cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17617/3.z0hmmh
title: Data and code for publication Species–specific circuitry of double cone photoreceptors in two avian retinas

description: Contains data reported in the paper "Species–specific circuitry of double cone photoreceptors in two avian retinas" and the code for data analysis and generation of figures. The raw EM dataset is not included due to size limitations but a link to the dataset is provided in the paper. Any further information required to re-analyse the data will be made available by the lead contact upon request.
DOI: 10.17617/3.g0aep5
title: Coordination of shoot apical meristem shape and identity by APETALA2 during floral transition in Arabidopsis

description: Plants flower in response to environmental signals. These signals change the shape and developmental identity of the shoot apical meristem (SAM), causing it to form flowers and inflorescences. We show that the increases in SAM width and height during floral transition correlate with changes in size of the central zone (CZ), defined by CLAVATA3 expression, and involve a transient increase in the height of the organizing center (OC), defined by WUSCHEL expression. The APETALA2 (AP2) transcription factor is required for the rapid increases in SAM height and width, by maintaining the width of the OC and increasing the height and width of the CZ. AP2 expression is repressed in the SAM at the end of floral transition, and extending the duration of its expression increases SAM width. Transcriptional repression by SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) represents one of the mechanisms reducing AP2 expression during floral transition. Moreover, AP2 represses SOC1 transcription, and we find that reciprocal repression of SOC1 and AP2 contributes to synchronizing precise changes in meristem shape with floral transition.
DOI: 10.17617/3.ntkshk
title: Collective self-caging of active filaments in virtual confinement

description: Data set for the publication "Collective self-caging of active filaments in virtual confinement"
DOI: 10.17617/3.vzs5tl
title: Data Architectures of Syntopia

description: The data-sets show the derived/compiled data on beetle-infested wood harvest for the case study in Feldbuch (Franconia, Germany) presented in the article "Architectures of Syntopia".
DOI: 10.17617/3.zqmoj3
title: Additional dataset for: Peering into the world of wild passerines with 3D-SOCS: synchronized video capture for posture estimation

description: This dataset includes sample data to reproduce the 3D-SOCS pipeline, as well as an annotated dataset and trained model weights for object detection and 2D keypoint estimation for Great tits and Blue tits. 

For more details, code and implementation of the pipeline, we refer to: https://github.com/alexhang212/3D-SOCS
DOI: 10.21233/mekc-7d83
title: LDDsite1712 ostracode surface sample dataset

description: Raw data for the LDDsite1712 ostracode surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.17617/3.yk9i4b
title: :unav

description: :unav
DOI: 10.17617/3.ako5sf
title: Phenylphenalenones and Linear Diarylheptanoid Derivatives are Biosynthesized via Parallel Routes in Musella lasiocarpa, the Chinese Dwarf Banana

description: NMR data for compounds mentioned in the manuscript.
DOI: 10.17617/3.yu9fg9
title: How Rainfall Events Modify Trace Gas Mixing Ratios in Central Amazonia

description: Codes and Data used on the article.
DOI: 10.17617/3.boletg
title: Data for "pH-mediated Manipulation of the Histidine Brace in LPMOs and Generation of a Tri-anionic Variant, Investigated by EPR, ENDOR, ESEEM and HYSCORE Spectroscopy"

description: Data for manuscript "pH-mediated Manipulation of the Histidine Brace in LPMOs and Generation of a Tri-anionic Variant, Investigated by EPR, ENDOR, ESEEM and HYSCORE Spectroscopy"
DOI: 10.17617/3.nkwopo
title: DNA sequences - Supplementary Material - CORE cycle

description: DNA sequence maps and analysis pipeline for whole-genome resequencing of evolved E. coli strains isolated from adaptive laboratory evolution (breseq)
DOI: 10.17617/3.5pee52
title: Evolvability

description: &lt;h1&gt;Introduction&lt;/h1&gt;
This record contains data accompanying the paper:
&lt;br&gt;
&lt;br&gt;
Experimental evolution of evolvability
Michael Barnett, Lena Zeller, Paul B. Rainey
&lt;a href=https://doi.org/10.1101/2024.05.01.592015&gt;doi:10.1101/2024.05.01.592015&lt;/a&gt;
&lt;br&gt;
&lt;br&gt;
&lt;h1&gt;Content of expevolv.zip&lt;/h1&gt;
The folder 'Population B whole-genome seq' contains all fastQ files derived from whole-genome re-sequencing of clones within 'meta-population B' that were used to identify and order mutations. A GenBank file 'OV986001-SBW25_genome' provides the appropriate reference genome for mapping these sequences. 
&lt;br&gt;
&lt;br&gt;
Names of fastQs files accord to the table 'interactive-pop-B.csv', which itself is the input used to visualise lineage dynamics of meta-population B within the paper via the software 'Colgen'. The interactive lineage visualization of meta-population B can be accessed at &lt;a href=https://micropop.evolbio.mpg.de/data/evolve&gt;https://micropop.evolbio.mpg.de/data/evolve&lt;/a&gt;.
&lt;br&gt;
&lt;br&gt;
Colgen can be found here:
&lt;a href=https://gitlab.com/ecoevomath/colgen&gt;https://gitlab.com/ecoevomath/colgen&lt;/a&gt;
And its accompanying paper here:
&lt;a href= https://doi.org/10.1101/2024.05.10.593459&gt;doi:10.1101/2024.05.10.593459&lt;/a&gt;
&lt;br&gt;
&lt;br&gt;
The folder 'Sanger seq from T10-M3 cel+ transposon mutagenesis' contains all Sanger sequences used to identify transposon insertion sites following transposon mutagenesis. These can be mapped to the GenBank reference file.

&lt;h1&gt;Contents of genetic_constructs.zip&lt;/h1&gt;
The folder 'Genetic constructs' contains annotated GenBank files for the novel donor plasmids used in this study to introduce genetic changes.
description: colgen
DOI: 10.17617/3.qmxnsh
title: Source data for "A glycan foldamer that uses carbohydrate-aromatic interactions to perform catalysis"

description: In nature, the ability to catalyse reactions is primarily associated with proteins and ribozymes. Inspired by these systems, peptide-based catalysts have been designed to accelerate chemical reactions and/or ensure regio- and stereoselective transformations. We wondered whether other biomolecules (such as glycans) could be designed to perform catalytic functions, expanding the portfolio of synthetic functional oligomers. Here we report a glycan foldamer inspired by the natural Sialyl Lewis X antigen that acts as catalyst in a chemical reaction. This glycan-based catalyst benefits from structural rigidity and modular adaptability, incorporating a substrate-recognition motif alongside a catalytic active site. Leveraging the inherent ability of carbohydrates to engage in CH–π interactions with aromatic substrates, we demonstrate the recruitment and functionalization of a tryptophan via a Pictet–Spengler transformation. Our modular glycan catalyst accelerates the reaction kinetics, enabling the modification of tryptophan-containing peptides in aqueous environments. Our findings pave the way for the development of glycan-based catalysts and suggest the possibility of catalytic capabilities of glycans in biological contexts.
DOI: 10.17617/3.gelg53
title: Local readout and control of current and kinetic energy operators in optical lattices

description: Data presented in the publication.
DOI: 10.17617/3.mbe4aa
title: Waves 2024

description: Proceedings of The 16th International Conference on Mathematical and Numerical Aspects of Wave Propagation.
DOI: 10.17617/3.us5bbt
title: Unbiased Phenotype Detection Using Negative Controls data set

description: Phenotypic screens using automated microscopy allow comprehensive measurement of the effects of compounds on cells due to the number of markers that can be scored and the richness of the parameters that can be extracted. The high dimensionality of the data is both a rich source of information and a source of noise that might hide information. Many methods have been proposed to deal with this complex data in order to reduce the complexity and identify interesting phenotypes. Nevertheless, the majority of laboratories still only use one or two parameters in their analysis, likely due to the computational challenges of carrying out a more sophisticated analysis. Here, we present a novel method that allows discovering new, previously unknown phenotypes based on negative controls only. The method is compared with L1-norm regularization, a standard method to obtain a sparse matrix. The analytical pipeline is implemented in the open-source software KNIME, allowing the implementation of the method in many laboratories, even ones without advanced computing knowledge.

As the data set for this paper is large we recommend using a download tool (or browser) that is capable of resuming. 

PubMed ID 30616488
WebOfScience Link WOS:000459287100004
description: KNIME
DOI: 10.17617/3.cmukkn
title: E4Warning Bird Species Distribution local predictions

description: These folders contain raster files of the four study sites in four European countries (Switzerland, Germany, Spain and Greece), which were created in frame of the E4Warning project (https://www.e4warning.eu). Each raster corresponds to the monthly prediction of habitat suitability for the year 2022 for a total of 228 unique bird species. The R script created to calculate the habitat suitability and to produce the rasters are made available on Github: https://github.com/E4Warning/WP5/tree/main/Deliverable_D5.1. An R script that helps to summarize and evaluate the information about the contents of rasters is also available on Github.
DOI: 10.17617/3.6hyxc4
title: Hexagonal electrohydraulic modules for rapidly reconfigurable high-speed robots

description: Data, code and design files for "Hexagonal electrohydraulic modules for rapidly reconfigurable high-speed robots."
DOI: 10.17617/3.z8y7om
title: GlycoMerge Software Operative Module Codes

description: Code files for executing operative synthetic modules during automated glycan assembly in a Glyconeer 3.1, the device control by the Software GlycoMerge where this operation packages are refer as processes. The software was developed in LabView. Each Process consists of a process file (.pro), a variable file (.var) and a rule file (.rul), all under the same name within the corresponding process folder.
description: GlycoMerge, V2.4.7
DOI: 10.17617/3.3rlihr
title: Full-length RNA transcript sequencing traces brain isoform diversity in house mouse natural populations

description: Using a newly developed full-length transcripts enrichment protocol with 5’ CAP selection, we sequenced full-length RNA transcripts of 48 individuals from outbred populations and subspecies of Mus musculus, and from the closely related sister species Mus spretus and Mus spicilegus as outgroups. The dataset represents the most extensive full-length high-quality isoform catalog at the population level to date.
DOI: 10.17617/3.bfam0e
title: Diversity, functionality, and evolutionary history of bacterial symbionts in false click beetles

description: Symbiotic relationships with microbes are widespread in insects, traversing a broad spectrum of reciprocal dependency, intimacy, duration, and cooperation. Many insect taxa are only able to establish in their ecological niche because of the help or bacterial partners. The false click beetles (Coleoptera, Throscidae) are a small, but globally distributed family of beetles that live in leaf litter and decaying wood and were previously reported to harbor intracellular symbionts in specialized bacteriomes. In this study, we investigated three of the four extant genera of Throscidae beetles for their symbiotic microbes and provide insights into host-symbiont interactions based on symbiont genomes and localization. The ancient Shikimatogenerans symbiont with a highly eroded genome of ~150 kbp and ~12% GC was present in all examined taxa, probably supplying tyrosine precursors for cuticle biosynthesis as its only contribution to the host. Beyond this, several secondary symbionts from the Enterobacterales (e.g. Sodalis and Symbiodolus ) and Flavobacteriales with variable tissue tropism, genome sizes, and encoded metabolic capabilities were present, suggesting multiple symbiont acquisition events. Their inferred roles based on genome content and localization range from parasitic by manipulating host reproduction, to mutualistic, supplying multiple amino acids and cofactors. Thus, beyond deepening our understanding of tyrosine-supplementing symbionts across a broad range of beetle families with different ecologies, the Throscidae provide insights into a dynamic evolutionary history with multiple co-occurring symbionts and expand our view on multipartite symbiotic interactions in insects.
DOI: 10.17617/3.hs2ee6
title: Spot contrasts from 3D MHD MURaM simulations

description: Spatially averaged 1D MHD atmosphere for M0 and K0 stars and the disk integrated fluxes for G2V, K0V and M0V stars
DOI: 10.17617/3.gvbmeq
title: Quantitive variation of male and female-specific compounds in 99 drosophilid flies

description: Variation in sex pheromones is regarded as one of the causes of reproductive isolation and speciation. We recently identified 51 male- and female-specific compounds – many of which function as sex pheromones – in 99 drosophilid species1. Here, we report that despite many of these compounds being shared between species, their quantities differ significantly. For example, although 34 drosophilid species share the male-specific compound cis-vaccenyl acetate (cVA), which plays a critical role in regulating various social and sexual behaviors, the amount of cVA can differ by up to 600-fold between different species. Additionally, we found 7-tricosene, the cuticular hydrocarbon pheromone, present in 35 Drosophila species. Our findings indicate that 7-tricosene is equally present in both sexes of 14 species, more abundant in males of 14 species, and more abundant in females of 7 species. We provide raw data on the concentration of potential pheromone components in the 99 drosophilids, which can provide important insights for further research on the behavior and evolution of these species. Quantitative variations highlight species-specific patterns, suggesting an additional mechanism for reproductive isolation built on specific combinations of compounds at set concentrations.
DOI: 10.17617/3.iamk5u
title: Growth of a tessellation: Geometric rules drive development of stingray skeletal patterns

description: The skeletons of sharks and rays, fashioned from cartilage, and armored by a veneer of mineralized tiles (tesserae) present a mathematical challenge: How can the continuous covering be maintained as the skeleton expands? This study, using microCT and custom visual data analyses of growing stingray skeletons, systematically examines tessellation patterns and morphologies of the many thousand interacting tesserae covering the hyomandibula (a skeletal element critical to feeding), over a two-fold developmental change in hyomandibula length. The number of tesserae remains surprisingly constant, even as the hyomandibula expands isometrically, with all hyomandibulae displaying self-similar distributions of tesserae shapes/sizes. Although the distribution of tesserae geometries largely agrees with the rules for polyhedra tiling of complex surfaces—dominated by hexagons and a minor fraction of pentagons and heptagons, but very few other polygons—the agreement with Euler's classic mathematical laws is not perfect. Contrary to the assumed uniform growth rate (which is shown would create geometric incompatibilities), larger tesserae grow faster to accommodate skeletal expansion. It is hypothesized that this local regulation of global system complexity is driven by tension (from cartilaginous core expansion) in the fibers connecting tesserae, with strain-responsive cells orchestrating local mineral apposition.
DOI: 10.17617/3.dif595
title: Pair distributions and membrane-mediated interactions of arc-shaped particles on spherical and tubular vesicles

description: This dataset contains data from Monte Carlo simulations of triangulated membrane vesicles with segmented, bound arc-shaped particles of two different sizes (in hdf5 format) and Mathematica notebooks to determine pair distributions, 2-dimensional free energy landscapes, and 1-dimensional energy profiles from the data, and to visualise the results. In the Monte Carlo simulations, the tubular or spherical shapes of the membrane vesicles are pre-determined by the volume-to-area ratio of the vesicles. In the Mathematica notebooks, the curvature-mediated pair interaction free energies and energies are calculated for the different vesicle shapes at three different area coverages x of the bound particles.
description: Mathematica, 13.0
DOI: 10.17617/3.0v1odv
title: Lipidic folding pathway of α-Synuclein via a toxic oligomer

description: Initial coordinate and simulation input files and a coordinate file of the final output.
DOI: 10.17617/3.4g3boj
title: Source data for "On resin synthesis of phosphoethanolamine cellulose"

description: NMR data
DOI: 10.17617/3.h40yyt
title: Closing the solar dynamo loop: poloidal field generation at the surface

description: ASH simulation results at surface.
Python/Numpy files
DOI: 10.15468/dl.5jrvak
title: Occurrence Download

description: A dataset containing 105252 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Meligethes atramentarius Förster, 1849, Eupteryx immaculatifrons (Kirschbaum, 1868), Ascochyta papaveris Oudem., Loxodonta cyclotis (Matschie, 1900), Schneidereria platyphracta (Meyrick, 1935), Caloptilia thymophanes (Meyrick, 1928), Atacira melanephra, Anufrievia zelta Dworakowska, 1977, Anufrievia cervena Dworakowska, 1977, Anufrievia maculosa Dworakowska, 1977, Aconophora compressa Walker, Frankliniella lantanae Mound, Nakahara & Day, 2005, Teleonemia harleyi Froeschner, 1970, Chelonoidis chathamensis (Van Denburgh, 1907), Emberiza capensis Linnaeus, 1767, Bertholdia steinbachi Rothschild, 1909, Oedicentra albipennis Warren, 1902, Scopula actuaria (Walker, 1861), Nola fasciata (Walker, 1866), Coptobasis lunalis (Guenée, 1854), Lobesia sitophaga Meyrick, 1922, Lobesia fetialis (Meyrick, 1920), Microsarotis palamedes (Meyrick, 1916), Hylica paradoxa Stål, 1863, Chidaea crassa Löcker & Holzinger, 2019, Sibovia tunicata (Fowler, 1900), Apogonalia sanguinipes (Van Duzee, 1907), Graphogonalia vicina Young, 1977, Apogonalia krameri Young, 1977, Rhabdotalebra octolineata (Baker, 1903), Euhyloptera corticalis Fennah, 1945, Caprona ransonnettii potiphera (Hewitson, 1873), Hasora badra badra, Cigaritis nipalicus, Hasora vitta (Butler, 1870), Papilio alcmenor Felder & Felder, 1864, Microlophus bivittatus (Peters, 1871), Hyarotis stubbsi Eliot, 1959, Amazilis amazilia amazilia, Tajuria cippus maxentius Fruhstorfer, 1912, Ideopsis gaura Horsfield, 1829, Cethosia nietneri mahratta Moore, 1872, Vagrans sinha, Ideopsis juventa (Cramer), Cethosia myrina C.Felder & R.Felder, 1865, Prioneris philonome (Boisduval, 1836), Piezodorus oceanicus (Montrouzier, 1864), Troides helena cerberus, Microlophus indefatigabilis (Baur, 1890), Chlorostilbon assimilis Lawrence, 1861)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 105252 records from 142 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010461-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60545/2yjzvi
title: Colección de Lepidóptera del Museo de Artrópodos del Laboratorio de Entomología Agrícola Fitosanitario.

description: La presente colección, perteneciente al Museo de Artrópodos del Laboratorio de Entomología Agrícola Fitosanitario, está conformada por ejemplares del orden Lepidóptera, comúnmente conocidos como mariposas. Estos insectos se caracterizan por poseer alas recubiertas de escamas microscópicas de colores variados, lo que les confiere una notable diversidad morfológica. Los lepidópteros cumplen funciones ecológicas fundamentales, destacando como polinizadores y bioindicadores de la salud ambiental.
DOI: 10.15468/dl.er6zuw
title: Occurrence Download

description: A dataset containing 111 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"equals","key":"GADM_LEVEL_2_GID","value":"USA.3.5_1","matchCase":false},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 111 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007265-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.28845323.v1
title: DATA.xlsx

description: Data for analysis
DOI: 10.3535/j4t-w84-c6s
title: Turritriton labiosus (W. Wood, 1828)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/gr2-1qs-nwn
title: Cancellaria ventricosa Hinds, 1843

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/sgd-eas-a2y
title: Ameranna milleri (Nowell-Usticke, 1959)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/nnl-032-231
title: Mimachlamys gloriosa (Reeve, 1853)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/w4p-83d-wgx
title: Donax clathratus Reeve, 1854

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/6qm-sbr-cd5
title: Rissoella inflata (Monterosato, 1880)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/der-skv-ezw
title: Sinum perspectivum (Say, 1831)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/wz3-4m1-rde
title: Conus villepinii P. Fischer & Bernardi, 1857

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/xgd-sw8-nsg
title: Chicoreus brevifrons (Lamarck, 1822)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/s66-4ym-abb
title: Leptochiton algesirensis (Capellini, 1859)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/tcc-8rk-mnh
title: Acanthochitona fascicularis (Linnaeus, 1767)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/2hd-dr3-gkx
title: Caecum subannulatum de Folin, 1870

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/sqt-km0-ymh
title: Pusillina radiata (R. A. Philippi, 1836)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/04a-xw9-4q3
title: Conus catus Hwass, 1792

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/mkr-mpy-9m8
title: Spirula spirula (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.