nils-herrmann/clean_scirepeval huggingface dataset:
Huddling behavior in emperor penguins: Dynamics of huddling
Venue: Physiology & Behavior

Although huddling was shown to be the key by which emperor penguins (Aptenodytes forsteri) save energy and sustain their breeding fast during the Antarctic winter, the intricacies of this social behavior have been poorly studied. We recorded abiotic variables with data loggers glued to the feathers of eight individually marked emperor penguins to investigate their thermoregulatory behavior and to estimate their "huddling time budget" throughout the breeding season (pairing and incubation period). Contrary to the classic view, huddling episodes were discontinuous and of short and variable duration, lasting 1.6+/-1.7 (S.D.) h on average. Despite heterogeneous huddling groups, birds had equal access to the warmth of the huddles. Throughout the breeding season, males huddled for 38+/-18% (S.D.) of their time, which raised the ambient temperature that birds were exposed to above 0 degrees C (at average external temperatures of -17 degrees C). As a consequence of tight huddles, ambient temperatures were above 20 degrees C during 13+/-12% (S.D.) of their huddling time. Ambient temperatures increased up to 37.5 degrees C, close to birds' body temperature. This complex social behavior therefore enables all breeders to get a regular and equal access to an environment which allows them to save energy and successfully incubate their eggs during the Antarctic winter.
Neurology: An ancient sensory organ in crocodilians
Venue: Nature

Crocodilians hunt at night, waiting half-submerged for land-bound prey to disturb the water surface. Here I show that crocodilians have specialized sensory organs on their faces that can detect small disruptions in the surface of the surrounding water, and which are linked to a dedicated, hypertrophied nerve system. Such 'dome' pressure receptors are also evident in fossils from the Jurassic period, indicating that these semi-aquatic predators solved the problem of combining armour with tactile sensitivity many millions of years ago.
Evolution of the dragonfly head-arresting system
Venue: Proceedings of The Royal Society B: Biological Sciences

The arrester or fixation system of the head in adult Odonata is unique among arthropods. This system involves the organs of two body segments: the head and the neck. It consists of a skeleton–muscle apparatus that sets the arrester parts in motion. The parts comprise formations covered with complicated microstructures: fields of microtrichia on the rear surface of the head and post–cervical sclerites of the neck. The arrester immobilizes the head during feeding or when the dragonfly is in tandem flight. Thus, it may serve as an adaptation to save the head from violent mechanical disturbance and to stabilize gaze in a variety of behavioural situations. This study shows the evolutionary trend of the arrester in the order Odonata by using scanning electron microscopy and measurements of arrester structures in 227 species from 26 odonate families. The arrester design occurring in the Epiophlebiidae, Gomphidae, Neopetaliidae, Petaluridae and Chlorogomphinae is suggested to be the basic one. Two convergent pathways of head–arrester evolution among Zygoptera and Anisoptera are proposed. The possible functional significance of the arrester system is discussed.
Membrane Thickness Cue for Cold Sensing in a Bacterium
Venue: Current Biology

Thermosensors are ubiquitous integral membrane proteins found in all kinds of life. They are involved in many physiological roles, including membrane remodeling, chemotaxis, touch, and pain [1-3], but, the mechanism by which their transmembrane (TM) domains transmit temperature signals is largely unknown. The histidine kinase DesK from Bacillus subtilis is the paradigmatic example of a membrane-bound thermosensor suited to remodel membrane fluidity when the temperature drops below approximately 30°C [1, 4] providing, thus, a tractable system for investigating the mechanism of TM-mediated input-output control of thermal adaptation. Here we show that the multimembrane-spanning domain from DesK can be simplified into a chimerical single-membrane-spanning minimal sensor (MS) that fully retains, in vivo and in vitro, the sensing properties of the parental system. The MS N terminus contains three hydrophilic amino acids near the lipid-water interface creating an instability hot spot. Mutational analysis of this boundary-sensitive beacon revealed that membrane thickness controls the signaling state of the sensor by dictating the hydration level of the metastable hydrophilic spot. Guided by these results we biochemically demonstrated that the MS signal transmission activity is sensitive to bilayer thickness. Membrane thickness could be a general cue for sensing temperature in many organisms.
Strong ultralight foams based on nanocrystalline cellulose for high-performance insulation.
Venue: Carbohydrate Polymers

Environmentally friendly, sustainable, and high-performance thermal insulators are in high demand. Petroleum-based insulator foams usually have high thermal conductivity and pose health hazards. Here, we report ultralight composite foams that are highly strong, elastic, and super-insulating. The foams are composed of nanocrystalline cellulose (NCC) (74 wt%), polyvinyl alcohol (7.5 wt%), and a crosslinking agent (18.5 wt%). The fabrication process is simple and uses only water. The composite foams exhibit an elastic strain of ˜13% at a modulus of 250 K Pa and a stress of 73 K Pa at 50% strain (100+ and 18 times, respectively, higher than those of pure NCC foam); both exceed the values of reported nanocellulose-based foams with no reinforcement. The foams exhibit a thermal conductivity of 0.027 Wm-1 K-1, which is superior to those of traditional insulating materials. The structural integrity is also preserved after burning. Our results show that NCC-based materials can be engineered towards high-performance insulation applications.
Characterization of the nanocomposite laminate structure occurring in fish scales from Arapaima Gigas
Venue: Materials Science and Engineering: C

In the present paper, the nanocomposite laminate structure of scales from the Amazonian fish Arapaima Gigas is investigated. The structure and composition of the scales were assessed by means of X-ray diffraction (XRD) and Fourier Transform Infrared spectroscopy (FTIR). The theory of Fickian diffusion is used and discussed in order to rationalize the water absorption and desorption behavior of the scales. Morphology studies and fracture analysis of the native scales were carried out using Transmission Electron Microscopy (TEM), Light Optical Microscopy (LOM) and Scanning Electron Microscopy (SEM). A fibrous layer of collagen and a plywood-like structure were observed. In order to study the mineral phase, the native scales were burned at 600 °C until all the organic components were degraded. The remaining ashes were then observed under the microscope and weighed to determine ratio of organic and inorganic components. The mechanical behavior of dry and wet scales was assessed by tensile tests and the effect of water in mechanical properties is also discussed.
From eye spots to eye shine
Venue: British Journal of Ophthalmology

In the marginalia of Darwin's On the Origin of Species , the author's spouse wondered if, indeed, an eye could possibly “evolve” since it is so complex. Others, more recently, have asked the same question. Fortunately, similar doubt did not afflict Darwin. A review of the evolutionary evidence reveals ample evidence that eyes can and do evolve. For example, there are creatures that have multiple and very specific eyes, suggesting that eyes are not only rather easy to evolve, but, in some creatures, ocular evolution can be quite rapid.

The process of organism photoreception probably started shortly after life began on this planet, stimulated by the sun. Ocular evolution responded to the sun's energy by producing phototaxis leading to crude eye spots, then ascending to the complex and elegant ocular structure of certain birds having two foveae and asymmetric lenses for precise focusing. Fantastic adaptations, often beyond imagination, have occurred and are with us today, including irregularly shaped eyes and special photopigments to view ultraviolet, infrared, and bioluminescence. The extension of the interpretation of electromagnetic waves into realms we cannot understand must create a fantastic panoply of colours and stimulations. And, yet, as ophthalmologists, we rarely consider that any visual system is significantly better than or even that different from our own. This is folly for many species have evolved spectacular and stunning adaptations to the visual imperatives of their world.

The crepuscular aerial drama of a swallow on the wing hunting for a small erratic insect illustrates the profoundly complex visual processing necessary to provide identification, tracking, pursuit, and eventual capture in a dimly lit and almost clueless three dimensional environment. Yet, a swallow does this hundreds of times a day. Similarly, a bathypelagic piscine predator, living at a depth of 1500 metres, must face staggering problems merely identifying …
Ants recognize foes and not friends
Venue: Proceedings of The Royal Society B: Biological Sciences

Discriminating among individuals and rejecting non-group members is essential for the evolution and stability of animal societies. Ants are good models for studying recognition mechanisms, because they are typically very efficient in discriminating ‘friends’ (nest-mates) from ‘foes’ (non-nest-mates). Recognition in ants involves multicomponent cues encoded in cuticular hydrocarbon profiles. Here, we tested whether workers of the carpenter ant Camponotus herculeanus use the presence and/or absence of cuticular hydrocarbons to discriminate between nest-mates and non-nest-mates. We supplemented the cuticular profile with synthetic hydrocarbons mixed to liquid food and then assessed behavioural responses using two different bioassays. Our results show that (i) the presence, but not the absence, of an additional hydrocarbon elicited aggression and that (ii) among the three classes of hydrocarbons tested (unbranched, mono-methylated and dimethylated alkanes; for mono-methylated alkanes, we present a new synthetic pathway), only the dimethylated alkane was effective in eliciting aggression. Our results suggest that carpenter ants use a fundamentally different mechanism for nest-mate recognition than previously thought. They do not specifically recognize nest-mates, but rather recognize and reject non-nest-mates bearing odour cues that are novel to their own colony cuticular hydrocarbon profile. This begs for a reappraisal of the mechanisms underlying recognition systems in social insects.
Pollen Cell Wall Patterns Form from Modulated Phases
Venue: Cell

The ornately geometric walls of pollen grains have inspired scientists for decades. We show that the evolved diversity of these patterns is entirely recapitulated by a biophysical model in which an initially uniform polysaccharide layer in the extracellular space, mechanically coupled to the cell membrane, phase separates to a spatially modulated state. Experiments reveal this process occurring in living cells. We observe that in ∼10% of extant species, this phase separation reaches equilibrium during development such that individual pollen grains are identical and perfectly reproducible. About 90% of species undergo an arrest of this process prior to equilibrium such that individual grains are similar but inexact copies. Equilibrium patterns have appeared multiple times during the evolution of seed plants, but selection does not favor these states. This framework for pattern development provides a route to rationalizing the surface textures of other secreted structures, such as cell walls and insect cuticle.
Bacterial rhodopsin: evidence for a new type of phototrophy in the sea.
Venue: Science

Extremely halophilic archaea contain retinal-binding integral membrane proteins called bacteriorhodopsins that function as light-driven proton pumps. So far, bacteriorhodopsins capable of generating a chemiosmotic membrane potential in response to light have been demonstrated only in halophilic archaea. We describe here a type of rhodopsin derived from bacteria that was discovered through genomic analyses of naturally occuring marine bacterioplankton. The bacterial rhodopsin was encoded in the genome of an uncultivated gamma-proteobacterium and shared highest amino acid sequence similarity with archaeal rhodopsins. The protein was functionally expressed in Escherichia coli and bound retinal to form an active, light-driven proton pump. The new rhodopsin exhibited a photochemical reaction cycle with intermediates and kinetics characteristic of archaeal proton-pumping rhodopsins. Our results demonstrate that archaeal-like rhodopsins are broadly distributed among different taxa, including members of the domain Bacteria. Our data also indicate that a previously unsuspected mode of bacterially mediated light-driven energy generation may commonly occur in oceanic surface waters worldwide.
Regional and global concerns over wetlands and water quality.
Venue: Trends in Ecology and Evolution

Water quality in many stream catchments and river basins is severely impacted by nutrient enrichment as a result of agriculture. Water-resource managers worldwide are considering the potential role of riparian zones and floodplain wetlands in improving stream-water quality, as there is evidence at the site scale that such wetlands are efficient at removing nutrients from through-flowing water. However, recent studies have highlighted disadvantages of such use of wetlands, including emissions of greenhouse gases and losses of biodiversity that result from prolonged nutrient loading. Here, we discuss the water purification function of wetlands at the site and catchment scale and suggest ways in which these disadvantages could be overcome.
Sticking ability in Spix's disk-winged bat, Thyroptera tricolor (Microchiroptera: Thyropteridae)
Venue: Canadian Journal of Zoology

Roosting Spix's disk-winged bats, Thyroptera tricolor, use disks on their wrists and ankles to cling to smooth leaves. In 584 trials we tested the ability of 31 T. tricolor and 121 other bats lacking disks (461 trials with 18 species from three families) to adhere to (i) medium-grade sandpaper, (ii) Lexan polycarbonate, (iii) solid sheet aluminum, and (iv) porous sheet aluminum. While T. tricolor readily adhered to smooth surfaces, the other species did not. Thyroptera tricolor did not show the same ability to adhere to rough surfaces as the other species that were tested. As was demonstrated by their performance on porous aluminum and sandpaper, the disks of T. tricolor worked by suction and sometimes by wet adhesion. In the course of adapting to adhere to smooth surfaces, T. tricolor appear to have lost some ability to roost on rough ones, although one adult T. tricolor climbed on a screen covering the inside walls of the polycarbonate cage by interlocking its thumb claws with the surface.
Study of the geometry and folding pattern of leaves of Mimosa pudica
Venue: Journal of Bionic Engineering

Many structural and functional properties possessed by plants have great potentials to stimulate new concepts and innovative ideas in the field of biomimetic engineering. The key inputs from biology can be used for creation of efficient and optimized structures. The study of the geometry and folding pattern of leaves of Mimosa pudica, referred as Sensitive Plant, reveals some of the peculiar characteristics during folding and unfolding. When the leaf is touched, it quickly folds its leaflets and pinnae and droops downward at the petiole attachment. With the help of experiments on simulation model, the variations in angle of leaflets and degree of compaction after folding are investigated.
Biology of Wolbachia.
Venue: Annual Review of Entomology

Wolbachia are a common and widespread group of bacteria found in reproductive tissues of arthropods. These bacteria are transmitted through the cytoplasm of eggs and have evolved various mechanisms for manipulating reproduction of their hosts, including induction of reproductive incompatibility, parthenogenesis, and feminization. Wolbachia are also transmitted horizontally between arthropod species. Significant recent advances have been made in the study of these interesting microorganisms. In this paper, Wolbachia biology is reviewed, including their phylogeny and distribution, mechanisms of action, population biology and evolution, and biological control implications. Potential directions for future research are also discussed.
Bioluminescence in the benthopelagic holothurian Enypniastes eximia
Venue: Journal of the Marine Biological Association of the United Kingdom

Enypniastes eximia (Echinodermata: Holothuroidea) is a prominent member of the benthic boundary layer community in deep Caribbean waters. Like most holothurians it feeds on benthic sediments. Feeding is episodic and after collecting food on the bottom it returns to the water column at altitudes within about 50 m of the sea floor. Direct observations from submersibles and laboratory studies of living specimens have shown how bioluminescence is produced. Light production in E. eximia is triggered mechanically, and is produced by hundreds of granular bodies within the gelatinous integument of the animal. Local stimulation yields a localized response which gradually spreads to the entire surface of the animal. Broad impact yields a whole-body luminescent response. The integument of E. eximia is quite fragile, and strong physical contact readily causes the skin to be sloughed off in a glowing cloud. The degree of luminous response is a function of the severity of contact. In the laboratory the skin of E. eximia , along with its luminescent capability, regenerated rapidly. The anti-predatory role of bioluminescence in this species is apparently a ‘burglar alarm’ strategy. In the dark, near-bottom habitat, physical contact by a predator elicits light production which reveals the presence of the attacker to its own visually-cued predators.
Mechanisms of phagocytosis in macrophages.
Venue: Annual Review of Immunology

Phagocytosis of pathogens by macrophages initiates the innate immune response, which in turn orchestrates the adaptive response. In order to discriminate between infectious agents and self, macrophages have evolved a restricted number of phagocytic receptors, like the mannose receptor, that recognize conserved motifs on pathogens. Pathogens are also phagocytosed by complement receptors after relatively nonspecific opsonization with complement and by Fc receptors after specific opsonization with antibodies. All these receptors induce rearrangements in the actin cytoskeleton that lead to the internalization of the particle. However, important differences in the molecular mechanisms underlying phagocytosis by different receptors are now being appreciated. These include differences in the cytoskeletal elements that mediate ingestion, differences in vacuole maturation, and differences in inflammatory responses. Infectious agents, such as M. tuberculosis, Legionella pneumophila, and Salmonella typhimurium, enter macrophages via heterogeneous pathways and modify vacuolar maturation in a manner that favors their survival. Macrophages also play an important role in the recognition and clearance of apoptotic cells; a notable feature of this process is the absence of an inflammatory response.
Selectivity in biomineralization of barium and strontium.
Venue: Journal of Structural Biology

The desmid green alga Closterium moniliferum belongs to a small number of organisms that form barite (BaSO(4)) or celestite (SrSO(4)) biominerals. The ability to sequester Sr in the presence of an excess of Ca is of considerable interest for the remediation of (90)Sr from the environment and nuclear waste. While most cells dynamically regulate the concentration of the second messenger Ca(2+) in the cytosol and various organelles, transport proteins rarely discriminate strongly between Ca, Sr, and Ba. Herein, we investigate how these ions are trafficked in C. moniliferum and how precipitation of (Ba,Sr)SO(4) crystals occurs in the terminal vacuoles. Towards this goal, we simultaneously visualize intracellular dynamics of multiple elements using X-ray fluorescence microscopy (XFM) of cryo-fixed/freeze-dried samples. We correlate the resulting elemental maps with ultrastructural information gleaned from freeze-fracture cryo-SEM of frozen-hydrated cells and use micro X-ray absorption near edge structure (micro-XANES) to determine sulfur speciation. We find that the kinetics of Sr uptake and efflux depend on external Ca concentrations, and Sr, Ba, and Ca show similar intracellular localization. A highly ion-selective cross-membrane transport step is not evident. Based on elevated levels of sulfate detected in the terminal vacuoles, we propose a "sulfate trap" model, where the presence of dissolved barium leads to preferential precipitation of (Ba,Sr)SO(4) due to its low solubility relative to SrSO(4) and CaSO(4). Engineering the sulfate concentration in the vacuole may thus be the most direct way to increase the Sr sequestered per cell, an important consideration in using desmids for phytoremediation of (90)Sr.
Proposed Carbon Dioxide Concentrating Mechanism in Chlamydomonas reinhardtii
Venue: Eukaryotic Cell

Aquatic photosynthetic microorganisms account for almost 50% of the world's photosynthesis ([19][1]). These organisms face several challenges in acquiring CO2 from the environment. The first challenge is presented by the properties of ribulose bisphosphate carboxylase-oxygenase (Rubisco).
A Comparative Study of Age-Related Hearing Loss in Wild Type and Insulin-Like Growth Factor I Deficient Mice
Venue: Frontiers in Neuroanatomy

Insulin-like growth factor-I (IGF-I) belongs to the family of insulin-related peptides that fulfils a key role during the late development of the nervous system. Human IGF1 mutations cause profound deafness, poor growth and mental retardation. Accordingly, Igf1−/− null mice are dwarfs that have low survival rates, cochlear alterations and severe sensorineural deafness. Presbycusis (age-related hearing loss) is a common disorder associated with aging that causes social and cognitive problems. Aging is also associated with a decrease in circulating IGF-I levels and this reduction has been related to cognitive and brain alterations, although there is no information as yet regarding the relationship between presbycusis and IGF-I biodisponibility. Here we present a longitudinal study of wild type Igf1+/+ and null Igf1−/− mice from 2 to 12 months of age comparing the temporal progression of several parameters: hearing, brain morphology, cochlear cytoarchitecture, insulin-related factors and IGF gene expression and IGF-I serum levels. Complementary invasive and non-invasive techniques were used, including auditory brainstem-evoked response (ABR) recordings and in vivo MRI brain imaging. Igf1−/− null mice presented profound deafness at all the ages studied, without any obvious worsening of hearing parameters with aging. Igf1+/+ wild type mice suffered significant age-related hearing loss, their auditory thresholds and peak I latencies augmenting as they aged, in parallel with a decrease in the circulating levels of IGF-I. Accordingly, there was an age-related spiral ganglion degeneration in wild type mice that was not evident in the Igf1 null mice. However, the Igf1−/− null mice in turn developed a prematurely aged stria vascularis reminiscent of the diabetic strial phenotype. Our data indicate that IGF-I is required for the correct development and maintenance of hearing, supporting the idea that IGF-I-based therapies could contribute to prevent or ameliorate age-related hearing loss.