nils-herrmann/clean_scirepeval huggingface dataset:
Bone-inspired microarchitectures achieve enhanced fatigue life
Venue: Proceedings of the National Academy of Sciences of the United States of America

Microarchitectured materials, such as foams and lattice structures, can achieve high stiffness and strength while remaining extremely lightweight. Applying high-porosity microarchitectured materials to durable devices, such as vehicles, however, will require the materials to also resist failure during cyclic loading. Here, we identify an aspect of microstructure in cancellous bone that greatly influences failure under cyclic loading and show that the effect is generalizable to synthetic microarchitectured materials. Our findings demonstrate that a common design strategy to improve stiffness and strength of microarchitectured materials comes at the cost of impaired service life. Our findings are useful for the design and application of microarchitectured materials and additionally provide insight into human health in situations of osteoporosis. Microarchitectured materials achieve superior mechanical properties through geometry rather than composition. Although ultralightweight microarchitectured materials can have high stiffness and strength, application to durable devices will require sufficient service life under cyclic loading. Naturally occurring materials provide useful models for high-performance materials. Here, we show that in cancellous bone, a naturally occurring lightweight microarchitectured material, resistance to fatigue failure is sensitive to a microarchitectural trait that has negligible effects on stiffness and strength—the proportion of material oriented transverse to applied loads. Using models generated with additive manufacturing, we show that small increases in the thickness of elements oriented transverse to loading can increase fatigue life by 10 to 100 times, far exceeding what is expected from the associated change in density. Transversely oriented struts enhance resistance to fatigue by acting as sacrificial elements. We show that this mechanism is also present in synthetic microlattice structures, where fatigue life can be altered by 5 to 9 times with only negligible changes in density and stiffness. The effects of microstructure on fatigue life in cancellous bone and lattice structures are described empirically by normalizing stress in traditional stress vs. life (S-N) curves by √ψ, where ψ is the proportion of material oriented transverse to load. The mechanical performance of cancellous bone and microarchitectured materials is enhanced by aligning structural elements with expected loading; our findings demonstrate that this strategy comes at the cost of reduced fatigue life, with consequences to the use of microarchitectured materials in durable devices and to human health in the context of osteoporosis.
Attachment to challenging substrates – fouling, roughness and limits of adhesion in the northern clingfish (Gobiesox maeandricus)
Venue: The Journal of Experimental Biology

Northern clingfish use a ventral suction disc to stick to rough substrates in the intertidal zone. Bacteria, algae and invertebrates grow on these surfaces (fouling) and change the surface properties of the primary substrate, and therefore the attachment conditions for benthic organisms. In this study, we investigate the influence of fouling and surface roughness on the adhesive strength of northern clingfish, Gobiesox maeandricus. We measured clingfish tenacity on unfouled and fouled substrates over four surface roughnesses. We exposed surfaces for 6 weeks in the Pacific Ocean, until they were covered with periphyton. Clingfish tenacity is equivalent on both fouled and unfouled smooth substrates; however, tenacity on fouled rough surfaces is less compared with tenacity on unfouled ones. We hypothesize that parts of biofilm may act as a lubricant and decrease friction of the disc margin, thereby making disc margins slip inwards and fail at lower tenacities. Nevertheless, even on fouled surfaces the adhesive forces are approximately 150 times the body weight of the fish. To identify the upper threshold of surface roughness the fish can cling to, we tested seven unfouled substrates of increasing surface roughness. The threshold roughness at which northern clingfish failed increased with specimen size. We hypothesize that because of the elastic properties of the disc margin, a larger disc can adapt to larger surface irregularities. The largest specimens (length 10–12 cm) were able to cling to surfaces with 2–4 mm grain size. The fish can attach to surfaces with roughness between 2 and 9% of the suction disc width.
Bioinspired Materials with Self-Adaptable Mechanical Properties.
Venue: Advanced Materials

Natural structural materials, such as bone, can autonomously modulate their mechanical properties in response to external loading to prevent failure. These material systems smartly control the addition/removal of material in locations of high/low mechanical stress by utilizing local resources guided by biological signals. On the contrary, synthetic structural materials have unchanging mechanical properties limiting their mechanical performance and service life. Inspired by the mineralization process of bone, a material system that adapts its mechanical properties in response to external mechanical loading is reported. It is found that charges from piezoelectric scaffolds can induce mineralization from surrounding media. It is shown that the material system can adapt to external mechanical loading by inducing mineral deposition in proportion to the magnitude of the stress and the resulting piezoelectric charges. Moreover, the mineralization mechanism allows a simple one-step route for fabricating functionally graded materials by controlling the stress distribution along the scaffold. The findings can pave the way for a new class of self-regenerating materials that reinforce regions of high stress or induce deposition of minerals on the damaged areas from the increase in mechanical stress to prevent/mitigate failure. It is envisioned that the findings can contribute to addressing the current challenges of synthetic materials for load-bearing applications from self-adaptive capabilities.
Beaver-induced spatiotemporal patch dynamics affect landscape-level environmental heterogeneity
Venue: Environmental Research Letters

Beavers (Castor sp.) are ecosystem engineers that cause significant changes to their physical environment and alter the availability of resources to other species. We studied flood dynamics created by American beaver (C. canadensis K.) in a southern boreal landscape in Finland in 1970-2018. We present for the first time, to our knowledge, a temporally continuous long-term study of beaver-induced flood disturbances starting from the appearance of beaver in the area. During the 49 years, the emergence of new sites flooded by beaver and repeated floods (61% of the sites) formed a dynamic mosaic characterized by clustered patterns of beaver sites. As beaver dispersal proceeded, connectivity of beaver sites increased significantly. The mean flood duration was approximately three years, which highlights the importance of datasets with high-temporal resolution in detecting beaver-induced disturbances. An individual site was often part of the active flood mosaic over several decades, although the duration and the number of repeated floods at different sites varied considerably. Variation of flood-inundated and post-flood phases at individual sites resulted in a cumulative number of unique patches that contribute to environmental heterogeneity in space and time. A disturbance mosaic consisting of patches differing by successional age and flood history is likely to support species richness and abundance of different taxa and facilitate whole species communities. Beavers are thus a suitable means to be used in restoration of riparian habitat due to their strong and dynamic influence on abiotic environment and its biotic consequences.
Synthesis and characterization of molybdenum disulfide nanoparticles in Shewanella oneidensis MR-1 biofilms.
Venue: Biointerphases

Shewanella oneidensis MR-1 is a dissimilatory metal-reducing bacterium capable of reducing various metal and sulfur compounds and precipitating them in nanoparticulate form. Here, we report the synthesis of molybdenum disulfide nanomaterials at the site of S. oneidensis biofilms grown in the presence of molybdenum trioxide and sodium thiosulfate. Samples from the growth medium were imaged using scanning electron microscopy and characterized using transmission electron microscopy, energy-dispersive x-ray spectroscopy, absorbance spectroscopy, and x-ray diffraction. These methods revealed the presence of molybdenum disulfide nanoparticle aggregates 50-300 nm in diameter with both hexagonal and rhombohedral polytypes. As a biosynthesis method for molybdenum sulfide, the use of S. oneidensis offers the advantage of significantly reduced heat and chemical solvent input compared to conventional methods of synthesizing molybdenum disulfide nanoparticles.
Soy and Arabidopsis receptor-like kinases respond to polysaccharide signals from Spodoptera species and mediate herbivore resistance
Venue: Communications Biology

Plants respond to herbivory by perceiving herbivore danger signal(s) (HDS(s)), including “elicitors”, that are present in herbivores’ oral secretions (OS) and act to induce defense responses. However, little is known about HDS-specific molecules and intracellular signaling. Here we explored soybean receptor-like kinases (RLKs) as candidates that might mediate HDS-associated RLKs’ (HAKs’) actions in leaves in response to OS extracted from larvae of a generalist herbivore, Spodoptera litura. Fractionation of OS yielded Frα, which consisted of polysaccharides. The GmHAKs composed of their respective homomultimers scarcely interacted with Frα. Moreover, Arabidopsis HAK1 homomultimers interacted with cytoplasmic signaling molecule PBL27, resulting in herbivory resistance, in an ethylene-dependent manner. Altogether, our findings suggest that HAKs are herbivore-specific RLKs mediating HDS-transmitting, intracellular signaling through interaction with PBL27 and the subsequent ethylene signaling for plant defense responses in host plants. Uemura et al. study the mechanism of herbivore resistance in soybean and Arabidopsis. They show that receptor-like kinases (HAK1/2) respond to a polysaccharide in the oral secretions of Spodoptera litura and then interact with PBL27, resulting in an ethylene-dependent herbivore resistance.
B cell zone reticular cell microenvironments shape CXCL13 gradient formation
Venue: Nature Communications

Through the formation of concentration gradients, morphogens drive graded responses to extracellular signals, thereby fine-tuning cell behaviors in complex tissues. Here we show that the chemokine CXCL13 forms both soluble and immobilized gradients. Specifically, CXCL13+ follicular reticular cells form a small-world network of guidance structures, with computer simulations and optimization analysis predicting that immobilized gradients created by this network promote B cell trafficking. Consistent with this prediction, imaging analysis show that CXCL13 binds to extracellular matrix components in situ, constraining its diffusion. CXCL13 solubilization requires the protease cathepsin B that cleaves CXCL13 into a stable product. Mice lacking cathepsin B display aberrant follicular architecture, a phenotype associated with effective B cell homing to but not within lymph nodes. Our data thus suggest that reticular cells of the B cell zone generate microenvironments that shape both immobilized and soluble CXCL13 gradients. Morphogens such as chemokines form gradients to direct graded responses and modulate cell behaviors. Here the authors show, using imaging and computer simulation, that the chemokine CXCL13 originated from follicular reticular cells in the lymph nodes forms both soluble and immobilized gradients to regulate B cell recruitment and migration.
The immunogenetics of sexual parasitism
Venue: Science

Reconfiguring an immune response The deep sea is a vast and generally empty environment. Finding a mate can thus be difficult. In response to this situation, one group of deep-sea denizens, the anglerfishes, have evolved a system in which males attach to females, in some cases permanently, through fusion of tissues and connection of circulatory systems. Such attachment greatly challenges the immune systems of the fish. Swann et al. found that these challenges have been met by the evolution of increasingly reduced immune responses among anglerfish species, including the loss of what have been considered essential vertebrate responses. These shifts suggest that vertebrate immune systems may be more flexible over evolutionary time than was previously thought. Science, this issue p. 1608 Anglerfish display altered immune responses to accommodate an unusual male attachment reproductive strategy. Sexual parasitism has evolved as a distinctive mode of reproduction among deep-sea anglerfishes. The permanent attachment of males to host females observed in these species represents a form of anatomical joining, which is otherwise unknown in nature. Pronounced modifications to immune facilities are associated with this reproductive trait. The genomes of species with temporarily attaching males lack functional aicda genes that underpin affinity maturation of antibodies. Permanent attachment is associated with additional alterations, culminating in the loss of functional rag genes in some species, abolishing somatic diversification of antigen receptor genes, the hallmark of canonical adaptive immunity. In anglerfishes, coevolution of innate and adaptive immunity has been disentangled, implying that an alternative form of immunity supported the emergence of this evolutionarily successful group of vertebrates.
Stochastic resonance in MoS2 photodetector
Venue: Nature Communications

In this article, we adopt a radical approach for next generation ultra-low-power sensor design by embracing the evolutionary success of animals with extraordinary sensory information processing capabilities that allow them to survive in extreme and resource constrained environments. Stochastic resonance (SR) is one of those astounding phenomena, where noise, which is considered detrimental for electronic circuits and communication systems, plays a constructive role in the detection of weak signals. Here, we show SR in a photodetector based on monolayer MoS2 for detecting ultra-low-intensity subthreshold optical signals from a distant light emitting diode (LED). We demonstrate that weak periodic LED signals, which are otherwise undetectable, can be detected by a MoS2 photodetector in the presence of a finite and optimum amount of white Gaussian noise at a frugal energy expenditure of few tens of nano-Joules. The concept of SR is generic in nature and can be extended beyond photodetector to any other sensors.
Shaping the zebrafish myotome by intertissue friction and active stress
Venue: Proceedings of the National Academy of Sciences of the United States of America

How do tissues self-organize to generate the complex organ shapes observed in vertebrates? Organ formation requires the integration of chemical and mechanical information, yet how this is achieved is poorly understood for most organs. Muscle compartments in zebrafish display a V shape, which is believed to be required for efficient swimming. We investigate how this structure emerges during zebrafish development, combining live imaging and quantitative analysis of cellular movements. We use theoretical modeling to understand how cell differentiation and mechanical interactions between tissues guide the emergence of a specific tissue morphology. Our work reveals how spatially modulating the mechanical environment around and within tissues can lead to complex organ shape formation. Organ formation is an inherently biophysical process, requiring large-scale tissue deformations. Yet, understanding how complex organ shape emerges during development remains a major challenge. During zebrafish embryogenesis, large muscle segments, called myotomes, acquire a characteristic chevron morphology, which is believed to aid swimming. Myotome shape can be altered by perturbing muscle cell differentiation or the interaction between myotomes and surrounding tissues during morphogenesis. To disentangle the mechanisms contributing to shape formation of the myotome, we combine single-cell resolution live imaging with quantitative image analysis and theoretical modeling. We find that, soon after segmentation from the presomitic mesoderm, the future myotome spreads across the underlying tissues. The mechanical coupling between the future myotome and the surrounding tissues appears to spatially vary, effectively resulting in spatially heterogeneous friction. Using a vertex model combined with experimental validation, we show that the interplay of tissue spreading and friction is sufficient to drive the initial phase of chevron shape formation. However, local anisotropic stresses, generated during muscle cell differentiation, are necessary to reach the acute angle of the chevron in wild-type embryos. Finally, tissue plasticity is required for formation and maintenance of the chevron shape, which is mediated by orientated cellular rearrangements. Our work sheds light on how a spatiotemporal sequence of local cellular events can have a nonlocal and irreversible mechanical impact at the tissue scale, leading to robust organ shaping.
Collective Computation in Animal Fission-Fusion Dynamics
Venue: Frontiers in Robotics and AI

Recent work suggests that collective computation of social structure can minimize uncertainty about the social and physical environment, facilitating adaptation. We explore these ideas by studying how fission-fusion social structure arises in spider monkey (Ateles geoffroyi) groups, exploring whether monkeys use social knowledge to collectively compute subgroup size distributions adaptive for foraging in variable environments. We assess whether individual decisions to stay in or leave subgroups are conditioned on strategies based on the presence or absence of others. We search for this evidence in a time series of subgroup membership. We find that individuals have multiple strategies, suggesting that the social knowledge of different individuals is important. These stay-leave strategies provide microscopic inputs to a stochastic model of collective computation encoded in a family of circuits. Each circuit represents an hypothesis for how collectives combine strategies to make decisions, and how these produce various subgroup size distributions. By running these circuits forward in simulation we generate new subgroup size distributions and measure how well they match food abundance in the environment using transfer entropies. We find that spider monkeys decide to stay or go using information from multiple individuals and that they can collectively compute a distribution of subgroup size that makes efficient use of ephemeral sources of nutrition. We are able to artificially tune circuits with subgroup size distributions that are a better fit to the environment than the observed. This suggests that a combination of measurement error, constraint, and adaptive lag are diminishing the power of collective computation in this system. These results are relevant for a more general understanding of the emergence of ordered states in multi-scale social systems with adaptive properties–both natural and engineered.
Microbial diversity drives carbon use efficiency in a model soil
Venue: Nature Communications

Empirical evidence for the response of soil carbon cycling to the combined effects of warming, drought and diversity loss is scarce. Microbial carbon use efficiency (CUE) plays a central role in regulating the flow of carbon through soil, yet how biotic and abiotic factors interact to drive it remains unclear. Here, we combine distinct community inocula (a biotic factor) with different temperature and moisture conditions (abiotic factors) to manipulate microbial diversity and community structure within a model soil. While community composition and diversity are the strongest predictors of CUE, abiotic factors modulated the relationship between diversity and CUE, with CUE being positively correlated with bacterial diversity only under high moisture. Altogether these results indicate that the diversity × ecosystem-function relationship can be impaired under non-favorable conditions in soils, and that to understand changes in soil C cycling we need to account for the multiple facets of global changes. Microbial carbon use efficiency has an important role in soil C cycling. Here the authors test the interactive effects of temperature and moisture and manipulate microbial community composition in soil microcosms, showing a positive relationship between microbial diversity and CUE that is contingent on abiotic conditions.
Spatial mapping of polymicrobial communities reveals a precise biogeography associated with human dental caries
Venue: Proceedings of the National Academy of Sciences of the United States of America

Dental caries remains an unresolved public health problem. The etiology is poorly understood, as the oral cavity harbors diverse communities of microorganisms. Using multiple imaging modalities on human teeth from patients with caries, we discovered a microbial community precisely arranged in a corona-like architecture. Moreover, this organization is mediated by the pathogen Streptococcus mutans through production of an extracellular scaffold that directs positioning of other oral microbes. We developed a methodology to quantify the spatial structure of microbial communities at the micron scale and found a precise spatial patterning of bacteria associated with localized caries onset. These findings are relevant as we approach the post-microbiome era, whereby quantifying the community structural organization may be essential for understanding microbiome function. Tooth decay (dental caries) is a widespread human disease caused by microbial biofilms. Streptococcus mutans, a biofilm-former, has been consistently associated with severe childhood caries; however, how this bacterium is spatially organized with other microorganisms in the oral cavity to promote disease remains unknown. Using intact biofilms formed on teeth of toddlers affected by caries, we discovered a unique 3D rotund-shaped architecture composed of multiple species precisely arranged in a corona-like structure with an inner core of S. mutans encompassed by outer layers of other bacteria. This architecture creates localized regions of acidic pH and acute enamel demineralization (caries) in a mixed-species biofilm model on human teeth, suggesting this highly ordered community as the causative agent. Notably, the construction of this architecture was found to be an active process initiated by production of an extracellular scaffold by S. mutans that assembles the corona cell arrangement, encapsulating the pathogen core. In addition, this spatial patterning creates a protective barrier against antimicrobials while increasing bacterial acid fitness associated with the disease-causing state. Our data reveal a precise biogeography in a polymicrobial community associated with human caries that can modulate the pathogen positioning and virulence potential in situ, indicating that micron-scale spatial structure of the microbiome may mediate the function and outcome of host–pathogen interactions.