nils-herrmann/clean_scirepeval huggingface dataset:
The anatomy of a crushing bite: The specialised cranial mechanics of a giant extinct kangaroo
Venue: PLOS ONE

The Sthenurinae were a diverse subfamily of short-faced kangaroos that arose in the Miocene and diversified during the Pliocene and Pleistocene. Many species possessed skull morphologies that were relatively structurally reinforced with bone, suggesting that they were adapted to incorporate particularly resistant foods into their diets. However, the functional roles of many unique, robust features of the sthenurine cranium are not yet clearly defined. Here, the finite element method is applied to conduct a comprehensive analysis of unilateral biting along the cheek tooth battery of a well-represented sthenurine, Simosthenurus occidentalis. The results are compared with those of an extant species considered to be of most similar ecology and cranial proportions to this species, the koala (Phascolarctos cinereus). The simulations reveal that the cranium of S. occidentalis could produce and withstand comparatively high forces during unilateral biting. Its greatly expanded zygomatic arches potentially housed enlarged zygomaticomandibularis muscles, shown here to reduce the risk of dislocation of the temporomandibular joint during biting with the rear of a broad, extensive cheek tooth row. This may also be a function of the zygomaticomandibularis in the giant panda (Ailuropoda melanoleuca), another species known to exhibit an enlarged zygomatic arch and hypertrophy of this muscle. Furthermore, the expanded frontal plates of the S. occidentalis cranium form broad arches of bone with the braincase and deepened maxillae that each extend from the anterior tooth rows to their opposing jaw joints. These arches are demonstrated here to be a key feature in resisting high torsional forces during unilateral premolar biting on large, resistant food items. This supports the notion that S. occidentalis fed thick, lignified vegetation directly to the cheek teeth in a similar manner to that described for the giant panda when crushing mature bamboo culms.
Agricultural land use disrupts biodiversity mediation of virus infections in wild plant populations
Venue: New Phytologist

Human alteration of natural habitats may change the processes governing species interactions in wild communities. Wild populations are increasingly impacted by agricultural intensification, yet it is unknown whether this alters biodiversity mediation of disease dynamics. We investigated the association between plant diversity (species richness, diversity) and infection risk (virus richness, prevalence) in populations of Plantago lanceolata in natural landscapes as well as those occurring at the edges of cultivated fields. Altogether, 27 P. lanceolata populations were surveyed for population characteristics and sampled for PCR detection of five recently characterized viruses. We find that plant species richness and diversity correlated negatively with virus infection prevalence. Virus species richness declined with increasing plant diversity and richness in natural populations while in agricultural edge populations species richness was moderately higher, and not associated with plant richness. This difference was not explained by changes in host richness between these two habitats, suggesting potential pathogen spill‐over and increased transmission of viruses across the agro‐ecological interface. Host population connectivity significantly decreased virus infection prevalence. We conclude that human use of landscapes may change the ecological laws by which natural communities are formed with far reaching implications for ecosystem functioning and disease.
Active perception during angiogenesis: filopodia speed up Notch selection of tip cells in silico and in vivo
Venue: Philosophical Transactions of the Royal Society B

How do cells make efficient collective decisions during tissue morphogenesis? Humans and other organisms use feedback between movement and sensing known as ‘sensorimotor coordination’ or ‘active perception’ to inform behaviour, but active perception has not before been investigated at a cellular level within organs. Here we provide the first proof of concept in silico/in vivo study demonstrating that filopodia (actin-rich, dynamic, finger-like cell membrane protrusions) play an unexpected role in speeding up collective endothelial decisions during the time-constrained process of ‘tip cell’ selection during blood vessel formation (angiogenesis). We first validate simulation predictions in vivo with live imaging of zebrafish intersegmental vessel growth. Further simulation studies then indicate the effect is due to the coupled positive feedback between movement and sensing on filopodia conferring a bistable switch-like property to Notch lateral inhibition, ensuring tip selection is a rapid and robust process. We then employ measures from computational neuroscience to assess whether filopodia function as a primitive (basal) form of active perception and find evidence in support. By viewing cell behaviour through the ‘basal cognitive lens' we acquire a fresh perspective on the tip cell selection process, revealing a hidden, yet vital time-keeping role for filopodia. Finally, we discuss a myriad of new and exciting research directions stemming from our conceptual approach to interpreting cell behaviour. This article is part of the theme issue ‘Basal cognition: multicellularity, neurons and the cognitive lens’.
Dragondrop: a novel passive mechanism for aerial righting in the dragonfly
Venue: Proceedings of The Royal Society B: Biological Sciences

Dragonflies perform dramatic aerial manoeuvres when chasing targets but glide for periods during cruising flights. This makes dragonflies a great system to explore the role of passive stabilizing mechanisms that do not compromise manoeuvrability. We challenged dragonflies by dropping them from selected inverted attitudes and collected 6-degrees-of-freedom aerial recovery kinematics via custom motion capture techniques. From these kinematic data, we performed rigid-body inverse dynamics to reconstruct the forces and torques involved in righting behaviour. We found that inverted dragonflies typically recover themselves with the shortest rotation from the initial body inclination. Additionally, they exhibited a strong tendency to pitch-up with their head leading out of the manoeuvre, despite the lower moment of inertia in the roll axis. Surprisingly, anaesthetized dragonflies could also complete aerial righting reliably. Such passive righting disappeared in recently dead dragonflies but could be partially recovered by waxing their wings to the anaesthetised posture. Our kinematics data, inverse dynamics model and wind-tunnel experiments suggest that the dragonfly's long abdomen and wing posture generate a rotational tendency and passive attitude recovery mechanism during falling. This work demonstrates an aerodynamically stable body configuration in a flying insect and raises new questions in sensorimotor control for small flying systems.
An Investigation on Surface Characteristics of Hair Fibres of Cold-Resistant Animals
Venue: Research journal of textile and apparel

Cold weather and the subsequent demand for lightweight apparel have prompted research work in the field of thermal insulation clothing. In addition to natural fibres, such as wool and cashmere, hollow chemical fibres, such as polyester or polypropylene fibre, have been studied and used to make thermal-insulation clothing. Primarily, modifications are made to increase the hollow ratio; however, this results in the fibre becoming brittle and prone to collapse. Yet many animals survive in harsh and cold conditions, and their hair plays a key role in keeping the body warm. In the research under discussion, 4 types of cold-resistant animals are selected for observation of their hair fibres based on optical and scanning electronic microscopies. The characteristics of the hair fibres of cold-resistant animals are examined, including colour, scale density, scale thickness, medullary distribution and morphology of cross sections. The conclusions show that there are some common characteristics among cold-resistant ...
Thermoregulation in reindeer
Venue: Rangifer

Thermoregulation was studied in Finnish reindeer (Rangifer tarandus L) on captive and herded individuals during 1977-85. Newborn calves maintained a high rectal temperature (Tre) (+39 to +41°C) even at —23°C by increasing heat production 5- to 6-fold through non-shivering thermogenesis, stimulated by cold-induced noradrenaline (NA). Plasma NA and thyroxine (T4) were high (18 ng/ml and 459 nmol/1) in neonatal reindeer. Sensitivity to exogenous NA was lost during the first 3-4 weeks of life. At +20°C and above, calves increased Tre (ca 1°C), oxygen consumption and heart rate, thereby showing poor heat tolerance. Thermal conductance was low in a cold environment, but rose sharply as ambient temperature (Ta) increased above + 10°C. The Tre of adults (+ 38 to +39°C) was independent of Ta (—28 to +15°C). Coarse (hollow) hair density and length in adults averaged 2000/cm2 and 12 mm on the legs, 1000/cm3 and 30 mm on the abdomen and 1700/cm2 and 30 mm on the back (calves 3200/cm2, 10 mm), respectively. The dependence of skin temperature on the Ta was linear in excised fur samples, but complex in living animals being strongest in the legs. Serum adrenaline correlated with the weight, age and total lipids. Serum NA and dopamine-fi-hydroxylase were highest in spring and decreased by autumn. Serum T4 was highest in summer and lowest in spring.
Neural correlates of mating system diversity: oxytocin and vasopressin receptor distributions in monogamous and non-monogamous Eulemur
Venue: Scientific Reports

Contemporary theory that emphasizes the roles of oxytocin and vasopressin in mammalian sociality has been shaped by seminal vole research that revealed interspecific variation in neuroendocrine circuitry by mating system. However, substantial challenges exist in interpreting and translating these rodent findings to other mammalian groups, including humans, making research on nonhuman primates crucial. Both monogamous and non-monogamous species exist within Eulemur, a genus of strepsirrhine primate, offering a rare opportunity to broaden a comparative perspective on oxytocin and vasopressin neurocircuitry with increased evolutionary relevance to humans. We performed oxytocin and arginine vasopressin 1a receptor autoradiography on 12 Eulemur brains from seven closely related species to (1) characterize receptor distributions across the genus, and (2) examine differences between monogamous and non-monogamous species in regions part of putative “pair-bonding circuits”. We find some binding patterns across Eulemur reminiscent of olfactory-guided rodents, but others congruent with more visually oriented anthropoids, consistent with lemurs occupying an ‘intermediary’ evolutionary niche between haplorhine primates and other mammalian groups. We find little evidence of a “pair-bonding circuit” in Eulemur akin to those proposed in previous rodent or primate research. Mapping neuropeptide receptors in these nontraditional species questions existing assumptions and informs proposed evolutionary explanations about the biological bases of monogamy.
Navigation by extrapolation of geomagnetic cues in a migratory songbird
Venue: Current Biology

Displacement experiments have demonstrated that experienced migratory birds translocated thousands of kilometers away from their migratory corridor can orient toward and ultimately reach their intended  This implies that they are capable of "true navigation," commonly defined2-4 as the ability to return to a known destination after displacement to an unknown location without relying on familiar surroundings, cues that emanate from the destination, or information collected during the outward journey.5-13 In birds, true navigation appears to require previous migratory experience5-7,14,15 (but see Kishkinev et al.16 and Piersma et al.17). It is generally assumed that, to correct for displacements outside the familiar area, birds initially gather information within their year-round distribution range, learn predictable spatial gradients of environmental cues within it, and extrapolate from those to unfamiliar magnitudes-the gradient hypothesis.6,9,18-22 However, the nature of the cues and evidence for actual extrapolation remain elusive. Geomagnetic cues (inclination, declination, and total intensity) provide predictable spatial gradients across large parts of the globe and could serve for navigation. We tested the orientation of long-distance migrants, Eurasian reed warblers, exposing them to geomagnetic cues of unfamiliar magnitude encountered beyond their natural distribution range. The birds demonstrated re-orientation toward their migratory corridor as if they were translocated to the corresponding location but only when all naturally occurring magnetic cues were presented, not when declination was changed alone. This result represents direct evidence for migratory birds' ability to navigate using geomagnetic cues extrapolated beyond their previous experience.
Social signals mediate oviposition site selection in Drosophila suzukii
Venue: Scientific Reports

The information that female insects perceive and use during oviposition site selection is complex and varies by species and ecological niche. Even in relatively unexploited niches, females interact directly and indirectly with conspecifics at oviposition sites. These interactions can take the form of host marking and re-assessment of prior oviposition sites during the decision-making process. Considerable research has focused on the niche breadth and host preference of the polyphagous invasive pest Drosophila suzukii Matsumura (Diptera: Drosophilidae), but little information exists on how conspecific signals modulate oviposition behavior. We investigated three layers of social information that female D. suzukii may use in oviposition site selection—(1) pre-existing egg density, (2) pre-existing larval occupation, and (3) host marking by adults. We found that the presence of larvae and host marking, but not egg density, influenced oviposition behavior and that the two factors interacted over time. Adult marking appeared to deter oviposition only in the presence of an unmarked substrate. These results are the first behavioral evidence for a host marking pheromone in a species of Drosophila . These findings may also help elucidate D. suzukii infestation and preference patterns within crop fields and natural areas.
Diminishing returns drive altruists to help extended family
Venue: Nature Ecology and Evolution

Altruism between close relatives can be easily explained. However, paradoxes arise when organisms divert altruism towards more-distantly-related recipients. In some social insects, workers ‘drift’ extensively between colonies and help raise less-related foreign brood, seemingly reducing inclusive fitness. Since being highlighted by W. D. Hamilton, three hypotheses (bet-hedging, indirect reciprocity, and diminishing returns to cooperation) have been proposed for this surprising behaviour. Here we show using inclusive fitness theory that bet-hedging and indirect reciprocity could only drive cooperative drifting under improbable conditions. However, diminishing returns to cooperation create a simple context in which sharing workers is adaptive. Using a longitudinal dataset comprising over a quarter of a million nest-cell observations, we quantify cooperative payoffs in the Neotropical wasp Polistes canadensis, where drifting occurs at high levels. As the worker-to-brood ratio rises in a worker’s home colony, the predicted marginal benefit of a worker for expected colony productivity diminishes. Helping on related colonies can allow effort to be focused on related brood that are more in need of care. Finally, we use simulations to show that cooperative drifting evolves under diminishing returns when dispersal is local, allowing altruists to focus their efforts on related recipients. Our results indicate the power of nonlinear fitness effects to shape social organisation, and suggest that models of eusocial evolution should be extended to include neglected social interactions within colony networks.
Soft Matter Mechanics and the Mechanisms Underpinning the Infrared Vision of Snakes
Venue: Matter

Pit-bearing snakes (vipers, pythons, and boas) have the extraordinary ability to “see” and accurately locate their prey and predators in total darkness. These animals use the infrared radiation emanating from objects that are warmer relative to the background environment to form a thermal image. Although enormous progress has been made to identify the key physiological features that enable the infrared vision of these snakes and a few other animals, the precise thermoelectric transduction mechanism that mediates the conversion of infrared heat to processable electrical signals has remained elusive. In this work, we quantitatively outline how cells in the snake's pit membrane organ act as apparent pyroelectric materials and convert infrared radiation into electrical signals. Despite the exceptional simplicity of our proposed mechanism and model, we are able to explain many central experimental results pertaining to the transduction process.
Pseudoflowers produced by Fusarium xyrophilum on yellow-eyed grass (Xyris spp.) in Guyana: a novel floral mimicry system?
Venue: Fungal Genetics and Biology

Pseudoflower formation is arguably the rarest outcome of a plant-fungus interaction. Here we report on a novel putative floral mimicry system in which the pseudoflowers are composed entirely of fungal tissues in contrast to modified leaves documented in previous mimicry systems. Pseudoflowers on two perennial Xyris species (yellow-eyed grass, X. setigera and X. surinamensis) collected from savannas in Guyana were produced by Fusarium xyrophilum, a novel Fusarium species. These pseudoflowers mimic Xyris flowers in gross morphology and are ultraviolet reflective. Axenic cultures of F. xyrophilum produced two pigments that had fluorescence emission maxima in light ranges that trichromatic insects are sensitive to and volatiles known to attract insect pollinators. One of the volatiles emitted by F. xyrophilum cultures (i.e., 2-ethylhexanol) was also detected in the head space of X. laxifolia var. iridifolia flowers, a perennial species native to the New World. Results of microscopic and PCR analyses, combined with examination of gross morphology of the pseudoflowers, provide evidence that the fungus had established a systemic infection in both Xyris species, sterilized them and formed fungal pseudoflowers containing both mating type idiomorphs. Fusarium xyrophilum cultures also produced the auxin indole-3-acetic acid (IAA) and the cytokinin isopentenyl adenosine (iPR). Field observations revealed that pseudoflowers and Xyris flowers were both visited by bees. Together, the results suggest that F. xyrophilum pseudoflowers are a novel floral mimicry system that attracts insect pollinators, via visual and olfactory cues, into vectoring its conidia, which might facilitate outcrossing of this putatively heterothallic fungus and infection of previously uninfected plants.
Conus venom fractions inhibit the adhesion of Plasmodium falciparum erythrocyte membrane protein 1 domains to the host vascular receptors.
Venue: Journal of Proteomics

Using high-throughput BioPlex assays, we determined that six fractions from the venom of Conus nux inhibit the adhesion of various recombinant PfEMP-1 protein domains (PF08_0106 CIDR1α3.1, PF11_0521 DBL2β3, and PFL0030c DBL3X and DBL5e) to their corresponding receptors (CD36, ICAM-1, and CSA, respectively). The protein domain-receptor interactions permit P. falciparum-infected erythrocytes (IE) to evade elimination in the spleen by adhering to the microvasculature in various organs including the placenta. The sequences for the main components of the fractions, determined by tandem mass spectrometry, yielded four T-superfamily conotoxins, one (CC-Loop-CC) with I-IV, II-III connectivity and three (CC-Loop-CXaaC) with a I-III, II-IV connectivity. The 3D structure for one of the latter, NuxVA = GCCPAPLTCHCVIY, revealed a novel scaffold defined by double turns forming a hairpin-like structure stabilized by the two disulfide bonds. Two other main fraction components were a miniM conotoxin, and a O2-superfamily conotoxin with cysteine framework VI/VII. This study is the first one of its kind suggesting the use of conotoxins for developing pharmacological tools for anti-adhesion adjunct therapy against malaria. Similarly, mitigation of emerging diseases like AIDS and COVID-19, can also benefit from conotoxins as inhibitors of protein-protein interactions as treatment.  Among the 850+ species of cone snail species there are hundreds of thousands of diverse venom exopeptides that have been selected throughout several million years of evolution to capture prey and deter predators. They do so by targeting several surface proteins present in target excitable cells. This immense biomolecular library of conopeptides can be explored for potential use as therapeutic leads against persistent and emerging diseases affecting non-excitable systems. We aim to expand the pharmacological reach of conotoxins/conopeptides by revealing their in vitro capacity to disrupt protein-protein and protein-polysaccharide interactions that directly contribute to pathology of Plasmodium falciparum malaria. This is significant for severe forms of malaria, which might be deadly even after treated with current parasite-killing drugs because of persistent cytoadhesion of P. falciparum infected erythrocytes even when parasites within red blood cells are dead. Anti-adhesion adjunct drugs would de-sequester or prevent additional sequestration of infected erythrocytes and may significantly improve survival of malaria patients. These results provide a lead for further investigations into conotoxins and other venom peptides as potential candidates for anti-adhesion or blockade-therapies. This study is the first of its kind and it suggests that conotoxins can be developed as pharmacological tools for anti-adhesion adjunct therapy against malaria. Similarly, mitigation of emerging diseases like AIDS and COVID-19, can also benefit from conotoxins as potential inhibitors of protein-protein interactions as treatment.