nils-herrmann/clean_scirepeval huggingface dataset:
Wetting properties of the multiscaled nanostructured polymer and metallic superhydrophobic surfaces.
Venue: Langmuir

A superhydrophobic surface is produced from industrial grade polymer materials. The surface comprises partly disordered triple-scaled arrays of polyvinylidene fluoride (PVDF) globules. An inherently superhydrophobic metallic surface is produced with polymer template. The mathematical model based on the Cassie-Baxter hypothesis of air trapping under a water drop is built, which gives the apparent contact angle on the manifold-scaled interface. The presence of several scales itself is not a sufficient condition of hydrophobicity of inherently wettable surfaces. The geometrical features favoring the increase of the vapor-water interface fraction are necessary for this phenomenon.
Why tree-crop interactions in agroforestry appear at odds with tree-grass interactions in tropical savannahs
Venue: Agroforestry Systems

This paper describes recent research findings on resource sharing between trees and crops in the semiarid tropics and attempts to reconcile this information with current knowledge of the interactions between savannah trees and understorey vegetation by examining agroforestry systems from the perspective of succession. In general, productivity of natural vegetation under savannah trees increases as rainfall decreases, while the opposite occurs in agroforestry. One explanation is that in the savannah, the beneficial effects of microclimatic improvements (e.g. lower temperatures and evaporation losses) are greater in more xeric environments. Mature savannah trees have a high proportion of woody above-ground structure compared to foliage, so that the amount of water 'saved' (largely by reduction in soil evaporation) is greater than water 'lost' through transpiration by trees. By contrast, in agroforestry practices such as alley cropping where tree density is high, any beneficial effects of the trees on microclimate are negated by reductions in soil moisture due to increasing interception losses and tree transpiration. While investment in woody structure can improve the water economy beneath agroforestry trees, it inevitably reduces the growth rate of the trees and thus increases the time required for improved understorey productivity. Therefore, agroforesters prefer trees with more direct and immediate benefits to farmers. The greatest opportunity for simultaneous agroforestry practices is therefore to fill niches within the landscape where resources are currently under-utilised by crops. In this way, agroforestry can mimic the large scale patch dynamics and successional progression of a natural ecosystem.
Bacterial microcompartments
Venue: Microporous and Mesoporous Materials; Annual Review of Microbiology

Bacterial microcompartments (BMCs) are self-assembling organelles that consist of an enzymatic core that is encapsulated by a selectively permeable protein shell. The potential to form BMCs is widespread and found across the kingdom Bacteria. BMCs have crucial roles in carbon dioxide fixation in autotrophs and the catabolism of organic substrates in heterotrophs. They contribute to the metabolic versatility of bacteria, providing a competitive advantage in specific environmental niches. Although BMCs were first visualized more than 60 years ago, it is mainly in the past decade that progress has been made in understanding their metabolic diversity and the structural basis of their assembly and function. This progress has not only heightened our understanding of their role in microbial metabolism but is also beginning to enable their use in a variety of applications in synthetic biology. In this Review, we focus on recent insights into the structure, assembly, diversity and function of BMCs.
Hydrogen and bioenergetics in the Yellowstone geothermal ecosystem.
Venue: Proceedings of the National Academy of Sciences of the United States of America

The geochemical energy budgets for high-temperature microbial ecosystems such as occur at Yellowstone National Park have been unclear. To address the relative contributions of different geochemistries to the energy demands of these ecosystems, we draw together three lines of inference. We studied the phylogenetic compositions of high-temperature (>70 degrees C) communities in Yellowstone hot springs with distinct chemistries, conducted parallel chemical analyses, and carried out thermodynamic modeling. Results of extensive molecular analyses, taken with previous results, show that most microbial biomass in these systems, as reflected by rRNA gene abundance, is comprised of organisms of the kinds that derive energy for primary productivity from the oxidation of molecular hydrogen, H2. The apparent dominance by H2-metabolizing organisms indicates that H2 is the main source of energy for primary production in the Yellowstone high-temperature ecosystem. Hydrogen concentrations in the hot springs were measured and found to range up to >300 nM, consistent with this hypothesis. Thermodynamic modeling with environmental concentrations of potential energy sources also is consistent with the proposed microaerophilic, hydrogen-based energy economy for this geothermal ecosystem, even in the presence of high concentrations of sulfide.
Venom kinematics during prey capture in Conus: the biomechanics of a rapid injection system
Venue: The Journal of Experimental Biology

Cone snails use an extensile, tubular proboscis as a conduit to deliver a potent cocktail of bioactive venom peptides into their prey. Previous studies have focused mainly on understanding the venom's role in prey capture but successful prey capture requires both rapid physiological and biomechanical mechanisms. Conus catus, a fish-hunting species, uses a high-speed hydraulic mechanism to inject its hollow, spear-like radular tooth into prey. We take an integrated approach to investigating the biomechanics of this process by coupling kinematic studies with morphological analyses. Taking advantage of the opaque venom and translucent proboscis of a mollusc-hunting juvenile cone snail, Conus pennaceus, we have determined that a high-speed prey capture mechanism is not unique to cone species that hunt fish prey. Two morphological structures were found to play crucial roles in this process. A constriction of the lumen near the tip of the proboscis, composed of tall epithelial cells densely packed with microfilaments, impedes forward movement of the radular tooth prior to its propulsion. Proximal to the constriction, a muscular sphincter was found to regulate venom flow and pressurization in the proboscis. In C. pennaceus, the rapid appearance and flushing of venom within the proboscis during prey capture suggests a mechanism involving the delivery of a discrete quantity of venom. The interplay between these elements provides a unique and effective biomechanical injection system for the fast-acting cone snail venom peptides.
Metal reduction kinetics in Shewanella
Venue: Bioinformatics

Metal reduction kinetics have been studied in cultures of dissimilatory metal reducing bacteria which include the Shewanella oneidensis strain MR-1. Estimation of system parameters from time-series data faces obstructions in the implementation depending on the choice of the mathematical model that captures the observed dynamics. The modeling of metal reduction is often based on Michaelis-Menten equations. These models are often developed using initial in vitro reaction rates and seldom match with in vivo reduction profiles.



For metal reduction studies, we propose a model that is based on the power law representation that is effectively applied to the kinetics of metal reduction. The method yields reasonable parameter estimates and is illustrated with the analysis of time-series data that describes the dynamics of metal reduction in S.oneidensis strain MR-1. In addition, mixed metal studies involving the reduction of Uranyl (U(VI)) to the relatively insoluble tetravalent form (U(IV)) by S. alga strain (BR-Y) were studied in the presence of environmentally relevant iron hydrous oxides. For mixed metals, parameter estimation and curve fitting are accomplished with a generalized least squares formulation that handles systems of ordinary differential equations and is implemented in Matlab. It consists of an optimization algorithm (Levenberg-Marquardt, LSQCURVEFIT) and a numerical ODE solver. Simulation with the estimated parameters indicates that the model captures the experimental data quite well. The model uses the estimated parameters to predict the reduction rates of metals and mixed metals at varying concentrations.



Supplementary data are available at Bioinformatics online.
Irregular fog as a water source for desert dune beetles
Venue: Oecologia

SummaryThree methods of fog-water uptake have been observed in three tribes of Namib desert dune tenebrionid beetles, Adesmiini, Eurychorini and Zophosini. The methods used correlate with distribution and gross morphology of each species but cut across phylogenetic affinities. Of the three methods described, none involve obvious fine anatomical or physical adaptations of the beetles for fog-water uptake. Rather, the beetles have evolved specific behavioural patterns for drinking water condensed on vegetation, their own dorsum or sand.Use of fog-water necessitates surface activity at times when surface temperatures and wind velocities are not optimal for these diurnal or crepuscular species. Behavioural adaptation has enabled these beetles to use irregular and unpredictable fogs as a moisture source.
Genetic Control of Surface Curvature
Venue: Science

Although curvature of biological surfaces has been considered from mathematical and biophysical perspectives, its molecular and developmental basis is unclear. We have studied the cinmutant of Antirrhinum, which has crinkly rather than flat leaves. Leaves of cin display excess growth in marginal regions, resulting in a gradual introduction of negative curvature during development. This reflects a change in the shape and the progression of a cell-cycle arrest front moving from the leaf tip toward the base. CIN encodes a TCP protein and is expressed downstream of the arrest front. We propose that CIN promotes zero curvature (flatness) by making cells more sensitive to an arrest signal, particularly in marginal regions.
Water balance and osmoregulation in Physadesmia globosa, a diurnal tenebrionid beetle from the Namib desert
Venue: Journal of Insect Physiology

Dehydration (10 days at 26°C) of the Namib tenebrionid beetle Physadesmia globosa resulted in rapid weight loss (approx. 19%), and a substantial decline in haemolymph volume (61%). Although the lipid content decreased significantly during this period, metabolic water production was insufficient to maintain total body water. Rehydration (no food) resulted in increases in body weight and haemolymph volume (sub-normal), and total body water to normality. Haemolymph osmolality, sodium, potassium and chloride concentrations increased during dehydration, but despite a marked decrease in the volume of haemolymph, changes in these parameters were subject to osmoregulatory control. Protein concentrations increased during dehydration and decreased during rehydration. Rapid rehydration (1 h) is well-controlled: while haemolymph volume increased dramatically, haemolymph osmolality, sodium, potassium and chloride were strongly regulated. However, extended rehydration (over 4 days) appears not to be as well managed by Physadesmia, with haemolymph osmolality and sodium concentrations decreasing despite no significant change in haemolymph volume from immediate post-rehydration (1 h) values. The potassium and chloride concentrations, however, appeared to be under stricter control during this period. Drinking (when fog water is available) probably contributes largely to the total water input of Physadesmia, and this together with efficient water conservation must serve to maintain effectively long-term water balance in these insects.
The influence of stochastic behavior on the human threshold of hearing
Venue: Chaos Solitons & Fractals

The inner hair cells in the cochlea perform the crucial task of transforming mechanical sound signals into electrical activity. The cochlear nerve fibers code this information and convey it to the brain for further processing. This study investigates the performance of the system inner hair cell – primary auditory afferent nerve fibers at the physical limit of the mechano-electrical transduction for the human auditory frequency range. The Brownian motion of the hair cell’s receptive organelle, the hair bundle, does not blunt the sensitivity, but in fact enlarges – especially in frequency regions which are most important for the perception of music and speech – via the mechanism of nonlinear stochastic resonance (SR) the dynamical range of the mechano-electrical transduction by at least one order of magnitude. The coding efficiency of small sinusoidal hair bundle deflections shows basic properties of the human hearing threshold curve for pure tones and corresponds to experimental results of noise-induced tuning curves in mechano-receptors in the rat foot. Furthermore, the model explains how altered coding efficiency contributes to pathological changes in the spiking pattern which arise from morphological changes in the hair bundle structure (e.g., in noise-induced sensorineural hearing loss of cochlear origin).
Sensory allometry, foraging task specialization and resource exploitation in honeybees
Venue: Behavioral Ecology and Sociobiology

Insect societies are important models for evolutionary biology and sociobiology. The complexity of some eusocial insect societies appears to arise from self-organized task allocation and group cohesion. One of the best-supported models explaining self-organized task allocation in social insects is the response threshold model, which predicts specialization due to inter-individual variability in sensitivity to task-associated stimuli. The model explains foraging task specialization among honeybee workers, but the factors underlying the differences in individual sensitivity remain elusive. Here, we propose that in honeybees, sensory sensitivity correlates with individual differences in the number of sensory structures, as it does in solitary species. Examining European and Africanized honeybees, we introduce and test the hypothesis that body size and/or sensory allometry is associated with foraging task preferences and resource exploitation. We focus on common morphological measures and on the size and number of structures associated with olfactory sensitivity. We show that the number of olfactory sensilla is greater in pollen and water foragers, which are known to exhibit higher sensory sensitivity, compared to nectar foragers. These differences are independent of the distribution of size within a colony. Our data also suggest that body mass and number of olfactory sensilla correlate with the concentration of nectar gathered by workers, and with the size of pollen loads they carry. We conclude that sensory allometry, but not necessarily body size, is associated with resource exploitation in honeybees and that the differences in number of sensilla may underlie the observed differences in sensitivity between bees specialized on water, pollen and nectar collection.
Ganglion-specific splicing of TRPV1 underlies infrared sensation in vampire bats
Venue: Nature

Vampire bats (Desmodus rotundus) are obligate blood feeders that have evolved specialized systems to suit their sanguinary lifestyle. Chief among such adaptations is the ability to detect infrared radiation as a means of locating hotspots on warm-blooded prey. Among vertebrates, only vampire bats, boas, pythons and pit vipers are capable of detecting infrared radiation. In each case, infrared signals are detected by trigeminal nerve fibres that innervate specialized pit organs on the animal’s face. Thus, vampire bats and snakes have taken thermosensation to the extreme by developing specialized systems for detecting infrared radiation. As such, these creatures provide a window into the molecular and genetic mechanisms underlying evolutionary tuning of thermoreceptors in a species-specific or cell-type-specific manner. Previously, we have shown that snakes co-opt a non-heat-sensitive channel, vertebrate TRPA1 (transient receptor potential cation channel A1), to produce an infrared detector. Here we show that vampire bats tune a channel that is already heat-sensitive, TRPV1, by lowering its thermal activation threshold to about 30 °C. This is achieved through alternative splicing of TRPV1 transcripts to produce a channel with a truncated carboxy-terminal cytoplasmic domain. These splicing events occur exclusively in trigeminal ganglia, and not in dorsal root ganglia, thereby maintaining a role for TRPV1 as a detector of noxious heat in somatic afferents. This reflects a unique organization of the bat Trpv1 gene that we show to be characteristic of Laurasiatheria mammals (cows, dogs and moles), supporting a close phylogenetic relationship with bats. These findings reveal a novel molecular mechanism for physiological tuning of thermosensory nerve fibres.
Propulsive force calculations in swimming frogs I. A momentum–impulse approach
Venue: The Journal of Experimental Biology

Frogs are animals that are capable of locomotion in two physically different media, aquatic and terrestrial. A comparison of the kinematics of swimming frogs in a previous study revealed a difference in propulsive impulse between jumping and swimming. To explore this difference further, we determined the instantaneous forces during propulsion in swimming using an impulse–momentum approach based on DPIV flow data. The force profile obtained was compared with force profiles obtained from drag–thrust equilibrium of the centre of mass and with the force profiles generated during jumping. The new approach to quantifying the instantaneous forces during swimming was tested and proved to be a valid method for determining the external forces on the feet of swimming frogs. On the kinematic profiles of swimming, leg extension precedes propulsion. This means that it is not only the acceleration of water backwards that provides thrust, but also that the deceleration of water flowing towards the frog as a result of recovery accelerates the centre of mass prior to leg extension. The force profile obtained from the impulse–momentum approach exposed an overestimation of drag by 30% in the drag–thrust calculations. This means that the difference in impulse between jumping and swimming in frogs is even larger than previously stated. The difference between the force profiles, apart from a slightly higher peak force during jumping, lies mainly in a difference in shape. During swimming, maximal force is reached early in the extension phase, 20% into it, while during jumping, peak force is attained at 80% of the extension phase. This difference is caused by a difference in inter-limb coordination.
Congruence of epicuticular hydrocarbons and tarsal secretions as a principle in beetles
Venue: Chemoecology

Within beetles, those species that are adapted to life on plants have developed widened tarsi with specialised hairy attachment structures. The capability to adhere to smooth surfaces is based on a liquid film on the surface of these structures, the composition of which is similar to the cuticular lipids. By means of a cluster analysis based on chemical similarities between samples obtained from tarsi or elytra of 35 species using solid phase microextraction, the present study strongly suggests that this chemical congruence is a principle in beetles. This supports the idea of tarsal liquids being part of the cuticular lipid layer and contributes to the understanding of liquid-mediated attachment systems.
Notch Signaling in Osteoblasts
Venue: Science Signaling

Bone remodeling is the result of the coordinated activity of osteoblasts, which form new matrix, and osteoclasts, which resorb bone. Notch proteins are single-pass transmembrane receptors that determine cell fate. Recent gain-of-function and loss-of-function experiments reveal a suppressive effect of Notch in osteoblast and osteoclast differentiation in development and in the postnatal bone, which establishes a role for Notch signaling in bone remodeling.
Structure and dynamics of cross-linked actin networks
Venue: Soft Matter

The actin cytoskeleton, a network of protein-polymers, is responsible for the mechanical stability of cells. This biopolymer network is also crucial for processes that require spatial and temporal variations in the network structure such as cell migration, division and intracellular transport. The cytoskeleton therefore has to combine structural integrity and mechanical stability with the possibility of fast and efficient network reorganization and restructuring. Cells meet this challenge by using proteins to link filamentous actin (F-actin) and construct complex networks. The molecular properties of the cross-linking proteins determine to a large extent the (micro)structure, viscoelastic properties and dynamics of the resulting networks. This review focuses on the structural polymorphism that can be induced by cross-linking proteins in reconstituted F-actin networks and summarizes recent results on how the molecular properties of cross-linking proteins dictate the ensuing viscoelastic properties.
Application of P450s for biosensing: combination of biotechnology and electrochemistry
Venue: Materials Science and Engineering: C

P 450s are heme-containing proteins which catalyze monooxygenation and other reactions in oxidative metabolism of lipophilic compounds. They are promising enzymes for the application of biosensing probes. Biosensing of various compounds is possible when P 450s are immobilized on oxygen electrode or on ion-sensitive field effect transistor (ISFET). Competition assay with other substrate is another biosensing method based on the biochemical assay. Optical biosensor based on a resonance mirror was also reported. Genes in the upstream region of P 450 gene including the promoter is utilized to construct reporter gene system (RGS). The system responds to a trace amount of endocrine-disrupting substance to induce luciferase. Various biosensing methods with P 450s and P 450-related genes will be useful for medical application and ecological application in the near future.
Molecular nanomechanics of nascent bone: fibrillar toughening by mineralization
Venue: Nanotechnology

Mineralized collagen fibrils are highly conserved nanostructural building blocks of bone. By a combination of molecular dynamics simulation and theoretical analysis it is shown that the characteristic nanostructure of mineralized collagen fibrils is vital for its high strength and its ability to sustain large deformation, as is relevant to the physiological role of bone, creating a strong and tough material. An analysis of the molecular mechanisms of protein and mineral phases under large deformation of mineralized collagen fibrils reveals a fibrillar toughening mechanism that leads to a manifold increase of energy dissipation compared to fibrils without mineral phase. This fibrillar toughening mechanism increases the resistance to fracture by forming large local yield regions around crack-like defects, a mechanism that protects the integrity of the entire structure by allowing for localized failure. As a consequence, mineralized collagen fibrils are able to tolerate microcracks of the order of several hundred micrometres in size without causing any macroscopic failure of the tissue, which may be essential to enable bone remodelling. The analysis proves that adding nanoscopic small platelets to collagen fibrils increases their Young's modulus and yield strength as well as their fracture strength. We find that mineralized collagen fibrils have a Young's modulus of 6.23 GPa (versus 4.59 GPa for the collagen fibril), yield at a tensile strain of 6.7% (versus 5% for the collagen fibril) and feature a fracture stress of 0.6 GPa (versus 0.3 GPa for the collagen fibril).