cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.v41ns1s2f
title: Museomics unveil systematics, diversity and evolution of Australian cycad-pollinating weevils

description: Weevils have been shown to play significant roles in the obligate
 pollination of Australian cycads. In this study we apply museomics to
 produce a first molecular phylogeny estimate of the Australian cycad
 weevils, allowing an assessment of their monophyly, placement and
 relationships. Divergence dating suggests that the Australian cycad
 weevils originated from the late Oligocene to the middle Miocene and that
 the main radiation of the cycad-pollinating groups occurred from the
 middle to the late Miocene, which is congruent with the diversification of
 the Australian cycads, thus refuting any notion of an ancient ciophilous
 system in Australia. Taxonomic studies reveal the existence of nineteen
 Australian cycad weevil species and that their associations with their
 hosts are mostly non-species-specific. Co-speciation analysis shows no
 extensive co-speciation events having occurred in the ciophilous system of
 Australian cycads. The distribution pattern suggests that geographic
 factors, rather than diversifying co-evolution, constitute the overriding
 process shaping the Australian cycad weevil diversity. The synchronous
 radiation of cycads and weevil pollinators is suggested to be a result of
 the post-Oligocene diversification common in Australian organisms.
description: All methods are described in the manuscript and supplementary
 materials in detail.
DOI: 10.5061/dryad.rjdfn2zj1
title: Predators can sequester and use novel toxins from exotic non-coevolved prey

description: Here, we chose a well-known system of invasive species to test whether
 non-coevolved predators can sequester and use toxins from exotic
 prey. Together with the invasive prickly pear plants, cochineal bugs
 (Dactylopius spp.) are spreading worldwide from their native range in the
 Americas. These insects produce carminic acid, a defensive anthraquinone
 that some specialized predators of cochineal bugs sequester for their own
 defense. We carried out a series of experiments to test whether
 non-coevolved predators in the exotic range of cochineal bugs can also
 sequester carminic acid and potentially benefit from this substance. We
 designed a series of experiments to test whether non-coevolved predators
 that feed on exotic cochineal bugs can sequester carminic acid and use it
 to release it on demand and repel their potential enemies. We first
 identified and quantified the resident predators that exploit cochineal
 bugs in the Mediterranean basin, an area invaded by cochineal bugs. Then,
 we determined whether the most abundant coccinellid predator tolerated,
 sequestered, and released carminic acid in the reflex-bleeding. Finally,
 we quantified the deterrent effect of carminic acid against antagonistic
 ants present in the invaded area. This data collection gathers different
 datasets collected by Ángel Plata between 2020 and 2022. It is organized
 in three different folders according to previously stated objectives. Each
 folder contains a file with the collected data. Besides the data, each
 folder contains README files that explain the methodology for collecting
 the data and README files that describe the structure of the data. When
 necessary, the calculation sheets and the codes related to statistical
 analysis and generation of figures are also included.
description: # Data from: Use of a novel toxin sequestered from exotic prey by a
 non-coevolved predator This collection gathers different datasets that
 have been used to generate the paper "Use of a novel toxin from
 exotic diet by a non-coevolved predator". These data have been
 collected by ngel Plata between 2020 and 2022. Each file folder contains
 the data used for the different sections explained in detail in the
 methodology of the above-mentioned paper. Folder 1 (two data sets):
 Exploitation of cochineal bugs by resident predators Folder 2 (one data
 set): Sequestration of carminic acid by C. montrouzieri Folder 3 (two data
 sets): Deterrence of carminic acid against C. montrouzieri potential
 enemies Besides the data, each folder includes several files:
 README_data_collection: it explains the methodology for collecting the
 data. README_files_description: it describes each file contained in the
 folder and the structure of the data. When necessary, the calculation
 sheets and the codes related to statistical analysis and generation of
 figures are also included.
DOI: 10.15151/esrf-dc-2324015771
title: From Pharmacophore to Warhead: NAD+-Targeting Triazoles as Mechanism-Based Sirtuin Inhibitors

description: Sirtuins (SIRTs) are nicotinamide adenine dinucleotide (NAD+)-dependent lysine deacylases linked to key physiological and disease processes. Here, we report a new class of mechanism-based 1,2,3-triazole inhibitors that hijack SIRT catalysis by forming stalled triazolium– or triazole–ADP-ribose (ADPR) adducts derived from the cofactor NAD+. These trapped adducts inhibit the enzyme without covalent protein modification, prompting us to term the compounds “Sirtuin Trapping Ligands” (SirTraps). X-ray crystallography and kinetics, together with mass spectrometry confirming adduct formation both in vitro and in cellulo, reveal that the triazole N3 of peptide- and small-molecule-based SirTraps triggers nucleophilic attack at C1’ of the nicotinamide riboside moiety of NAD+, mimicking the first deacylation step. Adduct formation critically depends on precise triazole positioning within the acyl-lysine channel and can be tuned through scaffold design, enabling potent and isoform-selective inhibition. Unlike thiocarbonyl-based NAD+-targeting SIRT inhibitors, which may suffer from instability and off-target effects, SirTraps combine high stability, synthetic accessibility, and structural tunability, while demonstrating nanomolar cellular target engagement confirmed by NanoBRET assays. Beyond SIRTs, this inhibition strategy may extend to other NAD+-dependent enzymes, including ADP-ribosyltransferases, opening new avenues for mechanism-driven drug discovery.
DOI: 10.5061/dryad.dz08kps31
title: Hydrobates spp. – Circadian locomotor output cycles kaput (Clock) gene poly-glutamine repeats

description: Annual cues in the environment result in physiological changes that allow
 organisms to time reproduction during periods of optimal resource
 availability. Understanding how circadian rhythm genes sense these
 environmental cues and stimulate the appropriate physiological changes in
 response is important for determining the adaptability of species,
 especially in the advent of changing climate. A first step involves
 characterizing the environmental correlates of natural variation in these
 genes. Band-rumped and Leach’s storm-petrels (Hydrobates spp.) are pelagic
 seabirds that breed across a wide range of latitudes. Importantly, some
 populations have undergone allochronic divergence, in which sympatric
 populations use the same breeding sites at different times of year. We
 investigated the relationship between variation in key functional regions
 of four genes that play an integral role in the cellular clock mechanism –
 Clock, Bmal1, Cry2 and Per2 – with both breeding season and absolute
 latitude in these two species complexes.  We discovered that
 allele frequencies in two genes, Clock and Bmal1, differed between
 seasonal populations in one archipelago, and also correlated with absolute
 latitude of breeding colonies. These results indicate that variation in
 these circadian rhythm genes may be involved in allochronic speciation, as
 well as adaptation to photoperiod at breeding locations.
description: This dataset contains Clock allele length information for samples
 of band-rumped storm-petrel (<em>Hydrobates</em>
 <em>castro</em>) and Leach's storm-petrel
 (<em>Hydrobates leucorhoa</em>) populations located throughout
 the Atlantic and Pacific oceans. The data were collected from 1995 to
 2011. The data were collected by the following individuals:
 Yuliana Bedolla-Guzman Petra
 Quillfeldt Juan F. Masello Petra
 Deane Vicki L. Friesen 
 Polymerase Chain Reaction (PCR) was performed to isolate the
 <em>Clock</em> gene for all samples in the study. Sequences
 were aligned using BioEdit (v7.0.9) to confirm amplification of the
 intended target. A Beckman-Coulter CEQ 8000 was then used to screen for
 variation in allele lengths in all individuals. The Beckman-Coulter CE
 8000 Genetic Analysis software was used to score the resulting
 chromatograms. Clock allele lengths and sequences of 10 individuals were
 compared to determine the corresponding number of polyQ repeats based on
 allele length. Basic Local Alignment Search Tool (BLAST) searches on
 GenBank were used to confirm that the target genes were correctly
 amplified.
description: The data files included are in CSV format and can be opened using
 a plain text editor (e.g. Notepad), Microsoft Excel, VS Code,
 etc.
DOI: 10.7280/d1611w
title: Data from: Catalytic materials enabled by a programmable assembly of synthetic polymers and bacterial spores

description: Natural biological materials are formed by self-assembly processes and
 catalyze a myriad of reactions. Here, we report a programmable molecular
 assembly of designed synthetic polymers with engineered Bacillus subtilis
 spores. The bacterial spore-based materials possess modular mechanical and
 functional properties derived from the independent design and assembly of
 synthetic polymers and engineered spores .  We discovered that
 phenylboronic acid (PBA) derivatives form tunable and reversible dynamic
 covalent bonds with the spore surface glycan. Spore labeling was performed
 using fluorescent PBA probes and monitored by fluorescence microscopy and
 spectroscopy. Binding affinities of PBA derivatives to spore surface
 glycan was controlled by aryl substituent effects. On the basis of this
 finding, PBA-functionalized statistical copolymers were synthesized and
 assembled with B. subtilis spores to afford macroscopic materials that
 exhibited programmable stiffness, self-healing, prolonged dry storage, and
 recyclability. These material properties could be examined using shear
 rheology, tensile testing, and NMR experiments.  Integration of
 engineered spores with surface enzymes yielded reusable biocatalytic
 materials with exceptional operational simplicity and high benchtop
 stability. The reaction progress of the biocatalyses could be monitored
 with fluorescence specroscopy and absorption measurements, while spore
 leakage could be monitored by changes in solution turbidity (OD600). The
 use of bacterial spores as an active partner in dynamic covalent
 crosslinking sets our material apart from previous examples and grants
 control over biocontainment as well as the subsequent fate of the spores
 through stimuli-responsive reversal of the crosslink.
description: All experimental methods are briefly described in the README.md
 file, and fully detailed in the Supporting Information file for the paper
 article "Catalytic materials enabled by a programmable assembly of
 synthetic polymers and engineered bacterial spores".
DOI: 10.5061/dryad.7m0cfxq0x
title: Large mammalian herbivores affect arthropod food webs via changes in vegetation characteristics and microclimate

description: Large mammalian herbivores are vital components of terrestrial ecosystems,
 influencing the plants they feed on, but also serving as ecosystem
 engineers that impact the occurrence and survival of many other organisms.
 Arthropods are the most abundant and diverse animal group on earth,
 filling all trophic levels in food webs and facilitating essential
 ecosystem services. However, the impacts of large herbivores on arthropod
 communities and the mechanisms via which these impacts are mediated are
 not fully understood.  Here, we experimentally separated the
 mechanistic pathways whereby large herbivores affect arthropod food webs
 using a 24-year manipulative multi-site field experiment in the
 Netherlands. We analyzed the abundance, biomass, and community composition
 of arthropods in the plant canopy and on the soil surface, both in grazed
 sites or sites where large herbivores were excluded. We found that the
 presence of large herbivores resulted in considerable differences in
 vegetation properties and microclimate which influenced the abundance and
 biomass of arthropods to varying trophic levels. Large herbivore grazing
 enhanced the overall abundance and biomass of arthropod herbivores,
 pollinators, omnivores, and soil-dwelling predators, but reduced that of
 detritivores, scavengers, parasitoids, and canopy predators. Structural
 equation models revealed that different trophic groups are affected by
 grazing via different pathways. Specially, large herbivores facilitated
 herbivores via increasing plant quality and enhanced ground-dwelling
 predators via increasing plant diversity. In contrast, plant-dwelling
 predators were suppressed via decreased plant quantity, and parasitoids
 were mainly affected by changes in microclimate conditions. 
 Synthesis. Our results show that large mammalian herbivores play a
 significant role in shaping grassland arthropod food webs and that these
 impacts were independently mediated by multiple aspects of vegetation
 properties, i.e., physical structure, plant diversity, standing crop
 biomass, and leaf nutrient content. Arthropods of different trophic groups
 responded differently to the large herbivores, and these functional
 group-specific responses in turn may have strong cascading effects on
 numerous ecosystem services.
DOI: 10.5061/dryad.f7m0cfz2d
title: Strain localization in sandstone-derived fault gouges under conditions relevant to earthquake nucleation

description: Constraining strain localization and the growth of shear fabrics within
 brittle fault zones at sub-seismic slip rates are important for
 understanding fault strength and frictional stability. We conducted direct
 shear experiments on simulated sandstone-derived fault gouges at an
 effective normal stress of 40 MPa, pore fluid pressure of 15 MPa, and
 temperature of 100°C. Using a passive strain marker and X-ray Computed
 Tomography (XCT), we analyzed the spatial deformation of the gouge samples
 obtained from the strain-hardening stage to strain-softening stage to
 steady-state at shearing velocities of 1, 30, and 1000 µm/s. We developed
 a machine-learning-based automatic boundary detection method to recognize
 the shear zone fabrics and quantify the slip partitioning between each
 fabric element. Our results show that R1 and Y (or boundary) shears are
 the two major shear zone fabrics. At velocities of 1 and 30 µm/s, the
 relative amount of slip on R1 shears is displacement dependent and
 increases to ~20% at the strain-softening stage and then decreases to
 ~10–18% at steady-state. This trend is absent at high velocity with an
 amount of ~18% through all investigated stages. At all velocities, the
 relative amount of slip on Y and boundary shears increases linearly with
 displacement to a total of more than 50% at steady-state. Our study
 provides constraints for the development of the active slip zone, which is
 an important input parameter for the heat budget for small-magnitude
 earthquakes with limited slip (mm-dm), such as those occurring in induced
 seismicity.
description: The raw data.zip is generated by conducting direct shear
 experiments on sandstone-derived fault gouges. The
 processed data.zip is generated by executing
 automatic_boundary_detection_code in Jupyter Notebook on X-ray CT images
 in the raw data. The automatic boundary detection code
 was developed based on the custom-designed machine-learning trainable
 segmentation tool from the scikit-image, an open-source image processing
 library (https://scikit-image.org/)
DOI: 10.5061/dryad.gb5mkkwvq
title: Lipidomics analysis of WT and CLN5-deficient HEK293T cells, iPSCs, and iNeurons

description: Lysosomes critically rely on bis(monoacylglycero)phosphate (BMP) to
 stimulate lipid catabolism, cholesterol homeostasis, and lysosomal
 function. Alterations in BMP levels in monogenic and complex
 neurodegeneration suggest an essential function in human health. However,
 the site and mechanism responsible for BMP synthesis have been subject to
 debate for decades. Here, we report that the Batten disease gene product
 CLN5 is the elusive BMP synthase (BMPS). BMPS-deficient cells exhibit a
 massive accumulation of the BMP synthesis precursor
 lysophosphatidylglycerol (LPG), depletion of BMP species, and
 dysfunctional lipid metabolism. Mechanistically, we demonstrate that BMPS
 mediates synthesis through an energy-independent base exchange reaction
 between two LPG molecules with increased activity on BMP-laden vesicles.
 Our study resolves the long-sought BMP biosynthetic route and reveals a
 novel anabolic function of late endosomes/lysosomes.
description: ## Lipidomics of CLN5-deficient and WT HEK293T cells, iPSCs, and iNeurons
 Dataset contains raw files for analysis in free softwares FreeStyle and
 MS-DIAL. #### Description of the Data and file structure * P = positive
 mode * N = negative mode * Pos = positive mode * Neg = negative mode * B =
 LysoIP Fraction * 101-103 = WT iPSCs * 91-93 = CLN5 KO iPSCs * 91B-94B =
 CLN5 KO HEK293Ts * 11B-14B = WT HEK293Ts * W1-3 = WT iNeurons * 51-53 =
 CLN5 KO iNeurons * "93B_pos_20230102182818" refers to 93B_pos
 iPSCs, HEK293Ts, and iNeurons should be analyzed as groups
DOI: 10.5061/dryad.ghx3ffbv0
title: Volunteers in Public Service Production: Modeling the Contributions of Volunteers to Organizational Performance

description: Volunteer use is an alternative service delivery arrangement in which
 public organizations directly involve volunteers in service production
 through a quasi-employment relationship. However, research evaluating the
 contributions of volunteer labor to organizational performance is
 relatively few. This article fills this gap by drawing from two
 theoretical insights. First, we test a linear model based on the
 traditional human resource management approach of interchangeability in
 which volunteers constitute a one-on-one substitute for paid employees.
 Second, we draw insight from critical mass theory to test a nonlinear
 model based on the assumption that the productivity of one volunteer may
 not be equal to that of one paid employee due to the systematic
 limitations of volunteer labor. Analyzing a large-N panel dataset of law
 enforcement agencies in the United States that utilize sworn volunteers
 with general arrest powers, the findings indicate that an increase in the
 number of sworn volunteers has a linear negative effect on clearing
 violent crimes in sheriffs' offices. However, we also find some
 evidence that volunteer use displays curvilinear effects on clearing
 violent crimes in police departments. This article suggests the need to
 account for the systematic limitations of volunteer labor when measuring
 performance and to explore multiple indicators. This study contributes to
 theory building and testing by enabling a two-way understanding of the
 relationship between volunteer involvement and organizational performance
 in the public sector.
description: STATA
DOI: 10.5061/dryad.12jm63z3m
title: A type 2 immune circuit in the stomach controls mammalian adaptation to dietary chitin

description: Dietary fiber improves metabolic health, but host-encoded mechanisms for
 digesting fibrous polysaccharides are unclear. Here, we describe a
 mammalian adaptation to dietary chitin that is coordinated by gastric
 innate immune activation and acidic mammalian chitinase (AMCase). Chitin
 consumption causes gastric distension and cytokine production by stomach
 tuft cells and group 2 innate lymphoid cells (ILC2s), driving expansion of
 AMCase-expressing zymogenic chief cells that facilitate chitin digestion.
 Although chitin influences microbial composition, ILC2-mediated tissue
 adaptation and gastrointestinal responses are preserved in germ-free mice.
 In the absence of AMCase, sustained chitin intake leads to heightened
 basal type 2 immunity, reduced adiposity, and resistance to obesity. These
 data define an endogenous metabolic circuit that enables nutrient
 extraction from an insoluble dietary constituent by enhancing digestive
 function.
DOI: 10.5061/dryad.7sqv9s4xs
title: Overlapping representations of food and social stimuli in VTA dopamine neurons

description: 2-photon imaging and behavioral data accompanying publication of
 "Overlapping representations of food and social stimuli in VTA
 dopamine neurons" (Lindsay Willmore, Adelaide Minerva, Ben Engelhard,
 Brenna McMannon, Nirja Oak, Stephan Thiberge, Malavika Murugan, Catherine
 Jensen Pena, Ilana Witten). This dataset contains all information required
 to recreate figures from the paper. 
description: Transgenic mice expressing the calcium-sensitive fluorescent
 indicator GCamp6f in dopamine neurons were used to perform 2-photon
 calcium imaging of ventral tegmental area as mice were presented with
 various social and food stimuli. See paper for detailed paradigm methods.
 Regions of interest (ROIs) containing putative single neurons were
 extracted using suite2p.  Contents of this dataset
 include: 2p_aligned: aligned time traces
 for imaging ROIs & neuropil; syncing signals for behavior
 analysis 2p_ops: output ROIs and statistics from
 suite2p for each imaging session body: DeepLabCut
 tracking files for points on the body of the imaged and stimulus mice for
 each relevant imaging session pupil: DeepLabCut
 tracking files for points on the pupil of the imaged mouse for each
 relevant imaging session tongue: tracking of if the
 tongue was seen as a proxy for licking for each relevant imaging
 session usv: syllable_sequence files from MUPET
 across sessions, usv_count summary syllable count data across sessions,
 example raw data from a single session 
 Analysis code: https://github.com/lwillmore/SocialVTA2p
DOI: 10.17882/111835
title: COSTOF2, technical data from SeaMoN East, node of the EMSO-Azores observatory, 2024-2025

description: This dataset contains the technical log that has been done with the COSTOF2 n° 002 (COmmunication and STOrage Front-end 2), the SeaMoN East datalogger unit. This station is dedicated to biological observations on Lucky Strike site.