Pseudomonas aeruginosa. These secretions were shown to be highly stable as a freeze‐dried preparation and, considering the activity against organisms typically associated with clinical infection, may be a source of novel antibiotic‐like compounds that may be used for infection control and in the fight against MRSA.
Predator-released hydrocarbons repel oviposition by a mosquito.
Venue: Ecology Letters

Prey species commonly use predator-released kairomones (PRKs) to detect risk of predation, yet the chemical identity of PRKs remains elusive. Chemical identification of PRKs will facilitate the study of predator-prey interactions and the risk of predation, and when the prey are pests, will potentially provide environmentally friendly means of pest control. In temporary pools of the Mediterranean and Middle East, larvae of the mosquito Culiseta longiareolata Macquart are highly vulnerable to the common predatory backswimmer, Notonecta maculata Fabricius. We demonstrate that N. maculata releases two hydrocarbons, n-heneicosane and n-tricosane, which repel ovipositing females of C. longiareolata. In behavioural tests with environmentally relevant chemical concentrations in outdoor mesocosm experiments, the repellent effects of the two compounds were additive at the tested concentrations.
PREHENSILE USE OF PERIORAL BRISTLES DURING FEEDING AND ASSOCIATED BEHAVIORS OF THE FLORIDA MANATEE (TRICHECHUS MANATUS LATIROSTRIS)
Venue: Marine Mammal Science

The use of perioral bristles (modified vibrissae) by 17 captive Florida manatees and approximately 20 wild manatees was analyzed. Captive manatees were fed six species of aquatic vegetation normally eaten in the wild (four freshwater species and two seagrasses). Inanimate objects were placed in the holding tanks with manatees at Lowry Park Zoological Gardens (Tampa, FL) to determine the degree to which perioral bristles were used in exploration and to define the range of manipulative behavior. In addition, behavioral observations were made on the use of perioral bristles during social interactions with conspecifics. Observations were recorded using a Hi8-format video camera. Florida manatees possess an unusually large degree of fine motor control of the snout and perioral bristles. The large and robust perioral bristle fields of the upper lip were used in a prehensile manner during feeding. Bristle use by manatees feeding on submerged vegetation differed from that seen during feeding on floating vegetation. Other behavioral use of the perioral bristles shows variation depending upon the situation encountered. The degree of plasticity of perioral bristle use supports our hypothesis that the vibrissal-muscular complex of the Florida manatee has evolved to increase the efficiency of grazing and browsing on aquatic vegetation and to fully maximize the potential of the manatee as a generalist feeder. The manipulative and sensitive nature of the manatee snout is likely a manifestation of a complex sensory and motor system which has evolved for marine mammal aquatic herbivores living in shallow turbid habitats.
THE MUSCULAR HYDROSTAT OF THE FLORIDA MANATEE (TRICHECHUS MANATUS LATIROSTRIS): A FUNCTIONAL MORPHOLOGICAL MODEL OF PERIORAL BRISTLE USE
Venue: Marine Mammal Science

Facial musculature was examined in the Florida manatee, Tricbecbus manatus latirostris, in order to develop a functional model of perioral bristle use. Muscles identified include the M. levator nasolabialis, M. buccinatorius, M. maxillonasolabialis, M. centralis nasi, M. lateralis nasi, M. spbincter colli profundus pars oris, M. orbicularis oris, M. mandibularis, and M. mentalis. A new muscle, M. centralis nasi, has been named and is an integral part of perioral bristle movement. The snout of the Florida manatee is capable of performing complex movements. The prehensile ability of Florida manatees can be explained in the context of a muscular hydrostat as defined by Kier and Smith (1985). Eversion of certain bristles in the upper lip occurs by shortening longitudinal, transverse, and semicircular muscles in combination with volume displacement due to compensatory changes in the shape of the snout. Midline sweeping of these bristles is accomplished by the contraction of M. centralis nasi. Eversion of bristles on the lower jaw is a result of shortening of M. mentalis. Contraction of M. orbicularis oris pushes vegetation into the oral cavity. All observed movement patterns and uses of perioral bristles can be explained by variation of these sequences within the context of muscular hydrostat function.
Mycosporine‐glutaminol‐glucoside, a UV‐absorbing compound of two Rhodotorula yeast species
Venue: Yeast

High‐performance liquid chromatography (HPLC), alone or in combination with mass spectrometry (MS), was used to screen the basidiomycetous yeasts Rhodotorula minuta and R. slooffiae isolated from lakes for the presence of UV‐absorbing compounds. Mycosporine‐glutaminol‐glucoside (maximum absorption, 310 nm), a UV‐photoprotective mycosporine known in terrestrial fungi, was the major UV‐absorbing compound found in these species. This is the first identification of a mycosporine in yeasts. The presence of this compound seems to be a promising chemotaxonomical marker for yeast systematics.
Novel barnacle underwater adhesive protein is a charged amino acid-rich protein constituted by a Cys-rich repetitive sequence.

Barnacle cement is an underwater adhesive that is used for permanent settlement, and is an insoluble protein complex. A method for rendering soluble the cement of Megabalanus rosa has been developed, and three major proteins have been identified in a previous study. To survey the M. rosa cement proteins in a lower molecular mass range, the cement proteins were separated by reversed-phase HPLC and a previously unidentified protein named 20 kDa M. rosa cement protein (Mrcp-20k) was found. Mrcp-20k cDNA was cloned to reveal its primary structure. This cDNA was 902 bp long and encoded a 202 amino acid-long open reading frame, including 19 amino acids of the signal sequence. The molecular mass in the disulphide form was calculated to be 20357 Da and the isoelectric point of the mature polypeptide was 4.72. Mrcp-20k was characterized by an abundance of Cys residues and charged amino acids. The most common amino acid was Cys (17.5%), with Asp (11.5%), Glu (10.4%) and His (10.4%) following in order of magnitude. The alignment of the Cys residues indicated the primary structure of this protein to consist of six degenerated repeats, each about 30 residues long. Mrcp-20k has no intermolecular disulphide bonds and no free thiol groups of Cys in the insoluble cement complex. Abundant Cys is thought to play a role in maintaining the topology of charged amino acids on the molecular surface by intramolecular disulphide-bond formation. The possible function of abundant charged amino acids, including the interaction with a variety of surface metals on the substratum, is discussed.
Eisenia fetida (Oligochaeta, Lumbricidae) Activates Fungal Growth, Triggering Cellulose Decomposition During Vermicomposting
Venue: Microbial Ecology

Cellulose is the most abundant polymer in nature and constitutes a large pool of carbon for microorganisms, the main agents responsible for soil organic matter decomposition. Cellulolysis occurs as the result of the combined action of fungi and bacteria with different requirements. Earthworms influence decomposition indirectly by affecting microbial population structure and dynamics and also directly because the guts of some species possess cellulolytic activity. Here we assess whether the earthworm Eisenia fetida (Savigny 1826) digests cellulose directly (i.e., with its associated gut microbiota) and also whether the effects of E. fetida on microbial biomass and activity lead to a change in the equilibrium between fungi and bacteria. By enhancing fungal communities, E. fetida would presumably trigger more efficient cellulose decomposition. To evaluate the role of E. fetida in cellulose decomposition, we carried out an experiment in which pig slurry, a microbial-rich substrate, was treated in small-scale vermireactors with and without earthworms. The presence of earthworms in vermireactors significantly increased the rate of cellulose decomposition (0.43 and 0.26% cellulose loss day−1, with and without earthworms, respectively). However, the direct contribution of E. fetida to degradation of cellulose was not significant, although its presence increased microbial biomass (Cmic) and enzyme activity (cellulase and β-glucosidase). Surprisingly, as fungi may be part of the diet of earthworms, the activity of E. fetida triggered fungal growth during vermicomposting. We suggest that this activation is a key step leading to more intense and efficient cellulolysis during vermicomposting of organic wastes.
The avian “hibernation” enigma: thermoregulatory patterns and roost choice of the common poorwill
Venue: Oecologia

Compared to mammals, there are relatively few studies examining heterothermy in birds. In 13 bird families known to contain heterothermic species, the common poorwill (Phalaenoptilus nuttallii) is the only species that ostensibly hibernates. We used temperature-sensitive radio-transmitters to collect roost and skin temperature (Tskin) data, and winter roost preferences for free-ranging poorwills in southern Arizona. Further, to determine the effect of passive rewarming on torpor bout duration and active rewarming (i.e., the use of metabolic heat to increase Tskin), we experimentally shaded seven birds during winter to prevent them from passively rewarming via solar radiation. Poorwills selected winter roosts that were open to the south or southwest, facilitating passive solar warming in the late afternoon. Shaded birds actively rewarmed following at least 3 days of continuous torpor. Average torpor bout duration by shaded birds was 122 h and ranged from 91 to 164 h. Active rewarming by shaded birds occurred on significantly warmer days than those when poorwills remained torpid. One shaded bird remained inactive for 45 days, during which it spontaneously rewarmed actively on eight occasions. Our findings show that during winter poorwills exhibit physiological patterns and active rewarming similar to hibernating mammals.
Oysters produce an organic-inorganic adhesive for intertidal reef construction.
Venue: Journal of the American Chemical Society

Coastal ecosystems rely upon oyster reefs to filter water, provide protection from storms, and build habitat for other species. From a chemistry perspective, few details are available to illustrate how these shellfish construct such extensive reef systems. Experiments presented here show that oysters generate a biomineralized adhesive material for aggregating into large communities. This cement is an organic-inorganic hybrid and differs from the surrounding shells by displaying an alternate CaCO(3) crystal form, a cross-linked organic matrix, and an elevated protein content. Emerging themes and unique aspects are both revealed when comparing oyster cement to the adhesives of other marine organisms. The presence of cross-linked proteins provides an analogy to mussel and barnacle adhesives whereas the high inorganic content is exclusive to oysters. With a description of oyster cement in hand we gain strategies for developing synthetic composite materials as well as a better understanding of the components needed for healthy coastal environments.
Antifreeze glycoprotein activity correlates with long-range protein-water dynamics.
Venue: Journal of the American Chemical Society

Antifreeze proteins (AFPs) and antifreeze glycoproteins (AFGPs) enable the survival of organisms living in subfreezing habitats and serve as preservatives. Although their function is known, the underlying molecular mechanism was not understood. Mutagenesis experiments questioned the previous assumption of hydrogen bonding as the dominant mechanism. We use terahertz spectroscopy to show that antifreeze activity is directly correlated with long-range collective hydration dynamics. Our results provide evidence for a new model of how AFGPs prevent water from freezing. We suggest that antifreeze activity may be induced because the AFGP perturbs the aqueous solvent over long distances. Retarded water dynamics in the large hydration shell does not favor freezing. The complexation of the carbohydrate cis-hydroxyl groups by borate suppresses the long-range hydration shell detected by terahertz absorption. The hydration dynamics shift toward bulk water behavior strongly reduces the AFGP antifreeze activity, further supporting our model.
Hydrodynamic Trail-Following in Harbor Seals (Phoca vitulina)
Venue: Science

Marine mammals often forage in dark or turbid waters. Whereas dolphins use echolocation under such conditions, pinnipeds apparently lack this sensory ability. For seals hunting in the dark, one source of sensory information may consist of fish-generated water movements, which seals can detect with their highly sensitive whiskers. Water movements in the wake of fishes persist for several minutes. Here we show that blindfolded seals can use their whiskers to detect and accurately follow hydrodynamic trails generated by a miniature submarine. This shows that hydrodynamic information can be used for long-distance prey location.
Bacterial nitric oxide synthases.
Venue: Annual Review of Biochemistry

Nitric oxide synthases (NOSs) are multidomain metalloproteins first identified in mammals as being responsible for the synthesis of the wide-spread signaling and protective agent nitric oxide (NO). Over the past 10 years, prokaryotic proteins that are homologous to animal NOSs have been identified and characterized, both in terms of enzymology and biological function. Despite some interesting differences in cofactor utilization and redox partners, the bacterial enzymes are in many ways similar to their mammalian NOS (mNOS) counterparts and, as such, have provided insight into the structural and catalytic properties of the NOS family. In particular, spectroscopic studies of thermostable bacterial NOSs have revealed key oxyheme intermediates involved in the oxidation of substrate L-arginine (Arg) to product NO. The biological functions of some bacterial NOSs have only more recently come to light. These studies disclose new roles for NO in biology, such as taking part in toxin biosynthesis, protection against oxidative stress, and regulation of recovery from radiation damage.