cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.18337869
title: Accompanying files for "A bridge-like lipid transfer protein is critical for generation of invasive stages in malaria parasites"

description: This upload contains files documented in a preprint.

Preprint: https://doi.org/10.1101/2025.07.25.666630

The files uploaded here are:

Structures:



Alphafold3 (1) predictions for PfVPS13L1 (split in 2 pieces: 1-3600; 3281-5988), PfVPS13L2 (split in 3 pieces: 1-2822; 2140-5096; 4401-7594), PfVPS13L5 (split in 2 pieces: 1-4805; 3668-6769), PfVPS13L16 (split in 2 pieces: 1-4916; 3868-5415) and PgVPS13L6 used for the domain cartoons presented in Fig. 3D and Extended Data Fig. 4. Five confidence-ranked structures are presented for each protein sequence. The annotated full length structure of PfVPS13L1 (presented in Fig. 4B-D) was aligned on PyMOL (2) and is also included in the PfVPS13L1 zip as a .pse file. The domain colored structures of PfVPS13L2, 5 and 6  and PgVPS13L6 (presented in Extended Data Fig. 4b) are included in the corresponding zip files as .pse files.

Alphafold3 (1) interaction prediction of PfVPS13L1 N-term (a.a. 1-2976) and PfVAP (presented in Extended Data Fig. 6F).

Alphafold3 (1) interaction prediciton of the C-terminal PH domain of PfVPS13L1 (a.a. 5864-5988) and the C-terminal HEPN-L domain of PfAegerolysin presented in Fig. 5 (a.a. 681-827) (presented in Fig. 5f and Extended Data Fig. 8h). Sequences and alignments used for conservation coloring in Fig. 5f are also included in the .zip file. 


Plasmids:



All partially annotated sequences for all transfected plasmids in the study, organized into 4 categories.


Code:



Python codes for identifying FFAT motifs in a given fasta file using the scoring matrix from Slee et al. (3) or the one proposed for Plasmodium in this article (the latter was removed from the second version of the article). The code was partially written by ChatGPT (OpenAI, 2025).


 

References

1. Abramson, J et al. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature (2024).

2. The PyMOL Molecular Graphics System, Version 2.0. Schrödinger LLC.

3. Slee, J.A. & Levine, T.P. Systematic prediction of FFAT motifs across eukaryote proteomes identifies nucleolar and eisosome proteins with the predicted capacity to form bridges to the endoplasmic reticulum. Contact (Thousand Oaks) (2019).
DOI: 10.17632/j3bwsb7grg
title: Three-dimensional electrical resistivity datasets of the Choushui River Alluvial Fan, Pingtung Plain, and Yilan Plain, Taiwan

description: This repository provides three-dimensional (3D) electrical resistivity model datasets for three major groundwater regions in Taiwan: the Choushui River Alluvial Fan (CRAF), the Pingtung Plain, and the Yilan Plain. The datasets characterize regional-scale subsurface resistivity structures and are intended to support interdisciplinary research involving subsurface characterization, including hydrogeology, engineering geology, environmental studies, geophysics, and Earth system science. The 3D resistivity models were constructed by integrating site-based one-dimensional (1D) resistivity profiles derived from transient electromagnetic (TEM), vertical electrical sounding (VES), and borehole resistivity (BR) surveys. To ensure consistency among heterogeneous data sources, all 1D profiles were processed using a unified workflow that included depth resampling at 1 m intervals, standardization to a maximum investigation depth of 200 m, and normalization of resistivity values to minimize systematic differences between survey methods. The processed profiles were subsequently spatially interpolated to generate volumetric resistivity distributions representing the subsurface structure of each study area. The repository structure and data formats are designed to facilitate straightforward reuse and extension across multiple research disciplines.
DOI: 10.17632/j3bwsb7grg.1
title: Three-dimensional electrical resistivity datasets of the Choushui River Alluvial Fan, Pingtung Plain, and Yilan Plain, Taiwan

description: This repository provides three-dimensional (3D) electrical resistivity model datasets for three major groundwater regions in Taiwan: the Choushui River Alluvial Fan (CRAF), the Pingtung Plain, and the Yilan Plain. The datasets characterize regional-scale subsurface resistivity structures and are intended to support interdisciplinary research involving subsurface characterization, including hydrogeology, engineering geology, environmental studies, geophysics, and Earth system science. The 3D resistivity models were constructed by integrating site-based one-dimensional (1D) resistivity profiles derived from transient electromagnetic (TEM), vertical electrical sounding (VES), and borehole resistivity (BR) surveys. To ensure consistency among heterogeneous data sources, all 1D profiles were processed using a unified workflow that included depth resampling at 1 m intervals, standardization to a maximum investigation depth of 200 m, and normalization of resistivity values to minimize systematic differences between survey methods. The processed profiles were subsequently spatially interpolated to generate volumetric resistivity distributions representing the subsurface structure of each study area. The repository structure and data formats are designed to facilitate straightforward reuse and extension across multiple research disciplines.
DOI: 10.17632/5ck563dp3b
title: Exogenous carbon complexity and C:N stoichiometric ratio co-regulate soil priming effect in a subtropical forest

description: The quality of exogenous substrates have strong influences on the direction and magnitude of soil priming effect (PE). However, the synergistic regulation of PE by the molecular-structure complexity and carbon-to‑nitrogen (C:N) stoichiometric ratio of added substrates remains poorly understood, particularly regarding how the underlying mechanisms shift with changes in edaphic factors such as nutrient availability, microbial biomass, and enzyme activities.
DOI: 10.17632/5ck563dp3b.1
title: Exogenous carbon complexity and C:N stoichiometric ratio co-regulate soil priming effect in a subtropical forest

description: The quality of exogenous substrates have strong influences on the direction and magnitude of soil priming effect (PE). However, the synergistic regulation of PE by the molecular-structure complexity and carbon-to‑nitrogen (C:N) stoichiometric ratio of added substrates remains poorly understood, particularly regarding how the underlying mechanisms shift with changes in edaphic factors such as nutrient availability, microbial biomass, and enzyme activities.
DOI: 10.17632/3zygrwcj4t
title: The contribution of native protein complexes to targeted protein degradation

description: Targeted protein degradation (TPD) destroys proteins of interest (POIs) by hijacking the cellular proteolytic machinery. Most proteins in cells exist and function as part of multi-protein or macromolecular complexes, thereby allowing a single protein to control multiple biological processes. Therefore, when a small molecule degrader induces proximity between an E3 ligase and the POI, the macromolecular context of the POI potentially influences the degradation outcomes of the POI and of the complex components. Here, we explore degradation of the eight CK1α-SACK1 (formerly known as FAM83A-H) complexes initiated by molecular glue degraders primarily designed to target Ser/Thr kinase CK1α. We demonstrate that lenalidomide-derived degraders DEG-77 and SJ3149, which selectively target the CK1α isoform, co-degrade multiple SACK1 proteins. We show that the degradation of SACK1 proteins by DEG-77 and SJ3149 requires CK1α, the CUL4ACRBN E3 ligase complex and the proteasome. In cells derived from palmoplantar keratoderma patients harbouring the CK1α-binding deficient SACK1GR265P mutation, DEG-77 targets CK1α and mitotic SACK1D but not SACK1GR265P, highlighting the requirement for CK1α-SACK1 interaction to achieve co-degradation. Our study underscores the importance of POI context in TPD and reinforces the potential for selectively targeting specific protein complexes for degradation.
DOI: 10.17632/3zygrwcj4t.1
title: The contribution of native protein complexes to targeted protein degradation

description: Targeted protein degradation (TPD) destroys proteins of interest (POIs) by hijacking the cellular proteolytic machinery. Most proteins in cells exist and function as part of multi-protein or macromolecular complexes, thereby allowing a single protein to control multiple biological processes. Therefore, when a small molecule degrader induces proximity between an E3 ligase and the POI, the macromolecular context of the POI potentially influences the degradation outcomes of the POI and of the complex components. Here, we explore degradation of the eight CK1α-SACK1 (formerly known as FAM83A-H) complexes initiated by molecular glue degraders primarily designed to target Ser/Thr kinase CK1α. We demonstrate that lenalidomide-derived degraders DEG-77 and SJ3149, which selectively target the CK1α isoform, co-degrade multiple SACK1 proteins. We show that the degradation of SACK1 proteins by DEG-77 and SJ3149 requires CK1α, the CUL4ACRBN E3 ligase complex and the proteasome. In cells derived from palmoplantar keratoderma patients harbouring the CK1α-binding deficient SACK1GR265P mutation, DEG-77 targets CK1α and mitotic SACK1D but not SACK1GR265P, highlighting the requirement for CK1α-SACK1 interaction to achieve co-degradation. Our study underscores the importance of POI context in TPD and reinforces the potential for selectively targeting specific protein complexes for degradation.
DOI: 10.5281/zenodo.18414866
title: Data k článku "Zachování vápnitých fosilií pozdně čtvrtohorní fauny v sedimentárních výplních pískovcových jeskyní kaňonu Labe"

description: Data k článku "Zachování vápnitých fosilií pozdně čtvrtohorní fauny v sedimentárních výplních pískovcových jeskyní kaňonu Labe" publikované ve Zprávách o geologických výzkumech 17.12.2025.
DOI: 10.5281/zenodo.18414865
title: Data k článku "Zachování vápnitých fosilií pozdně čtvrtohorní fauny v sedimentárních výplních pískovcových jeskyní kaňonu Labe"

description: Data k článku "Zachování vápnitých fosilií pozdně čtvrtohorní fauny v sedimentárních výplních pískovcových jeskyní kaňonu Labe" publikované ve Zprávách o geologických výzkumech 17.12.2025.
DOI: 10.5878/003007
title: The Regional Western Sweden SOM Survey 2016
title: Den västsvenska SOM-undersökningen 2016
title: Väst-SOM 2016

description: Western SOM has been conducted yearly since 1992, but was initially limited to residents of Gothenburg and its surrounding municipalities. In 1998, the survey was extended to include the entire Västra Götaland County plus the municipality of Kungsbacka. 

The purpose of the regional surveys is to enable SOM researchers to study attitudes and behaviour linked to local and regional issues. They emphasise public services and media, although many of the questions are identical with those used in National SOM in order to make the answers comparable both between the regions and with Sweden at large.

Purpose:

Study attitudes and behaviours that are linked to local and regional issues and phenomena.
description: Väst-SOM har genomförts varje höst sedan 1992. Fram till 1997 omfattade studien Göteborg med kranskommuner. Undersökningen utökades sedan till att omfatta hela Västra Götalands län samt Kungsbacka kommun. Väst-SOM genomförs i samverkan med Västra Götalandsregionen, och är en del av regionens långsiktiga utvärderingsarbete. 

Flertalet frågor har ställts i många år och svaren bidrar till att bibehålla tidsserier som sträcker sig från undersökningens början 1992. Frågorna har tonvikt på attityder och beteenden inom områdena offentlig service och medier. Många av frågorna är identiska med frågor i den nationella SOM-undersökningen vilket ger möjlighet att jämföra data både på regional och på nationell nivå.

Syfte:

Studera attityder och beteenden som är knutna till lokala och regionala frågor och företeelser.
DOI: 10.5878/003003
title: The Regional Western Sweden SOM Survey 2016
title: Den västsvenska SOM-undersökningen 2016
title: Väst-SOM 2016

description: Western SOM has been conducted yearly since 1992, but was initially limited to residents of Gothenburg and its surrounding municipalities. In 1998, the survey was extended to include the entire Västra Götaland County plus the municipality of Kungsbacka. 

The purpose of the regional surveys is to enable SOM researchers to study attitudes and behaviour linked to local and regional issues. They emphasise public services and media, although many of the questions are identical with those used in National SOM in order to make the answers comparable both between the regions and with Sweden at large.

Purpose:

Study attitudes and behaviours that are linked to local and regional issues and phenomena.
description: Väst-SOM har genomförts varje höst sedan 1992. Fram till 1997 omfattade studien Göteborg med kranskommuner. Undersökningen utökades sedan till att omfatta hela Västra Götalands län samt Kungsbacka kommun. Väst-SOM genomförs i samverkan med Västra Götalandsregionen, och är en del av regionens långsiktiga utvärderingsarbete. 

Flertalet frågor har ställts i många år och svaren bidrar till att bibehålla tidsserier som sträcker sig från undersökningens början 1992. Frågorna har tonvikt på attityder och beteenden inom områdena offentlig service och medier. Många av frågorna är identiska med frågor i den nationella SOM-undersökningen vilket ger möjlighet att jämföra data både på regional och på nationell nivå.

Syfte:

Studera attityder och beteenden som är knutna till lokala och regionala frågor och företeelser.
DOI: 10.5281/zenodo.18415254
title: Table 2 in Distributions and phylogeographic data of rheophilic freshwater fishes provide evidences on the geographic extension of a central-brazilian amazonian palaeoplateau in the area of the present day Pantanal Wetland

description: Table 2. Local populations statistics: n = sample size, N = number of haplotypes, h = haplotype diversity, ð = nucleotide diversity.
LocalitiesnNhπ1661.0000.0029402111.0000.0000003320.66670.0010434510.0000.0000005221.0000.0015656430.83330.0054777630.60000.00104381030.37780.0011829530.80000.00156510810.0000.00011430.83330.00156512510.0000.00013720.28570.00044714720.28570.000447
description: Published as part of Ribeiro, Alexandre C., Jacob, Rodrigo M., Silva, Ronnayana R. S. R., Lima, Flávio C. T., Ferreira, Daniela C., Ferreira, Katiane M., Mariguela, Tatiane C., Pereira, Luiz H. G. & Oliveira, Claudio, 2013, Distributions and phylogeographic data of rheophilic freshwater fishes provide evidences on the geographic extension of a central-brazilian amazonian palaeoplateau in the area of the present day Pantanal Wetland, pp. 323 in Neotropical Ichthyology 11 (2) on page 323, DOI: 10.1590/S1679-62252013000200010, http://zenodo.org/record/12652431
DOI: 10.5281/zenodo.18415255
title: Table 2 in Distributions and phylogeographic data of rheophilic freshwater fishes provide evidences on the geographic extension of a central-brazilian amazonian palaeoplateau in the area of the present day Pantanal Wetland

description: Table 2. Local populations statistics: n = sample size, N = number of haplotypes, h = haplotype diversity, ð = nucleotide diversity.
LocalitiesnNhπ1661.0000.0029402111.0000.0000003320.66670.0010434510.0000.0000005221.0000.0015656430.83330.0054777630.60000.00104381030.37780.0011829530.80000.00156510810.0000.00011430.83330.00156512510.0000.00013720.28570.00044714720.28570.000447
description: Published as part of Ribeiro, Alexandre C., Jacob, Rodrigo M., Silva, Ronnayana R. S. R., Lima, Flávio C. T., Ferreira, Daniela C., Ferreira, Katiane M., Mariguela, Tatiane C., Pereira, Luiz H. G. & Oliveira, Claudio, 2013, Distributions and phylogeographic data of rheophilic freshwater fishes provide evidences on the geographic extension of a central-brazilian amazonian palaeoplateau in the area of the present day Pantanal Wetland, pp. 323 in Neotropical Ichthyology 11 (2) on page 323, DOI: 10.1590/S1679-62252013000200010, http://zenodo.org/record/12652431
DOI: 10.15468/dl.9byvh2
title: Occurrence Download

description: A dataset containing 256 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Gymnotus inaequilabiatus"
 ]
}

 The dataset includes 256 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000037-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18415256
title: Table 3 in Distributions and phylogeographic data of rheophilic freshwater fishes provide evidences on the geographic extension of a central-brazilian amazonian palaeoplateau in the area of the present day Pantanal Wetland

description: Table 3. Analysis of molecular variance (AMOVA) testing for partitioning of genetic variation among populations, grouped according to localities of Jupiaba acanthogaster.
Source of variationDegree of freedomSum of squaresVariance% totalAmong groups2264.4297.552 Va75.36Among populations within groups11117.6312.107 Vb21.02Within populations5921.3640.362 Vc3.61Total72403.4251.002.056
description: Published as part of Ribeiro, Alexandre C., Jacob, Rodrigo M., Silva, Ronnayana R. S. R., Lima, Flávio C. T., Ferreira, Daniela C., Ferreira, Katiane M., Mariguela, Tatiane C., Pereira, Luiz H. G. & Oliveira, Claudio, 2013, Distributions and phylogeographic data of rheophilic freshwater fishes provide evidences on the geographic extension of a central-brazilian amazonian palaeoplateau in the area of the present day Pantanal Wetland, pp. 323 in Neotropical Ichthyology 11 (2) on page 323, DOI: 10.1590/S1679-62252013000200010, http://zenodo.org/record/12652431
DOI: 10.5281/zenodo.18415257
title: Table 3 in Distributions and phylogeographic data of rheophilic freshwater fishes provide evidences on the geographic extension of a central-brazilian amazonian palaeoplateau in the area of the present day Pantanal Wetland

description: Table 3. Analysis of molecular variance (AMOVA) testing for partitioning of genetic variation among populations, grouped according to localities of Jupiaba acanthogaster.
Source of variationDegree of freedomSum of squaresVariance% totalAmong groups2264.4297.552 Va75.36Among populations within groups11117.6312.107 Vb21.02Within populations5921.3640.362 Vc3.61Total72403.4251.002.056
description: Published as part of Ribeiro, Alexandre C., Jacob, Rodrigo M., Silva, Ronnayana R. S. R., Lima, Flávio C. T., Ferreira, Daniela C., Ferreira, Katiane M., Mariguela, Tatiane C., Pereira, Luiz H. G. & Oliveira, Claudio, 2013, Distributions and phylogeographic data of rheophilic freshwater fishes provide evidences on the geographic extension of a central-brazilian amazonian palaeoplateau in the area of the present day Pantanal Wetland, pp. 323 in Neotropical Ichthyology 11 (2) on page 323, DOI: 10.1590/S1679-62252013000200010, http://zenodo.org/record/12652431
DOI: 10.5281/zenodo.18415258
title: Table 4 in Distributions and phylogeographic data of rheophilic freshwater fishes provide evidences on the geographic extension of a central-brazilian amazonian palaeoplateau in the area of the present day Pantanal Wetland

description: Table 4. Genetic differentiation (Fst) between group pairs. Significance level p<0.05 in 1000 permutations. *significative results.
Groupsupper rio Xinguupper rio Paraguayupper rio Tapajósupper rio Xingu0.00000upper rio Paraguay0.84056*0.00000upper rio Tapajós0.97518*0.73615*0.00000
description: Published as part of Ribeiro, Alexandre C., Jacob, Rodrigo M., Silva, Ronnayana R. S. R., Lima, Flávio C. T., Ferreira, Daniela C., Ferreira, Katiane M., Mariguela, Tatiane C., Pereira, Luiz H. G. & Oliveira, Claudio, 2013, Distributions and phylogeographic data of rheophilic freshwater fishes provide evidences on the geographic extension of a central-brazilian amazonian palaeoplateau in the area of the present day Pantanal Wetland, pp. 324 in Neotropical Ichthyology 11 (2) on page 324, DOI: 10.1590/S1679-62252013000200010, http://zenodo.org/record/12652431
DOI: 10.5281/zenodo.18415259
title: Table 4 in Distributions and phylogeographic data of rheophilic freshwater fishes provide evidences on the geographic extension of a central-brazilian amazonian palaeoplateau in the area of the present day Pantanal Wetland

description: Table 4. Genetic differentiation (Fst) between group pairs. Significance level p<0.05 in 1000 permutations. *significative results.
Groupsupper rio Xinguupper rio Paraguayupper rio Tapajósupper rio Xingu0.00000upper rio Paraguay0.84056*0.00000upper rio Tapajós0.97518*0.73615*0.00000
description: Published as part of Ribeiro, Alexandre C., Jacob, Rodrigo M., Silva, Ronnayana R. S. R., Lima, Flávio C. T., Ferreira, Daniela C., Ferreira, Katiane M., Mariguela, Tatiane C., Pereira, Luiz H. G. & Oliveira, Claudio, 2013, Distributions and phylogeographic data of rheophilic freshwater fishes provide evidences on the geographic extension of a central-brazilian amazonian palaeoplateau in the area of the present day Pantanal Wetland, pp. 324 in Neotropical Ichthyology 11 (2) on page 324, DOI: 10.1590/S1679-62252013000200010, http://zenodo.org/record/12652431
DOI: 10.82136/dataset/08de5f29-c29d-475e-88af-a93f6272df4b
title: PM2.5 Air Quality Grid Dataset (Thessaloniki) (v1) (new)

description: Spatial grid of PM2.5 air quality concentrations in Thessaloniki.
DOI: 10.5281/zenodo.18414193
title: Atom Addition Formation of Thionylimide (HNSO) on Interstellar Dust Grains: Chemical routes requiring oxygen and nitrogen atom surface diffusion

description: Set of optimized structures regarding the article "Atom Addition Formation of Thionylimide (HNSO) on Interstellar Dust Grains: Chemical routes requiring oxygen and nitrogen atom surface diffusion". Any further query regarding the strucutres can be made to the corresponding author of the article.
DOI: 10.5281/zenodo.18414194
title: Atom Addition Formation of Thionylimide (HNSO) on Interstellar Dust Grains: Chemical routes requiring oxygen and nitrogen atom surface diffusion

description: Set of optimized structures regarding the article "Atom Addition Formation of Thionylimide (HNSO) on Interstellar Dust Grains: Chemical routes requiring oxygen and nitrogen atom surface diffusion". Any further query regarding the strucutres can be made to the corresponding author of the article.
DOI: 10.15468/dl.dz99wm
title: Occurrence Download

description: A dataset containing 3854 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((13.06862 47.8903,13.06793 47.89145,13.06745 47.89222,13.06548 47.89242,13.06225 47.88905,13.06068 47.88748,13.05849 47.88709,13.05946 47.88458,13.0631 47.88265,13.06729 47.88485,13.07 47.88742,13.07163 47.88987,13.07166 47.89049,13.06862 47.8903))",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 3854 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000038-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48717/ye9w-yg32
title: EVN Observation EL079A
DOI: 10.48717/c4d7-6a30
title: EVN Experiment EL079
DOI: 10.48717/tzqr-zg40
title: EVN Observation EL079B
DOI: 10.5281/zenodo.18415640
title: Loupežnická jeskyně, Labské pískovce

description: Data k výstupu "Specializovaná mapa Loupežnické jeskyně"
DOI: 10.5281/zenodo.18415641
title: Loupežnická jeskyně, Labské pískovce

description: Data k výstupu "Specializovaná mapa Loupežnické jeskyně"