nils-herrmann/clean_scirepeval huggingface dataset:
The origin of traveling waves in an emperor penguin huddle
Venue: New Journal of Physics

Emperor penguins breed during the Antarctic winter and have to endure temperatures as low as 50 C and wind speeds of up to 200kmh 1 . To conserve energy, they form densely packed huddles with a triangular lattice structure. Video recordings from previous studies revealed coordinated movements in regular wave-like patterns within these huddles. It is thought that these waves are triggered by individual penguins that locally disturb the huddle structure, and that the traveling wave serves to remove the lattice defects and restore order. The mechanisms that govern wave propagation are currently unknown, however. Moreover, it is unknown if the waves are always triggered by the same penguin in a huddle. Here, we present a model in which the observed wave patterns emerge from simple rules involving only the interactions between directly neighboring individuals, similar to the interaction rules found in other jammed systems, e.g. between cars in a traffic jam. Our model predicts that a 6 Authors to whom any correspondence should be addressed.
The Interaction between Plants and Bacteria in the Remediation of Petroleum Hydrocarbons: An Environmental Perspective
Venue: Frontiers in Microbiology

Widespread pollution of terrestrial ecosystems with petroleum hydrocarbons (PHCs) has generated a need for remediation and, given that many PHCs are biodegradable, bio- and phyto-remediation are often viable approaches for active and passive remediation. This review focuses on phytoremediation with particular interest on the interactions between and use of plant-associated bacteria to restore PHC polluted sites. Plant-associated bacteria include endophytic, phyllospheric, and rhizospheric bacteria, and cooperation between these bacteria and their host plants allows for greater plant survivability and treatment outcomes in contaminated sites. Bacterially driven PHC bioremediation is attributed to the presence of diverse suites of metabolic genes for aliphatic and aromatic hydrocarbons, along with a broader suite of physiological properties including biosurfactant production, biofilm formation, chemotaxis to hydrocarbons, and flexibility in cell-surface hydrophobicity. In soils impacted by PHC contamination, microbial bioremediation generally relies on the addition of high-energy electron acceptors (e.g., oxygen) and fertilization to supply limiting nutrients (e.g., nitrogen, phosphorous, potassium) in the face of excess PHC carbon. As an alternative, the addition of plants can greatly improve bioremediation rates and outcomes as plants provide microbial habitats, improve soil porosity (thereby increasing mass transfer of substrates and electron acceptors), and exchange limiting nutrients with their microbial counterparts. In return, plant-associated microorganisms improve plant growth by reducing soil toxicity through contaminant removal, producing plant growth promoting metabolites, liberating sequestered plant nutrients from soil, fixing nitrogen, and more generally establishing the foundations of soil nutrient cycling. In a practical and applied sense, the collective action of plants and their associated microorganisms is advantageous for remediation of PHC contaminated soil in terms of overall cost and success rates for in situ implementation in a diversity of environments. Mechanistically, there remain biological unknowns that present challenges for applying bio- and phyto-remediation technologies without having a deep prior understanding of individual target sites. In this review, evidence from traditional and modern omics technologies is discussed to provide a framework for plant–microbe interactions during PHC remediation. The potential for integrating multiple molecular and computational techniques to evaluate linkages between microbial communities, plant communities and ecosystem processes is explored with an eye on improving phytoremediation of PHC contaminated sites.
Optical solar energy adaptations and radiative temperature control of green leaves and tree barks
Venue: Solar Energy Materials and Solar Cells

Trees have adapted to keep leaves and barks cool in sunshine and can serve as interesting bionic model systems for radiative cooling. Silicon solar cells, on the other hand, loose up to one third of their energy efficiency due to heating in intensive sunshine. It is shown that green leaves minimize absorption of useful radiation and allow efficient infrared thermal emission. Since elevated temperatures are detrimental for tensile water flow in the Xylem tissue below barks, the optical properties of barks should also have evolved so as to avoid excessive heating. This was tested by performing optical studies with tree bark samples from representative trees. It was found that tree barks have optimized their reflection of incoming sunlight between 0.7 and 2 μm. This is approximately the optical window in which solar light is transmitted and reflected by green vegetation. Simultaneously, the tree bark is highly absorbing and thus radiation emitting between 6 and 10 μm. These two properties, mainly provided by tannins, create optimal conditions for radiative temperature control. In addition, tannins seem to have adopted a function as mediators for excitation energy towards photo-antioxidative activity for control of radiation damage. The results obtained are used to discuss challenges for future solar cell optimization.
K9 Water Searches: Scent and Scent Transport Considerations
Venue: Journal of Forensic Sciences

Increased use of water search dogs for detecting submerged bodies has created the need for a better understanding of scent emanating from the bodies and how it transits the water to the dog’s nose. A review of recent literature identifies likely scent sources, potential scent transport processes, and research needs. Scent sources include gases in bubbles or dissolved in the water, liquids as buoyant plumes and droplets or dissolved in the water, and solids consisting of buoyant particulates with secretions, bacteria, and body fluids. Potential transport processes through the water include buoyancy, entrainment, and turbulence. Transport processes from the water surface into the air include volatilization and evaporation enhanced by bubble bursting, breaking waves, splashing, and wind spray. Implications for the use of water search dogs are examined. Observations of submerged, decomposing bodies are needed to quantify the physical and chemical characteristics of the scent and scent transport processes.
Flaw tolerance of nuclear intermediate filament lamina under extreme mechanical deformation.
Venue: ACS Nano

The nuclear lamina, composed of intermediate filaments, is a structural protein meshwork at the nuclear membrane that protects genetic material and regulates gene expression. Here we uncover the physical basis of the material design of nuclear lamina that enables it to withstand extreme mechanical deformation of >100% strain despite the presence of structural defects. Through a simple in silico model we demonstrate that this is due to nanoscale mechanisms including protein unfolding, alpha-to-beta transition, and sliding, resulting in a characteristic nonlinear force-extension curve. At the larger microscale this leads to an extreme delocalization of mechanical energy dissipation, preventing catastrophic crack propagation. Yet, when catastrophic failure occurs under extreme loading, individual protein filaments are sacrificed rather than the entire meshwork. This mechanism is theoretically explained by a characteristic change of the tangent stress-strain hardening exponent under increasing strain. Our results elucidate the large extensibility of the nuclear lamina within muscle or skin tissue and potentially many other protein materials that are exposed to extreme mechanical conditions, and provide a new paradigm toward the de novo design of protein materials by engineering the nonlinear stress-strain response to facilitate flaw-tolerant behavior.
High-speed microscopic imaging of flagella motility and swimming in Giardia lamblia trophozoites
Venue: Proceedings of the National Academy of Sciences of the United States of America

We report, in this paper, several findings about the swimming and attachment mechanisms of Giardia lamblia trophozoites. These data were collected using a combination of a high-contrast CytoViva imaging system and a particle image velocimetry camera, which can capture images at speeds greater than 800 frames/s. Using this system, we discovered that, during rapid swimming of Giardia trophozoites, undulations of the caudal region contributed to forward propulsion combined with the beating of the flagella pairs. It was also discovered, in contrast to previous studies with 10 times slower image sampling technique, that the anterior and posterolateral flagella beat with a clearly defined power stroke and not symmetrical undulations. During the transition from free swimming to attachment, trophozoites modified their swimming behavior from a rapid rotating motion to a more stable planar swimming. While using this planar swimming motion, the trophozoites used the flagella for propulsion and directional control. In addition to examination of the posterolateral and anterior flagella, a model to describe the motion of the ventral flagella was derived, indicating that the ventral flagella beat in an expanding sine wave. In addition, the structure of the ventrocaudal groove creates boundary conditions that determine the form of beating of the ventral flagella. The results from this study indicate that Giardia is able to simultaneously generate both ciliary beating and typical eukaryotic flagellar beating using different pairs of flagella.
Humidity affects the extensibility of an orb-weaving spider's viscous thread droplets
Venue: The Journal of Experimental Biology

The prey-capture threads found in most spider orb webs rely on viscous droplets for their stickiness. Each droplet is formed of a central mass of viscoelastic glycoprotein glue surrounded by an aqueous covering, both of which incorporate hydrophilic components. We found that the extensibility of droplets on Larinioides cornutus threads increased as humidity increased. However, the deflection of the droplets' supporting axial lines did not change, indicating that atmospheric water uptake increases glycoprotein plasticity, but not glycoprotein adhesion. The extensibility of droplets, along with that of the thread's supporting axial fibers, is responsible for summing the adhesion of multiple thread droplets. Therefore, daily changes in humidity have the potential to significantly alter the performance of viscous threads and orb webs.
Lipids of the Stratum Corneum Vary with Cutaneous Water Loss among Larks along a Temperature‐Moisture Gradient
Venue: Physiological and Biochemical Zoology

We explored the relationship between lipids of the stratum corneum (SC), the barrier to water‐vapor diffusion of the skin, and cutaneous water loss (CWL) of species of free‐living larks along a temperature‐moisture gradient. Our results showed that free fatty acids, cholesterol, and ceramides were the major constituents of SC in larks from different environments including the Netherlands, a mesic environment; Iran, a semiarid region; and several areas in Saudi Arabia, a hot dry desert. We found that CWL was reduced among larks inhabiting deserts, but our data did not support the hypothesis that birds from desert environments have larger quantities of lipids per unit dry mass of the SC than larks from more mesic environments. Instead, larks in arid environments had a higher proportion of ceramides, especially the more polar fractions 4–6, and a smaller proportion of free fatty acids in their SC, an adjustment that apparently reduced their CWL. Subtle changes in the ratios of lipid classes can apparently alter the movement of water vapor through the skin. We hypothesize that desert birds have higher proportions of ceramides in their SC and lower proportions of free fatty acids because this combination allows the lipid lamellae to exist in a more highly ordered crystalline phase and consequently creates a tighter barrier to water‐vapor diffusion.
A dinoflagellate exploits toxins to immobilize prey prior to ingestion
Venue: Proceedings of the National Academy of Sciences of the United States of America

Toxins produced by the harmful algal bloom (HAB) forming, mixotrophic dinoflagellate Karlodinium veneficum have long been associated with fish kills. To date, the perceived ecological role for toxins has been relief from grazing pressures. Here, we demonstrate that karlotoxins also serve as a predation instrument. Using high-speed holographic microscopy, we measure the swimming behavior of several toxic and nontoxic strains of K. veneficum and their prey, Storeatula major, within dense suspensions. The selected strains produce toxins with varying potency and dosages, including a nontoxic one. Results clearly show that mixing the prey with the predatory, toxic strains causes prey immobilization at rates that are consistent with the karlotoxins’ potency and dosage. Even prey cells that continue swimming slow down after exposure to toxic predators. The swimming characteristics of predators vary substantially in pure suspensions, as quantified by their velocity, radii of helical trajectories, and direction of helical rotation. When mixed with prey, all toxic strains that are involved in predation slow down. Furthermore, they substantially reduced their predominantly vertical migration, presumably to remain in the vicinity of their prey. Conversely, the nontoxic control strain does not alter its swimming and does not affect prey behavior. In separate experiments, we show that exposing prey to exogenous toxins also causes prey immobilization at rates consistent with potency. Clearly, the toxic predatory strains use karlotoxins as a means of stunning their prey, before ingesting it. These findings add a substantiated critical understanding for why some HAB species produce such complex toxin molecules.
Giant bent-core mesogens in the thread forming process of marine mussels.
Venue: Biomacromolecules

In marine mussels (Mytilus), byssal threads are made in minutes from prefabricated smectic polymer liquid crystals by a process resembling reaction injection molding. The mesogens in these arrays are known to be natural block copolymers with rodlike collagen cores. Using atomic force microscopy, it was shown that these collagenous mesogens are bent-core or banana-shaped in a manner that is consistent with and predictable from their amino acid sequence. The overall bend angle in preCOL-NG in Mytilus galloprovincialis is about 130 degrees. The mesogens have a center-to-center separation of approximately 22 nm and a length of 200 nm. It is evident that the smectic structure of the prefabricated mesophases remains largely intact over 1-3 microm distances in the molded fibers and is presumably locked in place during molding by cross-linking. Like the smectic liquid crystals of many synthetic banana mesogens, the collagenous mesogens of the byssal threads exhibit SmC(2) symmetry with a characteristic tilt of 24.6 degrees. At about 100% extension, this tilt is considerably reduced and the globular end domains are no longer visible presumably because they have been unraveled.
SECRETION OF GASES AGAINST HIGH PRESSURES IN THE SWIMBLADDER OF DEEP SEA FISHES II. THE RETE MIRABILE
Venue: The Biological Bulletin

1. The structure and dimensions are given for the rete mirabile. It is interpreted as a counter current diffusion exchange mechanism between the afferent and efferent . This diffusion exchange has been quantitatively evaluated for O2, CO2, and N2. The arrangement makes possible the maintenance of a steep tension gradient within the rete, so that the oxygen loss from the leaving blood can be extremely low.3. Quantitative evaluation of the efficiency of the rete diffusion makes it clear that the limiting equilibrium pressure in the swimbladder could be extremely high, and that the limiting factor lies mainly in the dissociation pressure of the chemical or physical reaction which ultimately splits off the oxygen.4. The nature of the responsible compound and reaction is unknown. The anatomical arrangement of the glandular structure and the rete is suggestive of a cellular secretion of oxygen rather than of a mechanism that splits off oxygen in the blood.5. Data on the deposition of nitrogen against high...
Tuning of color contrast signals to visual sensitivity maxima of tree shrews by three Bornean highland Nepenthes species
Venue: Plant Signaling & Behavior

Three species of Nepenthes pitcher plants (Nepenthes rajah, Nepenthes lowii and Nepenthes macrophylla) specialize in harvesting nutrients from tree shrew excreta in their pitchers. In all three species, nectaries on the underside of the pitcher lid are the focus of the tree shrews' attention. Tree shrews are dichromats, with visual sensitivity in the blue and green wavebands. All three Nepenthes species were shown to produce visual signals, in which the underside of the pitcher lid (the area of highest nectar production) stood out in high contrast to the adjacent area on the pitcher (i.e., was brighter), in the blue and green wavebands visible to the tree shrews. N. rajah showed the tightest degree of “tuning,” notably in the green waveband. Conversely, pitchers of Nepenthes burbidgeae, a typical insectivorous species sympatric with N. rajah, did not produce a color pattern tuned to tree shrew sensitivity maxima.
Adhesion forces measured at the level of a terminal plate of the fly's seta
Venue: Proceedings of The Royal Society B: Biological Sciences

The attachment pads of fly legs are covered with setae, each ending in small terminal plates coated with secretory fluid. A cluster of these terminal plates contacting a substrate surface generates strong attractive forces that hold the insect on smooth surfaces. Previous research assumed that cohesive forces and molecular adhesion were involved in the fly attachment mechanism. The main elements that contribute to the overall attachment force, however, remained unknown. Multiple local force–volume measurements were performed on individual terminal plates by using atomic force microscopy. It was shown that the geometry of a single terminal plate had a higher border and considerably lower centre. Local adhesion was approximately twice as strong in the centre of the plate as on its border. Adhesion of fly footprints on a glass surface, recorded within 20 min after preparation, was similar to adhesion in the centre of a single attachment pad. Adhesion strongly decreased with decreasing volume of footprint fluid, indicating that the layer of pad secretion covering the terminal plates is crucial for the generation of a strong attractive force. Our data provide the first direct evidence that, in addition to Van der Waals and Coulomb forces, attractive capillary forces, mediated by pad secretion, are a critical factor in the fly's attachment mechanism.
Exploration types of ectomycorrhizae

Venue: Mycorrhiza

There is a need to quantify and qualify the ability of ectomycorrhizae to improve tree growth and nutrition and, in particular, to define criteria to classify ectomycorrhizae with respect to ecologically relevant features. Whereas the numbers of ectomycorrhizae and morphotypes give useful information when related to root biomass, root length or soil volume, the development and differentiation of the extramatrical mycelium may represent important predicative features relevant to the ecological classification of ectomycorrhizae. Here, different exploration types of ectomycorrhizae are distinguished based on the amount of emanating hyphae or the presence and differentiation of rhizomorphs. Their putative ecological importance is discussed.
Pointillist structural color in Pollia fruit
Venue: Proceedings of the National Academy of Sciences of the United States of America

Biological communication by means of structural color has existed for at least 500 million years. Structural color is commonly observed in the animal kingdom, but has been little studied in plants. We present a striking example of multilayer-based strong iridescent coloration in plants, in the fruit of Pollia condensata. The color is caused by Bragg reflection of helicoidally stacked cellulose microfibrils that form multilayers in the cell walls of the epicarp. We demonstrate that animals and plants have convergently evolved multilayer-based photonic structures to generate colors using entirely distinct materials. The bright blue coloration of this fruit is more intense than that of any previously described biological material. Uniquely in nature, the reflected color differs from cell to cell, as the layer thicknesses in the multilayer stack vary, giving the fruit a striking pixelated or pointillist appearance. Because the multilayers form with both helicoidicities, optical characterization reveals that the reflected light from every epidermal cell is polarized circularly either to the left or to the right, a feature that has never previously been observed in a single tissue.
The acacia ants revisited: convergent evolution and biogeographic context in an iconic ant/plant mutualism
Venue: Proceedings of The Royal Society B: Biological Sciences

Phylogenetic and biogeographic analyses can enhance our understanding of multispecies interactions by placing the origin and evolution of such interactions in a temporal and geographical context. We use a phylogenomic approach—ultraconserved element sequence capture—to investigate the evolutionary history of an iconic multispecies mutualism: Neotropical acacia ants (Pseudomyrmex ferrugineus group) and their associated Vachellia hostplants. In this system, the ants receive shelter and food from the host plant, and they aggressively defend the plant against herbivores and competing plants. We confirm the existence of two separate lineages of obligate acacia ants that convergently occupied Vachellia and evolved plant-protecting behaviour, from timid ancestors inhabiting dead twigs in rainforest. The more diverse of the two clades is inferred to have arisen in the Late Miocene in northern Mesoamerica, and subsequently expanded its range throughout much of Central America. The other lineage is estimated to have originated in southern Mesoamerica about 3 Myr later, apparently piggy-backing on the pre-existing mutualism. Initiation of the Pseudomyrmex/Vachellia interaction involved a shift in the ants from closed to open habitats, into an environment with more intense plant herbivory. Comparative studies of the two lineages of mutualists should provide insight into the essential features binding this mutualism.
The behavior in flow of the morphologically variable seaweed Hedophyllum sessile (C. Ag.) Setchell
Venue: Hydrobiologia

Drag force was measured on individual specimens of Hedophyllum sessile in a variable-speed flow tank. Those from sheltered localities, which are broad, bullate blades, experience greater drag at a given water velocity than ones from localities more exposed to the action of waves, which have smooth, deeply dissected blades. All specimens rearranged their blades as water velocity increased, resulting in a decrease in effective drag at higher water speeds, but individuals with smooth, dissected blades assumed a more compact shape at high current speeds and thus reduced their effective drag over that of broad-bladed individuals at the same speed. In habitats chronically exposed to strong wave action, drag reduction may be an important survival mechanism; in calm habitats the turbulence induced by lack of such streamlining may enhance mixing of the water in the immediate vicinity of a plant.