nils-herrmann/clean_scirepeval huggingface dataset:
Arsenic Hyperaccumulator Fern Pteris vittata: Utilities for Arsenic Phytoremediation and Plant Biotechnology
Venue: Reviews in Environmental Science and Bio\/technology

Arsenic is a toxic metalloid that is widespread in the environment due to both man-made and natural causes. Soils, food, and ground water contaminated with arsenic pose serious health risks to millions of people in different parts of the World. While engineering methods to remediate arsenic-contaminated environments are available, they are often prohibitively expensive and cumbersome. It was discovered about a decade ago that the Chinese brake fern (Pteris vittata) had an extraordinary ability to tolerate and hyperaccumulate arsenic, up to about 2% of dry weight in its fronds. This opened up new opportunities to develop the brake fern for a cost-effective green technology to remediate arsenic-contaminated environments. The objective of this review is to highlight some of the salient findings on this and related ferns regarding their arsenic tolerance and hyperaccumulation traits. Investigations have shown that arsenic hyperaccumulation in brake fern has evolved as a defense against herbivory. Research employing molecular biology tools have identified some of the key genes and proteins important for arsenic metabolism in this species including genes for arsenic-induced oxidative stress. Comparative biochemistry of how organisms adapt to arsenic suggests that many other fern genes related to arsenic transport and metabolism are yet to be characterized in this fern. Our research indicates that brake fern could be a source of genes that could inform us about how plants adapt to abiotic stress factors such as high temperature stress and drought that have oxidative stress as a component. Some of these genes can be expected to be valuable for improving crops for increased tolerance to stress.
An Intertidal Sea Star Adjusts Thermal Inertia to Avoid Extreme Body Temperatures
Venue: The American Naturalist

The body temperature of ectotherms is influenced by the interaction of abiotic conditions, morphology, and behavior. Although organisms living in different thermal habitats may exhibit morphological plasticity or move from unfavorable locations, there are few examples of animals adjusting their thermal properties in response to short‐term changes in local conditions. Here, we show that the intertidal sea star Pisaster ochraceus modulates its thermal inertia in response to prior thermal exposure. After exposure to high body temperature at low tide, sea stars increase the amount of colder‐than‐air fluid in their coelomic cavity when submerged during high tide, resulting in a lower body temperature during the subsequent low tide. Moreover, this buffering capacity is more effective when seawater is cold during the previous high tide. This ability to modify the volume of coelomic fluid provides sea stars with a novel thermoregulatory “backup” when faced with prolonged exposure to elevated aerial temperatures.
Investigation of microstructure, natural frequencies and vibration modes of dragonfly wing
Venue: Journal of Bionic Engineering

In the present work, a thorough investigation on the microstructural and morphological aspects of dragonfly wings was carried out using scanning electron microscope. Then, based on this study and the previous reports, a precise three-dimensional numerical model was developed and natural frequencies and vibration modes of dragonfly forewing were determined by finite element method. The results shown that dragonfly wings are made of a series of adaptive materials, which form a very complex composite structure. This bio-composite fabrication has some unique features and potential benefits. Furthermore, the numerical results show that the first natural frequency of dragonfly wings is about 168 Hz and bending is the predominant deformation mode in this stage. The accuracy of the present analysis is verified by comparison of calculated results with experimental data. This paper may be helpful for micro aerial vehicle design concerning dynamic response.
DISSECTING INSECT FLIGHT
Venue: Annual Review of Fluid Mechanics

▪ Abstract “What force does an insect wing generate?” Finding answers to this enduring question is an essential step toward our understanding of interactions of moving objects with fluids that enable most living species such as insects, birds, and fish to travel efficiently and us to follow similar suit with sails, oars, and airfoils. We give a brief history of research in insect flight and discuss recent findings in unsteady aerodynamics of flapping flight at intermediate range Reynolds numbers (10–104). In particular, we examine the unsteady mechanisms in uniform and accelerated motions, forward and hovering flight, as well as passive flight of free-falling objects. The results obtained by “taking the insects apart” helped us to resolve previous puzzles about the force estimates in hovering insects, to ellucidate basic mechanisms essential to flapping flight, and to gain insights about the efficieny of flight.
A three-dimensional study of sub-foliar condensation in desert rhubarb (Rheum palaestinum, Polygonaceae)
Venue: Plant Ecology and Evolution

The rare perennial plant species Rheum palaestinum Feinbr. (Polygonaceae), commonly known as desert rhubarb, is endemic to Jordan and southern Israel and grows in areas with low annual rainfall (Al-Eisawi 1998). It has an underground woody stem and grows mostly in shallow ravines of stonysandy terrains during the winter and early spring in years with above-normal precipitation. It produces one to four rounded leaves, 20–60 cm in diameter, with a wrinkled surface (fig. 1). The large leaf size of this species is atypical within arid ecosystems; in the presence of abundant sun, small leaf size is considered as one of the most common patterns of desert plants to decrease transpiration rates and increase water-use efficiency (Gibson 1996). The annual precipitation in Jordan’s desert is less than 75 mm, and January is the wettest month (Tarawneh & Kadıoğlu 2002). A preliminary study of the relationship between precipitation patterns and leaf growth suggested complex and under-studied water-absorption strategies for plants growing in arid environments. Our personal observations showed some unique morphologies and timing patterns that perennial plants in the tableland desert of Jordan have developed as survival strategies. A previous study showed that the large size and surface morphology of rhubarb leaves help to create a self-irrigation system and increase rainwater harvesting by 16-fold compared to other desert plants (Lev-Yadun et al. 2008). A simple leaf morphology can effectively drain rainwater without the need for wrinkles that dramatically increase leaf transpiration area, as has been shown for the lotus leaf (Barthlott & Neinhuis 1996). The leaf morphology of rhubarb may not play a crucial role in water collection, as rainfall is limited during its maximum growth period (March–April). Additionally, the leaves are tightly attached to the ground and the margins are bent downward to contact the soil; these morphological features favour the function of a vapour-trapping system under the leaf rather than water drainage on the upper surface. Rainwater collection is related to the leaf horizontal catchment area and not to the surface area maximized by the wrinkles. Because the water absorption rate needs to be higher than the transpiration rate, rhubarb leaf wrinkles increase the leaf surface area relative to the leaf footprint and
Three-dimensional structures of avidin and the avidin-biotin complex.
Venue: Proceedings of the National Academy of Sciences of the United States of America

The crystal structures of a deglycosylated form of the egg-white glycoprotein avidin and of its complex with biotin have been determined to 2.6 and 3.0 A, respectively. The structures reveal the amino acid residues critical for stabilization of the tetrameric assembly and for the exceptionally tight binding of biotin. Each monomer is an eight-stranded antiparallel beta-barrel, remarkably similar to that of the genetically distinct bacterial analog streptavidin. As in streptavidin, binding of biotin involves a highly stabilized network of polar and hydrophobic interactions. There are, however, some differences. The presence of additional hydrophobic and hydrophilic groups in the binding site of avidin (which are missing in streptavidin) may account for its higher affinity constant. Two amino acid substitutions are proposed to be responsible for its susceptibility to denaturation relative to streptavidin. Unexpectedly, a residual N-acetylglucosamine moiety was detected in the deglycosylated avidin monomer by difference Fourier synthesis.
Elastic energy storage in the mantis shrimp's fast predatory strike
Venue: The Journal of Experimental Biology

Storage of elastic energy is key to increasing the power output of many biological systems. Mantis shrimp (Stomatopoda) must store considerable elastic energy prior to their rapid raptorial strikes; however, little is known about the dynamics and location of elastic energy storage structures in this system. We used computed tomography (CT) to visualize the mineralization patterns in Gonodactylaceus falcatus and high speed videography of Odontodactylus scyllarus to observe the dynamics of spring loading. Using a materials testing apparatus, we measured the force and work required to contract the elastic structures in G. falcatus. There was a positive linear correlation between contraction force and contraction distance; alternative model tests further supported the use of a linear model. Therefore, we modeled the system as a Hookean spring. The force required to fully compress the spring was positively correlated with body mass and appendage size, but the spring constant did not scale with body size, suggesting a possible role of muscle constraints in the scaling of this system. One hypothesized elastic storage structure, the saddle, only contributed approximately 11% of the total measured force, thus suggesting that primary site of elastic energy storage is in the mineralized ventral bars found in the merus segment of the raptorial appendages. Furthermore, the intact system exhibited 81% resilience and severing the saddle resulted in a non-significant reduction to 77% resilience. The remarkable shapes and mineralization patterns that characterize the mantis shrimp's raptorial appendage further reveal a highly integrated mechanical power amplification system based on exoskeletal elastic energy storage.
An experimental test of the contributions and condition dependence of microstructure and carotenoids in yellow plumage coloration
Venue: Proceedings of The Royal Society B: Biological Sciences

A combination of structural and pigmentary components is responsible for many of the colour displays of animals. Despite the ubiquity of this type of coloration, neither the relative contribution of structures and pigments to variation in such colour displays nor the relative effects of extrinsic factors on the structural and pigment-based components of such colour has been determined. Understanding the sources of colour variation is important because structures and pigments may convey different information to conspecifics. In an experiment on captive American goldfinches Carduelis tristis, we manipulated two parameters, carotenoid availability and food availability, known to affect the expression of carotenoid pigments in a full-factorial design. Yellow feathers from these birds were then analysed in two ways. First, we used full-spectrum spectrometry and high-performance liquid chromatography to examine the extent to which variation in white structural colour and total carotenoid content was associated with variation in colour properties of feathers. The carotenoid content of yellow feathers predicted two colour parameters (principal component 1—representing high values of ultraviolet and yellow chroma and low values of violet–blue chroma—and hue). Two different colour parameters (violet–blue and yellow chroma) from white de-pigmented feathers, as well as carotenoid content, predicted reflectance measurements from yellow feathers. Second, we determined the relative effects of our experimental manipulations on white structural colour and yellow colour. Carotenoid availability directly affected yellow colour, while food availability affected it only in combination with carotenoid availability. None of our manipulations had significant effects on the expression of white structural colour. Our results suggest that the contribution of microstructures to variation in the expression of yellow coloration is less than the contribution of carotenoid content, and that carotenoid deposition is more dependent on extrinsic variability than is the production of white structural colour.
Numerical simulation of electroosmotic flow near earthworm surface
Venue: Journal of Bionic Engineering

The electroosmotic flow near an earthworm surface is simulated numerically to further understand the anti soil adhesion mechanism of earthworm. A lattice Poisson method is employed to solve electric potential and charge distributions in the electric double layer along the earthworm surface. The external electric field is obtained by solving a Laplace equation. The electroosmotic flow controlled by the Navier-Stokes equations with external body force is simulated by the lattice Boltzmann method. A benchmark test shows that accurate electric potential distributions can be obtained by the LPM. The simulation shows that the moving vortices, which probably contribute to anti soil adhesion, are formed near earthworm body surface by the nonuniform and variational electrical force.
Mutations perturbing petal cell shape and anthocyanin synthesis influence bumblebee perception of Antirrhinum majus flower colour
Venue: Arthropod-plant Interactions

We wished to understand the effects on pollinator behaviour of single mutations in plant genes controlling flower appearance. To this end, we analysed snapdragon flowers (Antirrhinum majus), including the mixta and nivea mutants, in controlled laboratory conditions using psychophysical tests with bumblebees. The MIXTA locus controls petal epidermal cell shape, and thus the path that incident light takes within the pigment-containing cells. The effect is that mixta mutant flowers are pink in comparison to the wild type purple flowers, and mutants lack the sparkling sheen of wild type flowers that is clearly visible to human observers. Despite their fundamentally different appearance to humans, and even though bees could discriminate the flowers, inexperienced bees exhibited no preference for either type, and the flowers did not differ in their detectability in a Y-maze—either when the flowers appeared in front of a homogeneous or a dappled background. Equally counterintuitive effects were found for the non-pigmented, UV reflecting nivea mutant: even though the overall reflectance intensity and UV signal of nivea flowers is several times that of wild type flowers, their detectability was significantly reduced relative to wild type flowers. In addition, naïve foragers preferred wild type flowers over nivea mutants, even though these generated a stronger signal in all receptor types. Our results show that single mutations affecting flower signal can have profound effects on pollinator behaviour—but not in ways predictable by crude assessments via human perception, nor simple quantification of UV signals. However, current models of bee visual perception predict the observed effects very well.
Birch (Betula spp.) leaves adsorb and re-release volatiles specific to neighbouring plants--a mechanism for associational herbivore resistance?
Venue: New Phytologist

Plant-emitted semi-volatile compounds have low vaporization rates at 20-25 degrees C and may therefore persist on surfaces such as plant foliage. The passive adsorption of arthropod-repellent semi-volatiles to neighbouring foliage could convey associational resistance, whereby a plant's neighbours reduce damage caused by herbivores. We found that birch (Betula spp.) leaves adsorb and re-release the specific arthropod-repelling C(15) semi-volatiles ledene, ledol and palustrol produced by Rhododendron tomentosum when grown in mixed association in a field setup. In a natural habitat, a higher concentration of ledene was released from birches neighbouring R. tomentosum than from birches situated > 5 m from R. tomentosum. Emission of alpha-humulene, a sesquiterpene synthesized by both Betula pendula and R. tomentosum, was also increased in R. tomentosum-neighbouring B. pendula. In assessments for associational resistance, we found that the polyphagous green leaf weevils (Polydrusus flavipes) and autumnal moth (Epirrita autumnata) larvae both preferred B. pendula to R. tomentosum. P. flavipes also preferred birch leaves not exposed to R. tomentosum to leaves from mixed associations. In the field, a reduction in Euceraphis betulae aphid density occurred in mixed associations. Our results suggest that plant/tree species may be protected by semi-volatile compounds emitted by a more herbivore-resistant heterospecific neighbour.
Nitrogen retention in wetlands, lakes and rivers
Venue: Hydrobiologia

As human activities continue to alter the global nitrogen cycle, the ability to predict the impact of increased nitrogen loading to freshwater systems is becoming more and more important. Nitrogen retention is of particular interest because it is through its combined processes (denitrification, nitrogen sedimentation and uptake by aquatic plants) that local and downstream nitrogen concentrations are reduced. Here, we compare the magnitude of nitrogen retention and its components in wetlands, lakes and rivers. We show that wetlands retain the highest proportion of total nitrogen loading, followed by lakes and then rivers. The differences in the proportion of N retained among systems is explained almost entirely by differences in water discharge. Denitrification is the primary mechanism of nitrogen retention, followed by nitrogen sedimentation and uptake by aquatic plants.
Genetic evidence for natural product-mediated plant-plant allelopathy in rice (Oryza sativa).
Venue: New Phytologist

There is controversy as to whether specific natural products play a role in directly mediating antagonistic plant-plant interactions - that is, allelopathy. If proved to exist, such phenomena would hold considerable promise for agronomic improvement of staple food crops such as rice (Oryza sativa). • However, while substantiated by the presence of phytotoxic compounds at potentially relevant concentrations, demonstrating a direct role for specific natural products in allelopathy has been difficult because of the chemical complexity of root and plant litter exudates. This complexity can be bypassed via selective genetic manipulation to ablate production of putative allelopathic compounds, but such an approach previously has not been applied. • The rice diterpenoid momilactones provide an example of natural products for which correlative biochemical evidence has been obtained for a role in allelopathy. Here, we apply reverse genetics, using knock-outs of the relevant diterpene synthases (copalyl diphosphate synthase 4 (OsCPS4) and kaurene synthase-like 4 (OsKSL4)), to demonstrate that rice momilactones are involved in allelopathy, including suppressing growth of the widespread rice paddy weed, barnyard grass (Echinochloa crus-galli). • Thus, our results not only provide novel genetic evidence for natural product-mediated allelopathy, but also furnish a molecular target for breeding and metabolic engineering of this important crop plant.
Can the ecosystem mimic hypotheses be applied to farms in African savannahs?
Venue: Agroforestry Systems

The first ecosystem mimic hypothesis suggests clear advantages if man-made land use systems do not deviate greatly in their resource use patterns from natural ecosystems typical of a given climatic zone. The second hypothesis claims that additional advantages will accrue if agroecosystems also maintain a substantial part of the diversity of natural systems. We test these hypotheses for the savannah zone of sub-Saharan Africa, with its low soil fertility and variable rainfall. Where annual food crops replace the natural grass understorey of savannah systems, water use will decrease and stream and groundwater flow change, unless tree density increases relative to the natural situation. Increasing tree density, however, will decrease crop yields, unless the trees meet specific criteria. Food crop production in the parkland systems may benefit from lower temperatures under tree canopies, but water use by trees providing this shade will prevent crops from benefiting. In old parkland trees that farmers have traditionally retained when opening fields for crops, water use per unit shade is less than in most fast growing trees introduced for agroforestry trials. Strong competition between plants adapted to years with different rainfall patterns may stabilise total system productivity -- but this will be appreciated by a farmer only if the components are of comparable value. The best precondition for farmers to maintain diversity in their agroecosystem hinges on the availability of a broad basket of choices, without clear winners or 'best bets'.
Evolution of the Mechanisms Underlying Insect Respiratory Gas Exchange
Venue: Advances in Insect Physiology

Many factors influence gas exchange patterns in insects and are generally treated in isolation from one another. Here, we provide a review of the current state of knowledge on the physics of gas exchange, insect respiratory chemoreceptors, the diversity and the methods typically used in the characterisation of respiratory pattern types, briefly covering some of the new tools and techniques that are being incorporated into this field. We then discuss the functional significance of insect gas exchange pattern variation, and possible evolutionary explanations of discontinuous gas exchange as a derived control mechanism for effecting physiological change in the context of (a) adaptive hypotheses, (b) non-adaptive hypotheses and (c) mathematical modelling of gas exchange. The lack of consensus in the literature for all proposed adaptive or mechanistic hypotheses suggests that multiple factors influence which gas exchange pattern is displayed by any particular insect during a given experiment. Thus, while the primary function of a breathing pattern is to meet an animal's gas exchange requirements, it is an interacting hierarchy of constraints that most likely determines how this demand may be met. We conclude the review with a brief discussion of future directions for the field.
A Biological Solution to a Fundamental Distributed Computing Problem
Venue: Science

Modeling of development in the fruit fly yields an algorithm useful in designing wireless communication networks. Computational and biological systems are often distributed so that processors (cells) jointly solve a task, without any of them receiving all inputs or observing all outputs. Maximal independent set (MIS) selection is a fundamental distributed computing procedure that seeks to elect a set of local leaders in a network. A variant of this problem is solved during the development of the fly’s nervous system, when sensory organ precursor (SOP) cells are chosen. By studying SOP selection, we derived a fast algorithm for MIS selection that combines two attractive features. First, processors do not need to know their degree; second, it has an optimal message complexity while only using one-bit messages. Our findings suggest that simple and efficient algorithms can be developed on the basis of biologically derived insights.