nils-herrmann/clean_scirepeval huggingface dataset:
Biodeterioration of crude oil and oil derived products: a review
Venue: Reviews in Environmental Science and Bio\/technology

Biodeterioration of crude oil and oil fuels is a serious economic and an environmental problem all over the world. It is impossible to prevent penetration of microorganisms in oil and fuels both stored in tanks or in oilfields after drilling. Both aerobic and anaerobic microorganisms tend to colonise oil pipelines and oil and fuel storage installations. Complex microbial communities consisting of both hydrocarbon oxidizing microorganisms and bacteria using the metabolites of the former form an ecological niche where they thrive. The accumulation of water at the bottom of storage tanks and in oil pipelines is a primary prerequisite for development of microorganisms in fuels and oil and their subsequent biological fouling. Ability of microorganisms to grow both in a water phase and on inter-phase of water/hydrocarbon as well as the generation of products of their metabolism worsen the physical and chemical properties of oils and fuels. This activity also increases the amount of suspended solids, leads to the formation of slimes and creates a variety of operational problems. Nowadays various test-systems are utilized for microbial monitoring in crude oils and fuels; thus allowing an express determination of both the species and the quantities of microorganisms present. To suppress microbial growth in oils and fuels, both physico-mechanical and chemical methods are applied. Among chemical methods, the preference is given to substances such as biocides, additives, the anti-freezing agents etc that do not deteriorate the quality of oil and fuels and are environmentally friendly. This review is devoted to the analysis of the present knowledge in the field of microbial fouling of crude oils and oil products. The methods utilized for monitoring of microbial contamination and prevention of their undesirable activities are also evaluated. The special focus is given to Russian scientific literature devoted to crude oil and oil products biodeterioration.
The function of the sawfish's saw
Venue: Current Biology

Jawed fishes that possess an elongated rostrum use it to either sense prey or to manipulate it, but not for both. The billfish rostrum, for instance, lacks any sensory function and is used to stun prey , while paddlefishes use their rostrum to detect and orient towards electric fields of plankton . Sturgeons search through the substrate with their electroreceptive rostrum, and engulf prey by oral suction . Here, we show that juvenile freshwater sawfish Pristis microdon are active predators that use their toothed rostrum — the saw — to both sense prey-simulating electric fields and capture prey. Prey encountered in the water column is attacked with lateral swipes of the saw that can stun and/or impale it. We compare sawfish to shovelnose rays, which share a common shovelnose ray-like ancestor  and lack a saw.
Super-lampreys and wave energy: Optimised control of artificially-evolved, simulated swimming lamprey
Venue: Neurocomputing

Propulsion in the lamprey, an eel-like fish, is governed by activity in its spinal neural network (called a central pattern generator (CPG)). This CPG is simulated, in accordance with Ekeberg's original model, and optimised alternatives are generated with genetic algorithms (GAs). A two-phase GA is adopted: (1) to evolve neuron-descriptive parameters and synaptic weights of the neural oscillator for a single lamprey segment, (2) to generate interconnections between segments. Results demonstrate that Ekeberg's prototype is not a unique solution and that simpler versions with wider operational ranges can be generated. Evolved solutions outperform the swimming capabilities of a modelled biological organism, as an initial step in understanding how to control wave power devices, with similar motion to the lamprey.
Effect of abiotic factors on the foraging strategy of the orb-web spider Argiope keyserlingi (Araneae: Araneidae)
Venue: Austral Ecology

Environmental conditions such as light level, background contrast and temperature might influence a spider's prey capture success and risk of predation. Thus it may often be advantageous for spiders to adjust web-building behaviour in response to variation in these environmental conditions. This hypothesis was examined in a study of the construction of webs and web decorations (conspicuous strands of silk at the hub of the web) of the orb-web spider Argiope keyserlingi. Web decorations are thought to have one or more separate functions. They may attract prey, deter predators or advertise the web to oncoming birds, thus preventing web damage. In this series of experiments, relationships between weather parameters and the construction of webs and web decorations were considered. In complementary laboratory experiments, A. keyserlingi spiders were exposed to two different light levels (700 and 90 lx), background contrasts (black and white) and temperature conditions (20 and 26°C). Of the available weather parameters, only temperature was significantly related to web decorating behaviour but not to web size. In the laboratory, temperature also influenced web-decorating behaviour, and spiders in dim light (700 lx) constructed larger webs and longer decorations.  contrast did not significantly alter web size or web decorations. These data suggest that when prey availability is reduced at low temperatures, spiders may use web decorations to attract prey to the web. Similarly, in dim light, spiders may build more and larger decorations to increase the visual signal to approaching prey or to advertise the web to oncoming birds.
Anatomically diverse butterfly scales all produce structural colours by coherent scattering
Venue: The Journal of Experimental Biology

The structural colours of butterflies and moths (Lepidoptera) have been attributed to a diversity of physical mechanisms, including multilayer interference, diffraction, Bragg scattering, Tyndall scattering and Rayleigh scattering. We used fibre optic spectrophotometry, transmission electron microscopy (TEM) and 2D Fourier analysis to investigate the physical mechanisms of structural colour production in twelve lepidopteran species from four families, representing all of the previously proposed anatomical and optical classes of butterfly nanostructure. The 2D Fourier analyses of TEMs of colour producing butterfly scales document that all species are appropriately nanostructured to produce visible colours by coherent scattering, i.e. differential interference and reinforcement of scattered, visible wavelengths. Previously hypothesized to produce a blue colour by incoherent, Tyndall scattering, the scales of Papilio zalmoxis are not appropriately nanostructured for incoherent scattering. Rather, available data indicate that the blue of P. zalmoxis is a fluorescent pigmentary colour. Despite their nanoscale anatomical diversity, all structurally coloured butterfly scales share a single fundamental physical color production mechanism - coherent scattering. Recognition of this commonality provides a new perspective on how the nanostructure and optical properties of structurally coloured butterfly scales evolved and diversified among and within lepidopteran clades.
Self-organized lane formation and optimized traffic flow in army ants
Venue: Proceedings of The Royal Society B: Biological Sciences

We show how the movement rules of individual ants on trails can lead to a collective choice of direction and the formation of distinct traffic lanes that minimize congestion. We develop and evaluate the results of a new model with a quantitative study of the behaviour of the army ant Eciton burchelli. Colonies of this species have up to 200 000 foragers and transport more than 3000 prey items per hour over raiding columns that exceed 100 m. It is an ideal species in which to test the predictions of our model because it forms pheromone trails that are densely populated with very swift ants. The model explores the influences of turning rates and local perception on traffic flow. The behaviour of real army ants is such that they occupy the specific region of parameter space in which lanes form and traffic flow is maximized.
Raptorial jaws in the throat help moray eels swallow large prey
Venue: Nature

Most bony fishes rely on suction mechanisms to capture and transport prey. Once captured, prey are carried by water movement inside the oral cavity to a second set of jaws in the throat, the pharyngeal jaws, which manipulate the prey and assist in swallowing. Moray eels display much less effective suction-feeding abilities. Given this reduction in a feeding mechanism that is widespread and highly conserved in aquatic vertebrates, it is not known how moray eels swallow large fish and cephalopods. Here we show that the moray eel (Muraena retifera) overcomes reduced suction capacity by launching raptorial pharyngeal jaws out of its throat and into its oral cavity, where the jaws grasp the struggling prey animal and transport it back to the throat and into the oesophagus. This is the first described case of a vertebrate using a second set of jaws to both restrain and transport prey, and is the only alternative to the hydraulic prey transport reported in teleost fishes. The extreme mobility of the moray pharyngeal jaws is made possible by elongation of the muscles that control the jaws, coupled with reduction of adjacent gill-arch structures. The discovery that pharyngeal jaws can reach up from behind the skull to grasp prey in the oral jaws reveals a major innovation that may have contributed to the success of moray eels as apex predators hunting within the complex matrix of coral reefs. This alternative prey transport mode is mechanically similar to the ratcheting mechanisms used in snakes—a group of terrestrial vertebrates that share striking morphological, behavioural and ecological convergence with moray eels.
Defensive and chemical characterization of the froth produced by the cercopid Aphrophora cribrata
Venue: Chemoecology

Nymphs of the cercopid Aphrophora cribrata cover themselves with a frothy exudate while ingesting sap from their preferred host plant, the eastern white pine, Pinus strobus. Chemical analyses of froth collected from A. cribrata nymphs revealed an array of metabolites belonging to five chemical classes, including fatty acid-derived alcohols, γ-lactones and a single 1-monoacylglycerol, as well as the polyol pinitol and the polyhydroxyalkanoate, poly-3-hydroxybutyrate. Bioassays showed the natural A. cribata froth, as well as a synthetic mixture comprised of representative compound classes identified therein, to be repellent to ants but largely devoid of topical irritancy in tests with cockroaches.
Entrapment of bed bugs by leaf trichomes inspires microfabrication of biomimetic surfaces
Venue: Journal of the Royal Society Interface

Resurgence in bed bug infestations and widespread pesticide resistance have greatly renewed interest in the development of more sustainable, environmentally friendly methods to manage bed bugs. Historically, in Eastern Europe, bed bugs were entrapped by leaves from bean plants, which were then destroyed; this purely physical entrapment was related to microscopic hooked hairs (trichomes) on the leaf surfaces. Using scanning electron microscopy and videography, we documented the capture mechanism: the physical impaling of bed bug feet (tarsi) by these trichomes. This is distinct from a Velcro-like mechanism of non-piercing entanglement, which only momentarily holds the bug without sustained capture. Struggling, trapped bed bugs are impaled by trichomes on several legs and are unable to free themselves. Only specific, mechanically vulnerable locations on the bug tarsi are pierced by the trichomes, which are located at effective heights and orientations for bed bug entrapment despite a lack of any evolutionary association. Using bean leaves as templates, we microfabricated surfaces indistinguishable in geometry from the real leaves, including the trichomes, using polymers with material properties similar to plant cell walls. These synthetic surfaces snag the bed bugs temporarily but do not hinder their locomotion as effectively as real leaves.
Surfactants tailored by the class Actinobacteria
Venue: Frontiers in Microbiology

Globally the change towards the establishment of a bio-based economy has resulted in an increased need for bio-based applications. This, in turn, has served as a driving force for the discovery and application of novel biosurfactants. The class Actinobacteria represents a vast group of microorganisms with the ability to produce a diverse range of secondary metabolites, including surfactants. Understanding the extensive nature of the biosurfactants produced by actinobacterial strains can assist in finding novel biosurfactants with new potential applications. This review therefore presents a comprehensive overview of the knowledge available on actinobacterial surfactants, the chemical structures that have been completely or partly elucidated, as well as the identity of the biosurfactant-producing strains. Producer strains of not yet elucidated compounds are discussed, as well as the original habitats of all the producer strains, which seems to indicate that biosurfactant production is environmentally driven. Methodology applied in the isolation, purification and structural elucidation of the different types of surface active compounds, as well as surfactant activity tests, are also discussed. Overall, actinobacterial surfactants can be summarized to include the dominantly occurring trehalose-comprising surfactants, other non-trehalose containing glycolipids, lipopeptides and the more rare actinobacterial surfactants. The lack of structural information on a large proportion of actinobacterial surfactants should be considered as a driving force to further explore the abundance and diversity of these compounds. This would allow for a better understanding of actinobacterial surface active compounds and their potential for biotechnological application.
Common mycorrhizal networks provide a potential pathway for the transfer of hydraulically lifted water between plants.
Venue: Journal of Experimental Botany

Plant roots may be linked by shared or common mycorrhizal networks (CMNs) that constitute pathways for the transfer of resources among plants. The potential for water transfer by such networks was examined by manipulating CMNs independently of plant roots in order to isolate the role(s) of ectomycorrhizal (EM) and arbuscular mycorrhizal fungal (AMF) networks in the plant water balance during drought (soil water potential -5.9 MPa). Fluorescent tracer dyes and deuterium-enriched water were used to follow the pathways of water transfer from coastal live oak seedlings (Quercus agrifolia Nee; colonized by EM and AMF) conducting hydraulic lift (HL) into the roots of water-stressed seedlings connected only by EM (Q. agrifolia) or AMF networks (Q. agrifolia, Eriogonum fasciculatum Benth., Salvia mellifera Greene, Keckiella antirrhinoides Benth). When connected to donor plants by hyphal linkages, deuterium was detected in the transpiration flux of receiver oak plants, and dye-labelled extraradical hyphae, rhizomorphs, mantles, and Hartig nets were observed in receiver EM oak roots, and in AMF hyphae of Salvia. Hyphal labelling was scarce in Eriogonum and Keckiella since these species are less dependent on AMF. The observed patterns of dye distribution also indicated that only a small percentage of mycorrhizal roots and extraradical hyphae were involved with water transfer among plants. Our results suggest that the movement of water by CMNs is potentially important to plant survival during drought, and that the functional ecophysiological traits of individual mycorrhizal fungi may be a component of this mechanism.
Structural Strengthening of Urchin Skeletons by Collagenous Sutural Ligaments.
Venue: The Biological Bulletin

Sea urchin skeletons are strengthened by flexible collagenous ligaments that bind together rigid calcite plates at sutures. Whole skeletons without ligaments (removed by bleaching) broke at lower apically applied forces than did intact, fresh skeletons. In addition, in three-point bending tests on excised plate combinations, sutural ligaments strengthened sutures but not plates. The degree of sutural strengthening by ligaments depended on sutural position; in tensile tests, ambital and adapical sutures were strengthened more than adoral sutures. Adapical sutures, which grow fastest, were also the loosest, suggesting that strengthening by ligaments is associated with growth. In fed, growing urchins, sutures overall were looser than in unfed urchins. Looseness was demonstrated visually and by vibration analysis: bleached skeletons of unfed urchins rang at characteristic frequencies, indicating that sound traveled across tightly fitting sutures; skeletons of fed urchins damped vibrations, indicating loss of vibrational energy across looser sutures. Furthermore, bleached skeletons of fed urchins broke at lower apically applied forces than bleached skeletons of unfed urchins, indicating that the sutures of fed urchins had been held together relatively loosely by sutural ligaments. Thus, the apparently rigid dome-like skeleton of urchins sometimes transforms into a flexible, jointed membrane as sutures loosen and become flexible during growth.
Carbon acquisition by diatoms
Venue: Photosynthesis Research

Diatoms are responsible for up to 40% of primary productivity in the ocean, and complete genome sequences are available for two species. However, there are very significant gaps in our understanding of how diatoms take up and assimilate inorganic C. Diatom plastids originate from secondary endosymbiosis with a red alga and their Form ID Rubisco (ribulose-1,5-bisphosphate carboxylase-oxygenase) from horizontal gene transfer, which means that embryophyte paradigms can only give general guidance as to their C acquisition mechanisms. Although diatom Rubiscos have relatively high CO2 affinity and CO2/O2 selectivity, the low diffusion coefficient for CO2 in water has the potential to restrict the rate of photosynthesis. Diatoms growing in their natural aquatic habitats operate inorganic C concentrating mechanisms (CCMs), which provide a steady-state CO2 concentration around Rubisco higher than that in the medium. How these CCMs work is still a matter of debate. However, it is known that both CO2 and HCO3− are taken up, and an obvious but as yet unproven possibility is that active transport of these species across the plasmalemma and/or the four-membrane plastid envelope is the basis of the CCM. In one marine diatom there is evidence of C4-like biochemistry which could act as, or be part of, a CCM. Alternative mechanisms which have not been eliminated include the production of CO2 from HCO3− at low pH maintained by a H+ pump, in a compartment close to that containing Rubisco.
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
Venue: Science

Chromosomal Mapping The conformation of the genome in the nucleus and contacts between both proximal and distal loci influence gene expression. In order to map genomic contacts, Lieberman-Aiden et al.  developed a technique to allow the detection of all interactions between genomic loci in the eukaryotic nucleus followed by deep sequencing. This technology was used to map the organization of the human genome and to examine the spatial proximity of chromosomal loci at one megabase resolution. The map suggests that the genome is partitioned into two spatial compartments that are related to local chromatin state and whose remodeling correlates with changes in the chromatin state. Chromosomes are organized in a fractal knot-free conformation that is densely packed while easily folded and unfolded. We describe Hi-C, a method that probes the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. We constructed spatial proximity maps of the human genome with Hi-C at a resolution of 1 megabase. These maps confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free, polymer conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. The fractal globule is distinct from the more commonly used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes.
Egg Longevity and Time-Integrated Fertilization in a Temperate Sea Urchin (Strongylocentrotus droebachiensis)
Venue: The Biological Bulletin

Recent field experiments have suggested that fertilization levels in sea urchins (and other broadcast spawners that release their gametes into the water column) may often be far below 100%. However, past experiments have not considered the potentially positive combined effects of an extended period of egg longevity and the release of gametes in viscous fluids (which reduces dilution rates). In a laboratory experiment, we found that eggs of the sea urchin Strongylocentrotus droebachiensis had high viability for 2 to 3 d. Fertilization levels of eggs held in sperm-permeable egg baskets in the field and exposed to sperm slowly diffusing off a spawning male increased significantly with exposure from 15 min to 3 h. In a field survey of time-integrated fertilizations (over 24, 48, and 72 h) during natural sperm release events, eggs held in baskets accrued fertilizations over as much as 48 h and attained fairly high fertilization levels. Our results suggest that an extended period of egg longevity and the release of gametes in viscous fluids may result in higher natural fertilization levels than currently expected from short-term field experiments.
Naturally occurring nanoparticles from English ivy: an alternative to metal-based nanoparticles for UV protection
Venue: Journal of Nanobiotechnology

BackgroundOver the last decade safety concerns have arisen about the use of metal-based nanoparticles in the cosmetics field. Metal-based nanoparticles have been linked to both environmental and animal toxicity in a variety of studies. Perhaps the greatest concern involves the large amounts of TiO2 nanoparticles that are used in commercial sunscreens. As an alternative to using these potentially hazardous metal-based nanoparticles, we have isolated organic nanoparticles from English ivy (Hedera helix). In this study, ivy nanoparticles were evaluated for their potential use in sunscreens based on four criteria: 1) ability to absorb and scatter ultraviolet light, 2) toxicity to mammalian cells, 3) biodegradability, and 4) potential for diffusion through skin.ResultsPurified ivy nanoparticles were first tested for their UV protective effects using a standard spectrophotometric assay. Next the cell toxicity of the ivy nanoparticles was compared to TiO2 nanoparticles using HeLa cells. The biodegradability of these nanoparticles was also determined through several digestion techniques. Finally, a mathematical model was developed to determine the potential for ivy nanoparticles to penetrate through human skin. The results indicated that the ivy nanoparticles were more efficient in blocking UV light, less toxic to mammalian cells, easily biodegradable, and had a limited potential to penetrate through human skin. When compared to TiO2 nanoparticles, the ivy nanoparticles showed decreased cell toxicity, and were easily degradable, indicating that they provided a safer alternative to these nanoparticles.ConclusionsWith the data collected from this study, we have demonstrated the great potential of ivy nanoparticles as a sunscreen protective agent, and their increased safety over commonly used metal oxide nanoparticles.