cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccdc.csd.cc2nbsf7
title: CCDC 2453229: Experimental Crystal Structure Determination

description: Related Article: Rafael Stieler, Paulo Henrique Schneider, Douglas Bernardo Paixão|2025|CSD Communication|||
description: Related Article: Douglas B. Paixão, Anita B. Kessler, Fabiano S. Rodembusch, Rafael Stieler, Daniel S. Rampon, Paulo H. Schneider|2026|Org.Lett.|||doi:10.1021/acs.orglett.5c05364
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5061/dryad.j6q573nk9
title: The genetics of immune and infection phenotypes in wild mice, Mus musculus domesticus

description: Wild animals are under constant threat from a wide range of micro- and
 macroparasites in their environment. Animals make immune responses against
 parasites, and these are important in affecting the dynamics of parasite
 populations. Individual animals vary in their anti-parasite immune
 responses. Genetic polymorphism of immune-related loci contributes to
 inter-individual differences in immune responses, but most of what we know
 in this regard comes from studies of humans or laboratory animals; there
 are very few such studies of wild animals naturally infected with
 parasites. Here we have investigated the effect of Single Nucleotide
 Polymorphisms (SNPs) in immune-related loci (the MHC, and loci coding for
 cytokines and Toll-like receptors) on a wide range of immune and infection
 phenotypes in UK wild house mice, Mus musculus domesticus. We found strong
 associations between SNPs in various MHC and cytokine-coding loci on both
 immune measures (antibody concentration and cytokine production) and on
 infection phenotypes (infection with mites, worms and viruses). Our study
 provides a comprehensive view of how polymorphism of immune-related loci
 affects immune and infection phenotypes in naturally infected wild rodent
 populations.
DOI: 10.5281/zenodo.18284671
title: Thermodynamic Costs of Symmetry Breaking in Molecular Motors: A Feedback-Based Bound

description: The three laws of thermodynamics (plus the zeroth) describe equilibrium and near-equilibrium systems but inadequately capture the far-from-equilibrium dynamics of living systems, characterized by active energy consumption, internal set points, and feedback mechanisms. This conceptual paper proposes a thermodynamic bound tailored to living systems: In living systems with internal set points and feedback control, the housekeeping entropy production rate Σ_{hk} is bounded below by a function of time-reversal asymmetry Λ, ensuring biological stability and functionality: Σ_{hk} ≥ f(Λ), where f incorporates thermodynamic uncertainty relations, information-theoretic measures, and information flow costs. We derive this rigorously using stochastic thermodynamics integrated with feedback control, support it with equations, analytical derivations, Python simulations of a kinesin motor model using real parameters, sensitivity analysis, Bayesian inference, uncertainty quantification, null model comparisons, and falsifiability. The framework draws on empirical data from actin cortex studies and recent research on kinesin thermodynamics, kinesin-8 and kinesin-14 specifics including their structures and roles in meiosis, kinesin-5's role in meiotic spindle bipolarity, the role of dynein in meiotic division including its structure, and thermodynamic laws in living cells, substantiated by peer-reviewed references from prestigious journals.
DOI: 10.5281/zenodo.18403563
title: Thermodynamic Costs of Symmetry Breaking in Molecular Motors: A Feedback-Based Bound

description: The three laws of thermodynamics (plus the zeroth) describe equilibrium and near-equilibrium systems but inadequately capture the far-from-equilibrium dynamics of living systems, characterized by active energy consumption, internal set points, and feedback mechanisms. This conceptual paper proposes a thermodynamic bound tailored to living systems: In living systems with internal set points and feedback control, the housekeeping entropy production rate Σ_{hk} is bounded below by a function of time-reversal asymmetry Λ, ensuring biological stability and functionality: Σ_{hk} ≥ f(Λ), where f incorporates thermodynamic uncertainty relations, information-theoretic measures, and information flow costs. We derive this rigorously using stochastic thermodynamics integrated with feedback control, support it with equations, analytical derivations, Python simulations of a kinesin motor model using real parameters, sensitivity analysis, Bayesian inference, uncertainty quantification, null model comparisons, and falsifiability. The framework draws on empirical data from actin cortex studies and recent research on kinesin thermodynamics, kinesin-8 and kinesin-14 specifics including their structures and roles in meiosis, kinesin-5's role in meiotic spindle bipolarity, the role of dynein in meiotic division including its structure, and thermodynamic laws in living cells, substantiated by peer-reviewed references from prestigious journals.
DOI: 10.6078/d1fd8g
title: Locomotor behavior of wolf spiders in the paramo

description: Ectothermic animals depend on ambient temperature to regulate internal
 temperature. This dependence affects their ecology and behavior, including
 locomotion, foraging, and reproduction. Additionally, ectotherms are more
 vulnerable in environments with extreme hourly temperature fluctuations,
 and their activity patterns likely match those of favorable temperatures.
 Here, we studied Pardosa wolf spiders (Lycosidae) in the highland tropical
 paramos of Costa Rica. We tested two hypotheses to elucidate the drivers
 of variation in locomotor behavior. First, we tested if locomotor behavior
 is driven by temperature variation. Spiders experimentally exposed to
 higher temperatures (30°C) moved 3.96 times faster than those exposed to
 lower temperatures (7°C). Second, we tested if locomotor behavior is
 modulated by the maternal care strategy of these spiders. Females carry an
 egg sac externally by holding it with the distal spinnerets. The egg sac
 can represent up to 36% of the spider's body size. Females moved at
 the same speed regardless of whether they carried an egg sac or not. This
 demonstrates that the maternal care strategy does not affect their
 locomotor performance. In contrast, temperature plays a crucial role in
 driving locomotion. These findings expand our understanding of how
 temperature fluctuations in extreme environments challenge ectotherms’
 ability to escape predators and locate potential mates and food.
description: We ran locomotor behavior trials in which we tested the relative
 velocity of female wolf spiders of Pardosa sp. (Araneae: Lycosidae).
 Spiders were experimentally subjected to cold or heat conditions, and we
 measured their velocity afterward. A portion of those females was carrying
 an external egg sac that represented up to ~1/3 of their body size. This
 allowed us to test the effect of carrying that object on their
 speed. We conducted this fieldwork in the highland
 paramo environment of Costa Rica.
DOI: 10.5061/dryad.x95x69pq7
title: A new species of Illacme from southern California (Siphonophorida, Siphonorhinidae)

description: The millipede fauna inhabiting deep soil are poorly known. They are small
 and threadlike, slow moving, lacking pigmentation, and rarely encountered
 due to their obscure underground way of life. One family, the
 Siphonorhinidae, encompasses four genera and 12 species in a fragmentary
 distribution in California, southern Africa, Madagascar, the Malay
 Archipelago, and Indo-Burma. The family is represented in the Western
 Hemisphere by a single genus, Illacme Cook & Loomis, 1928 from
 California, with its closest known relative, Nematozonium filum Verhoeff,
 1939, from southern Africa. We document a new species of this family from
 soil microhabitats in the Los Angeles metropolitan area, Illacme socal n.
 sp. Based on this discovery and the recent documentation of other endogean
 millipede species, we show that these grossly understudied subterranean
 fauna represent the next frontier of discovery. However, they are
 threatened by encroaching human settlement and habitat loss, and
 conservation of this species and other subterranean fauna is of high
 importance.
DOI: 10.5061/dryad.b5mkkwhj0
title: Dietary and niche analyses of four endemic and sympatric batoid species of the subtropical South Atlantic Ocean

description: We aimed to characterize the trophic ecology and test the hypothesis of
 niche overlap between four sympatric batoid species of the subtropical
 South Atlantic. Data were collected between 2017 and 2022 from two
 artisanal fishery communities in southern Brazil. Batoid’s stomach
 contents were identified, separated into categories, and weighed. We
 calculated the Levins, Pianka’s, and Prey-specific index of relative
 dietary importance (PSIRI) and performed a similarity test using PERMANOVA
 and the similarity percentage (SIMPER) for niche analysis. We analyzed 229
 stomachs of four batoid species, 187 containing foods. All species showed
 a narrow food niche. The most important diet items for each species
 were Leptochaela serratorbita and Onuphidae
 for Dasyatis hypostigma; Nematoda for Pseudobatos
 horkelii; L. serratorbita, Sicyonia
 dorsalis and Portunidae for Rioraja
 agassizii and Achelous spinicarpus and fish
 for Sympterygia bonapartii. The analyses showed dissimilarity
 among the species’ diets without significant niche overlap. Our results
 detected the absence of significant niche overlap among batoid species,
 suggesting other types of niche partitioning and spatiotemporal habitat
 variation. This information could be considered for local management
 plans.
description: Data were collected in two
 artisanal fisheries communities in coastal Southern Brazil (27° 22’ S, 48°
 20’ W,) from July 2017 to March 2022. The biometric data (total length –
 TL, disc width – DW, weight, sex, stage of maturation) were recorded for
 all batoid individuals. Stomachs were removed, fixed in 10% formalin, and
 sorted in the laboratory. The content was identified to the lowest
 possible taxonomic level, quantified, and weighed for each batoid species.
 We used family identification as the lowest taxonomic level to compare
 diet between species (i.e., Fish, Portunidae, Varunidae, Onuphidae,
 Sicyonidae). Seaweed and substrate were considered as accidental ingestion
 and excluded from analysis (Aguiar & Valentin,
 2010).
description: Excel and
 R Language for Statistical
 Computing 2022.
DOI: 10.5061/dryad.905qfttr1
title: Data from: Landscape variation in defense traits along gradients of multiple resources in a tropical savanna plant

description: Many plant species are widely distributed and consequently are exposed to
 multiple abiotic factors and diverse herbivores, each of which may
 distinctly affect the magnitude of different defense
 traits. Alternative theories for optimal allocation to plant
 defense traits predict both positive and negative associations between
 magnitude of defense and resource availability. These predictions may
 apply even within species. This suggests potential for a single species‘
 patterns of association of defense traits and resources to vary with both
 the type of defense and identity of resource, but relatively few studies
 have explored intraspecific variation in multiple defense traits along
 several resource gradients simultaneously. In order to address this gap,
 especially in an ecosystem dominated by large mammalian herbivores, we
 assessed relationships between multiple resources (rainfall, soil N, and
 soil P) and plant defense traits (prickle density, phenolics, and lignin
 content) using a widely distributed tropical savanna herb, Solanum
 incanum, growing in naturally occurring resource gradients within the
 Serengeti National Park. We found substantial intraspecific variation in
 all three defense traits across sites (n =43). Variation in prickle
 density was positively associated with rainfall and soil P, but not soil
 N. In contrast to prickle density, phenolics and lignin were uncorrelated
 with all three resource gradients. This independent association of soil P
 with a carbon-based defense, prickle density, suggests potential for
 resources that are not components of defenses to influence allocation to
 defense traits. Such influence may reflect association between resource
 and herbivore abundance and/or preference. These varied patterns in
 resource-defense associations further emphasize the tremendous variation
 in anti-herbivore traits which may be influenced by different plant
 resources and highlight the need to consider multiple resource gradients
 in understanding evolution of plant traits.
DOI: 10.5061/dryad.15dv41p2j
title: Data for: Northern crayfish form alternation morphometrics

description: Complex life histories are frequently associated with biological
 trade-offs, as the use of one trait can decrease the performance of a
 second trait due to the need to balance competing demands to maximize
 fitness. Here, we examine growth patterns in invasive adult male northern
 crayfish (Faxonius virilis) that are indicative of a potential trade-off
 between energy allocation for body size versus chelae size growth.
 Northern crayfish undergo cyclic dimorphism, a process characterized by
 seasonal morphological changes associated with reproductive status. We
 measured carapace length and chelae length before and after molting and
 compared these growth increments between the four morphological
 transitions of the northern crayfish. Consistent with our predictions,
 reproductive crayfish molting to the non-reproductive form and
 non-reproductive crayfish molting within the non-reproductive form
 experienced a larger carapace length growth increment. Reproductive
 crayfish molting within the reproductive form and non-reproductive
 crayfish molting to the reproductive form, on the other hand, experienced
 a larger growth increment in chelae length. The results of this study
 support that cyclic dimorphism evolved as a strategy for optimizing energy
 allocation for body and chelae size growth during discrete periods of
 reproduction in crayfish with complex life histories.
description: Morphometric data for the present study were derived
 opportunistically from adult male northern crayfish collected as part of
 separate experiments that took place over a two-year period. Crayfish in
 these separate experiments were held in the lab for behavioral
 measurements that included measuring activity (<em>n </em>=
 156) and aggression (<em>n</em> = 84). Depending on the nature
 of the experiment, crayfish were held in the laboratory for various
 lengths of time (3-6 weeks). As a result, long-term housing allowed us to
 capture morphological measurements before and after molting events as they
 occurred. Therefore, measurements for the present study were
 opportunistically collected from 33 of these crayfish that happened to
 molt while being held in the lab, as follows: 12 in 2019 and 21 in
 2020.
DOI: 10.5281/zenodo.18401711
title: Data on small mammal community composition and pathogen screening used for statistical analysis

description: Understanding the ecological mechanisms driving biodiversity and disease associations is critical for biodiversity conservation and public health strategies. However, despite numerous studies describing the direction of biodiversity-disease relationships, field-based evidence identifying the underlying ecological mechanisms remains scarce. Here, we combine extensive field data on 1) small mammal communities and 2) flea-borne pathogens collected across a gradient of land use disturbance in The Netherlands. Data was used to test whether dilution effects arise through shifts in host community composition or through interspecific interactions between low- and high-quality hosts.

Files included:

Comm_comp.csv: Data on small mammal community composition used for CA and PERMANOVA analyses, and for Figure 3 of the associated manuscript.

Model_manuscript.csv: Data used for all generalized linear mixed models and for Figures 4–6 of the associated manuscript.

These datasets accompany a manuscript currently under peer review and are made available to ensure transparency and reproducibility of the analyses.
DOI: 10.5281/zenodo.18401710
title: Data on small mammal community composition and pathogen screening used for statistical analysis

description: Understanding the ecological mechanisms driving biodiversity and disease associations is critical for biodiversity conservation and public health strategies. However, despite numerous studies describing the direction of biodiversity-disease relationships, field-based evidence identifying the underlying ecological mechanisms remains scarce. Here, we combine extensive field data on 1) small mammal communities and 2) flea-borne pathogens collected across a gradient of land use disturbance in The Netherlands. Data was used to test whether dilution effects arise through shifts in host community composition or through interspecific interactions between low- and high-quality hosts.

Files included:

Comm_comp.csv: Data on small mammal community composition used for CA and PERMANOVA analyses, and for Figure 3 of the associated manuscript.

Model_manuscript.csv: Data used for all generalized linear mixed models and for Figures 4–6 of the associated manuscript.

These datasets accompany a manuscript currently under peer review and are made available to ensure transparency and reproducibility of the analyses.
DOI: 10.5061/dryad.g1jwstqw6
title: Data from: Ecological genetics of local adaptation in Arabidopsis: an 8-year field experiment

description: There is considerable evidence for local adaptation in nature, yet
 important questions remain regarding its genetic basis. How many loci are
 involved? What are their effect sizes? What is the relative importance of
 conditional neutrality vs. genetic trade-offs?  Here we address
 these questions in the self-pollinating, annual plant Arabidopsis
 thaliana. We used 400 recombinant inbred lines (RIL) derived from two
 locally adapted populations in Italy and Sweden, grew the RILs and parents
 at the parental locations, and mapped quantitative trait loci (QTL) for
 mean fitness (fruits/seedling planted). We previously published results
 from the first three years of the study, and here add five additional
 years, providing a unique opportunity to assess how temporal variation in
 selection might affect QTL detection and classification. We found ten
 adaptive and one maladaptive QTL in Italy, and six adaptive and four
 maladaptive QTL in Sweden. The discovery of maladaptive QTL at both sites
 suggests that even locally adapted populations are not always at their
 genotypic optimum. Mean effect sizes for adaptive QTL, 0.97 and 0.55
 fruits in Italy and Sweden respectively, were large relative to the mean
 fitness of the RILs (approximately 8 fruits/seedling planted at both
 sites). Both genetic trade-offs (four cases) and conditional neutrality
 (seven cases) contribute to local adaptation in this system. The
 eight-year dataset provided greater power to detect QTL and to estimate
 their locations compared to our previous three-year study, identifying one
 new genetic trade-off and reclassifying one QTL from genetic trade-off to
 conditionally neutral.
DOI: 10.5061/dryad.tdz08kq49
title: Supporting isotopic data for: Amino acid isotope analysis reveals variation in gut microbial contribution to host protein metabolism in a wild small mammal community

description: Herbivory is a dominant feeding strategy among animals, yet herbivores are
 often protein limited. The gut microbiome is hypothesized to help maintain
 host protein balance by provisioning essential macromolecules, but this
 has never been tested in wild consumers. Using amino acid carbon (δ13C)
 and nitrogen (δ15N) isotope analysis, we estimated the proportional
 contributions of essential amino acids (AAESS) synthesized by gut microbes
 to five co-occurring desert rodents representing herbivorous, omnivorous,
 and insectivorous functional groups. We found that herbivorous rodents
 occupying lower trophic positions (Dipodomys spp.) routed a substantial
 proportion (~40–50%) of their AAESS from gut microbes, while higher
 trophic level omnivores (Peromyscus spp.) and insectivores (Onychomys
 arenicola) obtained most of their AAESS (~58%) from plant-based energy
 channels but still received ~20% of their AAESS from gut microbes. These
 findings empirically demonstrate that gut microbes play a key functional
 role in host protein metabolism in wild animals.
DOI: 10.6078/d1xd96
title: Precursor recommendation for inorganic synthesis by machine learning materials similarity from scientific literature

description: Synthesis prediction is a key accelerator for the rapid design of advanced
 materials. However, determining synthesis variables such as the choice of
 precursor materials is challenging for inorganic materials because the
 sequence of reactions during heating is not well understood. In this work,
 we use a knowledge base of 29,900 solid-state synthesis recipes,
 text-mined from the scientific literature, to automatically learn which
 precursors to recommend for the synthesis of a novel target material. The
 data-driven approach learns chemical similarity of materials and refers
 the synthesis of a new target to precedent synthesis procedures of similar
 materials, mimicking human synthesis design. When proposing five precursor
 sets for each of 2,654 unseen test target materials, the recommendation
 strategy achieves a success rate of at least 82%. Our approach captures
 decades of heuristic synthesis data in a mathematical form, making it
 accessible for use in recommendation engines and autonomous laboratories.
DOI: 10.5061/dryad.8pk0p2nsw
title: A broader flight season for Norway’s Odonata across a century and a half

description: As global climate continues to change, so too will phenology of a wide
 range of insects. Changes in flight season usually are characterised as
 shifts to earlier dates or means, with attention less often paid to flight
 season breadth or whether seasons are now skewed. We amassed flight season
 data for the insect order Odonata, the dragonflies and damselflies, for
 Norway over the past century-and-a-half to examine the form of flight
 season change. By means of Bayesian analyses that incorporated uncertainty
 relative to annual variability in survey effort, we estimated shifts in
 flight season mean, breadth, and skew. We focussed on flight season
 breadth, positing that it will track documented growing season expansion.
 A specific mechanism explored was shifts in voltinism, the number of
 generations per year, which tends to increase with warming. We found
 strong evidence for an increase in  flight season breadth but
 much less for a shift in mean, with any shift of the latter tending toward
 a later mean. Skew has become rightward for suborder Zygoptera, the
 damselflies, but not for Anisoptera, the dragonflies, or for the Odonata
 as a whole. We found weak support for voltinism as a predictor of broader
 flight season; instead, voltinism acted interactively with use of
 human-modified habitats, including decrease in shading (e.g., from timber
 extraction). Other potential mechanisms that link warming with broadening
 of flight season include protracted emergence and cohort splitting, both
 of which have been documented in the Odonata. It is likely that
 warming-induced broadening of flight seasons of these widespread insect
 predators will have wide-ranging consequences for freshwater ecosystems.
description: Data was extracted from Artsdatabanken, a public database for
 Norway.  Data were cleaned, and useable records served as the basis for
 analyses.
description: Excel.