nils-herrmann/clean_scirepeval huggingface dataset:
Surface Temperatures of Cacti‐‐Influences of Environmental and Morphological Factors
Venue: Ecology

An energy budget model predicted the average stem surface temperatures of a Mam- millaria dioica 9.4 cm tail and a Carnegiea gigantea 5.64 m tail within 1?C of the hourly measured temperatures over 24-h periods. For the ranges of various environmental factors considered in a sensitivity analysis, the average surface temperature of the stem was most influenced by air temper? ature. Greater diurnal extremes of stem temperature occurred at lower wind velocities. Asymmetrical heating of the stem by direct solar irradiation was clearly evident in the measurements and the simulations. The model was used to study the effect of changes in spine coverage, apical pubescence, stem absorptance, tissue thermal properties, plant height, and diameter on stem surface temperatures. In the absence of spines the average surface temperature of Mammillaria became 1 to 2?C cooler at night and 2 to 6?C warmer during the day. The effect of spines on the simulated diurnal temperature variation was even greater for the apical meristem, which had the most dense coverage of spines. A mat of pubescence additionally protected the apical meristem of Carnegiea and Ferocactus acan- thodes, substantially reducing diurnal temperature extremes there. Simulated decreases in the di? ameter of Carnegiea increased the daily range of temperatures of the apical meristem, suggesting that some adaptive optimization of plant diameter may have occurred. Simulations for the 3 species under the same environmental conditions showed that the lowest stem and apical temperatures occurred for Carnegiea, consistent with its restriction to lower (presumably warmer) elevations than Ferocactus and Mammillaria.
Insect tricks: two-phasic foot pad secretion prevents slipping
Venue: Journal of the Royal Society Interface

Many insects cling to vertical and inverted surfaces with pads that adhere by nanometre-thin films of liquid secretion. This fluid is an emulsion, consisting of watery droplets in an oily continuous phase. The detailed function of its two-phasic nature has remained unclear. Here we show that the pad emulsion provides a mechanism that prevents insects from slipping on smooth substrates. We discovered that it is possible to manipulate the adhesive secretion in vivo using smooth polyimide substrates that selectively absorb its watery component. While thick layers of polyimide spin-coated onto glass removed all visible hydrophilic droplets, thin coatings left the emulsion in its typical form. Force measurements of stick insect pads sliding on these substrates demonstrated that the reduction of the watery phase resulted in a significant decrease in friction forces. Artificial control pads made of polydimethylsiloxane showed no difference when tested on the same substrates, confirming that the effect is caused by the insects’ fluid-based adhesive system. Our findings suggest that insect adhesive pads use emulsions with non-Newtonian properties, which may have been optimized by natural selection. Emulsions as adhesive secretions combine the benefits of ‘wet’ adhesion and resistance against shear forces.
A Role for Parasites in Stabilising the Fig-Pollinator Mutualism
Venue: PLOS Biology

Mutualisms are interspecific interactions in which both players benefit. Explaining their maintenance is problematic, because cheaters should outcompete cooperative conspecifics, leading to mutualism instability. Monoecious figs (Ficus) are pollinated by host-specific wasps (Agaonidae), whose larvae gall ovules in their “fruits” (syconia). Female pollinating wasps oviposit directly into Ficus ovules from inside the receptive syconium. Across Ficus species, there is a widely documented segregation of pollinator galls in inner ovules and seeds in outer ovules. This pattern suggests that wasps avoid, or are prevented from ovipositing into, outer ovules, and this results in mutualism stability. However, the mechanisms preventing wasps from exploiting outer ovules remain unknown. We report that in Ficus rubiginosa, offspring in outer ovules are vulnerable to attack by parasitic wasps that oviposit from outside the syconium. Parasitism risk decreases towards the centre of the syconium, where inner ovules provide enemy-free space for pollinator offspring. We suggest that the resulting gradient in offspring viability is likely to contribute to selection on pollinators to avoid outer ovules, and by forcing wasps to focus on a subset of ovules, reduces their galling rates. This previously unidentified mechanism may therefore contribute to mutualism persistence independent of additional factors that invoke plant defences against pollinator oviposition, or physiological constraints on pollinators that prevent oviposition in all available ovules.
Dermal bone in early tetrapods: a palaeophysiological hypothesis of adaptation for terrestrial acidosis
Venue: Proceedings of The Royal Society B: Biological Sciences

The dermal bone sculpture of early, basal tetrapods of the Permo-Carboniferous is unlike the bone surface of any living vertebrate, and its function has long been obscure. Drawing from physiological studies of extant tetrapods, where dermal bone or other calcified tissues aid in regulating acid–base balance relating to hypercapnia (excess blood carbon dioxide) and/or lactate acidosis, we propose a similar function for these sculptured dermal bones in early tetrapods. Unlike the condition in modern reptiles, which experience hypercapnia when submerged in water, these animals would have experienced hypercapnia on land, owing to likely inefficient means of eliminating carbon dioxide. The different patterns of dermal bone sculpture in these tetrapods largely correlates with levels of terrestriality: sculpture is reduced or lost in stem amniotes that likely had the more efficient lung ventilation mode of costal aspiration, and in small-sized stem amphibians that would have been able to use the skin for gas exchange.
Evolution-guided discovery of antibiotics that inhibit peptidoglycan remodelling
Venue: Nature

Addressing the ongoing antibiotic crisis requires the discovery of compounds with novel mechanisms of action that are capable of treating drug-resistant infections 1 . Many antibiotics are sourced from specialized metabolites produced by bacteria, particularly those of the Actinomycetes family 2 . Although actinomycete extracts have traditionally been screened using activity-based platforms, this approach has become unfavourable owing to the frequent rediscovery of known compounds. Genome sequencing of actinomycetes reveals an untapped reservoir of biosynthetic gene clusters, but prioritization is required to predict which gene clusters may yield promising new chemical matter 2 . Here we make use of the phylogeny of biosynthetic genes along with the lack of known resistance determinants to predict divergent members of the glycopeptide family of antibiotics that are likely to possess new biological activities. Using these predictions, we uncovered two members of a new functional class of glycopeptide antibiotics—the known glycopeptide antibiotic complestatin and a newly discovered compound we call corbomycin—that have a novel mode of action. We show that by binding to peptidoglycan, complestatin and corbomycin block the action of autolysins—essential peptidoglycan hydrolases that are required for remodelling of the cell wall during growth. Corbomycin and complestatin have low levels of resistance development and are effective in reducing bacterial burden in a mouse model of skin MRSA infection. The glycopeptide antibiotic-related compounds complestatin and corbomycin function by binding to peptidoglycan and blocking the action of autolysins—peptidoglycan hydrolase enzymes that remodel the cell wall during growth.
Incidence and mechanical significance of pneumatization in the long bones of birds
Venue: Zoological Journal of the Linnean Society

The incidence of pneumatization in avian long bones was studied, by direct observation, in a large sample of species. Only proximal bones (humerus and femur) presented pneumatization in the sample studied. The incidence obtained was related to the variation of the maximum cortical thickness and mechanical properties, such as bending strength and flexural Young's modulus. Cortical thickness, bending strength and flexural Young's modulus were significantly lower in pneumatized bones than in marrow-filled bones. Furthermore, some congruence was found between pneumatization and systematic groups when compared. In this sense, Charadriformes was the only order studied with total absence of long bone pneumatization. Results on cortical thickness appear to be in agreement with modelling predictions previously made and with results obtained on other groups of flying vertebrates. The possible selective advantage of reduction in cortical thickness in relation to flying is suggested.
Design of superior spider silk: from nanostructure to mechanical properties.
Venue: Biophysical Journal

Spider dragline silk is of practical interest because of its excellent mechanical properties. However, the structure of this material is still largely unknown. In this article, we report what we believe is a new model of the hierarchical structure of silk based on scanning electron microscope and atomic force microscope images. This hierarchical structure includes beta-sheet, polypeptide chain network, and silk fibril. It turns out that an exceptionally high strength of the spider dragline silk can be obtained by decreasing the size of the crystalline nodes in the polypeptide chain network while increasing the degree of orientation of the crystalline nodes. Based on this understanding, how the reeling speed affects mechanical properties of spider dragline silk can be understood properly. Hopefully, the understanding obtained in this study will shed light on the formation of spider silk, and consequently, on the principles for the design of ultrastrong silk.
Trap geometry in three giant montane pitcher plant species from Borneo is a function of tree shrew body size.
Venue: New Phytologist

*Three Bornean pitcher plant species, Nepenthes lowii, N. rajah and N. macrophylla, produce modified pitchers that 'capture' tree shrew faeces for nutritional benefit. Tree shrews (Tupaia montana) feed on exudates produced by glands on the inner surfaces of the pitcher lids and defecate into the pitchers. Here, we tested the hypothesis that pitcher geometry in these species is related to tree shrew body size by comparing the pitcher characteristics with those of five other 'typical' (arthropod-trapping) Nepenthes species. We found that only pitchers with large orifices and lids that are concave, elongated and oriented approximately at right angles to the orifice capture faeces. The distance from the tree shrews' food source (that is, the lid nectar glands) to the front of the pitcher orifice precisely matches the head plus body length of T. montana in the faeces-trapping species, and is a function of orifice size and the angle of lid reflexion. Substantial changes to nutrient acquisition strategies in carnivorous plants may occur through simple modifications to trap geometry. This extraordinary plant-animal interaction adds to a growing body of evidence that Nepenthes represents a candidate model for adaptive radiation with regard to nitrogen sequestration strategies.
Cleaving C-Hg bonds: two thiolates are better than one
Venue: Nature Chemical Biology

Organomercurial lyase (MerB) catalyzes the difficult cleavage of C-Hg bonds to hydrocarbon and mercuric dithiol products. Model compounds providing two or three thiolate ligands activate organomercurials toward acidic cleavage under mild conditions, which supports a mechanism in which MerB enzymes use two conserved active-site cysteines to activate the substrate.
Arsenic and selenium in microbial metabolism.
Venue: Annual Review of Microbiology

Arsenic and selenium are readily metabolized by prokaryotes, participating in a full range of metabolic functions including assimilation, methylation, detoxification, and anaerobic respiration. Arsenic speciation and mobility is affected by microbes through oxidation/reduction reactions as part of resistance and respiratory processes. A robust arsenic cycle has been demonstrated in diverse environments. Respiratory arsenate reductases, arsenic methyltransferases, and new components in arsenic resistance have been recently described. The requirement for selenium stems primarily from its incorporation into selenocysteine and its function in selenoenzymes. Selenium oxyanions can serve as an electron acceptor in anaerobic respiration, forming distinct nanoparticles of elemental selenium that may be enriched in (76)Se. The biogenesis of selenoproteins has been elucidated, and selenium methyltransferases and a respiratory selenate reductase have also been described. This review highlights recent advances in ecology, biochemistry, and molecular biology and provides a prelude to the impact of genomics studies.
Leaf dynamics, self-shading and carbon gain in seedlings of a tropical pioneer tree
Venue: Oecologia

We examined leaf dynamics and leaf age gradients of photosynthetic capacity and nitrogen concentration in seedlings of the tropical pioneer tree, Heliocarpus appendiculatus, grown in a factorial design under controlled conditions with two levels each of nutrients, ambient light (light levels incident above the canopy), and self-shading (the gradient of light levels from upper to lower leaves on the shoot). Correlations among these parameters were examined in order to determine the influence of self-shading, and the regulation of standing leaf numbers, on leaf longevity and its association with leaf photosynthetic capacity. Leaf longevity and the number of leaves on the main shoot were both reduced in high light, while in the low light environment, they were reduced in the steeper self-shading gradient. In high nutrients, leaf longevity was reduced whereas leaf number increased. Leaf initiation rates were higher in the high nutrient treatment but were not influenced by either light treatment. Maximum-light saturated photosynthetic rate, on an area basis, was greater in the high light and nutrient treatments, while the decline in photosynthetic capacity in realtion to leaf position on the shoot was more rapid in high light and in low nutrients. Leaf longevity was negatively correlated among treatments with initial photosynthetic capacity. The leaf position at which photosynthetic capacity was predicted to reach zero was positively correlated with the number of leaves on the shoot, supporting the hypothesis that leaf numbers are regulated by patterns of self-shading. The negative association of longevity and initial photosynthetic capacity apparently arises from different associations among gradients of photosynthetic capacity, leaf numbers and leaf initiation rates in relation to light and nutrient availability. The simultaneous consideration of age and position of leaves illuminates the role of self-shading as an important factor influencing leaf senescence and canopy structure and dynamics.
Bile Acid Secreted by Male Sea Lamprey That Acts as a Sex Pheromone
Venue: Science

We show that reproductively mature male sea lampreys release a bile acid that acts as a potent sex pheromone, inducing preference and searching behavior in ovulated female lampreys. The secreted bile acid 7α,12α,24-trihydroxy-5α-cholan-3-one 24-sulfate was released in much higher amounts relative to known vertebrate steroid pheromones and may be secreted through the gills. Hence, the male of this fish species signals both its reproductive status and location to females by secreting a pheromone that can act over long distances.
The structure of aquaporins
Venue: Quarterly Reviews of Biophysics

1.  1.1 The elusive water pores 362 1.2 CHIP28 362 2. Studies on AQP-1 363 2.1 Expression of AQP1 cDNA in Xenopus oocytes 363 2.2 Reconstitution of purified AQP1 into artificial lipid bilayers 364 2.3 Structural information deduced from the primary sequence 365 2.4 Evolution and mammalian AQPs 365 3. Chronological overview over AQP structures 368 3.1 AQP1 – the red blood cell water pore 368 3.2 GlpF – the E. coli glycerol facilitator 371 3.3 AQPZ – the E. coli water pore 372 3.4 AQP0 – the lens-specific aquaporin 373 3.5 AQP4 – the main aquaporin in brain 377 3.6 SoPiP2;1 – a plant aquaporin 379 3.7 AQPM – an archaeabacterial aquaporin 379 4. Proton exclusion 380 5. Substrate selectivity 382 6. Pore regulation 385 6.1 Hormonal regulation of AQP trafficking 385 6.2 Influence of pH on AQP water conduction 386 6.3 Regulation of AQP pore conductance by protein binding 387 6.4 Pore closure by conformational changes in the AQP0 pore 388 7. Unresolved questions 390 8. Acknowledgments 390 9. References 391 The ubiquitous members of the aquaporin (AQP) family form transmembrane pores that are either exclusive for water (aquaporins) or are also permeable for other small neutral solutes such as glycerol (aquaglyceroporins). The purpose of this review is to provide an overview of our current knowledge of AQP structures and to describe the structural features that define the function of these membrane pores. The review will discuss the mechanisms governing water conduction, proton exclusion and substrate specificity, and how the pore permeability is regulated in different members of the AQP family.
Sea urchin spawning in benthic boundary layers: Are eggs fertilized before advecting away from females?
Venue: Limnology and Oceanography

Past work on fertilization in echinoids and other egg-broadcasting, free-spawning invertebrates suggests that these organisms might be extremely sperm limited in the field unless individuals spawn in close proximity and under nearly ideal flow conditions. However, virtually all previous experiments have used one or more techniques (surrogates for males and females, and short sampling duration) that bypassed two potentially important aspects of echinoid reproductive biology: the release of gametes in viscous fluids that cling to tests and spines, and extended longevity of eggs and undiluted sperm. We hypothesized that these attributes might interact with some flow regimes to facilitate time-integrated fertilization. Consequently, we explored fertilization processes in sea urchins induced to spawn in a benthic boundary layer in a flow-through flume, with a male 0.5 m upstream of a female. Our observations and data suggest that at free‐stream flow velocities of 2.5 and 8.5 cm s 21 , gametes were slowly and continually advected from the aboral surfaces of spawning animals. Eggs on the surface of the aboral mass were often fertilized before they ablated from the surface; many advected eggs were fertilized after being trapped in the vortex downstream of the female. Gamete advection and fertilization continued for several hours, with the actual time course depending on flow velocity. Fertilization levels declined only slightly with increasing flow velocity. These results suggest that fertilization in echinoderms and other free-spawners with viscous, long-lived gametes could be much less sperm-limited than currently envisioned and have additional implications for population dynamics and selection on gamete characteristics.
Acclimation or Innate Protection of Anemonefishes from Sea Anemones
Venue: Copeia

Studies have shown that anemonefishes can acquire protection from the stinging tentacles of their host anemones through a behavioral process called "acclimation." However, some investigators have suggested that anemonefishes are innately protected from all species of host anemones. To definitively test whether anemonefishes are innately protected from anemones, we forced "naive" anemonefishes, bred and raised in complete isolation from anemones, to contact the tentacles of Macrodactyla doreensis, Heteractis crispa, and Stichodactyla haddoni. Individuals of Amphiprion clarkii were protected when forced to contact the tentacles of all three anemone species. However, individuals of A. ocellaris and A. perideraion were stung by some anemones. All fishes went through acclimation behavior after the initial forced contact with anemones. Thus, anemonefishes are innately protected from some anemone species but must acclimate to live with others.
In Situ Imaging of Barnacle (Balanus amphitrite) Cyprid Cement Using Confocal Raman Microscopy
Venue: Journal of Adhesion

Barnacles are a model for research on permanent underwater adhesion and the wider process of marine biofouling. A detailed understanding of the permanent adhesive secreted by the cypris larva for permanent settlement, the so-called cyprid cement, has potential to lead to novel antifouling solutions. There is a need for micro-analytical chemical in situ methods to gain more insight into the process of adhesion and the chemical composition of the cement. In this study, the applicability of confocal Raman microscopy for imaging the cyprid cement beneath permanently attached juvenile barnacles (Balanus amphitrite) was explored. Based on acquired area scans Raman images for characteristic chemical functional groups were obtained. In addition to showing the morphology of the attachment apparatus, the images provided information on chemical composition, in particular the hydration state of the cement, and demonstrated the potential of this method for in situ studies of adhesion at the micro-scale.
Avoidance and tolerance of freezing in ectothermic vertebrates
Venue: The Journal of Experimental Biology

Ectothermic vertebrates have colonized regions that are seasonally or perpetually cold, and some species, particularly terrestrial hibernators, must cope with temperatures that fall substantially below 0°C. Survival of such excursions depends on either freeze avoidance through supercooling or freeze tolerance. Supercooling, a metastable state in which body fluids remain liquid below the equilibrium freezing/melting point, is promoted by physiological responses that protect against chilling injury and by anatomical and behavioral traits that limit risk of inoculative freezing by environmental ice and ice-nucleating agents. Freeze tolerance evolved from responses to fundamental stresses to permit survival of the freezing of a substantial amount of body water under thermal and temporal conditions of ecological relevance. Survival of freezing is promoted by a complex suite of molecular, biochemical and physiological responses that limit cell death from excessive shrinkage, damage to macromolecules and membranes, metabolic perturbation and oxidative stress. Although freeze avoidance and freeze tolerance generally are mutually exclusive strategies, a few species can switch between them, the mode used in a particular instance of chilling depending on prevailing physiological and environmental conditions.
Tendon elasticity and muscle function.
Venue: Comparative Biochemistry and Physiology A-molecular & Integrative Physiology

Vertebrate animals exploit the elastic properties of their tendons in several different ways. Firstly, metabolic energy can be saved in locomotion if tendons stretch and then recoil, storing and returning elastic strain energy, as the animal loses and regains kinetic energy. Leg tendons save energy in this way when birds and mammals run, and an aponeurosis in the back is also important in galloping mammals. Tendons may have similar energy-saving roles in other modes of locomotion, for example in cetacean swimming. Secondly, tendons can recoil elastically much faster than muscles can shorten, enabling animals to jump further than they otherwise could. Thirdly, tendon elasticity affects the control of muscles, enhancing force control at the expense of position control.