cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17592315
title: Trajectory data for bacterial motility in semi-solid agar

description: Description of data

This directory contains the trajectory data of bacterial swimming experiments, using the soil bacterium Pseudomonas putida, in porous agar gels. The subdirectories named WT_025 and WT_03 refer to the trajectory data corresponding to wild type Pseudomonas putida cells in 0.25% and 0.3% agar, respectively. The subdirectories motAB_025 and motCD_025 correspond to the trajectory data associated with the swimming experiments of two knockout mutants (MotAB and MotCD) of the same bacterium, details of which can be found in the references below [1,3].

Each subdirectory contains further subdirectories, including raw data (raw) and processed data for Refs. [1,2]. For experimental Materials and Methods, we refer to the respective publications.

In the raw subdirectory, each .csv file corresponds to a single trajectory (not processed), where the headers X and Y correspond to the coordinates of a single bacterium, in units of micrometers, with a temporal resolution of 20 frames per second, i.e. two successive coordinates are 0.05 seconds apart.In the processed_motility_paper subdirectory, each .csv file corresponds to a single processed and labeled trajectory (meaning of labels: run corresponds to motile swimming phases of bacteria whereas turn correspond to the intermittent non-motile phases). This dataset was used in Ref. [1].

Additionally, inside WT_025 and WT_03 datasets, a third subdirectory exists, namely, processed_chemotaxis_paper that contains labeled trajectories that were used in Ref. [2]. The spatial and temporal resolutions as well as the run-turn distinction criterion are identical to Ref. [1].

References



Agniva Datta, Sönke Beier, Veronika Pfeifer, Robert Großmann, and Carsten Beta. "Bacterial swimming in porous gels exhibits intermittent run motility with active turns and mechanical trapping." Scientific Reports 15 20320 (2025). URL

Sönke Beier, Veronika Pfeifer, Agniva Datta, Robert Großmann, and Carsten Beta. "Deciphering the dual chemotaxis strategy of bacteria in porous media." arXiv:2503.05286 (2025). URL

Veronika Pfeifer, Sönke Beier, Zahra Alirezaeizanjani, and Carsten Beta. "Role of the two flagellar stators in swimming motility of Pseudomonas putida." mBio 13(6) e02182-22 (2022) URL


Ref. [1] is based on the data in:



`/WT_025/processed_motility_paper'

`/WT_03/processed_motility_paper'

`/motAB_025/processed_motility_paper'

`/motCD_025/processed_motility_paper'


Ref. [2] is based on the data in:



`/WT_025/processed_chemotaxis_paper'

`/WT_03/processed_chemotaxis_paper'
DOI: 10.5281/zenodo.17592316
title: Trajectory data for bacterial motility in semi-solid agar

description: Description of data

This directory contains the trajectory data of bacterial swimming experiments, using the soil bacterium Pseudomonas putida, in porous agar gels. The subdirectories named WT_025 and WT_03 refer to the trajectory data corresponding to wild type Pseudomonas putida cells in 0.25% and 0.3% agar, respectively. The subdirectories motAB_025 and motCD_025 correspond to the trajectory data associated with the swimming experiments of two knockout mutants (MotAB and MotCD) of the same bacterium, details of which can be found in the references below [1,3].

Each subdirectory contains further subdirectories, including raw data (raw) and processed data for Refs. [1,2]. For experimental Materials and Methods, we refer to the respective publications.

In the raw subdirectory, each .csv file corresponds to a single trajectory (not processed), where the headers X and Y correspond to the coordinates of a single bacterium, in units of micrometers, with a temporal resolution of 20 frames per second, i.e. two successive coordinates are 0.05 seconds apart.In the processed_motility_paper subdirectory, each .csv file corresponds to a single processed and labeled trajectory (meaning of labels: run corresponds to motile swimming phases of bacteria whereas turn correspond to the intermittent non-motile phases). This dataset was used in Ref. [1].

Additionally, inside WT_025 and WT_03 datasets, a third subdirectory exists, namely, processed_chemotaxis_paper that contains labeled trajectories that were used in Ref. [2]. The spatial and temporal resolutions as well as the run-turn distinction criterion are identical to Ref. [1].

References



Agniva Datta, Sönke Beier, Veronika Pfeifer, Robert Großmann, and Carsten Beta. "Bacterial swimming in porous gels exhibits intermittent run motility with active turns and mechanical trapping." Scientific Reports 15 20320 (2025). URL

Sönke Beier, Veronika Pfeifer, Agniva Datta, Robert Großmann, and Carsten Beta. "Deciphering the dual chemotaxis strategy of bacteria in porous media." arXiv:2503.05286 (2025). URL

Veronika Pfeifer, Sönke Beier, Zahra Alirezaeizanjani, and Carsten Beta. "Role of the two flagellar stators in swimming motility of Pseudomonas putida." mBio 13(6) e02182-22 (2022) URL


Ref. [1] is based on the data in:



`/WT_025/processed_motility_paper'

`/WT_03/processed_motility_paper'

`/motAB_025/processed_motility_paper'

`/motCD_025/processed_motility_paper'


Ref. [2] is based on the data in:



`/WT_025/processed_chemotaxis_paper'

`/WT_03/processed_chemotaxis_paper'
DOI: 10.3535/ytg-65w-gx7
title: Achnatherum calamagrostis (L.) P.Beauv.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytg-7dh-d5h
title: Chenopodium giganteum D. Don

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytg-7gh-w3r
title: Geranium pusillum L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytg-f3m-p7v
title: Rhamphospermum arvense (L.) Andrz. ex Besser

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytg-m73-bbn
title: Medicago falcata L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytg-mfq-0m4
title: Plantae

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytg-qhy-2r6
title: Carex mackenziei V.I.Krecz.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytf-4mn-9qr
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/ytg-sp9-p0q
title: Carex elongata L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytg-xz6-118
title: Actaea spicata L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.15468/dl.62uhng
title: Occurrence Download

description: A dataset containing 30362 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GenusKey is Corybas",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is false",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
}

 The dataset includes 30362 records from 81 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0062872-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/yth-0l7-fbq
title: Lathyrus hirsutus L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/yth-6fx-aaj
title: Moehringia trinervia (L.) Clairv.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/yth-hpe-30z
title: Erysimum virgatum Roth

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/yth-r83-sqe
title: Poa annua L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytj-85t-9nh
title: Carex canescens L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/yth-k7g-rkk
title: Carex limosa L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytj-z0t-22z
title: Vicia tetrasperma (L.) Schreb.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytk-mvz-9g3
title: Lycopodiella inundata (L.) Holub

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytk-y44-mbl
title: Rumex longifolius DC.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytk-zfs-7ab
title: Alchemilla glaucescens Wallr.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytl-6jr-dnq
title: Carex cespitosa L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytl-89y-vgw
title: Spirodela polyrhiza (L.) Schleid.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytl-d6y-3bv
title: Juncus bulbosus L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytl-g4f-cl2
title: Hammarbya paludosa (L.) Kuntze

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytl-k0w-d09
title: Stratiotes aloides L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytl-d6j-190
title: Ononis arvensis L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytl-ntt-5me
title: Carex flava L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytl-rhx-dzh
title: Alnus glutinosa (L.) Gaertn.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytl-vd7-yq4
title: Trifolium hybridum L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytm-00q-vsn
title: Thalictrum simplex L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytm-20x-7ej
title: Botrychium lunaria (L.) Sw.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytm-8rs-6m5
title: Anthyllis vulneraria x ssp. lapponica × ssp. vulneraria

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytm-be1-32b
title: Alchemilla glomerulans Buser

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytm-brb-d1x
title: Cerastium holosteoides Fr.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytm-ejw-p8j
title: Carex rupestris All.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytm-fsc-6jp
title: Sparganium emersum Rehmann

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytm-jsg-v8v
title: Dianthus arenarius L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytm-q5k-dg2
title: Berberis vulgaris L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytm-wqv-fjh
title: Salix myrtilloides L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytm-ykh-1b8
title: Carex digitata L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytn-203-rf7
title: Potamogeton gramineus L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytn-2j8-df9
title: Eriophorum russeolum subsp. russeolum

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytn-cdb-svc
title: Arabidopsis × suecica (Fr.) Norrl.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytn-ece-49f
title: Potamogeton berchtoldii Fieber

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytn-vjt-gdm
title: Vicia cracca L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytn-yy4-4jd
title: Thalictrum flavum L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytp-12a-prq
title: Festuca rubra L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytp-3bn-p6w
title: Cystopteris fragilis (L.) Bernh.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytp-4sp-b3r
title: Plantae

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytp-app-y44
title: Poa pratensis L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytp-bqg-g76
title: Alchemilla micans Buser

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytp-c81-nsa
title: Salix caprea L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytp-cg6-ckc
title: Melilotus officinalis (L.) Lam.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.14459/2025mp1774973.001
title: TUM Bond Database (TUMBD): Full-Scale Beam Tests with Anchorages and Laps in Tension

description: The datasets include a large number of full-scale anchorage and lap splice tests on concrete beams and slabs conducted since 1955. They provide extensive information on material properties (concrete, reinforcement, rib geometry), geometric properties (dimensions, spacings, bond length), and test results compiled from literature and tests performed at TUM. The datasets are continuously updated.
DOI: 10.3535/ytp-n89-w6v
title: Stellaria palustris (Murray ex Ehrh.) Hoffm.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytn-wwt-hdk
title: Rabelera holostea (L.) M. T. Sharples & E. A. Tripp

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytq-0q7-q5w
title: Poa nemoralis L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytq-2sq-2ke
title: Sisymbrium officinale (L.) Scop.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytq-7te-fdc
title: Scleranthus annuus subsp. polycarpos (L.) Bonnier & Layens

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytq-9cr-j17
title: Salix myrsinifolia subsp. myrsinifolia

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytq-9v5-ach
title: Cerastium alpinum var. lanatum (Lam.) Hegetschw.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytq-dpl-6jl
title: Allium scorodoprasum L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytq-jar-6vh
title: Sagittaria × lunata C.D.Preston & Uotila

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytq-xyw-ndh
title: Atocion rupestre (L.) Oxelman

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytr-1f8-a1h
title: Plantago lanceolata L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytr-ajx-1tw
title: Carex flava L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.6084/m9.figshare.30932633
title: Raw NMR data

description: Raw NMR data.
DOI: 10.6084/m9.figshare.30932633.v1
title: Raw NMR data

description: Raw NMR data.
DOI: 10.3535/ytp-z9z-wmz
title: Luzula pallescens Sw.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytq-f1f-mj9
title: Sparganium emersum × erectum

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytr-ey9-hvw
title: Calamagrostis purpurea (Trin.) Trin.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytr-pfg-dzx
title: Rabelera holostea (L.) M. T. Sharples & E. A. Tripp

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/yts-2cy-bsy
title: Carex recta Boott

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/yts-4nk-x05
title: Allium oleraceum L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/yts-90w-dz9
title: Cerastium semidecandrum L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/yts-enl-lzl
title: Eriophorum vaginatum L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/yts-hk9-ec9
title: Diphasiastrum complanatum subsp. complanatum

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/yts-l1q-lzl
title: Ribes L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/yts-rd3-08m
title: Atriplex patula L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/yts-rvp-bn1
title: Alchemilla monticola Opiz

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/yts-tb9-fc8
title: Pulsatilla pratensis (L.) Mill.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/yts-vm7-hc8
title: Potamogeton alpinus Balb.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytt-0lw-df5
title: Carex vesicaria L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytt-2pb-bm3
title: Scolochloa festucacea (Willd.) Link

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytr-cdl-v65
title: Arenaria serpyllifolia L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytr-sn8-ce2
title: Erysimum cheiranthoides L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytr-t0n-rkz
title: Carex vaginata Tausch

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/yts-d2s-ww6
title: Salix rosmarinifolia subsp. rosmarinifolia

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytt-8cv-epq
title: Rumex longifolius DC.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytt-98e-5yd
title: Leymus arenarius (L.) Hochst.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytt-cc4-1a6
title: Pyrus pyraster (L.) Burgsd.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytt-fzd-bad
title: Carex mackenziei V.I.Krecz.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.5281/zenodo.17736075
title: User Metrics for Adaptive Interface Design

description: This repository contains the supplementary materials accompanying the manuscript "User Metrics for Adaptive Interface Design". The supplementary material includes five figures, five tables, the scenarios used in the validation phase, and the experimental results. The dataset is used to determine whether the value of the user metrics aligns with the user's preference.

 1. Figures:



Supplementary Figure A presents the results of the TLR process.

Supplementary Figure B presents the results of the linear regression for the skill characteristic.

Supplementary Figure C presents the results of the linear regression for the knowledge characteristic.

Supplementary Figure D presents the results of the linear regression for the device characteristic.

Supplementary Figure E presents the results of the linear regression for the interests characteristic.


 

2.  Tables:



Supplementary Table A presents a summary of related works.

Supplementary Table B presents the dependent variables of the experimental process.

Supplementary Table C presents the results of the mixed model for estimated characteristics.

Supplementary Table D presents the results of the mixed model for user preferences.

Supplementary Table E presents the results of the linear regression.


3. Tasks:



Include the statements of the 25 experimental tasks and the metrics calculated in each one.


 

4. Experimental Data:



Include the results of the experimental process.
DOI: 10.3535/ytt-gm7-86r
title: Scleranthus annuus subsp. polycarpos (L.) Bonnier & Layens

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ytt-hx3-a2a
title: Lepidium campestre (L.) W. T. Aiton

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.