cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.g4f4qrfvk
title: Patchy particle insights into self-assembly of transparent, graded index squid lenses

description: Squids have spherical, gradient index lenses that maximize optical
 sensitivity while minimizing light scattering and geometric aberration.
 Previous studies have shown that the constituent lens proteins behave like
 patchy particles, and that a density gradient of packing fraction $\sim
 0.01$ to $1$ assembles from a gradient of average particle valence,
 $\langle M\rangle$ $\approx 2.1$ to $\langle M\rangle$ $&gt;6$. A
 priori, transparency requires that all regions within the larger gradient
 must minimize density fluctuations at length scales close to the
 wavelength of visible light. It is not known how a material can achieve
 this at all possible packing fractions via attractive interactions. We
 also observe that the set of proteins making the lens is remarkably
 polydisperse (there are around 40 isoforms expressed). Why does nature
 employ so many geometrically similar isoforms when theory suggests a few
 would suffice, and what, if any, is the physical role of the
 polydispersity? This study focuses on answering these questions for the
 sparsest regions of the lens, where the patchy nature of the system will
 have the largest influence on the final structure. We first simulated
 mixtures of bi- and trivalent patchy particles and found a strong
 influence of patch angle on the percolation and gel structure of the
 system. We then investigated the influence of the interaction
 polydispersity on the structure of the $M=2.1$ system. We find that
 increasing the variance in patch energies and single-patch angle appears
 decrease the length scale of density fluctuations while also moving the
 percolation line to lower temperature. S-crystallin geometry and
 polydispersity appear to contribute to promoting regular percolation of a
 gel structure while also limiting density fluctuations to small length
 scales, thereby promoting transparency in the annealed structure.
DOI: 10.5061/dryad.34tmpg4qs
title: Data from: Relational values of nature in empirical research: A systematic review

description: In the past five years, scholarly and policy attention to relational
 values, a concept that articulates plural values of nature, has grown
 steadily. To date, there are no published syntheses of empirical research
 that explicitly address relational values. We perform a systematic
 literature review of n = 72 empirical studies of relational values to
 summarize the state of current research and to identify opportunities for
 future research and conceptual development. In our analysis, we categorize
 what authors identify as relational values and summarize study
 characteristics (e.g., study location, methods approach.) Authors
 collectively report n = 312 unique relational values. Categories of
 identity, social cohesion, livelihoods, connection to place/human-nature
 connection, and religion are most common. Scholarship that
 explicitly addresses relational values has increased since 2017 and
 exhibits substantial diversity: in how relational values are
 conceptualized (or not); in disciplinary associations; in geographical
 location; and in data collection methods. We find that most empirical
 research on relational values does not justify how its results reflect
 characteristics that establish the relational values concept as unique
 from other environmental values concepts. As a result, diverse
 interpretations of the relational values concept pose the risk of the
 relational values concept being so broad and inclusive that it becomes
 meaningless, or at least meaning-light.
DOI: 10.5061/dryad.931zcrjr9
title: Data for figures in: Modal petrology and mineral chemistry of Apollo 17 Drive Tube Section 73002

description: The Apollo 17 mission returned samples from the Taurus-Littrow Valley of
 the Moon. Key features of the site are a basaltic valley floor partially
 enclosed by South Massif and North Massif mountains and the Sculptured
 Hills, which consist of feldspar-rich, highland lithologies. A recently
 opened soil core sampled an inferred landslide deposit at the base of
 South Massif. Study of a suite of polished grain mounts of six size
 fractions of &lt;1 mm material from 14 depth intervals of the ~18 cm
 soil column shows that all size fractions from the upper 5–6 cm are richer
 in agglutinates, an indicator of surface exposure, than the deeper
 material, which is among the most agglutinate-poor Apollo 17 regolith
 reported. Regolith breccia, crystalline melt breccia, and noritic igneous
 rocks are the most abundant fragment types. Mare basalt, glasses, and
 agglutinates are minor components throughout. The observations are
 consistent with deposition of the highland-dominated material in a
 landslide, which did not preserve any previous stratigraphy, followed by
 in situ maturation, with only minor additions of mare lithologies from
 nearby basaltic regolith, due to the inefficiency of lateral transport on
 the Moon.
description: Backscattered electron imaging, quantitative energy dispersive
 analysis, calculations and sorting in Excel spreadsheets, graphic displays
 by KaleidaGraph modified in PowerPoint.
description: MS Excel
DOI: 10.5061/dryad.6wwpzgn41
title: Breastfeeding, carrying, grooming, and playing behaviours in wild Javan gibbons (Hylobates moloch)

description: In pair-living species, female and male pairs may maintain stable social
 bonds by adjusting spatial and social associations. Nevertheless, each sex
 invests differently to maintain the pair bond, and the investment can
 depend on the presence of paternal care or ‘male services.’ While most
 species live in pairs, the sex responsible for pair bond maintenance in
 gibbons is still controversial. We investigated pair bond maintenance and
 parental care in three pairs of wild Javan gibbons in Gunung Halimun-Salak
 National Park, Indonesia, for over 21 months. We found that Javan gibbon
 fathers groomed their offspring more than adult females, especially as
 offspring get older. While both parents increased playing time with
 offspring when offspring became older and more independent, fathers played
 with offspring 20 times more than mothers on average. Grooming within
 Javan gibbon pairs was male-biased, suggesting that pair bond maintenance
 was heavily the job of males. However, offspring age as a proxy for
 paternal care did not affect the pair bond maintenance. Our study
 highlights that adult male Javan gibbons may have an important role in
 pair bond maintenance and the care of juveniles.
description: The field site is in the
 Citalahab area of the Gunung Halimun-Salak National Park
 (6°44′S,
 106°31′E) in West Java,
 Indonesia. We collected data from three habituated wild Javan gibbon
 groups A, B, and S. All
 three groups consist of an adult female-male pair and their offspring
 (total N = 12). We
 followed the age classification (infant; 0-2 years, juvenile; 2-5 years,
 adolescent; 5-8 years, subadult; 8-dispersal). Groups A and B had two offspring each
 throughout the study. Group S had three offspring and we excluded the
 oldest offspring from the data analysis since the individual dispersed in
 April 2016, near the end of the study.
 We carried out all-day field
 observations on the three habituated gibbon groups from one sleeping tree
 to the next over 22 months between November 2014 and July 2016. We
 observed them for 2,209 h
 over 306 days (group A: 776.25 h over 105 days; B: 720.5 h over 101 days;
 S: 712.25 h over 100 days). During the study period, we collected data from an adult female-male
 pair in each group, and a
 younger offspring (10-30 mo), and an older offspring (45-65 mo) from group
 A, and two younger offspring (5-25 mo) and two older offspring (41-61 mo)
 from group B and S. We recorded the occurrence of social grooming
 (hereafter ‘grooming’) and social playing (hereafter ‘playing’) bouts
 between all family members using all occurrence
 sampling. We defined a
 grooming bout as grooming without ceasing for longer than one minute in
 between. Particularly for the mother-offspring dyad, we
 recorded the time mothers breastfeed and carry infants using 15-min focal
 sampling (all occurrence sampling during 15-min) for every
 hour.
DOI: 10.5061/dryad.1jwstqk0s
title: MtDNA genomes from Ranis individuals aligned with previously published ancient & modern humans

description: The Middle to Upper Palaeolithic transition in Europe is associated with
 the regional disappearance of Neanderthals and the spread of Homo sapiens.
 Archaeological evidence indicates the presence of technocomplexes at the
 interface of this transition, complicating our understanding of the period
 and the association of those with specific hominin groups. One such
 technocomplex where the maker is unknown is the
 Lincombian-Ranisian-Jerzmanowician (LRJ), which covers an area in
 northwestern and central Europe from the UK to Poland. This paper presents
 the morphological and proteomic species identification, mitochondrial DNA
 analysis, and direct radiocarbon dating of human remains directly
 associated to an LRJ assemblage at the cave site of Ilsenhöhle in Ranis
 (Germany).  
description: DNA was extracted from skeletal remains identified as hominin
 from the site Ranis, Germany following the protocol described in Rohland
 et al., 2018 (buffer 'D') and then converted into
 single-stranded double-indexed libraries according to the automated
 protocol in Gansauge et al., 2020. Libraries from all specimens except
 R10873 were then enriched for human mitochondrial (mt) DNA via automated
 hybridization capture (Zavala et al., 2022). Enriched and non-enriched
 libraries were sequenced on Illumina platforms with paired-end sequencing.
 The ancient parameters for BWA (‘-n 0.01 –o 2 –l 16500’) were used for
 aligning reads to the revised Cambridge Reference Sequence (rCRS). Reads
 shorter than 35 basepairs or with mapping qualities less than 25 and PCR
 duplicates were removed. Consensus bases were called for positions with at
 least 5 reads and 80% support when masking C-to-T substitutions on the
 terminal seven positions of reads. The resulting sequences were realigned
 to the rCRS with previously published mtDNA genomes from 54 modern humans,
 19 ancient humans, and two Neanderthals using MAFFT). 
description: The file is in fasta format and can be read with any text editor
 or viewed in any sequence alignment software (MEGA, Seaview,
 etc).
DOI: 10.5061/dryad.z08kprrjd
title: Transformable nano-antibiotics for mechanotherapy and immune activation against drug-resistant Gram-negative bacteria

description: The dearth of antibiotic candidates against Gram-negative bacteria and the
 rise of antibiotic resistance create a global health concern. The
 challenge lies in the unique Gram-negative bacterial outer membrane that
 provides the impermeable barrier for antibiotics and sequesters antigen
 presentation. We designed a transformable nano-antibiotics (TNA) which can
 transform from nontoxic nanoparticles to bactericidal nanofibrils with
 reasonable rigidity (Young’s modulus, 21.6 ± 5.9 MPa) after targeting
 β-barrel assembly machine A (BamA) and lipid polysaccharides (LPS) of
 Gram-negative bacteria. After morphological transformation, the TNA can
 penetrate and damage the bacterial envelope, disrupt electron transport
 and multiple conserved biosynthetic and metabolic pathways, burst
 bacterial antigen release from the outer membrane, and subsequently
 activate innate and adaptive immunity. TNA kills Gram-negative
 bacteria in vitro and in vivo with undetectable resistance
 through multiple bactericidal modes of action. TNA-treatment-induced
 vaccination results in rapid and long-lasting immune responses, protecting
 against lethal re-infections.
DOI: 10.5061/dryad.5hqbzkhbh
title: PPND: a comprehensive genomic data platform for plant-parasitic nematode research

description: Plant parasitic nematodes are important phytopathogens, they harm the
 growth of agricultural and forestry plants for a long time. Scientists
 have done a series of studies on them to prevent and solve the diseases
 that they cause. With the advent of the genomics era, genome sequencing of
 plant parasitic nematodes has been greatly accelerated, and a large amount
 of data has been generated. This study developed the Plant Parasitic
 Nematodes Database (http://nematode.org.cn/), a platform to bring all
 these data together. The PPND contains genomic, transcriptomic, protein,
 and functional annotation data. It allows users to conduct BLAST searches,
 genome browser analyses, and download bioinformatics data for deeper
 research. PPND will be continuously updated, and new data will be
 integrated. We hope that the PPND will become a comprehensive genomic data
 platform for plant parasitic nematode research.
DOI: 10.5061/dryad.tb2rbp05t
title: Data from: Social group composition modulates the role of last male sperm precedence in post-copulatory sexual selection

description: In many species, the order in which males mate with a female explains much
 of the variation in paternity arising from post-copulatory sexual
 selection. Research in Drosophila suggests that mating order may account
 for the majority of the variance in male reproductive success. However,
 the effects of mating order on paternity bias might not be static but
 could potentially vary with social or environmental factors. To test this
 idea, we used an existing dataset, collated from an experiment we
 previously published (Morimoto et al. 2016), with the addition of
 unpublished data from the same experiment. These previous experiments
 manipulated larval density in Drosophila melanogaster which generated
 variation in male and female body size, assembled groups of individuals of
 different sizes, and measured the mating success and paternity share of
 focal males. The data presented here provide information on each focal
 male’s mating order and the frequency in which focal males remated with
 the same females (‘repetitive matings’). We combined this
 information with our previously reported focal male reproductive success
 to partition variance in paternity into male mating order and repetitive
 matings across groups that differed in the body size composition of males
 and females. We found, as expected, that male mating order explained a
 considerable portion of the variance in male paternity. However, we also
 found that the impact of male mating order on male paternity was
 influenced by the body size composition of groups. Specifically, males
 that tended to mate last had a greater paternity advantage, and displayed
 lower variance, in groups containing a heterogenous mixture of male body
 sizes than in groups with a single male body size. Repetitive mating only
 had a minor contribution to the variance in male paternity share across
 all experiments. Overall, our findings contribute to the growing body of
 research showing that post-copulatory sexual selection is subject to
 socio-ecological influences.
description: R was used to analyse the data. Excel is needed to open the
 files.
DOI: 10.5061/dryad.3tx95x6mh
title: Amplicon sequence variants (ASV) of gut pathogens in hooded cranes and domestic geese

description: Driven by habitat loss from anthropogenic activities, wintering migratory
 birds forage together with poultry in paddy fields, and thus impose risks
 of cross transmitting pathogens. To date, there is little evidence for
 such risks of pathogen transmission between wild birds and poultry. Using
 the high-throughput sequencing, we report on detected potential pathogens
 of both wild hooded cranes Grus monacha and sympatric domestic geese Anser
 anser domesticus during the wintering period and infer the possibility of
 cross-species pathogen transmission. The results revealed that the number
 of shared amplicon sequence variants (ASVs) of potential pathogens between
 the gut microbiota of the two species was low during the early wintering
 stage (17.2%; 5 ASVs shared) but increased to 56.3% (18 ASVs shared)
 during the late wintering stage. That is, potential pathogens in the gut
 microbial communities of the two species became more similar through
 co-foraging in paddy fields, supporting cross-transmission of pathogens
 between hooded cranes and domestic geese during the wintering period.
 Importantly, transmission appeared to be largely from wild hooded cranes
 to domestic geese, although some potential pathogens may have become
 specialized to the domestic goose in late wintering stage. Humans are also
 facing the risks of contracting these potential pathogens from migratory
 birds through their frequent contact with domestic poultry. It is,
 therefore, necessary to closely monitor this pathway of pathogen
 transmission from wild birds to domestic animals and even to humans.
DOI: 10.5061/dryad.5mkkwh7bf
title: Restoration temporarily supports the resilience of sagebrush-steppe ecosystems subjected to repeated fires

description: Many ecosystems are experiencing increased fire frequencies and species
 invasions that can erode their resilience and cause a shift to alternative
 states. In the sagebrush-steppe, a semi-arid shrubland ecosystem in North
 America, restoration treatments are often implemented following wildfire
 to enhance their resilience to invasion. However, little is known about
 the long-term effectiveness of these treatments. We investigated whether
 repeated restoration efforts provide greater resilience in
 sagebrush-steppe communities initially dominated by species with different
 post-fire regeneration traits and subjected to compounding wildfires and
 invasion by Bromus tectorum over 25 years. We studied 37 permanent
 transects (Columbia Basin, Washington, USA) in which species abundance was
 recorded multiple times from 1992 to 2017. We quantified community change
 and its relationship with fire, restoration, and moisture availability.
 Resilience was evaluated by quantifying community resistance and stability
 indices. The greatest change occurred in communities where the obligate
 seeding shrub Artemisia tridentata was initially common. Repeated fires
 led to the extirpation of this shrub and eventual dominance of B.
 tectorum. Herbicide applications temporarily suppressed B. tectorum
 post-fire. Seeding treatments and above average precipitation initially
 increased native cover. Although communities where resprouting species
 were common showed the least change, repeated fires did lead to a gradual
 but substantial decline (86%) in resprouting shrubs. Synthesis and
 applications: Our findings show that repeated restoration efforts,
 together with elevated precipitation, can support native species
 re-establishment in systems experiencing altered disturbance regimes and
 species invasions. Our unique long-term dataset demonstrates, however,
 that many such interventions have short-lived effects due to the strong
 “unhelpful resilience” of highly invaded systems. This implicitly suggests
 that many such systems have experienced fundamental shifts in ecosystem
 state. The likelihood of this occurring is strongly associated with the
 dominant species post-fire regeneration traits. We predict that community
 composition and resilience will continue to degrade in the
 sagebrush-steppe unless management prioritizes fire suppression and an
 adaptive restoration approach that considers resource availability.
description: See published article in the Journal of Applied Ecology for
 method details.
description: Compilation of raw empirical species abundance and enviromental
 data utilized in the associated manuscript. To guide interpretation, a
 brief 'readme' tab is attached to each file.
DOI: 10.25345/c5nz81396
title: MassIVE MSV000100618 - BitterSweetDB: MS/MS database of phytochemical diversity across tissues and ontogeny in S. dulcamara
title: Phytochemical diversity in Solanum dulcamara tissues across ontogeny in three different genetic backgrounds.
DOI: 10.5061/dryad.h44j0zpr2
title: Data and code for: Building use-inspired species distribution models: using multiple data types to examine and improve model performance

description: Species distribution models (SDMs) are becoming an important tool for
 marine conservation and management. Yet while there is an increasing
 diversity and volume of marine biodiversity data for training SDMs, little
 practical guidance is available on how to leverage distinct data types to
 build robust models. We explored the effect of different data types on the
 fit, performance and predictive ability of SDMs by comparing models
 trained with four data types for a heavily exploited pelagic fish, the
 blue shark (Prionace glauca), in the Northwest Atlantic: two
 fishery-dependent (conventional mark-recapture tags, fisheries observer
 records) and two fishery-independent (satellite-linked electronic tags,
 pop-up archival tags). We found that all four data types can result in
 robust models, but differences among spatial predictions highlighted the
 need to consider ecological realism in model selection and interpretation
 regardless of data type. Differences among models were primarily
 attributed to biases in how each data type, and the associated
 representation of absences, sampled the environment and summarized the
 resulting species distributions. Outputs from model ensembles and a model
 trained on all pooled data both proved effective for combining inferences
 across data types and provided more ecologically realistic predictions
 than individual models. Our results provide valuable guidance for
 practitioners developing SDMs. With increasing access to diverse data
 sources, future work should further develop truly integrative modeling
 approaches that can explicitly leverage strengths of individual data types
 while statistically accounting for limitations, such as sampling
 biases. 
description: Please see the README document ("README.md") and the
 accompanying published article: Braun, C. D., M. C. Arostegui, N.
 Farchadi, M. Alexander, P. Afonso, A. Allyn, S. J. Bograd, S. Brodie, D.
 P. Crear, E. F. Culhane, T. H. Curtis, E. L. Hazen, A. Kerney, N.
 Lezama-Ochoa, K. E. Mills, D. Pugh, N. Queiroz, J. D. Scott, G. B. Skomal,
 D. W. Sims, S. R. Thorrold, H. Welch, R. Young-Morse, R. Lewison. In
 press. Building use-inspired species distribution models: using multiple
 data types to examine and improve model performance. Ecological
 Applications. Accepted. DOI: &lt; article DOI will be added when it is
 assigned &gt;