cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.16327921
title: Automatic Positioning and Contour Analysis of Complete Bone Models - data and code

description: 3D models (.wrl/.vrml) of modern mountain gazelle (Gazella gazella) astragali and calcanea.

PYTHON script for computing automatic alignment (Part 1- align_items) and contours (Part 1-Contours). 

This work accompanies the manuscript: Lebenzon, R., Dick, N., Munro, N.D., Grosman, L., under review. New Tools for Computational Zooarchaeology: Automatic Positioning and Contour Analysis of Complete Bone Models. Journal of Archaeological Science.

ABSTRACT: 

As staple tools in zooarchaeological research, morphometric analyses have contributed substantially to foundational research themes such as taxonomy, paleoenvironmental reconstruction and animal domestication. Thus, as the field of archaeology transforms with the rapid advancement of computational techniques, new methods that analyze the complete 3D model, herein called Complete Model Analysis (CMA), hold great promise for zooarchaeology. By extracting and analyzing the complete 3D mesh in a fully automated manner, CMA offers an accurate, repeatable and nuanced approach to bone shape analysis. However, until now, CMA has not been integrated into zooarchaeology due to the complexity and irregularity of some bone shapes which are incompatible with the existing automatic positioning methods that provide the essential first step in CMA analysis. Here, we address this challenge by introducing a three-step procedure that can automatically position any 3D mesh. This breakthrough enables the application of all existing CMA analytical protocols to faunal material. Additionally, we present a global contour tool that automatically generates geometric profiles to calculate assemblage variance. We demonstrate the applicability and utility of these two tools by exploring sex-related variability in a collection of modern mountain gazelle (Gazella gazella) skeletons. Ultimately, this paper opens the door to the development of new CMA analyses in zooarchaeology, including by machine learning.
DOI: 10.3535/12f-an1-b3r
title: Calamagrostis canescens (Weber) Roth

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12f-fam-gt0
title: Lipandra polysperma (L.) S. Fuentes, Uotila & Borsch

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12f-prb-n3m
title: Diplazium sibiricum (Turcz. ex Kunze) Sa. Kurata

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12f-v6v-4t1
title: Lepidium densiflorum Schrad.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12f-zhz-h6k
title: Carex flava L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12g-2t2-ypd
title: Salix phylicifolia L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12g-3ey-af0
title: Carex rhynchophysa Fisch., C.A.Mey. & Avé-Lall.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12g-963-t1k
title: Carex elongata L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12g-de1-87p
title: Elymus caninus (L.) L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12g-h27-vtx
title: Brassica L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12g-k2a-gxv
title: Persicaria lapathifolia (L.) Gray

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12h-023-8n6
title: Micranthes foliolosa (R. Br.) Gornall

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12h-2dn-kez
title: Berteroa incana (L.) DC.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12h-2jr-wev
title: Poa pratensis L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12h-31a-z62
title: Crassula aquatica (L.) Schönland

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12g-02q-tr5
title: Lolium temulentum L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12h-8rk-mgc
title: Salix myrtilloides L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12h-104-3rt
title: Trifolium arvense L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12h-91r-r3k
title: Geum urbanum L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12h-9be-zz7
title: Lycopodiella inundata (L.) Holub

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12h-grx-x65
title: Philadelphus L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12h-lgw-q2n
title: Deschampsia cespitosa (L.) P.Beauv.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12h-sz7-r8n
title: Agrimonia eupatoria L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12h-vn0-9mt
title: Equisetum hyemale L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12h-vvy-6y4
title: Triglochin maritima L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12j-177-t1w
title: Erysimum cheiranthoides subsp. cheiranthoides

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12j-18z-0g4
title: Blysmus rufus (Huds.) Link

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12j-1ha-zab
title: Elymus repens (L.) Gould

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12j-2gm-tgj
title: Cotoneaster integerrimus Medik.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12j-5la-bfd
title: Dactylorhiza sambucina (L.) Soó

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12j-6jw-a63
title: Carex echinata Murray

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12j-ajl-lgr
title: Dryopteris expansa (C. Presl) Fraser-Jenk. & Jermy

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12j-gvw-9tc
title: Lathyrus sylvestris L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12j-k28-m3j
title: Poa arctica R.Br.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12j-x5b-tbv
title: Carex demissa Hornem.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12h-wba-djz
title: Cerastium holosteoides Fr.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.15778/resif.zr2020
title: SEIS-ADELICE temporary experiment measuring the cryo-seismicity of the Astrolabe glacier in Terre Adelie, Antarctica (RESIF-SISMOB)

description: To analyze the dynamics of Antarctica coastal glaciers and their interaction with the ocean, SEIS-ADELICE aims at measuring the cryo-seismicity of the Astrolabe glacier (Terre Adélie, Antarctica) from land and ocean bottom seismic observations. The first instrumental deployments occurred in January and February 2022. They consisted in a network of 6 broad-band (BB) stations from the French INSU-SISMOB pool deployed on the grounding line of the Astrolabe glacier, together with 4 OBS deployed at sea few km off the floating tongue of the glacier. These stations were complemented by semi-permanent BB seismological stations deployed on stable ice around the glacier for long term (several years) recording of the ice and of the glacier cryogenic activity.
DOI: 10.3535/12k-5c6-yfp
title: Eriophorum vaginatum L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12k-9d8-h31
title: Agrostis capillaris L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12k-c5n-xa5
title: Betula pendula f. var. pendula f. lobulata

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12k-dza-fhh
title: Agrostis canina L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12k-gga-57c
title: Neottia cordata (L.) Rich.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12k-gxn-qmp
title: Ranunculus acris L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12k-lh3-fyg
title: Dactylorhiza maculata (L.) Soó

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12k-rxk-wlx
title: Carex echinata Murray

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12k-vx1-0ha
title: Rumex acetosella subsp. acetosella

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12k-ysn-mzy
title: Carex vaginata Tausch

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12l-0e0-n9k
title: Plantae

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12l-3k3-nyx
title: Carex digitata L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12l-4v6-jx6
title: Calamagrostis canescens (Weber) Roth

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12l-8bq-wwy
title: Melilotus officinalis (L.) Lam.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12l-8h3-805
title: Isatis tinctoria L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12l-8pb-b4c
title: Lipandra polysperma (L.) S. Fuentes, Uotila & Borsch

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12l-9ap-9w1
title: Alchemilla glomerulans Buser

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12l-025-20r
title: Luzula multiflora subsp. multiflora

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12l-a5s-gfc
title: Carex glareosa Schkuhr ex Wahlenb.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12l-wdb-93p
title: Eriophorum × medium Andersson

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12m-a63-efv
title: Dryopteris filix-mas (L.) Schott

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12m-ett-mb6
title: Dryopteris expansa (C. Presl) Fraser-Jenk. & Jermy

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12m-exr-ah5
title: Actaea rubra subsp. rubra

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12m-gz8-6c4
title: Carex bohemica Schreb.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12m-k9z-rz1
title: Plantae

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12m-pen-fwq
title: Equisetum sylvaticum L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12m-x6c-kxm
title: Carex bigelowii subsp. bigelowii

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12n-0w1-g64
title: Avenula pubescens (Huds.) Dumort.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12n-3dt-kn4
title: Chelidonium majus L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12n-cf7-kcg
title: Chenopodium L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12n-llv-6xc
title: Chenopodium hircinum Schrad.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12n-n84-yrk
title: Cerastium holosteoides Fr.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12n-nft-jd8
title: Trifolium medium L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12n-ppy-gtn
title: Carex cespitosa L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12n-sff-j6v
title: Potentilla norvegica L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12n-vyq-8f6
title: Prunus padus L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12n-ygq-phf
title: Hordeum murinum L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12p-2cc-015
title: Salix pentandra L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12p-fas-fvl
title: Poa remota Forselles

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12p-kw0-728
title: Alchemilla monticola Opiz

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12p-mx3-1f7
title: Poa palustris L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12p-7gw-ydn
title: Eleocharis quinqueflora (Hartmann) O.Schwarz

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12p-wwf-wzm
title: Ficaria verna Huds.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12p-fxr-kpn
title: Spirodela polyrhiza (L.) Schleid.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12q-1xy-bwt
title: Equisetum pratense Ehrh.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12q-3rv-85h
title: Calamagrostis epigejos (L.) Roth

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12q-3y2-lw0
title: Luzula parviflora (Ehrh.) Desv.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12q-7q6-ha7
title: Carex chordorrhiza L.f.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12q-cbg-p1v
title: Milium effusum L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12q-dqd-7bk
title: Potamogeton pusillus L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12q-fn9-ypq
title: Cardamine pratensis subsp. pratensis

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12q-kzc-q50
title: Trollius europaeus L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12q-lh8-95p
title: Potamogeton berchtoldii Fieber

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12q-q8x-s6b
title: Salix phylicifolia L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12q-qgt-2mj
title: Malus domestica (Suckow) Borkh.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12q-qrs-rj0
title: Spergula morisonii Boreau

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12q-sm3-rr1
title: Carex flava L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12q-vgy-1b4
title: Alchemilla monticola Opiz

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12q-z12-k0h
title: Lathyrus palustris L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12r-f7p-8fq
title: Lolium multiflorum var. westerwoldicum

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12r-g55-3wr
title: Poa nemoralis L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12r-kee-7wk
title: Cardamine pratensis L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12q-bdw-8fy
title: Dianthus deltoides L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/12q-vby-mmq
title: Trifolium repens L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.25345/c5m32np2p
title: MassIVE MSV000098142 - Profiling Methylation in MCF7 Cells with Commercially Available SCX tips and Heavy-Methyl SILAC
title: Methylation is an important post-translational modification that plays many roles in cellular processes; therefore, it is important to identify in complex, biological samples. Methylation is difficult to detect with proteomics because it is less common compared to other modifications, often localized on low-abundance peptides, and typically associated with false positives. Although methylation does not alter many physiochemical properties of amino acids, trypsin cannot cleave after methylated lysine or arginine due to sterics, leading to an increased positive charge on methylated peptides. Thus, strong-cation exchange (SCX) has been used to enrich methylated peptides. However, previous studies use custom-packed columns, cartridges, and tips with differing salts to elute peptides. Here, we assess commercially available SCX tips for the enrichment of methylated peptides to reduce variability caused by custom setups. Additionally, SCX has shown to yield complementary identifications to other methods. Our results show that commercially available SCX effectively fractions peptides by charge and missed cleavages. Further, SCX and no enrichment methods yield complementary methylation site identifications, differing by sequence motifs surrounding the methylation site. Ultimately, these results suggest that commercially available SCX and no enrichment methods are required to effectively profile the methylome of complex biological samples.
DOI: 10.15468/dl.mzg8gs
title: Occurrence Download

description: A dataset containing 4583 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Andrena tibialis (Kirby, 1802)"
 ]
}

 The dataset includes 4583 records from 86 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038610-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k2shyj
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ixianthes Benth.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((35.628 -23.023,35.6007 -22.9702,35.6007 -23.165,35.628 -23.023))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038612-250525065834625/datasets/export for details.
DOI: 10.15468/dl.u4pxqs
title: Occurrence Download

description: A dataset containing 115 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Andrena tscheki Morawitz, 1872"
 ]
}

 The dataset includes 115 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038611-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eawnq4
title: Occurrence Download

description: A dataset containing 130307 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Amelanchier ovalis Medik.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 130307 records from 570 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038591-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d6e6x8
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Achnanthes straubiana Lange-Bertalot, 1996",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((30.0251 -31.3959,30.5701 -30.7329,30.5701 -28.5786,25.5395 -28.5786,25.5395 -32.9007,28.2048 -32.9007,28.5753 -32.6569,29.4902 -31.7517,30.0251 -31.3959))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038614-250525065834625/datasets/export for details.