OSCR

Autophagy dysfunction in iPSCs-derived neurons and midbrain organoids carrying a SNCA triplication.

Code ↔ Paper

4 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 4 matches
  1. [1] § Methods › Live imaging in neuronal cultures ↔ Imaging/Rosella_staging_2D/Main_2.m, lines 5 to 13 · score 0.56 · Yokogawa CV8000, Cell carrier, ultra, plates · Report a mismatch
  2. [2] § Methods › Live imaging in neuronal cultures ↔ Imaging/Rosella_staging_2D/Template/Main.m, lines 5 to 15 · score 0.56 · Yokogawa CV8000, Cell carrier, ultra, plates · Report a mismatch
  3. [3] § Results › PD neuronal cultures show early and progressive autophagy impairment ↔ Data Processing and Plotting/AutophagyReporter_NeuronalCultures/Graphs_Autophagy_NeuronalCultures.Rmd, lines 287 to 346 · score 0.54 · autophagy reporter, autolysosome area, neuronal cultures, DsRed, cell area, b2 · Report a mismatch
  4. [4] § Results › PD hMOs show dopaminergic neuronal degeneration and functional decline ↔ Data Processing and Plotting/MEA/MEA_template_batch_template.R, lines 75 to 163 · score 0.52 · burst frequency, fire rate, intervals, Electrophysiological, MEA · Report a mismatch

Paper

Loaded from Europe PMC by your browser; OSCR does not store it: doi.org · Europe PMC

The paper is loaded when this pane is shown.

The authors' code

MATLAB · 102 lines · 5.1 KB · no license · 1 match

  1. %% Clear Matlab workspace
  2. clear
  3. clc
  5. %% User inputs per run
  6. DataPaths = { 'S:\YokogawaCV8000Standalone\BTSData\MeasurementData\javier\JJ_60X_384_Auto_snake_leftright_st_clplate1st_20210415_090510\AssayPlate_PerkinElmer_CellCarrier-384 Ultra',...
  7. 'S:\YokogawaCV8000Standalone\BTSData\MeasurementData\javier\JJ_60X_384_Auto_snake_leftright_st_clplate2st_20210416_093254\AssayPlate_PerkinElmer_CellCarrier-384 Ultra',...
  8. 'S:\YokogawaCV8000Standalone\BTSData\MeasurementData\javier\JJ_60X_384_Auto_snake_leftright_st_clplate3st_20210422_090156\AssayPlate_PerkinElmer_CellCarrier-384 Ultra',...
  9. 'S:\YokogawaCV8000Standalone\BTSData\MeasurementData\javier\JJ_60X_384_Auto_snake_leftright_st_clplate4st_20210423_092925\AssayPlate_PerkinElmer_CellCarrier-384 Ultra'};
  10. MesPaths = {'JJ_60X_384_Auto_snake_leftright_st'};
  11. %IncubationTimes = {'2_hours','5_hours','8_hours','22_hours'};
  13. for b = 3:size(DataPaths, 2) %loop over DataPaths
  14. %% Prepare folders
  15. clear OutPath
  16. DataPath = DataPaths{b};
  17. Mes = MesPaths{:};
  18. %IncubationTime = IncubationTimes{b};
  19. AnalysisTimeStamp = datestr(now, 'yyyymmdd_HHMMSS');
  20. %OutPath = ['S:\HCS_Platform\Data\JavierJarazo\LDC\Autophagy_screen\Development\',IncubationTime];
  21. OutPath = ['S:\HCS_Platform\Data\JavierJarazo\CL\Dose_curve_stress\Replicate_1'];
  22. MainPath = [OutPath , 'Plate_', num2str(b),'\Analysis_', AnalysisTimeStamp];
  23. MesPath = [DataPath, '\' , Mes,'.mes'];
  26. %% Create folders
  27. mkdir(MainPath)
  29. FileNameShort = mfilename;
  30. f_LogDependencies(FileNameShort, MainPath);
  32. %% Load Metadata
  33. ObjectsAll = {};
  34. MetaData = f_CV8000_getChannelInfo(DataPath, MesPath);
  35. InfoTable = MetaData.InfoTable{:};
  36. % Create a unique of table of the timelines
  37. TimeLines = unique(InfoTable.TimeLine);
  38. % Make a for loop for the unique values
  39. for t=1:1:numel(TimeLines)
  40. %Keep track of the TimeLine to add to table of analysis
  41. TimeLineThis = TimeLines{t};
  42. % Filter the InfoTable by the time line -> InfoTableThisTimeLine
  43. InfoTableThisTimeLine = InfoTable(str2double(InfoTable.TimeLine)==t,:);
  44. %make saving paths for the Time Line
  45. Savingpath = [MainPath ,filesep,'Timepoint_',TimeLineThis];
  46. PreviewPath = [Savingpath, filesep, 'Previews'];
  47. mkdir(Savingpath)
  48. mkdir(PreviewPath)
  49. %Then define unique wells
  50. Wells = unique(InfoTableThisTimeLine.Well);%instead of defining the unique wells here we have to first filter the wells of each timepoint
  52. fieldProgress = 0;
  53. for w = 1:numel(Wells)
  54. WellThis = Wells{w};
  55. InfoTableThisWell = InfoTableThisTimeLine(strcmp(InfoTableThisTimeLine.Well, WellThis),:);
  56. FieldsThisWell = unique(InfoTableThisWell.Field);
  57. for f = 1:numel(FieldsThisWell)
  58. fieldProgress = fieldProgress + 1;
  59. FieldThis = FieldsThisWell{f};
  60. InfoTableThisField = InfoTableThisWell(strcmp(InfoTableThisWell.Field, FieldsThisWell{f}),:);
  61. ChannelsThisField = unique(InfoTableThisField.Channel);
  62. ImPaths = cell(1, numel(ChannelsThisField));
  63. for c = 1:numel(ChannelsThisField)
  64. ChannelThis = ChannelsThisField{c};
  65. InfoTableThisChannel = InfoTableThisField(strcmp(InfoTableThisField.Channel,ChannelThis),:);
  66. InfoTableThisChannel = sortrows(InfoTableThisChannel, 'Plane', 'ascend');
  67. chThisPaths = cell(height(InfoTableThisChannel),1);
  68. for p = 1:height(InfoTableThisChannel)
  69. chThisPaths{p} = InfoTableThisChannel{p, 'file'}{:};
  70. end
  71. ImPaths{c} = chThisPaths;
  72. MesFile = MetaData.MeasurementSettingFileName;
  73. end
  74. FieldMetaData{fieldProgress} = {ImPaths, MesFile, Wells{w}, FieldsThisWell{f}};
  75. end
  76. end
  77. %% Image Analysis
  78. parfor i = 1:numel(FieldMetaData)
  79. try
  80. i
  81. ch1files = FieldMetaData{i}{1}{1};
  82. ch1Collector = cellfun(@(x) imread(x), ch1files, 'UniformOutput', false);
  83. ch1 = cat(3,ch1Collector{:}); % it(ch1) %pHluorin
  85. ch2files = FieldMetaData{i}{1}{2};
  86. ch2Collector = cellfun(@(x) imread(x), ch2files, 'UniformOutput', false);
  87. ch2 = cat(3,ch2Collector{:}); % it(ch2) %DsRed
  89. WellThis = FieldMetaData{i}{3};
  90. FieldThis = FieldMetaData{i}{4};
  91. [Objects] = f_Autophagy_imageanalysis(ch1, ch2, WellThis, FieldThis, TimeLineThis, PreviewPath);
  92. ObjectsAll{i} = Objects;
  93. catch
  94. continue
  95. end
  96. end
  97. %% Results saving
  98. Data = vertcat(ObjectsAll{:});
  99. save([Savingpath, filesep, 'data.mat'], 'Data');
  100. writetable(Data, [Savingpath, filesep, 'data.csv'], 'WriteRowNames', true)
  101. end %of TimeLines
  102. end %of Datapaths

Main_2.m at commit a86cc9c, no license · at the source

Overview

Authors: Catarina Serra-Almeida1,2, Javier Jarazo2,3, Gemma Gomez-Giro2, Isabel Rosety3, Alise Zagare2, Daniele Ferrante2, Cláudia Saraiva2, Daniela Frangenberg2, Jennifer Modamio-Chamarro2, Elisa Zuccoli2, Ana Clara Cristóvão1,4, Liliana Bernardino1, Jens Christian Schwamborn2
ORCID iDs: Alise Zagare, Elisa Zuccoli
  1. RISE-Health, Department of Medical Sciences, Faculty of Health Sciences, University of Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
  2. Luxembourg Center for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
  3. OrganoTherapeutics SARL, Esch-sur-Alzette, Luxembourg
  4. NeuroSoV, UBImedical, University of Beira Interior, Covilhã, Portugal
Institutions: University of Beira Interior (Portugal); University of Luxembourg (Luxembourg); Luxembourg Centre for Systems Biomedicine (Luxembourg)
Journal: NPJ Parkinson's disease, volume 12, issue 1, article 123
Dates: received 8 August 2025; accepted 16 March 2026; published online 31 March 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1038/s41531-026-01330-x · PMID 41917031 · PMCID PMC13199463 · OpenAlex W7143647240
Open access: gold, a free copy (OpenAlex)
Status: code verified (how the code is found and verified)
Categories: human (organism), Parkinson's (population), cellular / molecular (subfield)
Methods: Spectral & time-frequency, Statistics, Evoked potentials
Keywords: Cell biology, Neurology, Neuroscience, Stem cells
Topic: Parkinson's Disease Mechanisms and Treatments (Clinical Neurology, Medicine), according to OpenAlex
Funding: Fundação para a Ciência e a Tecnologia (SFRH/BD/149036/2019)
Citations: cited by 2 papers (Europe PMC); 64 references in the paper
Research resources: RRID:SCR_001622, RRID:SCR_001905, RRID:SCR_003070, RRID:SCR_016308, RRID:SCR_016495, RRID:SCR_018063, RRID:SCR_023270

Abstract

Parkinson’s disease (PD), characterized by α-Synuclein aggregation and dopaminergic neuronal loss, has no current cure. Autophagy is critical for α-Synuclein clearance, yet its real-time dynamics remain challenging to assess in human-relevant systems. Here, we used live-cell imaging to assess autophagy within human neuronal cultures and midbrain organoids (hMOs) derived from induced pluripotent stem cells (iPSCs) of PD patients carrying a triplication of the α-Synuclein gene (3xSNCA). Using the LC3-Rosella dual-fluorescent reporter, we quantified autolysosomes dynamics in real time. In 3xSNCA neuronal cultures, we detected early autophagy defects. In 3xSNCA hMOs, reduced autolysosome area, increased total and phosphorylated α-Synuclein (pS129), and decreased electrophysiological activity were observed at 50 days of differentiation (DoD). By 70 DoD, autophagy impairment became more pronounced, overlapping with dopaminergic neuron dysfunction. These findings support the use of human iPSCs-derived models to study autophagy dysfunction in PD and demonstrate a temporal correlation between impaired autophagy, α-Synuclein pathology and neuronal degeneration.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repository

Its files are read in the Code ↔ Paper reader above, with 4 matches between paragraphs and lines of code.

uniluxembourg/lcsb/developmental-and-cellular-biology/almeida_2025

License: none: the authors keep all their rights
State: the link answers, verified on 30 September 2026
Evidence: files inventoried
Commit: a86cc9c676b397ed46f97245278cd12b0065c1bf, 23 April 2026
Languages: MATLAB (24), R (9)
Size: 41 files, 33 scripts
Software Heritage: not archived
Found in: “Code availability”
Holds: README, 8 notebooks
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: ggplot2 (9 files), tidyverse (9 files), ggpubr (8 files), Image Processing Toolbox (8 files), rstatix (8 files), XGBoost (8 files), cowplot (2 files), data.table (2 files), reshape2 (1 file)
Availability: 1 check, the latest on 30 September 2026: the link answers
  • 30 September 2026: the link answers
34 files
At the source: gitlab.com/uniluxembourg/lcsb/developmental-and-cellular-biology/almeida_2025

Code availability

All scripts used to obtain, analyse and plot the data are available at https://gitlab.com/uniluxembourg/lcsb/developmental-and-cellular-biology/almeida_2025.

Reproduced under the paper's license (CC BY), from the paper cited above.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 33 scripts, each with its path and the digest of its content;
  • 4 matches between paragraphs of the paper and lines of the code (method lexical-v1);
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

No dataset and no data link were found in the paper.

Data Availability Statement

All data generated or analysed during this study as well as scripts that support the findings are available at 10.17881/gd2k-9685.

All scripts used to obtain, analyse and plot the data are available at https://gitlab.com/uniluxembourg/lcsb/developmental-and-cellular-biology/almeida_2025.

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 30 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 13 authors, 4 keywords, 1 funder, 63 references, 7 RRIDs.

Cite

This paper

Serra-Almeida, C., Jarazo, J., Gomez-Giro, G., Rosety, I., Zagare, A., Ferrante, D., Saraiva, C., Frangenberg, D., Modamio-Chamarro, J., Zuccoli, E., Cristóvão, A. C., Bernardino, L., & Schwamborn, J. C. (2026). Autophagy dysfunction in iPSCs-derived neurons and midbrain organoids carrying a SNCA triplication. NPJ Parkinson's disease, 12(1), 123. https://doi.org/10.1038/s41531-026-01330-x

BibTeX

@article{serraalmeida2026autophagy,
author = {Serra-Almeida, Catarina and Jarazo, Javier and Gomez-Giro, Gemma and Rosety, Isabel and Zagare, Alise and Ferrante, Daniele and Saraiva, Cláudia and Frangenberg, Daniela and Modamio-Chamarro, Jennifer and Zuccoli, Elisa and Cristóvão, Ana Clara and Bernardino, Liliana and Schwamborn, Jens Christian},
title = {{Autophagy dysfunction in iPSCs-derived neurons and midbrain organoids carrying a SNCA triplication}},
journal = {NPJ Parkinson's disease},
year = {2026},
month = mar,
volume = {12},
number = {1},
pages = {123},
publisher = {Nature Publishing Group},
issn = {2373-8057},
doi = {10.1038/s41531-026-01330-x},
url = {https://doi.org/10.1038/s41531-026-01330-x},
pmid = {41917031},
pmcid = {PMC13199463}
}

RIS

TY - JOUR
AU - Serra-Almeida, Catarina
AU - Jarazo, Javier
AU - Gomez-Giro, Gemma
AU - Rosety, Isabel
AU - Zagare, Alise
AU - Ferrante, Daniele
AU - Saraiva, Cláudia
AU - Frangenberg, Daniela
AU - Modamio-Chamarro, Jennifer
AU - Zuccoli, Elisa
AU - Cristóvão, Ana Clara
AU - Bernardino, Liliana
AU - Schwamborn, Jens Christian
TI - Autophagy dysfunction in iPSCs-derived neurons and midbrain organoids carrying a SNCA triplication
T2 - NPJ Parkinson's disease
J2 - NPJ Parkinsons Dis
PY - 2026
DA - 2026/03/31
VL - 12
IS - 1
SP - 123
SN - 2373-8057
PB - Nature Publishing Group
DO - 10.1038/s41531-026-01330-x
UR - https://doi.org/10.1038/s41531-026-01330-x
LA - en
ER -

CSL-JSON

{
"id": "10.1038/s41531-026-01330-x",
"type": "article-journal",
"title": "Autophagy dysfunction in iPSCs-derived neurons and midbrain organoids carrying a SNCA triplication",
"container-title": "NPJ Parkinson's disease",
"author": [
{
"family": "Serra-Almeida",
"given": "Catarina"
},
{
"family": "Jarazo",
"given": "Javier"
},
{
"family": "Gomez-Giro",
"given": "Gemma"
},
{
"family": "Rosety",
"given": "Isabel"
},
{
"family": "Zagare",
"given": "Alise"
},
{
"family": "Ferrante",
"given": "Daniele"
},
{
"family": "Saraiva",
"given": "Cláudia"
},
{
"family": "Frangenberg",
"given": "Daniela"
},
{
"family": "Modamio-Chamarro",
"given": "Jennifer"
},
{
"family": "Zuccoli",
"given": "Elisa"
},
{
"family": "Cristóvão",
"given": "Ana Clara"
},
{
"family": "Bernardino",
"given": "Liliana"
},
{
"family": "Schwamborn",
"given": "Jens Christian"
}
],
"container-title-short": "NPJ Parkinsons Dis",
"volume": "12",
"issue": "1",
"page": "123",
"DOI": "10.1038/s41531-026-01330-x",
"PMID": "41917031",
"PMCID": "PMC13199463",
"ISSN": "2373-8057",
"publisher": "Nature Publishing Group",
"URL": "https://doi.org/10.1038/s41531-026-01330-x",
"language": "en",
"issued": {
"date-parts": [
[
2026,
3,
31
]
]
}
}

The tracing map gets a citation of its own once an author has validated it and it has a DOI.

Similar papers

The papers with a page that share the most with this one: the tools found in their code, their categories, datasets, cited references and authors, the rarest counting most.

[1] doi:10.1038/s41531-023-00616-8 [code]
Impaired neuron differentiation in GBA-associated Parkinson's disease is linked to cell cycle defects in organoids.
Journal: NPJ Parkinson's disease
In common: XGBoost, rstatix, cowplot, 5 other tools, Parkinson's, 5 references, author Alise Zagare
[2] doi:10.1177/20417314241295928 [code]
Insulin resistance compromises midbrain organoid neuronal activity and metabolic efficiency predisposing to Parkinson's disease pathology.
Journal: Journal of tissue engineering
In common: rstatix, cowplot, reshape2, 4 other tools, Parkinson's, 4 references, author Alise Zagare
[3] doi:10.1016/j.isci.2026.114674 [code]
Single-cell transcriptomics revealed molecular vulnerability in a human midbrain-like organoid model of Parkinson's disease.
Journal: iScience
In common: rstatix, cowplot, reshape2, 4 other tools, Parkinson's, cellular / molecular, 5 references
[4] doi:10.1093/brain/awaf051 [code]
Parkinson's disease mutant Miro1 causes mitochondrial dysfunction and dopaminergic neuron loss.
Journal: Brain : a journal of neurology
In common: cowplot, ggpubr, Image Processing Toolbox, 2 other tools, Parkinson's, cellular / molecular, 4 references, author Alise Zagare
[5] doi:10.1002/mds.30039 [code]
Insulin Resistance Is a Modifying Factor for Parkinson's Disease.
Journal: Movement disorders : official journal of the Movement Disorder Society
In common: rstatix, ggpubr, Image Processing Toolbox, 1 other tool, Parkinson's, cellular / molecular, 4 references, author Alise Zagare
[6] doi:10.1038/s41540-025-00509-x [code]
MIRO1 mutation leads to metabolic maladaptation resulting in Parkinson's disease-associated dopaminergic neuron loss.
Journal: NPJ systems biology and applications
In common: rstatix, ggpubr, Image Processing Toolbox, 1 other tool, Parkinson's, cellular / molecular, 4 references, author Alise Zagare
[7] doi:10.1038/s42003-023-05548-w [code]
Omics data integration suggests a potential idiopathic Parkinson's disease signature.
Journal: Communications biology
In common: cowplot, ggpubr, ggplot2, 1 other tool, Parkinson's, cellular / molecular, 4 references, author Alise Zagare
[8] doi:10.1038/s41598-025-14735-0 [code]
Morphological profiling reveals neuroprotection via mitochondrial uncoupling in human dopaminergic neurons.
Journal: Scientific reports
In common: XGBoost, Parkinson's, cellular / molecular, 7 references
[9] doi:10.1038/s41467-025-67779-1 [code]
An in vivo and in vitro spatiotemporal profile of human midbrain development.
Journal: Nature communications
In common: cowplot, reshape2, ggpubr, 3 other tools, cellular / molecular, 3 references
[10] doi:10.1093/hmg/ddag024 [code]
A microbiome quantitative trait locus in SLC39A8 modulates disease severity in synucleinopathy-induced models of Parkinson's disease.
Journal: Human molecular genetics
In common: rstatix, cowplot, ggpubr, 2 other tools, Parkinson's, cellular / molecular, 3 references

Contribute

The authors of this paper can claim it, correct its record and validate its tracing map, and the maintainers of its code (its owner, or a public member of its organization) correct what it says of their repository; anyone signed in can ask for its removal. Every request goes to OSCR's own machine, which answers it; your account page follows them.

Sign in with ORCID to claim this paper as one of its authors, correct its record or validate its tracing map: when the paper's metadata lists your ORCID iD, you are recognized at once. Maintainers of its code: sign in with GitHub, then claim the repository on your account page.

Add the badge to the code's README

OSCR: the badge of this paper

If you are an author or a maintainer of this paper's code, you can add this badge. It says what OSCR knows of the paper (its code, its validated tracing map) and links the code to this page. Paste one of these snippets under the README's title. Keep the two marks around it, so that the badge can be replaced in place and is never added twice. OSCR changes nothing in your repository.

Markdown
<!-- oscr-badge:start -->
[![OSCR](https://openscicode.org/badge/doi/10.1038/s41531-026-01330-x.svg)](https://openscicode.org/badge/doi/10.1038/s41531-026-01330-x)
<!-- oscr-badge:end -->
reStructuredText
.. oscr-badge:start

.. image:: https://openscicode.org/badge/doi/10.1038/s41531-026-01330-x.svg
   :target: https://openscicode.org/badge/doi/10.1038/s41531-026-01330-x
   :alt: OSCR

.. oscr-badge:end
HTML
<!-- oscr-badge:start -->
<a href="https://openscicode.org/badge/doi/10.1038/s41531-026-01330-x"><img src="https://openscicode.org/badge/doi/10.1038/s41531-026-01330-x.svg" alt="OSCR"></a>
<!-- oscr-badge:end -->

If you choose to, you can have the badge kept up to date for you, with oscr badge --write from the command line or with the GitHub Action in your repository's workflows. Every other form and option (a card, AsciiDoc, LaTeX, shields.io) is on the badge page.

Request its removal

To ask OSCR to remove this record, the copies of its authors' scripts or its tracing map, use the removal request page: signed in, you say who you are, what to remove and why, then review and confirm the request. Published rules decide every request (how).

Discussion, reproductions, activity

Discussion: code errors and mismatches between the code and the paper about this paper and its code, from readers and its authors, beside the paper and its tracing map.

Report a mismatch between the code and the paper · Report a code error (signed in)

Reproductions: reports from readers who ran the authors' code and did not get the paper's result, what they ran, with which environment, commit and data.

Report a reproduction failure (signed in)

Activity: what happens around this paper: new versions of its record, its map's validation, discussions and reproductions. It opens with sign-in.