nils-herrmann/clean_scirepeval huggingface dataset:
A dehydration avoidance mechanism: Leaf rolling
Venue: Botanical Review

Plants have several defense mechanisms against unfavorable environmental conditions. One of these mechanisms is leaf rolling. In this review, leaf rolling as a response to water deficit stress and biochemical changes during leaf rolling in higher plants are reported. For instance, the activities of some enzymes and osmotic substances change during leaf rolling. Leaf rolling increases drought resistance in numerous species in theGramineae as well as inCtenanthe setosa, a perennial herbaceous plant that is a suitable model for use in studies of leaf rolling.ZusammenfassungPflanzen besitzen Schutzmechanismen gegen ungünstige Umweltbedingungen. Einer dieser Mechanismen ist das Einrollen der Blätter. In diesem Übersichtsartikel wird erstmals über die Bedeutung des Einrollens der Blätter als Antwort auf Wassermangel und von biochemischen Änderungen während des Einrollens der Blätter bei höheren Pflanzen berichtet. Das Einrollen der Blätter ist nicht nur eine Reaktion der Pflanze auf Wassermangel, es treten auch biochemische Veränderungen zusammen mit dem Einrollen der Blätter auf. Zum Beispiel verändern sich einige Enzymaktivitäten und osmotisch-aktive Stoffe während des Einrollens der Blätter. Das Einrollen der Blätter erhöht die Widerstandsfähigkeit gegen Trockenheit bei vielen Gramineen wieCtenanthe setosa. C. setosa, eine mehrjährige krautige Pflanze, ist eine gute Modellpflanze für Untersuchungen des Einrollens der Blätter.
A Pearl Spectrometer.
Venue: Nano Letters

Information recovery from incomplete measurements, typically performed by a numerical means, is beneficial in a variety of classical and quantum signal processing. Random and sparse sampling with nanophotonic and light scattering approaches has received attention to overcome the hardware limitations of conventional spectrometers and hyperspectral imagers but requires high-precision nanofabrications and bulky media. We report a simple spectral information processing scheme in which light transport through an Anderson-localized medium serves as an entropy source for compressive sampling directly in the frequency domain. As implied by the "lustrous" reflection originating from the exquisite multilayered nanostructures, a pearl (or mother-of-pearl) allows us to exploit the spatial and spectral intensity fluctuations originating from strong light localization for extracting salient spectral information with a compact and thin form factor. Pearl-inspired light localization in low-dimensional structures can offer an alternative of spectral information processing by hybridizing digital and physical properties at a material level.
Multiple Degrees of Freedom in the Fish Skull and Their Relation to Hydraulic Transport of Prey in Channel Catfish
Venue: Integrative Organismal Biology (Oxford, England)

Synopsis Fish perform many complex manipulation behaviors without hands or flexible muscular tongues, instead relying on more than 20 movable skeletal elements in their highly kinetic skulls. How fish use their skulls to accomplish these behaviors, however, remains unclear. Most previous mechanical models have represented the fish skull using one or more planar four-bar linkages, which have just a single degree of freedom (DoF). In contrast, truncated-cone hydrodynamic models have assumed up to five DoFs. In this study, we introduce and validate a 3D mechanical linkage model of a fish skull that incorporates the pectoral girdle and mandibular and hyoid arches. We validate this model using an in vivo motion dataset of suction feeding in channel catfish and then use this model to quantify the DoFs in the fish skull, to categorize the motion patterns of the cranial linkage during feeding, and to evaluate the association between these patterns and food motion. We find that the channel catfish skull functions as a 17-link, five-loop parallel mechanism. Despite having 19 potential DoFs, we find that seven DoFs are sufficient to describe most of the motion of the cranial linkage, consistent with the fish skull functioning as a multi-DoF, manipulation system. Channel catfish use this linkage to generate three different motion patterns (rostrocaudal wave, caudorostral wave, and compressive wave), each with its own associated food velocity profile. These results suggest that biomechanical manipulation systems must have a minimum number of DoFs to effectively control objects, whether in water or air.
Eyelashes divert airflow to protect the eye
Venue: Journal of the Royal Society Interface

Eyelashes are ubiquitous, although their function has long remained a mystery. In this study, we elucidate the aerodynamic benefits of eyelashes. Through anatomical measurements, we find that 22 species of mammals possess eyelashes of a length one-third the eye width. Wind tunnel experiments confirm that this optimal eyelash length reduces both deposition of airborne particles and evaporation of the tear film by a factor of two. Using scaling theory, we find this optimum arises because of the incoming flow's interactions with both the eye and eyelashes. Short eyelashes create a stagnation zone above the ocular surface that thickens the boundary layer, causing shear stress to decrease with increasing eyelash length. Long eyelashes channel flow towards the ocular surface, causing shear stress to increase with increasing eyelash length. These competing effects result in a minimum shear stress for intermediate eyelash lengths. This design may be employed in creating eyelash-inspired protection for optical sensors.
Eco-Mimicry Opens New Doors for Bioprocess Engineers
Venue: Joule

The natural world blends microenvironments to create a continuum of spatial niches wherein microbial consortia participate in metabolic exchanges. The capability with which nature selects a consortium to complement a given niche is often taken for granted. Not by Shahab et al. (2020), however, who created a synthetic microbial consortium to mediate a multi-step bioprocess in a single bioreactor system. The concept affords a fair degree of modularity in the choice of biocatalyst and a reasonable level of process control, thus making it an engineering tool.
Mammals repel mosquitoes with their tails
Venue: The Journal of Experimental Biology

The swinging of a mammal's tail has long been thought to deter biting insects, which, in cows, can drain up to 0.3 liters of blood per day. How effective is a mammal's tail at repelling insects? In this combined experimental and theoretical study, we filmed horses, zebras, elephants, giraffes and dogs swinging their tails. The tail swings at triple the frequency of a gravity-driven pendulum, and requires 27 times more power input. Tails can also be used like a whip to directly strike at insects. This whip-like effect requires substantial torques from the base of the tail on the order of 101–102 N m, comparable to the torque of a sedan, but still within the physical limits of the mammal. Based on our findings, we designed and built a mammal tail simulator to simulate the swinging of the tail. The simulator generates mild breezes of 1 m s–1, comparable to a mosquito's flight speed, and sufficient to deter up to 50% of mosquitoes from landing. This study may help us determine new mosquito-repelling strategies that do not depend on chemicals.  Mammals swing their tails three times faster than a gravity-driven pendulum. Our experiments with artificial tails show that tail motion generates winds sufficient to repel mosquitoes.
Honey bees (Apis cerana) use animal feces as a tool to defend colonies against group attack by giant hornets (Vespa soror)
Venue: PLOS ONE

Honey bees (genus Apis) are well known for the impressive suite of nest defenses they have evolved to protect their abundant stockpiles of food and the large colonies they sustain. In Asia, honey bees have evolved under tremendous predatory pressure from social wasps in the genus Vespa, the most formidable of which are the giant hornets that attack colonies in groups, kill adult defenders, and prey on brood. We document for the first time an extraordinary collective defense used by Apis cerana against the giant hornet Vespa soror. In response to attack by V. soror, A. cerana workers foraged for and applied spots of animal feces around their nest entrances. Fecal spotting increased after colonies were exposed either to naturally occurring attacks or to chemicals that scout hornets use to target colonies for mass attack. Spotting continued for days after attacks ceased and occurred in response to V. soror, which frequently landed at and chewed on entrances to breach nests, but not Vespa velutina, a smaller hornet that rarely landed at entrances. Moderate to heavy fecal spotting suppressed attempts by V. soror to penetrate nests by lowering the incidence of multiple-hornet attacks and substantially reducing the likelihood of them approaching and chewing on entrances. We argue that A. cerana forages for animal feces because it has properties that repel this deadly predator from nest entrances, providing the first report of tool use by honey bees and the first evidence that they forage for solids that are not derived from plants. Our study describes a remarkable weapon in the already sophisticated portfolio of defenses that honey bees have evolved in response to the predatory threats they face. It also highlights the strong selective pressure honey bees will encounter if giant hornets, recently detected in western North America, become established.
Structure, self-assembly, and properties of a truncated reflectin variant
Venue: Proceedings of the National Academy of Sciences of the United States of America

The investigation of protein-based materials has provided a better understanding of living systems and has led to the development of ubiquitous modern technologies. Within this context, unique cephalopod proteins called reflectins have exhibited promise for biophotonics and bioelectronics applications, but the exploration of reflectins as materials has been hindered by an incomplete understanding of their structures and properties. Here, we resolve the molecular-level structure of a model reflectin variant, establish a straightforward approach to controlling the assembly of this protein, and describe a correlation between its structural characteristics and light-manipulating properties. Taken together, our findings advance current understanding of reflectin-based materials, provide insight into the color-changing capabilities of cephalopods, and afford new opportunities in biochemistry, cellular biology, bioengineering, and optics. Naturally occurring and recombinant protein-based materials are frequently employed for the study of fundamental biological processes and are often leveraged for applications in areas as diverse as electronics, optics, bioengineering, medicine, and even fashion. Within this context, unique structural proteins known as reflectins have recently attracted substantial attention due to their key roles in the fascinating color-changing capabilities of cephalopods and their technological potential as biophotonic and bioelectronic materials. However, progress toward understanding reflectins has been hindered by their atypical aromatic and charged residue-enriched sequences, extreme sensitivities to subtle changes in environmental conditions, and well-known propensities for aggregation. Herein, we elucidate the structure of a reflectin variant at the molecular level, demonstrate a straightforward mechanical agitation-based methodology for controlling this variant’s hierarchical assembly, and establish a direct correlation between the protein’s structural characteristics and intrinsic optical properties. Altogether, our findings address multiple challenges associated with the development of reflectins as materials, furnish molecular-level insight into the mechanistic underpinnings of cephalopod skin cells’ color-changing functionalities, and may inform new research directions across biochemistry, cellular biology, bioengineering, and optics.
Limb work and joint work minimization reveal an energetic benefit to the elbows-back, knees-forward limb design in parasagittal quadrupeds
Venue: Proceedings of The Royal Society B: Biological Sciences

Quadrupedal animal locomotion is energetically costly. We explore two forms of mechanical work that may be relevant in imposing these physiological demands. Limb work, due to the forces and velocities between the stance foot and the centre of mass, could theoretically be zero given vertical limb forces and horizontal centre of mass path. To prevent pitching, skewed vertical force profiles would then be required, with forelimb forces high in late stance and hindlimb forces high in early stance. By contrast, joint work—the positive mechanical work performed by the limb joints—would be reduced with forces directed through the hip or shoulder joints. Measured quadruped kinetics show features consistent with compromised reduction of both forms of work, suggesting some degree of, but not perfect, inter-joint energy transfer. The elbows-back, knees-forward design reduces the joint work demand of a low limb-work, skewed, vertical force profile. This geometry allows periods of high force to be supported when the distal segment is near vertical, imposing low moments about the elbow or knee, while the shoulder or hip avoids high joint power despite high moments because the proximal segment barely rotates—translation over this period is due to rotation of the distal segment.
Dynamics of topological defects and structural synchronization in a forming periodic tissue
Venue: Nature Physics

Living organisms form a large variety of hierarchically structured extracellular functional tissues. Remarkably, these materials exhibit regularity and structural coherence across multiple length scales, far beyond the size of a single cell. Here, synchrotron-based nanotomographic imaging in combination with machine-learning-based segmentation is used to reveal the structural synchronization process of nacre forming in the shell of the mollusc Unio pictorum . We show that the emergence of this highly regular layered structure is driven by a disorder-to-order transition achieved through the motion and interaction of screw-like structural dislocations with an opposite topological sign. Using an analogy to similar processes observed in liquid-crystalline systems, we demonstrate that these microstructural faults act as dissipative topological defects coupled by an elastic distortion field surrounding their cores. Their mutual annihilation results in structural synchronization that is simulated using the classical Kuramoto model. The developed experimental, theoretical and numerical framework provides a comprehensive physical view of the formation of biogenic materials. Molluscs assemble layers of material in the shells around them with a high level of control. Here the authors observe the structural evolution of layer formation and propose a mechanism reminiscent of topological defect dynamics in liquid crystals.
Discovery and quantification of anaerobic nitrogen metabolisms among oxygenated tropical Cuban stony corals
Venue: The ISME Journal

Coral reef health depends on an intricate relationship among the coral animal, photosynthetic algae, and a complex microbial community. The holobiont can impact the nutrient balance of their hosts amid an otherwise oligotrophic environment, including by cycling physiologically important nitrogen compounds. Here we use 15 N-tracer experiments to produce the first simultaneous measurements of ammonium oxidation, nitrate reduction, and nitrous oxide (N 2 O) production among five iconic species of reef-building corals ( Acropora palmata , Diploria labyrinthiformis , Orbicella faveolata , Porites astreoides , and Porites porites ) in the highly protected Jardines de la Reina reefs of Cuba. Nitrate reduction is present in most species, but ammonium oxidation is low potentially due to photoinhibition and assimilatory competition. Coral-associated rates of N 2 O production indicate a widespread potential for denitrification, especially among D. labyrinthiformis , at rates of ~1 nmol cm −2  d −1 . In contrast, A. palmata displays minimal active nitrogen metabolism. Enhanced rates of nitrate reduction and N 2 O production are observed coincident with dark net respiration periods. Genomes of bacterial cultures isolated from multiple coral species confirm that microorganisms with the ability to respire nitrate anaerobically to either dinitrogen gas or ammonium exist within the holobiont. This confirmation of anaerobic nitrogen metabolisms by coral-associated microorganisms sheds new light on coral and reef productivity.
DNA Origami Design: A How-To Tutorial
Venue: Journal of Research of the National Institute of Standards and Technology

While the design and assembly of DNA origami are straightforward, its relative novelty as a nanofabrication technique means that the tools and methods for designing new structures have not been codified as well as they have for more mature technologies, such as integrated circuits. While design approaches cannot be truly formalized until design-property relationships are fully understood, this document attempts to provide a step-by-step guide to designing DNA origami nanostructures using the tools available at the current state of the art.
Assembly of infectious enteroviruses depends on multiple, conserved genomic RNA-coat protein contacts
Venue: PLOS Pathogens

Picornaviruses are important viral pathogens, but despite extensive study, the assembly process of their infectious virions is still incompletely understood, preventing the development of anti-viral strategies targeting this essential part of the life cycle. We report the identification, via RNA SELEX and bioinformatics, of multiple RNA sites across the genome of a typical enterovirus, enterovirus-E (EV-E), that each have affinity for the cognate viral capsid protein (CP) capsomer. Many of these sites are evolutionarily conserved across known EV-E variants, suggesting they play essential functional roles. Cryo-electron microscopy was used to reconstruct the EV-E particle at ~2.2 Å resolution, revealing extensive density for the genomic RNA. Relaxing the imposed symmetry within the reconstructed particles reveals multiple RNA-CP contacts, a first for any picornavirus. Conservative mutagenesis of the individual RNA-contacting amino acid side chains in EV-E, many of which are conserved across the enterovirus family including poliovirus, is lethal but does not interfere with replication or translation. Anti-EV-E and anti-poliovirus aptamers share sequence similarities with sites distributed across the poliovirus genome. These data are consistent with the hypothesis that these RNA-CP contacts are RNA Packaging Signals (PSs) that play vital roles in assembly and suggest that the RNA PSs are evolutionarily conserved between pathogens within the family, augmenting the current protein-only assembly paradigm for this family of viruses.
Cobalt Resistance via Detoxification and Mineralization in the Iron-Reducing Bacterium Geobacter sulfurreducens
Venue: Frontiers in Microbiology

Bacteria in the genus Geobacter thrive in iron- and manganese-rich environments where the divalent cobalt cation (CoII) accumulates to potentially toxic concentrations. Consistent with selective pressure from environmental exposure, the model laboratory representative Geobacter sulfurreducens grew with CoCl2 concentrations (1 mM) typically used to enrich for metal-resistant bacteria from contaminated sites. We reconstructed from genomic data canonical pathways for CoII import and assimilation into cofactors (cobamides) that support the growth of numerous syntrophic partners. We also identified several metal efflux pumps, including one that was specifically upregulated by CoII. Cells acclimated to metal stress by downregulating non-essential proteins with metals and thiol groups that CoII preferentially targets. They also activated sensory and regulatory proteins involved in detoxification as well as pathways for protein and DNA repair. In addition, G. sulfurreducens upregulated respiratory chains that could have contributed to the reductive mineralization of the metal on the cell surface. Transcriptomic evidence also revealed pathways for cell envelope modification that increased metal resistance and promoted cell-cell aggregation and biofilm formation in stationary phase. These complex adaptive responses confer on Geobacter a competitive advantage for growth in metal-rich environments that are essential to the sustainability of cobamide-dependent microbiomes and the sequestration of the metal in hitherto unknown biomineralization reactions.
Evolution of fold switching in a metamorphic protein
Venue: Science

One sequence encoding two structures Most proteins have stable, folded structures, but there are rare examples of metamorphic proteins that can switch between two different folds that may each have a different function. Dishman et al. investigated the evolution of XCL1, which is a member of the chemokine family that interconverts between the chemokine fold and a second, noncanonical fold that forms dimers. The authors used nuclear magnetic resonance spectroscopy to investigate the structures of inferred evolutionary ancestral sequences. Their results suggest that XCL1 evolved from an ancestor with the chemokine fold and then transitioned to prefer the noncanonical fold before reaching the modern-day metamorphic protein. Science, this issue p. 86 The human protein XCL1 evolved to switch between two completely different folds with different functions. Metamorphic proteins switch between different folds, defying the protein folding paradigm. It is unclear how fold switching arises during evolution. With ancestral reconstruction and nuclear magnetic resonance, we studied the evolution of the metamorphic human protein XCL1, which has two distinct folds with different functions, making it an unusual member of the chemokine family, whose members generally adopt one conserved fold. XCL1 evolved from an ancestor with the chemokine fold. Evolution of a dimer interface, changes in structural constraints and molecular strain, and alteration of intramolecular protein contacts drove the evolution of metamorphosis. Then, XCL1 likely evolved to preferentially populate the noncanonical fold before reaching its modern-day near-equal population of folds. These discoveries illuminate how one sequence has evolved to encode multiple structures, revealing principles for protein design and engineering.