POPri: Private Federated Learning using Preference-Optimized Synthetic Data
Paper • 2504.16438 • Published • 1
Dataset Preview
The full dataset viewer is not available (click to read why). Only showing a preview of the rows.
The dataset generation failed because of a cast error
Error code: DatasetGenerationCastError
Exception: DatasetGenerationCastError
Message: An error occurred while generating the dataset
All the data files must have the same columns, but at some point there are 1 new columns ({'funder'})
This happened while the json dataset builder was generating data using
hf://datasets/hazylavender/biorxiv-abstract/biorxiv_result_2025-07.json (at revision 11474938a0373f576cdb50d47a70423830b61b5c), [/tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2023-04-01_2024-08-31.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2023-04-01_2024-08-31.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2024-03.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2024-03.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2024-09.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2024-09.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2024-10.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2024-10.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2024-11.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2024-11.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2024-12.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2024-12.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-01.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-01.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-02.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-02.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-03.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-03.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-04.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-04.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-05.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-05.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-06.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-06.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-07.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-07.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-08.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-08.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-09.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-09.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-10.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-10.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-11.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-11.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-12.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-12.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2026-01.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2026-01.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2026-02.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2026-02.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2026-03.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2026-03.json)]
Please either edit the data files to have matching columns, or separate them into different configurations (see docs at https://hf.co/docs/hub/datasets-manual-configuration#multiple-configurations)
Traceback: Traceback (most recent call last):
File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1890, in _prepare_split_single
writer.write_table(table)
File "/usr/local/lib/python3.12/site-packages/datasets/arrow_writer.py", line 760, in write_table
pa_table = table_cast(pa_table, self._schema)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2272, in table_cast
return cast_table_to_schema(table, schema)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2218, in cast_table_to_schema
raise CastError(
datasets.table.CastError: Couldn't cast
title: string
authors: string
author_corresponding: string
author_corresponding_institution: string
doi: string
date: timestamp[s]
version: string
type: string
license: string
category: string
jatsxml: string
abstract: string
funder: extension<arrow.json>
published: string
server: string
-- schema metadata --
huggingface: '{"info": {"features": {"title": {"dtype": "string", "_type"' + 729
to
{'doi': Value('string'), 'title': Value('string'), 'authors': Value('string'), 'author_corresponding': Value('string'), 'author_corresponding_institution': Value('string'), 'date': Value('timestamp[s]'), 'version': Value('string'), 'type': Value('string'), 'license': Value('string'), 'category': Value('string'), 'jatsxml': Value('string'), 'abstract': Value('string'), 'published': Value('string'), 'server': Value('string')}
because column names don't match
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1347, in compute_config_parquet_and_info_response
parquet_operations = convert_to_parquet(builder)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 980, in convert_to_parquet
builder.download_and_prepare(
File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 884, in download_and_prepare
self._download_and_prepare(
File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 947, in _download_and_prepare
self._prepare_split(split_generator, **prepare_split_kwargs)
File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1739, in _prepare_split
for job_id, done, content in self._prepare_split_single(
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1892, in _prepare_split_single
raise DatasetGenerationCastError.from_cast_error(
datasets.exceptions.DatasetGenerationCastError: An error occurred while generating the dataset
All the data files must have the same columns, but at some point there are 1 new columns ({'funder'})
This happened while the json dataset builder was generating data using
hf://datasets/hazylavender/biorxiv-abstract/biorxiv_result_2025-07.json (at revision 11474938a0373f576cdb50d47a70423830b61b5c), [/tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2023-04-01_2024-08-31.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2023-04-01_2024-08-31.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2024-03.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2024-03.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2024-09.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2024-09.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2024-10.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2024-10.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2024-11.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2024-11.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2024-12.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2024-12.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-01.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-01.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-02.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-02.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-03.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-03.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-04.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-04.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-05.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-05.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-06.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-06.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-07.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-07.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-08.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-08.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-09.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-09.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-10.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-10.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-11.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-11.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-12.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2025-12.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2026-01.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2026-01.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2026-02.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2026-02.json), /tmp/hf-datasets-cache/medium/datasets/16281826296926-config-parquet-and-info-hazylavender-biorxiv-abst-63815e6b/hub/datasets--hazylavender--biorxiv-abstract/snapshots/11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2026-03.json (origin=hf://datasets/hazylavender/biorxiv-abstract@11474938a0373f576cdb50d47a70423830b61b5c/biorxiv_result_2026-03.json)]
Please either edit the data files to have matching columns, or separate them into different configurations (see docs at https://hf.co/docs/hub/datasets-manual-configuration#multiple-configurations)Need help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
doi string | title string | authors string | author_corresponding string | author_corresponding_institution string | date timestamp[us] | version string | type string | license string | category string | jatsxml string | abstract string | published string | server string |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
10.1101/719013 | Cell cycle variants during Drosophila accessory gland development | Box, A. M.; Ramesh, N. A.; Nandakumar, S.; Church, S. J.; Prasad, D.; Afrakhteh, A.; Taichman, R. S.; Buttitta, L. | Laura Buttitta | University of Michigan | 2024-02-01T00:00:00 | 4 | new results | cc_by_nc_nd | developmental biology | https://www.biorxiv.org/content/early/2024/02/01/719013.source.xml | The Drosophila melanogaster accessory gland is a functional analog of the mammalian prostate containing two secretory epithelial cell types, termed main and secondary cells. This tissue is responsible for making and secreting seminal fluid proteins and other molecules that contribute to successful reproduction. The cel... | NA | biorxiv |
10.1101/721696 | Myelin-reactive B cells exacerbate the severity of CD4+ T cell-driven CNS autoimmunity in an IL-23-dependent manner. | Fazazi, M. R.; Doss, P. M. I. A.; Pereira, R.; Fudge, N.; Regmi, A.; Joly-Beauparlant, C.; Akbar, I.; Yeola, A. P.; Mailhot, B.; Baillargeon, J.; Grenier, P.; Bertrand, N.; Lacroix, S.; Droit, A.; Moore, C. S.; Rojas, O. L.; Rangachari, M. | Manu Rangachari | Laval University | 2023-09-06T00:00:00 | 5 | new results | cc_by | immunology | https://www.biorxiv.org/content/early/2023/09/06/721696.source.xml | Multiple sclerosis (MS) is an autoimmune disorder of the central nervous system (CNS) that has traditionally been considered a T cell-mediated disease. However, accumulating evidence points to a crucial role for B cells in disease processes. IgH[MOG] mice possess a transgenic immunoglobulin heavy chain derived from a m... | 10.1038/s41467-024-49259-0 | biorxiv |
10.1101/722397 | A new QRS detector stress test combining temporal jitter and accuracy (JA) reveals significant performance differences amongst popular detectors | Porr, B.; Macfarlane, P. W. | Bernd Porr | University of Glasgow | 2023-07-27T00:00:00 | 5 | contradictory results | cc_by_nc_nd | bioengineering | https://www.biorxiv.org/content/early/2023/07/27/722397.source.xml | QRS detection within an electrocardiogram (ECG) is the basis of virtually any further processing and any error caused by this detection will propagate to further processing stages. However, standard benchmarking procedures of QRS detectors are seriously flawed because they report almost always close to 100% accuracy fo... | NA | biorxiv |
10.1101/722397 | A new QRS detector stress test combining temporal jitter and F-score (JF) reveals significant performance differences amongst popular detectors | Porr, B.; Macfarlane, P. W. | Bernd Porr | University of Glasgow | 2024-03-30T00:00:00 | 6 | contradictory results | cc_by_nc_nd | bioengineering | https://www.biorxiv.org/content/early/2024/03/30/722397.source.xml | QRS detection within an electrocardiogram (ECG) is the basis of virtually any further processing and any error caused by this detection will propagate to further processing stages. However, standard benchmarking procedures of QRS detectors are seriously flawed because they report almost always close to 100% accuracy fo... | NA | biorxiv |
10.1101/721001 | Small molecule modulation of a redox-sensitive stress granule protein dissolves stress granules with beneficial outcomes for familial amyotrophic lateral sclerosis models | Uechi, H.; Sridharan, S.; Nijssen, J.; Bilstein, J.; Iglesias-Artola, J. M.; Kishigami, S.; Casablancas-Antras, V.; Poser, I.; Martinez, E. J.; Boczek, E.; Wagner, M.; Tomschke, N.; de Jesus Domingues, A. M.; Pal, A.; Doeleman, T.; Kour, S.; Anderson, E. N.; Stein, F.; Lee, H. O.; Zhang, X.; Fritsch, A. W.; Jahnel, M.;... | Anthony A Hyman | Max Planck Institute of Molecular Cell Biology and Genetics | 2024-01-05T00:00:00 | 3 | new results | cc_by | cell biology | https://www.biorxiv.org/content/early/2024/01/05/721001.source.xml | Neurodegenerave diseases such as amyotrophic lateral sclerosis (ALS) are oten associated with mutaons in proteins that are associated with stress granules. Stress granules are condensates formed by liquid-liquid phase separaon which, when aberrant, can lead to altered condensaon behaviours and disease phenotypes. Here,... | NA | biorxiv |
10.1101/743435 | Association of Ddx5/p68 protein with the upstream erythroid enhancer element (EHS1) of the Klf1 gene | Chen, X.; Pillay, S.; Lohmann, F.; Bieker, J. J. | James J Bieker | Mount Sinai School of Medicine, New York, NY | 2023-04-03T00:00:00 | 2 | new results | cc_by_nc_nd | molecular biology | https://www.biorxiv.org/content/early/2023/04/03/743435.source.xml | EKLF/KLF1 is an essential transcription factor that plays a global role in erythroid transcriptional activation. Its own regulation is of interest, as it displays a highly restricted expression pattern, limited to erythroid cells and its progenitors. Here we use biochemical affinity purification to identify the Ddx5/p6... | NA | biorxiv |
10.1101/743120 | Shielding working memory from distraction is more effortful than flexible updating | Papadopetraki, D.; Froboese, M. I.; Westbrook, A. J.; Zandbelt, B. B.; Cools, R. | Danae Papadopetraki | Donders Institute for Congnitive Neuroimaging; Radboud University Nijmegen; Radboud university Medical Center, Department of Psychiatry, Nijmegen | 2024-05-24T00:00:00 | 2 | new results | cc_by_nd | neuroscience | https://www.biorxiv.org/content/early/2024/05/24/743120.source.xml | Exerting cognitive control is known to carry a subjective effort cost and people are generally biased to avoid it. Recent theorizing suggests that the cost of cognitive effort serves as a motivational signal to bias people away from excessive focusing and towards more cognitive flexibility. We asked whether the effort ... | NA | biorxiv |
10.1101/759506 | Cardiac competence of the paraxial head mesoderm fades concomitant with a shift towards the head skeletal muscle programme | Alzamrooni, A. M. A. M.; Mendes Vieira, P. J.; Murciano, N.; Wolton, M.; Schubert, F. R.; Robson, S. C.; Dietrich, S. | Susanne Dietrich | University of Portsmouth | 2023-05-14T00:00:00 | 3 | new results | cc_by_nc_nd | developmental biology | https://www.biorxiv.org/content/early/2023/05/14/759506.source.xml | The vertebrate head mesoderm provides the heart, the great vessels, some smooth and most head skeletal muscle, in addition to parts of the skull. It has been speculated that the ability to generate cardiac and smooth muscle is the evolutionary ground-state of the tissue. However, whether indeed the entire head mesoderm... | 10.1016/j.ydbio.2023.06.005 | biorxiv |
10.1101/761346 | A dual function of the IDA peptide in regulating cell separation and modulating plant immunity at the molecular level | Lalun, V. O.; Breiden, M.; Galindo-Trigo, S.; Smakowska-Luzan, E.; Simon, R.; Butenko, M. A. | Melinka Alonso Butenko | University of Oslo | 2024-02-15T00:00:00 | 3 | new results | cc_by_nc_nd | plant biology | https://www.biorxiv.org/content/early/2024/02/15/761346.source.xml | The abscission of floral organs and emergence of lateral roots in Arabidopsis is regulated by the peptide ligand INFLORESCENCE DEFICIENT IN ABSCISSION (IDA) and the receptor protein kinases HAESA (HAE) and HAESA-LIKE 2 (HSL2). During these cell separation processes, the plant induces defense-associated genes to protect... | 10.7554/eLife.87912 | biorxiv |
10.1101/761346 | A dual function of the IDA peptide in regulating cell separation and modulating plant immunity at the molecular level | Lalun, V. O.; Breiden, M.; Galindo-Trigo, S.; Smakowska-Luzan, E.; Simon, R.; Butenko, M. A. | Melinka Alonso Butenko | University of Oslo | 2024-03-26T00:00:00 | 4 | new results | cc_by_nc_nd | plant biology | https://www.biorxiv.org/content/early/2024/03/26/761346.source.xml | The abscission of floral organs and emergence of lateral roots in Arabidopsis is regulated by the peptide ligand INFLORESCENCE DEFICIENT IN ABSCISSION (IDA) and the receptor protein kinases HAESA (HAE) and HAESA-LIKE 2 (HSL2). During these cell separation processes, the plant induces defense-associated genes to protect... | 10.7554/eLife.87912 | biorxiv |
10.1101/751222 | A nonlinear relationship between prediction errors and learning rates in human reinforcement learning | Ikwunne, B.; Parham, J.; Pulcu, E. | Erdem Pulcu | University of Oxford | 2024-07-31T00:00:00 | 4 | new results | cc_by_nc_nd | neuroscience | https://www.biorxiv.org/content/early/2024/07/31/751222.source.xml | Reinforcement-learning (RL) models have been pivotal to our understanding of how agents perform learning-based adaptions in dynamically changing environments. However, the exact nature of the relationship (e.g. linear, logarithmic etc.) between key components of RL models such as prediction errors (PEs; the difference ... | NA | biorxiv |
10.1101/773507 | Gravity-based microfiltration reveals unexpected prevalence of circulating tumor cell clusters in ovarian and colorectal cancer | Meunier, A.; Hernandez-Castro, J. A.; Chahley, N.; Communal, L.; Kheireddine, S.; Koushki, N.; Davoudvandi, N.; Al Habyan, S.; Peant, B.; Lazaris, A.; Ng, A.; Veres, T.; McCaffrey, L.; Provencher, D.; Metrakos, P.; Mes-Masson, A.-M.; Juncker, D. | David Juncker | McGill University | 2023-12-05T00:00:00 | 2 | new results | cc_by_nc_nd | bioengineering | https://www.biorxiv.org/content/early/2023/12/05/773507.source.xml | Circulating tumor cells (CTCs) are rare (few cells per milliliter of blood) and mostly isolated as single cell CTCs (scCTCs). CTC clusters (cCTCs), even rarer, are of growing interest, notably because of their higher metastatic potential, but very difficult to isolate. Here, we introduce gravity-based microfiltration (... | NA | biorxiv |
10.1101/784678 | ISG15/USP18/STAT2 is a molecular hub regulating autocrine IFN I-mediated control of Dengue and Zika virus replication | Espada, C. E.; da Rocha, E. L.; Ricciardi-Jorge, T.; dos Santos, A. A.; Soares, Z. G.; Malaquias, G.; Patricio, D. d. O.; Kozlova, E. G.; dos Santos, P. F.; Bordignon, J.; Sanford, T. J.; Fajardo, T.; Sweeney, T.; Bafica, A.; Mansur, D. S. | Daniel Santos Mansur | Universidade Federal de Santa Catarina | 2023-07-15T00:00:00 | 4 | new results | cc_by_nc_nd | immunology | https://www.biorxiv.org/content/early/2023/07/15/784678.source.xml | The establishment of a virus infection is the result of the pathogens ability to replicate in a hostile environment generated by the hosts immune system. Here, we found that ISG15 restricts Dengue and Zika viruses replication through the stabilisation of its binding partner USP18. ISG15 expression was necessary to cont... | 10.3389/fimmu.2024.1331731 | biorxiv |
10.1101/784678 | ISG15/USP18/STAT2 is a molecular hub regulating autocrine IFN I-mediated control of Dengue and Zika virus replication | Espada, C. E.; da Rocha, E. L.; Ricciardi-Jorge, T.; dos Santos, A. A.; Soares, Z. G.; Malaquias, G.; Patricio, D. d. O.; Kozlova, E. G.; dos Santos, P. F.; Bordignon, J.; Sanford, T. J.; Fajardo, T.; Sweeney, T.; Bafica, A.; Mansur, D. S. | Daniel Santos Mansur | Universidade Federal de Santa Catarina | 2023-10-19T00:00:00 | 5 | new results | cc_by_nc_nd | immunology | https://www.biorxiv.org/content/early/2023/10/19/784678.source.xml | The establishment of a virus infection is the result of the pathogens ability to replicate in a hostile environment generated by the hosts immune system. Here, we found that ISG15 restricts Dengue and Zika viruses replication through the stabilisation of its binding partner USP18. ISG15 expression was necessary to cont... | 10.3389/fimmu.2024.1331731 | biorxiv |
10.1101/784678 | ISG15/USP18/STAT2 is a molecular hub regulating autocrine IFN I-mediated control of Dengue and Zika virus replication | Espada, C. E.; da Rocha, E. L.; Ricciardi-Jorge, T.; dos Santos, A. A.; Soares, Z. G.; Malaquias, G.; Patricio, D. d. O.; Kozlova, E. G.; dos Santos, P. F.; Bordignon, J.; Sanford, T. J.; Fajardo, T.; Sweeney, T.; Bafica, A.; Mansur, D. S. | Daniel Santos Mansur | Universidade Federal de Santa Catarina | 2023-11-01T00:00:00 | 6 | new results | cc_by_nc_nd | immunology | https://www.biorxiv.org/content/early/2023/11/01/784678.source.xml | The establishment of a virus infection is the result of the pathogens ability to replicate in a hostile environment generated by the hosts immune system. Here, we found that ISG15 restricts Dengue and Zika viruses replication through the stabilisation of its binding partner USP18. ISG15 expression was necessary to cont... | 10.3389/fimmu.2024.1331731 | biorxiv |
10.1101/784157 | Technical artifact drives apparent deviation from Hardy-Weinberg equilibrium at CCR5-Δ32 and other variants in gnomAD | Karczewski, K. J.; Gauthier, L. D.; Daly, M. J. | Konrad J Karczewski | Broad Institute | 2023-07-29T00:00:00 | 2 | contradictory results | cc_by | genomics | https://www.biorxiv.org/content/early/2023/07/29/784157.source.xml | Following an earlier report suggesting increased mortality due to homozygosity at the CCR5-{Delta}32 allele1, Wei and Nielsen recently suggested a deviation from Hardy-Weinberg Equilibrium (HWE) observed in public variant databases as additional supporting evidence for this hypothesis2. Here, we present a re-analysis o... | NA | biorxiv |
10.1101/790378 | Enhancing autophagy by redox regulation extends lifespan in Drosophila | Lennicke, C.; Bjedov, I.; Grönke, S.; Menger, K. E.; James, A. M.; Castillo-Quan, J. I.; van Leeuwen, L. A. G.; Foley, A.; Buricova, M.; Adcott, J.; Montoya, A.; Kramer, H. B.; Shliaha, P. V.; Logan, A.; Cabreiro, F.; Murphy, M. P.; Partridge, L.; Cocheme, H. M. | Helena M Cochemé | MRC London Institute of Medical Sciences, UK | 2024-05-10T00:00:00 | 2 | new results | cc_by | molecular biology | https://www.biorxiv.org/content/early/2024/05/10/790378.source.xml | Dysregulation of redox homeostasis has been implicated in the ageing process and the pathology of age-related diseases. To study redox signalling by H2O2 in vivo, we established a redox-shifted model by manipulating levels of the H2O2-degrading enzyme catalase in Drosophila. Here we report that ubiquitous over-expressi... | NA | biorxiv |
10.1101/793943 | Energy landscape steering mediates dynamic coupling in ATP-driven protein translocation by the bacterial Sec machinery | Crossley, J. A.; Allen, W. J.; Watkins, D. W.; Sabir, T.; Radford, S. E.; Tuma, R.; Collinson, I.; Fessl, T. | Roman Tuma | University of Leeds, United Kingdom and University of South Bohemia, Czech Republic | 2023-06-06T00:00:00 | 4 | new results | cc_by_nc_nd | biophysics | https://www.biorxiv.org/content/early/2023/06/06/793943.source.xml | The Sec translocon is a highly conserved membrane complex for transport of polypeptides across, or into, lipid bilayers. In bacteria, the core protein-channel SecYEG resides in the inner-membrane, through which secretion is powered by the cytosolic ATPase SecA. Here, we use single-molecule fluorescence to interrogate t... | NA | biorxiv |
10.1101/795930 | Human astrocytes and microglia show augmented ingestion of synapses in Alzheimer's disease via MFG-E8 | Tzioras, M.; Daniels, M. J.; Davies, C.; Baxter, P.; King, D.; McKay, S.; Varga, B. V.; Popovic, K.; Hernandez, M.; Stevenson, A. J.; Barrington, J.; Drinkwater, E.; Borella, J. A.; Holloway, R. K.; Tulloch, J.; Latta, C.; Kandasamy, J.; Sokol, D.; Smith, C.; Miron, V.; Karadottir, R. T.; Hardingham, G.; Henstridge, C.... | Tara L Spires-Jones | The University of Edinburgh | 2023-04-05T00:00:00 | 2 | new results | cc_by | neuroscience | https://www.biorxiv.org/content/early/2023/04/05/795930.source.xml | Synapse loss correlates with cognitive decline in Alzheimers disease (AD). Data from mouse models suggests microglia are important for synapse degeneration, but direct human evidence for any glial involvement in synapse removal in human AD remains to be established. Here we observe astrocytes and microglia from human b... | 10.1016/j.xcrm.2023.101175 | biorxiv |
10.1101/801563 | Overlap in synaptic neurological condition susceptibility pathways and the neural pannexin 1 interactome revealed by bioinformatics analyses | Frederiksen, S. D.; Wicki-Stordeur, L. E.; Swayne, L. A. | Leigh A. Swayne | University of Victoria | 2023-04-27T00:00:00 | 2 | new results | cc_by_nc_nd | neuroscience | https://www.biorxiv.org/content/early/2023/04/27/801563.source.xml | Many neurological conditions exhibit synaptic impairments, suggesting mechanistic convergence. Additionally, the pannexin 1 (PANX1) channel and signalling scaffold is linked to several of these neurological conditions and is an emerging regulator of synaptic development and plasticity; however, its synaptic pathogenic ... | 10.1080/19336950.2023.2253102 | biorxiv |
10.1101/801563 | Overlap in synaptic neurological condition susceptibility pathways and the neural pannexin 1 interactome revealed by bioinformatics analyses | Frederiksen, S. D.; Wicki-Stordeur, L. E.; Swayne, L. A. | Leigh A. Swayne | University of Victoria | 2023-05-10T00:00:00 | 3 | new results | cc_by_nc_nd | neuroscience | https://www.biorxiv.org/content/early/2023/05/10/801563.source.xml | Many neurological conditions exhibit synaptic impairments, suggesting mechanistic convergence. Additionally, the pannexin 1 (PANX1) channel and signalling scaffold is linked to several of these neurological conditions and is an emerging regulator of synaptic development and plasticity; however, its synaptic pathogenic ... | 10.1080/19336950.2023.2253102 | biorxiv |
10.1101/803205 | Caliban: Accurate cell tracking and lineage construction in live-cell imaging experiments with deep learning | Schwartz, M.; Moen, E.; Miller, G.; Dougherty, T.; Borba, E.; Ding, R.; Graf, W.; Pao, E.; Van Valen, D. A. | David Ashley Van Valen | California Institute of Technology | 2023-09-06T00:00:00 | 3 | new results | cc_by | bioinformatics | https://www.biorxiv.org/content/early/2023/09/06/803205.source.xml | While live-cell imaging is a powerful approach to studying the dynamics of cellular systems, converting these imaging data into quantitative, single-cell records of cellular behavior has been a longstanding challenge. Deep learning methods have proven capable of performing cell segmentation--a critical task for analyzi... | NA | biorxiv |
10.1101/803205 | Caliban: Accurate cell tracking and lineage construction in live-cell imaging experiments with deep learning | Schwartz, M.; Moen, E.; Miller, G.; Dougherty, T.; Borba, E.; Ding, R.; Graf, W.; Pao, E.; Van Valen, D. A. | David Ashley Van Valen | California Institute of Technology | 2023-09-12T00:00:00 | 4 | new results | cc_by | bioinformatics | https://www.biorxiv.org/content/early/2023/09/12/803205.source.xml | While live-cell imaging is a powerful approach to studying the dynamics of cellular systems, converting these imaging data into quantitative, single-cell records of cellular behavior has been a longstanding challenge. Deep learning methods have proven capable of performing cell segmentation--a critical task for analyzi... | NA | biorxiv |
10.1101/803205 | Caliban: Accurate cell tracking and lineage construction in live-cell imaging experiments with deep learning | Schwartz, M.; Moen, E.; Miller, G.; Dougherty, T.; Borba, E.; Ding, R.; Graf, W.; Pao, E.; Van Valen, D. A. | David Ashley Van Valen | California Institute of Technology | 2024-08-07T00:00:00 | 5 | new results | cc_by | bioinformatics | https://www.biorxiv.org/content/early/2024/08/07/803205.source.xml | While live-cell imaging is a powerful approach to studying the dynamics of cellular systems, converting these imaging data into quantitative, single-cell records of cellular behavior has been a longstanding challenge. Deep learning methods have proven capable of performing cell segmentation--a critical task for analyzi... | NA | biorxiv |
10.1101/805614 | An Improved Chromosome-scale Genome Assembly and Population Genetics resource for Populus tremula. | Robinson, K. M.; Schiffthaler, B.; Liu, H.; Westman, S. M.; Rendon-Anaya, M.; Ahlgren Kalman, T.; Kumar, V.; Canovi, C.; Bernhardsson, C.; Delhomme, N.; Jenkins, J.; Wang, J.; Mähler, N.; Richau, K. H.; Stokes, V.; A'Hara, S.; Cottrell, J.; Coeck, K.; Diels, T.; Vandepoele, K.; Mannapperuma, C.; Park, E.-J.; Plaisance... | Bastian Schiffthaler | Umea Plant Science Center | 2024-04-08T00:00:00 | 2 | new results | cc_by_nc_nd | genomics | https://www.biorxiv.org/content/early/2024/04/08/805614.source.xml | Aspen (Populus tremula L.) is a widely distributed keystone species and a model system for forest tree genomics, with extensive resources developed for population genetics and genomics. Here we present an updated resource comprising a chromosome-scale assembly of P. tremula and population genetics and genomics data int... | NA | biorxiv |
10.1101/810259 | Plasmid carriage and the unorthodox use of Fisher's theorem in evolutionary biology | Reding, C. | Carlos Reding | University of Exeter | 2023-05-04T00:00:00 | 11 | new results | cc_by_nc_nd | evolutionary biology | https://www.biorxiv.org/content/early/2023/05/04/810259.source.xml | The link between fitness and reproduction rate is a central tenet in microbiology, and indeed evolutionary biology: Mutants reproducing faster than the dominant wild-type are favoured by selection, but otherwise the mutation is lost. This link was given by Ronald Fisher in 1930 under the assumption that fitness can onl... | NA | biorxiv |
10.1101/810259 | Plasmid carriage and the unorthodox use of fitness in microbial genetics | Reding, C. | Carlos Reding | University of Exeter | 2023-08-28T00:00:00 | 12 | new results | cc_by_nc_nd | evolutionary biology | https://www.biorxiv.org/content/early/2023/08/28/810259.source.xml | The link between fitness and reproduction rate is a central tenet in microbiology, and indeed evolutionary biology: Mutants reproducing faster than the dominant wild-type are favoured by selection, but otherwise the mutation is lost. This link was given by Ronald Fisher in 1930 under the assumption that fitness can onl... | NA | biorxiv |
10.1101/810259 | Plasmid carriage and the unorthodox use of fitness in microbial genetics | Reding, C. | Carlos Reding | University of Exeter | 2023-11-20T00:00:00 | 13 | new results | cc_by_nc_nd | evolutionary biology | https://www.biorxiv.org/content/early/2023/11/20/810259.source.xml | The link between fitness and reproduction rate is a central tenet in microbiology, and indeed evolutionary biology: Mutants reproducing faster than the dominant wild-type are favoured by selection, but otherwise the mutation is lost. This link was given by Ronald Fisher in 1930 under the assumption that fitness can onl... | NA | biorxiv |
10.1101/812198 | Effective mechanical potential of cell-cell interaction explains three-dimensional morphologies during early embryogenesis | Koyama, H.; Okumura, H.; Ito, A. M.; Nakamura, K.; Otani, T.; Kato, K.; Fujimori, T. | Hiroshi Koyama | National Institute for Basic Biology | 2023-06-26T00:00:00 | 6 | new results | cc_by_nc_nd | biophysics | https://www.biorxiv.org/content/early/2023/06/26/812198.source.xml | Mechanical forces are critical for the emergence of diverse three-dimensional morphologies of multicellular systems. However, it remains unclear what kind of mechanical parameters at cellular level substantially contribute to tissue morphologies. This is largely due to technical limitations of live measurements of cell... | 10.1371/journal.pcbi.1011306 | biorxiv |
10.1101/839811 | The astrocyte-enriched gene CG11000 plays a crucial role in the development, locomotion and lifespan of D. melanogaster | Najafi, H.; Wong, K.; Salkini, A. H.; Miao, H.; Kim, W. J. | Woo Jae Kim | University of Ottawa | 2023-09-12T00:00:00 | 4 | new results | cc_by_nc_nd | genetics | https://www.biorxiv.org/content/early/2023/09/12/839811.source.xml | The brain of Drosophila melanogaster is a complex organ with various cell types, orchestrating the physiology and behaviors of the fly. While each cell type in the Drosophila brain is known to express a unique set of genes, their complete genetic profile is still unknown. Advances in the RNA-sequencing techniques at si... | NA | biorxiv |
10.1101/852129 | Sympathetic innervation directs Ankyrin G, voltage-gated Nav and KCNQ1 channels to the neuro-cardiac junctions | Shcherbakova, O. G. | Olga G Shcherbakova | Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC Kurchatov Institute | 2023-06-09T00:00:00 | 3 | new results | cc_by_nc_nd | neuroscience | https://www.biorxiv.org/content/early/2023/06/09/852129.source.xml | The sympathetic nervous system plays a central role in the cardiovascular response to acute stress by increasing heart rate and contractility. Despite the importance of functional connections between sympathetic nerves and cardiac myocytes, very little is known about the structural and functional organization of the ne... | NA | biorxiv |
10.1101/859942 | Prioritized neural processing of social threats during perceptual decision-making | El Zein, M.; Mennella, R.; Sequestro, M.; Meaux, E.; Wyart, V.; Grezes, J. | Emilie Meaux | INSERM U960, LNC2, Ecole Normale Superieure de Paris, PSL University | 2024-01-02T00:00:00 | 4 | new results | cc_by | neuroscience | https://www.biorxiv.org/content/early/2024/01/02/859942.source.xml | Emotional signals, notably those signaling threat, benefit from prioritized processing in the human brain. Yet, it remains unclear whether perceptual decisions about the emotional, threat-related aspects of stimuli involve specific or similar neural computations compared to decisions about their non-threatening/non-emo... | 10.1016/j.isci.2024.109951 | biorxiv |
10.1101/871020 | Quantitative Real-Time PCR assays for species-specific detection and quantification of Baltic Sea spring bloom dinoflagellates | Brink, A. M.; Kremp, A.; Gorokhova, E. | Annica M. Brink | Stockholm University | 2024-03-09T00:00:00 | 2 | new results | cc_by_nc_nd | molecular biology | https://www.biorxiv.org/content/early/2024/03/09/871020.source.xml | In the Baltic Sea, the dinoflagellates Apocalathium malmogiense, Biecheleria baltica, and Gymnodinium corollarium are important contributors to the spring bloom. However, their relative contribution to the bloom community cannot be unambiguously determined by conventional light microscopy due to lack of resolution of d... | NA | biorxiv |
10.1101/2019.12.13.875526 | An Alignment-free Method for Phylogeny Estimation using Maximum Likelihood | Zahin, T.; Abrar, M. H.; Rahman, M.; Tasnim, T.; Bayzid, M. S.; Rahman, A. | Atif Rahman | Bangladesh University of Engineering and Technology | 2024-07-29T00:00:00 | 2 | new results | cc_by_nd | bioinformatics | https://www.biorxiv.org/content/early/2024/07/29/2019.12.13.875526.source.xml | While alignment has traditionally been the primary approach for establishing homology prior to phylogenetic inference, alignment-free methods offer a simplified alternative, particularly beneficial when handling genome-wide data involving long sequences and complex events such as rearrangements. Moreover, alignment-fre... | NA | biorxiv |
10.1101/2019.12.12.868489 | Is N-Hacking Ever OK? A Simulation-based study | Reinagel, P. | Pamela Reinagel | UCSD | 2023-08-24T00:00:00 | 4 | new results | cc_by_nc_nd | scientific communication and education | https://www.biorxiv.org/content/early/2023/08/24/2019.12.12.868489.source.xml | After an experiment has been completed, a trend may be observed that is "not quite significant". Sometimes in this situation, researchers collect more data in an effort to achieve statistical significance. Such "N-hacking" is condemned because it can lead to an excess of false positive results. I use simulations to dem... | 10.1371/journal.pbio.3002345 | biorxiv |
10.1101/2019.12.12.868489 | Is N-Hacking Ever OK? A Simulation-based study | Reinagel, P. | Pamela Reinagel | UCSD | 2023-08-24T00:00:00 | 4 | new results | cc_by_nc_nd | scientific communication and education | https://www.biorxiv.org/content/early/2023/08/24/2019.12.12.868489.source.xml | After an experiment has been completed, a trend may be observed that is "not quite significant". Sometimes in this situation, researchers collect more data in an effort to achieve statistical significance. Such "N-hacking" is condemned because it can lead to an excess of false positive results. I use simulations to dem... | 10.1371/journal.pbio.3002345 | biorxiv |
10.1101/2019.12.20.884734 | Genetic erosion reduces biomass temporal stability in wild fish populations. | Prunier, J. G.; Chevalier, M.; Raffard, A.; Loot, G.; Poulet, N.; Blanchet, S. | Jerome G. Prunier | CNRS | 2023-04-05T00:00:00 | 3 | new results | cc_by_nc | ecology | https://www.biorxiv.org/content/early/2023/04/05/2019.12.20.884734.source.xml | Genetic diversity sustains species adaptation. However, it may also support key ecosystems functions and services that can be altered by the worldwide loss of genetic diversity. Here, using long-term wild fish data, we demonstrate that populations with high genetic diversity do not reach higher biomasses than populatio... | 10.1038/s41467-023-40104-4 | biorxiv |
10.1101/2019.12.20.884262 | Cognitive control of behavior and hippocampal information processing without medial prefrontal cortex | Park, E.; Reilly, K. O.; Grubbs, G.; Taborga, D.; Nicholas, K.; Ahmeda, A. S.; Ruiz, N.; Kim, N.; Segura-Carrillo, S.; Fenton, A. A. | Kally O'Reilly | Columbia University | 2024-04-11T00:00:00 | 3 | new results | cc_by_nd | neuroscience | https://www.biorxiv.org/content/early/2024/04/11/2019.12.20.884262.source.xml | Cognitive control tasks require using one class of information and ignoring competing classes of information. A central role for the medial prefrontal cortex (mPFC) in cognitive control is well established because mPFC damage impairs tasks that may require cognitive control, as inferred, typically from the task design.... | NA | biorxiv |
10.1101/2020.01.03.893776 | A long tail of truth and beauty: A zigzag pattern of feather formation explains the symmetry, complexity, and beauty of the peacock's tail | Singh, R. S.; Jagadeeshan, S. | Rama Shankar Singh | McMaster University | 2023-08-17T00:00:00 | 3 | new results | cc_by_nc_nd | evolutionary biology | https://www.biorxiv.org/content/early/2023/08/17/2020.01.03.893776.source.xml | One hundred and fifty years after the publication of Darwins sexual selection theory, the problem of the peacocks train remains unsolved. Darwin assumed that the peacocks long train was maladaptive and was the indirect effect of selection by female mate choice based on the trains beauty. While a relationship between th... | NA | biorxiv |
10.1101/2020.01.04.894907 | Genome-wide Functional Characterization of Escherichia coli Promoters and Sequence Elements Encoding Their Regulation | Urtecho, G.; Insigne, K.; Tripp, A. D.; Brinck, M.; Lubock, N. B.; Acree, C.; Kim, H.; Chan, T.; Kosuri, S. | Sriram Kosuri | UCLA | 2023-10-12T00:00:00 | 2 | new results | cc_by_nc | microbiology | https://www.biorxiv.org/content/early/2023/10/12/2020.01.04.894907.source.xml | Despite decades of intense genetic, biochemical, and evolutionary characterizations of bacterial promoters, we lack the ability to identify or predict transcriptional activities of promoters using primary sequence. Even in simple, well-characterized organisms such as E. coli there is little agreement on the number, loc... | NA | biorxiv |
10.1101/2020.01.09.900514 | Defective Function of α-Ketoglutarate Dehydrogenase Exacerbates Mitochondrial ATP Deficits during Complex I Deficiency | Piroli, G. G.; Manuel, A. M.; McCain, R. S.; Smith, H. H.; Ozohanics, O.; Mellid, S.; Cotham, W. E.; Walla, M. D.; Cascon, A.; Ambrus, A.; Frizzell, N. | Norma Frizzell | University of South Carolina | 2023-08-10T00:00:00 | 3 | new results | cc_by_nc_nd | biochemistry | https://www.biorxiv.org/content/early/2023/08/10/2020.01.09.900514.source.xml | The NDUFS4 knockout (KO) mouse phenotype resembles the human Complex I deficiency Leigh Syndrome. The irreversible succination of protein thiols by fumarate is increased in select regions of the NDUFS4 KO brain affected by neurodegeneration, suggesting a mechanistic role in neurodegenerative decline. We report that dih... | 10.1016/j.redox.2023.102932 | biorxiv |
10.1101/2020.01.11.899559 | Macromolecular and cytological changes in fission yeast G0 nuclei | Tan, Z. Y.; Cai, S.; Paithankar, S. A.; Nie, X.; Shi, J.; Gan, L. | Lu Gan | National University of Singapore | 2024-04-10T00:00:00 | 2 | new results | cc_by_nc_nd | cell biology | https://www.biorxiv.org/content/early/2024/04/10/2020.01.11.899559.source.xml | When starved of nitrogen, fission yeast Schizosaccharomyces pombe cells enter a quiescent "G0" state with smaller nuclei and transcriptional repression. The genomics of S. pombe G0 cells has been well studied, but much of its nuclear cell biology remains unknown. Here we use confocal microscopy, immunoblots, and electr... | NA | biorxiv |
10.1101/2020.01.12.903393 | Calcium-independent lipid release from astrocytes modulates neuronal excitability | Wang, F.; Bradshaw, H. B.; Jablonska, B.; Pena, S. E.; Xavier, J.; Gong, S.; Li, B.; Chandler-Militello, D.; Bekar, L. K.; Smith, N. A. | Nathan A Smith | Children's National Research Institute | 2024-05-19T00:00:00 | 6 | new results | cc_by_nc_nd | neuroscience | https://www.biorxiv.org/content/early/2024/05/19/2020.01.12.903393.source.xml | An accumulating amount of data suggests that Ca2+-dependent gliotransmitter release plays a key role in the modulation of neuronal networks. Here, we tested the hypothesis that in response to agonist exposure, astrocytes release lipid modulators through activation of Ca2+-independent phospholipase A2 (iPLA2) activity. ... | NA | biorxiv |
10.1101/2020.01.12.903393 | Calcium-independent lipid release from astrocytes modulates neuronal excitability | Wang, F.; Bradshaw, H. B.; Jablonska, B.; Pena, S. E.; Chittaranjan, S.; Xavier, J.; Gong, S.; Li, B.; Chandler-Militello, D.; Bekar, L. K.; Smith, N. A. | Nathan A Smith | Children's National Research Institute | 2024-07-30T00:00:00 | 7 | new results | cc_by_nc_nd | neuroscience | https://www.biorxiv.org/content/early/2024/07/30/2020.01.12.903393.source.xml | An accumulating amount of data suggests that Ca2+-dependent gliotransmitter release plays a key role in the modulation of neuronal networks. Here, we tested the hypothesis that in response to agonist exposure, astrocytes release lipid modulators through activation of Ca2+-independent phospholipase A2 (iPLA2) activity. ... | NA | biorxiv |
10.1101/2020.01.29.926022 | CopyMix: Mixture Model Based Single-Cell Clustering and Copy Number Profiling using Variational Inference | Safinianaini, N.; P. E. de Souza, C.; Roth, A.; Koptagel, H.; Toosi, H.; Lagergren, J. | Negar Safinianaini | School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, Stockholm, Sweden | 2023-10-17T00:00:00 | 6 | new results | cc_by | bioinformatics | https://www.biorxiv.org/content/early/2023/10/17/2020.01.29.926022.source.xml | Investigating tumor heterogeneity using single-cell sequencing technologies is imperative to understand how tumors evolve since each cell subpopulation harbors a unique set of genomic features that yields a unique phenotype, which is bound to have clinical relevance. Clustering of cells based on copy number data obtain... | NA | biorxiv |
10.1101/2020.01.30.926790 | Alu insertion-mediated dsRNA structure formation with pre-existing Alu elements as a novel disease-causing mechanism | Masson, E.; Maestri, S.; Bordeau, V.; Cooper, D. N.; Ferec, C.; Chen, J.-M. | Jian-Min Chen | Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France | 2024-04-03T00:00:00 | 2 | new results | cc_by_nc_nd | genetics | https://www.biorxiv.org/content/early/2024/04/03/2020.01.30.926790.source.xml | We previously identified a homozygous Alu insertion variant (Alu_Ins) in the 3-UTR of the SPINK1 gene as the cause of a novel pediatric disease. Although we established that Alu_Ins leads to the complete loss of SPINK1 mRNA expression, the precise mechanisms remained elusive. Here we aimed to elucidate these mechanisms... | NA | biorxiv |
10.1101/2020.02.03.926295 | The hidden cost of receiving favors: A theory of indebtedness | Gao, X.; Jolly, E.; Yu, H.; Liu, H.; Zhou, X.; Chang, L. J. | Luke J Chang | Peking University | 2023-05-26T00:00:00 | 4 | new results | cc_by_nc_nd | neuroscience | https://www.biorxiv.org/content/early/2023/05/26/2020.02.03.926295.source.xml | Receiving help or a favor from another person can sometimes have a hidden cost for the beneficiary. In this study, we explore these hidden costs by developing and validating a conceptual model of indebtedness across three studies that combine a large scale online questionnaire, an interpersonal game, computational mode... | NA | biorxiv |
10.1101/2020.02.09.940494 | Pathogen community composition and co-infection patterns in a wild community of rodents | Abbate, J. L.; Galan, M.; Razzauti, M.; Sironen, T.; Voutilainen, L.; Henttonen, H.; Gasqui, P.; Cosson, J.-F.; Charbonnel, N. | Nathalie Charbonnel | CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France | 2023-07-21T00:00:00 | 3 | new results | cc_by_nc_nd | ecology | https://www.biorxiv.org/content/early/2023/07/21/2020.02.09.940494.source.xml | Rodents are major reservoirs of pathogens that can cause disease in humans and livestock. It is therefore important to know what pathogens naturally circulate in rodent populations, and to understand the factors that may influence their distribution in the wild. Here, we describe the occurrence and distribution pattern... | 10.24072/pcjournal.370 | biorxiv |
10.1101/2020.02.09.940494 | Pathogen community composition and co-infection patterns in a wild community of rodents | Abbate, J. L.; Galan, M.; Razzauti, M.; Sironen, T.; Voutilainen, L.; Henttonen, H.; Gasqui, P.; Cosson, J.-F.; Charbonnel, N. | Nathalie Charbonnel | CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France | 2023-11-14T00:00:00 | 4 | new results | cc_by_nc_nd | ecology | https://www.biorxiv.org/content/early/2023/11/14/2020.02.09.940494.source.xml | Rodents are major reservoirs of pathogens that can cause disease in humans and livestock. It is therefore important to know what pathogens naturally circulate in rodent populations, and to understand the factors that may influence their distribution in the wild. Here, we describe the occurrence and distribution pattern... | 10.24072/pcjournal.370 | biorxiv |
10.1101/2020.02.13.946517 | Protein interaction mapping reveals widespread targeting of development-related host transcription factors by phytoplasma effectors | Correa Marrero, M.; Capdevielle, S.; Huang, W.; Al-Subhi, A. M.; Busscher, M.; Busscher-Lange, J.; van der Wal, F.; de Ridder, D.; van Dijk, A. D. J.; Hogenhout, S. A.; Immink, R. G. H. | Richard G.H. Immink | Wageningen University & Research | 2023-07-23T00:00:00 | 2 | new results | cc_by_nc_nd | plant biology | https://www.biorxiv.org/content/early/2023/07/23/2020.02.13.946517.source.xml | Phytoplasmas are pathogenic bacteria that reprogram plant host development for their own benefit. Previous studies have characterized a few different phytoplasma effector proteins that destabilize specific plant transcription factors. However, these are only a small fraction of the potential effectors used by phytoplas... | 10.1111/tpj.16546 | biorxiv |
10.1101/2020.02.13.948539 | Slow oscillation-spindle coupling predicts sequence-based language learning | Cross, Z. R.; Helfrich, R. F.; Corcoran, A. W.; Kohler, M. J.; Coussens, S.; Zou-Williams, L.; Schlesewsky, M.; Gaskell, M. G.; Knight, R. T.; Bornkessel-Schlesewsky, I. | Zachariah R Cross | Cognitive and Systems Neuroscience Research Hub, University of South Australia | 2023-11-27T00:00:00 | 3 | new results | cc_by_nd | neuroscience | https://www.biorxiv.org/content/early/2023/11/27/2020.02.13.948539.source.xml | Sentence comprehension involves the rapid decoding of semantic and grammatical information, a process fundamental to communication. As with other cognitive processes, language comprehension relies partly on long-term memory. However, the electrophysiological mechanisms underpinning the initial encoding and generalisati... | NA | biorxiv |
10.1101/2020.02.19.955351 | Is FAM19A5 an adipokine? Peripheral FAM19A5 in wild-type, FAM19A5 knock-out, and LacZ knock-in mice. | Kwak, H.; Cho, E.-H.; Cho, E. B.; Lee, Y.-N.; Shahapal, A.; Yong, H. J.; Reyes-Alcaraz, A.; Jeong, Y.; Lee, Y.; Lee, M.; Ha, N.; Oh, S.; Lee, J. K.; Lee, W. S.; Kim, W. K.; Hwang, J.-I.; Seong, J. Y. | Jae Young Seong | Graduate School of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea | 2024-07-26T00:00:00 | 2 | contradictory results | cc_by_nd | genetics | https://www.biorxiv.org/content/early/2024/07/26/2020.02.19.955351.source.xml | FAM19A5 is a novel secretory protein primarily expressed in the brain. However, a recent study reported that FAM19A5 is an adipocyte-derived adipokine that regulates vascular smooth muscle function through sphingosine-1-phosphate receptor 2 (S1PR2). In our study, we investigated FAM19A5 transcript and protein levels in... | NA | biorxiv |
10.1101/2020.02.20.957548 | A New World begomovirus infecting Cotton in Argentina | Delfosse, V.; Debat, H.; Zavallo, D.; Moyano, S.; Luna, F.; Bonacic Kresic, I.; Asurmendi, S.; Gomez-Talquenca, S.; Distefano, A. J. | Humberto Debat | IPAVE-CIAP-INTA | 2023-08-08T00:00:00 | 2 | new results | cc_by_nc_nd | microbiology | https://www.biorxiv.org/content/early/2023/08/08/2020.02.20.957548.source.xml | Cotton (Gossypium spp.) is a globally significant cash crop cultivated for its versatile fiber, widely used in the textile industry. Cotton, as other crops, is vulnerable to infectious pathogens. Several of them, including viruses, are a major threat to cotton production. Geminiviruses (family Geminiviridae) are insect... | NA | biorxiv |
10.1101/2020.02.25.965376 | A rapid, accurate approach to inferring pedigrees in endogamous populations | Williams, C. M.; Scelza, B.; Slack, S. D.; Mathias, R. A.; Watson, H.; Barnes, K. C.; Lange, E.; Johnson, R. K.; Gignoux, C. R.; Ramachandran, S.; Henn, B. M. | Brenna M Henn | Dept. of Anthropology and UC Davis Genome Center, University of California, Davis | 2024-07-16T00:00:00 | 3 | new results | cc_by_nc_nd | bioinformatics | https://www.biorxiv.org/content/early/2024/07/16/2020.02.25.965376.source.xml | Accurate reconstruction of pedigrees from genetic data remains a challenging problem. Pedigree inference algorithms are often trained only on European-descent families in urban locations. Many relationship categories can be difficult to distinguish (e.g. half-sibships versus avuncular) without external information. Fur... | NA | biorxiv |
10.1101/2020.02.27.968339 | Spiking attractor model of motor cortex explains modulation of neural and behavioral variability by prior target information | Rostami, V.; Rost, T.; Schmitt, F. J.; van Albada, S. J.; Riehle, A.; P. Nawrot, M. | Vahid Rostami | Computational Systems Neuroscience, Institute of Zoology, University of Cologne, Cologne, Germany | 2024-03-05T00:00:00 | 4 | new results | cc_by_nc_nd | neuroscience | https://www.biorxiv.org/content/early/2024/03/05/2020.02.27.968339.source.xml | When preparing a movement, we often rely on partial or incomplete information, which can decrement task performance. In behaving monkeys we show that the degree of cued target information is reflected in both, neural variability in motor cortex and behavioral reaction times. We study the underlying mechanisms in a spik... | 10.1038/s41467-024-49889-4 | biorxiv |
10.1101/2020.02.29.971424 | Trypanosoma brucei ultra-structure cell modifications caused by knockdown of the ribonuclease Rrp44/Dis3 | Cesaro, G.; Hiraiwa, P. M.; Carneiro, F. R. G.; Rouam, V.; Legrand, P.; Conesa, J. J.; Refregiers, M.; Pereiro, E.; Guimaraes, B. G.; Jamme, F.; Zanchin, N. I. T. | Nilson I. T. Zanchin | Carlos Chagas Institute, Oswaldo Cruz Foundation, FIOCRUZ-PR, Curitiba-PR, Brazil | 2024-01-31T00:00:00 | 2 | new results | cc_by_nc_nd | cell biology | https://www.biorxiv.org/content/early/2024/01/31/2020.02.29.971424.source.xml | Rrp44/Dis3 is an essential protein conserved in all eukaryotes that functions in the maturation of many different RNA precursors and RNA surveillance. The Trypanosoma brucei Rrp44/Dis3 homologue (TbRRP44) is required for maturation of pre-rRNA, spliced leader, and U3 snoRNA precursors. Its depletion leads to inhibition... | NA | biorxiv |
10.1101/2020.03.05.979468 | Neurons in the ventral striatopallidal complex modulate lateral hypothalamic orexin/hypocretin neuron activity: Implications for reward-seeking | Mitchell, C. S.; Mohammadkhani, A.; Manning, E. E.; Campbell, E. J.; Fisher, S. D.; Yeoh, J. W.; Pearl, A. J.; Iredale, J. A.; Burton, N. J.; Qiao, M.; Bains, J. S.; McNally, G. P.; Andrews, Z. A.; Graham, B. A.; Scammel, T. E.; Lowell, B. B.; Kong, D.; Borgland, S. L.; Dayas, C. V. | Christopher V Dayas | School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, NSW 2308, Australia. | 2024-03-03T00:00:00 | 2 | new results | cc_by_nc_nd | neuroscience | https://www.biorxiv.org/content/early/2024/03/03/2020.03.05.979468.source.xml | Reward-seeking involves the engagement and computation of multiple physiological and motivational parameters. The lateral hypothalamus (LH) is a necessary node in the circuits that control food-seeking and motivation. One group of cells that plays an important yet incompletely understood role in these processes are the... | NA | biorxiv |
10.1101/2020.03.11.988238 | Immune Digital Twin Blueprint: A Comprehensive Simulatable Model of the Human Immune System | Moore, R.; Amin, R.; Aghamiri, S.; Mohammed, A.; La Fleur, A.; Puniya, B. L.; Helikar, T. | Tomas Helikar | University of Nebraska - Lincoln | 2023-05-16T00:00:00 | 2 | new results | cc_by_nd | systems biology | https://www.biorxiv.org/content/early/2023/05/16/2020.03.11.988238.source.xml | The immune system is a complex and dynamic network, crucial for combating infections and maintaining health. Developing a comprehensive digital twin of the immune system requires incorporating essential cellular components and their interactions. This study presents the first blueprint for an immune system digital twin... | NA | biorxiv |
10.1101/2020.03.11.988238 | Immune Digital Twin Blueprint: A Comprehensive Mechanistic Model of the Human Immune System | Amin, R.; Aghamiri, S.; Puniya, B. L.; Mayo, L.; Startsev, D.; Poore, K.; Helikar, R. M.; Helikar, T. | Tomas Helikar | University of Nebraska - Lincoln | 2024-07-31T00:00:00 | 3 | new results | cc_by_nd | systems biology | https://www.biorxiv.org/content/early/2024/07/31/2020.03.11.988238.source.xml | The immune system is a complex and dynamic network, crucial for combating infections and maintaining health. Developing a comprehensive digital twin of the immune system requires incorporating essential cellular components and their interactions. This study presents the first blueprint for an immune system digital twin... | NA | biorxiv |
10.1101/2020.03.17.995431 | pyComBat, a Python tool for batch effects correction in high-throughput molecular data using empirical Bayes methods | Behdenna, A.; Colange, M.; Haziza, J.; Gema, A. P.; Appe, G.; Azencott, C.-A.; Nordor, A. | Akpéli Nordor | Epigene Labs, Paris, France | 2023-08-29T00:00:00 | 3 | confirmatory results | cc_by_nc_nd | bioinformatics | https://www.biorxiv.org/content/early/2023/08/29/2020.03.17.995431.source.xml | BackgroundVariability in datasets is not only the product of biological processes: they are also the product of technical biases. ComBat and ComBat-Seq are among the most widely used tools for correcting those technical biases, called batch effects, in, respectively, microarray and RNA-Seq expression data.
ResultsIn t... | 10.1186/s12859-023-05578-5 | biorxiv |
10.1101/2020.03.22.002618 | Solving the where problem in neuroanatomy: a generative framework with learned mappings to register multimodal, incomplete data into a reference brain | Tward, D. J.; Gray, B. D. P.; Li, X.; Huo, B.; Banerjee, S.; Savoia, S.; Mezias, C.; Das, S.; Miller, M.; Mitra, P. P. | Daniel Jacob Tward | Johns Hopkins University | 2024-02-28T00:00:00 | 2 | new results | cc_by | neuroscience | https://www.biorxiv.org/content/early/2024/02/28/2020.03.22.002618.source.xml | A current focus of research in neuroscience is to enumerate, map and annotate neuronal cell types in whole vertebrate brains using different modalities of data acquisition. Mapping these molecular and anatomical datasets into a common reference space remains a key challenge. While several brain-to-atlas mapping workflo... | NA | biorxiv |
10.1101/2020.03.23.003962 | Flagellar dynamics reveal fluctuations and kinetic limit in the Escherichia coli chemotaxis network | Bano, R.; Mears, P.; Golding, I.; Chemla, Y. R. | Yann R Chemla | University of Illinois at Urbana-Champaign | 2023-12-03T00:00:00 | 3 | new results | cc_by_nc_nd | biophysics | https://www.biorxiv.org/content/early/2023/12/03/2020.03.23.003962.source.xml | The Escherichia coli chemotaxis network, by which bacteria modulate their random run/tumble swimming pattern to navigate their environment, must cope with unavoidable number fluctuations ("noise") in its molecular constituents like other signaling networks. The probability of clockwise (CW) flagellar rotation, or CW bi... | NA | biorxiv |
10.1101/2020.03.23.003061 | Modality-independent effect of gravity in shaping the internal representation of 3D space | Theo, M.; Gabriela, H. A.; Leonardo, A.; Gilles, C.; Mathieu, B.; Joseph, M.; Michele, T. | Michele Tagliabue | Université de Paris, Integrative Neuroscience and Cognition Center, CNRS UMR 8002, F-75270 Paris, France. | 2023-06-11T00:00:00 | 2 | new results | cc_by_nc_nd | neuroscience | https://www.biorxiv.org/content/early/2023/06/11/2020.03.23.003061.source.xml | Human 3D perception of visual objects is flawed by distortions, which are influenced by non-visual factors, such as gravitational vestibular signals. Whether gravity acts specifically on the visual system or at a higher, modality-independent, level of information processing remains unknown. To test these modality-speci... | 10.1523/JNEUROSCI.2457-20.2023 | biorxiv |
10.1101/2020.03.26.009795 | Fifty shades of The Virtual Brain: Converging optimal working points yield biologically plausibleelectrophysiological and imaging features | Triebkorn, P.; Meier, J.; Zimmermann, J.; Stefanovski, L.; Roy, D.; Solodkin, A.; Jirsa, V.; Deco, G.; Breakspear, M.; Schirner, M.; McIntosh, A. R.; Ritter, P. | Paul Triebkorn | Charite Universitatsmedizin Berlin | 2024-05-15T00:00:00 | 2 | new results | cc_by | neuroscience | https://www.biorxiv.org/content/early/2024/05/15/2020.03.26.009795.source.xml | Brain network modeling studies are often limited with respect to the number of data features fitted, although capturing multiple empirical features is important to validate the models overall biological plausibility. Here we construct personalized models from multimodal data of 50 healthy individuals (18-80 years) with... | NA | biorxiv |
10.1101/2020.04.06.028092 | Post-transcriptional splicing can occur in a slow-moving zone around the gene | Cote, A. J.; O'Farrell, A.; Dardani, I.; Dunagin, M.; Cote, C. J.; Wan, Y.; Bayatpour, S.; Drexler, H. L.; Alexander, K. A.; Chen, F.; Wassie, A. T.; Patel, R.; Pham, K.; Boyden, E. S.; Berger, S.; Phillips-Cremins, J.; Churchman, L. S.; Raj, A. | Arjun Raj | University of Pennsylvania | 2023-06-13T00:00:00 | 3 | new results | cc_by | cell biology | https://www.biorxiv.org/content/early/2023/06/13/2020.04.06.028092.source.xml | Splicing is the stepwise molecular process by which introns are removed from pre-mRNA and exons are joined together to form mature mRNA sequences. The ordering and spatial distribution of these steps remain controversial, with opposing models suggesting splicing occurs either during or after transcription. We used sing... | 10.7554/eLife.91357 | biorxiv |
10.1101/2020.04.06.028092 | Post-transcriptional splicing can occur in a slow-moving zone around the gene | Cote, A. J.; O'Farrell, A.; Dardani, I.; Dunagin, M.; Cote, C. J.; Wan, Y.; Bayatpour, S.; Drexler, H. L.; Alexander, K. A.; Chen, F.; Wassie, A. T.; Patel, R.; Pham, K.; Boyden, E. S.; Berger, S.; Phillips-Cremins, J.; Churchman, L. S.; Raj, A. | Arjun Raj | University of Pennsylvania | 2023-11-13T00:00:00 | 4 | new results | cc_by | cell biology | https://www.biorxiv.org/content/early/2023/11/13/2020.04.06.028092.source.xml | Splicing is the stepwise molecular process by which introns are removed from pre-mRNA and exons are joined together to form mature mRNA sequences. The ordering and spatial distribution of these steps remain controversial, with opposing models suggesting splicing occurs either during or after transcription. We used sing... | 10.7554/eLife.91357 | biorxiv |
10.1101/2020.04.07.029009 | Disseminating cells in human tumours acquire an EMT cancer stem cell state that is predictive of metastasis | Youssef, G.; Gammon, L.; Ambler, L.; Lunetto, S.; Scemama, A.; Cottom, H.; Piper, K.; Mackenzie, I. C.; Philpott, M. P.; Biddle, A. | Adrian Biddle | Queen Mary University of London | 2023-05-03T00:00:00 | 2 | new results | cc_by | cancer biology | https://www.biorxiv.org/content/early/2023/05/03/2020.04.07.029009.source.xml | Cancer stem cells (CSCs) undergo epithelial-mesenchymal transition (EMT) to drive metastatic dissemination in experimental cancer models. However, tumour cells undergoing EMT have not been observed disseminating into the tissue surrounding human tumour specimens, leaving the relevance to human cancer uncertain. We have... | 10.7554/eLife.90298 | biorxiv |
10.1101/2020.04.20.049866 | The accelerated infectious disease risk in the Anthropocene: more outbreaks and wider global spread | Morand, S.; Walther, B. A. | Bruno Andreas Walther | National Sun Yat-sen University | 2023-08-24T00:00:00 | 2 | confirmatory results | cc_by_nc_nd | ecology | https://www.biorxiv.org/content/early/2023/08/24/2020.04.20.049866.source.xml | The greatly accelerated economic growth during the Anthropocene has resulted in astonishing improvements in many aspects of human well-being, but has also caused the acceleration of risks, such as the interlinked biodiversity and climate crisis. Here, we report on another risk: the accelerated infectious disease risk a... | NA | biorxiv |
10.1101/2020.04.22.043422 | Phenotypic innovation in one tooth induced concerted developmental evolution in another | Semon, M.; Gueguen, L.; Steklikova, K.; Mouginot, M.; Peltier, M.; Veber, P.; Pantalacci, S. | Marie Semon | LBMC / ENS Lyon | 2023-05-02T00:00:00 | 3 | new results | cc_by_nc_nd | evolutionary biology | https://www.biorxiv.org/content/early/2023/05/02/2020.04.22.043422.source.xml | Serial appendages are similar organs found at different places in the body, such as fore/hindlimbs or different teeth. They are bound to develop with the same pleiotropic genes, apart from identity genes. These identity genes have logically been implicated in cases where a single appendage evolved a drastically new sha... | NA | biorxiv |
10.1101/2020.04.24.014852 | HiTaC: a Hierarchical Taxonomic Classifier for Fungal ITS Sequences | Miranda, F. M.; Azevedo, V. A. C.; Ramos, R. T. J.; Renard, B. Y.; C. Piro, V. | Vitor C. Piro | Hasso Plattner Institut | 2023-06-04T00:00:00 | 4 | new results | cc_by | bioinformatics | https://www.biorxiv.org/content/early/2023/06/04/2020.04.24.014852.source.xml | BackgroundFungi play a key role in several important ecological functions, ranging from organic matter decomposition to symbiotic associations with plants. Moreover, fungi naturally inhabit the human body and can be beneficial when administered as probiotics. In mycology, the internal transcribed spacer (ITS) region wa... | 10.1186/s12859-024-05839-x | biorxiv |
10.1101/2020.04.24.014852 | HiTaC: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2 | Miranda, F. M.; Azevedo, V. A. C.; Ramos, R. T. J.; Renard, B. Y.; C. Piro, V. | Vitor C. Piro | Hasso Plattner Institut | 2024-03-15T00:00:00 | 5 | new results | cc_by | bioinformatics | https://www.biorxiv.org/content/early/2024/03/15/2020.04.24.014852.source.xml | BackgroundFungi play a key role in several important ecological functions, ranging from organic matter decomposition to symbiotic associations with plants. Moreover, fungi naturally inhabit the human body and can be beneficial when administered as probiotics. In mycology, the internal transcribed spacer (ITS) region wa... | 10.1186/s12859-024-05839-x | biorxiv |
10.1101/2020.04.24.059097 | Characterising a stable five-species microbial community for use in experimental evolution and ecology. | Castledine, M.; Pennycook, J.; Newbury, A.; Lear, L.; Erdos, Z.; Lewis, R.; Kay, S.; Sanders, D.; Sunderhauf, D.; Buckling, A.; Hesse, E.; Padfield, D. | Daniel Padfield | University of Exeter | 2024-04-11T00:00:00 | 2 | new results | cc_by_nd | ecology | https://www.biorxiv.org/content/early/2024/04/11/2020.04.24.059097.source.xml | Model microbial communities are regularly used to test ecological and evolutionary theory as they are easy to manipulate and have fast generation times, allowing for large-scale, high throughput experiments. A key assumption for most model microbial communities is that they stably coexist, but this is rarely tested exp... | NA | biorxiv |
10.1101/2020.04.25.061531 | WITHDRAWN: Recombinant BCG overexpressing a STING agonist elicits trained immunity and improved antitumor efficacy in non-muscle invasive bladder | Singh, A. K.; Praharaj, M.; Lombardo, K. A.; Yoshida, T.; Matoso, A.; Baras, A. S.; Zhao, L.; Prasad, P.; Powell, J. D.; Kates, M.; McConkey, D.; Pardoll, D. M.; Bishai, W. R.; Bivalacqua, T. J. | Trinity J. Bivalacqua | Johns Hopkins School of Medicine | 2023-12-20T00:00:00 | 4 | withdrawn | cc_by | cancer biology | https://www.biorxiv.org/content/early/2023/12/20/2020.04.25.061531.source.xml | Withdrawal StatementThe authors have withdrawn their manuscript owing to irregularities in the Source Data supporting some figures. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding authors. | 10.1038/s41467-022-28509-z | biorxiv |
10.1101/2020.04.27.063628 | Toxoplasma FER1 is a versatile and dynamic mediator of differential microneme trafficking and microneme exocytosis | Tagoe, D. N.; Ribeiro E Silva, A.; Drozda, A. A.; Coppens, I.; Coleman, B. I.; Gubbels, M.-J. | Marc-Jan Gubbels | Boston College | 2024-06-11T00:00:00 | 2 | new results | cc_by_nc_nd | cell biology | https://www.biorxiv.org/content/early/2024/06/11/2020.04.27.063628.source.xml | Toxoplasma gondii is a polarized cell concentrating several secretory organelles at the apical pole. The secretory micronemes come in two sub-populations differentiated by dependence on the Rab5A/C in their biogenesis. Calcium-dependent exocytosis of micronemes occurs at the very apical tip and is critical for parasite... | NA | biorxiv |
10.1101/2020.04.28.065755 | Single-cell copy number calling and event history reconstruction | Kuipers, J.; Tuncel, M. A.; Ferreira, P. F.; Jahn, K.; Beerenwinkel, N. | Niko Beerenwinkel | D-BSSE, ETH Zurich | 2024-06-03T00:00:00 | 2 | new results | cc_by_nc_nd | cancer biology | https://www.biorxiv.org/content/early/2024/06/03/2020.04.28.065755.source.xml | Copy number alterations are driving forces of tumour development and the emergence of intra-tumour heterogeneity. A comprehensive picture of these genomic aberrations is therefore essential for the development of personalised and precise cancer diagnostics and therapies. Single-cell sequencing offers the highest resolu... | NA | biorxiv |
10.1101/2020.04.29.069138 | Removing the Gβγ-SNAP25 brake on exocytosis enhances insulin action, promotes adipocyte browning, and protects against diet-induced obesity | Ceddia, R. P.; Zurawski, Z.; Thompson Gray, A.; Adegboye, F.; McDonald-Boyer, A.; Shi, F.; Liu, D.; Maldonado, J.; Feng, J.; Li, Y.; Alford, S.; Ayala, J. E.; McGuinness, O. P.; Collins, S.; Hamm, H. E. | Heidi E Hamm | Vanderbilt University | 2023-06-06T00:00:00 | 4 | new results | cc_by_nc_nd | physiology | https://www.biorxiv.org/content/early/2023/06/06/2020.04.29.069138.source.xml | Negative regulation of exocytosis from secretory cells throughout the body is accomplished through inhibitory signals from Gi/o G protein-coupled receptors by G{beta}{gamma} subunit inhibition of two common mechanisms: (i) decreased calcium entry and (ii) direct interaction of G{beta}{gamma} with the Soluble N-ethylmal... | NA | biorxiv |
10.1101/2020.05.04.075119 | Single-cell RNA sequencing reveals subset-specific functional reprogramming of CD4+ T-cells from PLHIV upon ex vivo HDAC inhibition and biomarkers of cells harbouring non-silent proviruses | Kazmierski, J.; Postmus, D.; Wyler, E.; Fadejeva, J.; Steijaert, T.; Fischer, C.; Jansen, J.; Koppe, U.; Gunsenheimer-Bartmeyer, B.; Meixenberger, K.; Vitcetz, S.; Sohn, M.; Loyal, L.; Thiel, A.; Sauer, S.; Bannert, N.; Landthaler, M.; GOFFINET, C. | Christine GOFFINET | Charite - Universitaetsmedizin Berlin | 2023-06-04T00:00:00 | 2 | new results | cc_by_nc | microbiology | https://www.biorxiv.org/content/early/2023/06/04/2020.05.04.075119.source.xml | Shock-and-kill is one of the most advanced, yet unrealized, concepts towards establishment of HIV-1 cure. Treatment with latency-reversing agents (LRAs), including histone deacetylase inhibitors (HDACis) exerting chromatin remodelling and gene expression reprogramming, combined with anti-retroviral therapy reactivates ... | NA | biorxiv |
10.1101/2020.05.04.075119 | Type I interferons sensitise HIV-1-reactivating T-cells for NK cell-mediated elimination despite HDACi-imposed dysregulation of innate immunity | Prigann, J.; Postmus, D.; Pietrobon, A. J.; Wyler, E.; Jansen, J.; Moeller, L.; Fadejeva, J.; Steijaert, T.; Fischer, C.; Koppe, U.; Gunsenheimer-Bartmeyer, B.; Meixenberger, K.; Vitcetz, S.; Sohn, M.; Loyal, L.; Thiel, A.; Sauer, S.; Sutter, K.; Dittmer, U.; Laue, M.; Bannert, N.; Landthaler, M.; GOFFINET, C. | Christine GOFFINET | Charite - Universitaetsmedizin Berlin | 2023-11-19T00:00:00 | 3 | new results | cc_by_nc | microbiology | https://www.biorxiv.org/content/early/2023/11/19/2020.05.04.075119.source.xml | Shock-and-kill is one of the most advanced, yet unrealized, concepts towards establishment of HIV-1 cure. Treatment with latency-reversing agents (LRAs), including histone deacetylase inhibitors (HDACis) exerting chromatin remodelling and gene expression reprogramming, combined with anti-retroviral therapy reactivates ... | NA | biorxiv |
10.1101/2020.05.08.080929 | The evolution of sex allocation in metapopulations | Roux, C.; Mullon, C. D. L.; Pannell, J. | John Pannell | Univ. of Lausanne | 2024-04-08T00:00:00 | 2 | new results | cc_by_nc_nd | evolutionary biology | https://www.biorxiv.org/content/early/2024/04/08/2020.05.08.080929.source.xml | Selection in inbred populations is expected to favor female-biased sex ratios in dioecious populations as a result of local mate competition, a prediction that finds strong support in situations where females have control of the sex ratio. Local mate competition due to inbreeding should also promote female-biased sex a... | NA | biorxiv |
10.1101/2020.05.08.084848 | Generating Synthetic Signaling Networks for in Silico Modeling Studies | Xu, J.; Wiley, H. S.; Sauro, H. M. | Herbert M. Sauro | University of Washington | 2023-05-15T00:00:00 | 2 | new results | cc_by_nc_nd | systems biology | https://www.biorxiv.org/content/early/2023/05/15/2020.05.08.084848.source.xml | Predictive models of signaling pathways have proven to be difficult to develop. Traditional approaches to developing mechanistic models rely on collecting experimental data and fitting a single model to that data. This approach works for simple systems but has proven unreliable for complex systems such as biological si... | NA | biorxiv |
10.1101/2020.05.08.084848 | Generating synthetic signaling networks for in silico modeling studies | Xu, J.; Wiley, S.; Sauro, H. M. | Herbert M. Sauro | University of Washington | 2024-02-01T00:00:00 | 3 | new results | cc_by_nc_nd | systems biology | https://www.biorxiv.org/content/early/2024/02/01/2020.05.08.084848.source.xml | Predictive models of signaling pathways have proven to be difficult to develop. Traditional approaches to developing mechanistic models rely on collecting experimental data and fitting a single model to that data. This approach works for simple systems but has proven unreliable for complex systems such as biological si... | NA | biorxiv |
10.1101/2020.05.08.084848 | Generating synthetic signaling networks for in silico modeling studies | Xu, J.; Wiley, S.; Sauro, H. M. | Herbert M. Sauro | University of Washington | 2024-06-07T00:00:00 | 4 | new results | cc_by_nc_nd | systems biology | https://www.biorxiv.org/content/early/2024/06/07/2020.05.08.084848.source.xml | Predictive models of signaling pathways have proven to be difficult to develop. Traditional approaches to developing mechanistic models rely on collecting experimental data and fitting a single model to that data. This approach works for simple systems but has proven unreliable for complex systems such as biological si... | NA | biorxiv |
10.1101/2020.05.12.079863 | Haplotype-based analysis distinguishes maternal-fetal genetic contribution to pregnancy-related outcomes | Srivastava, A. K.; Juodakis, J.; Sole-Navais, P.; Chen, J.; Bacelis, J.; Teramo, K.; Hallman, M.; Njolstad, P. R.; Evans, D. M.; Jacobsson, B.; Muglia, L. J.; Zhang, G. | Ge Zhang | Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, USA | 2023-06-30T00:00:00 | 2 | new results | cc_by_nc_nd | genetics | https://www.biorxiv.org/content/early/2023/06/30/2020.05.12.079863.source.xml | AbstractGenotype-based approaches for the estimation of SNP-based narrow-sense heritability [Formula] have limited utility in pregnancy-related outcomes due to confounding by the shared alleles between mother and child. Here, we propose a haplotype-based approach to estimate the genetic variance attributable to three h... | NA | biorxiv |
10.1101/2020.05.14.096032 | Mycobacteria inhibit neutrophil recruitment to avoid neutrophil-assisted killing by macrophages | Candel, S.; Ramakrishnan, L. | Lalita Ramakrishnan | University of Cambridge | 2023-07-26T00:00:00 | 4 | withdrawn | cc_by | molecular biology | https://www.biorxiv.org/content/early/2023/07/26/2020.05.14.096032.source.xml | This article was withdrawn on 29 July 2020 after inaccuracies were identified in the experiments reported in the manuscript. The corresponding author, Professor Lalita Ramakishnan, reported concerns regarding data in the manuscript to the University of Cambridge. An investigation by the University of Cambridge conclude... | NA | biorxiv |
10.1101/2020.05.14.096230 | scRNA-seq analysis of colon and esophageal tumors uncovers abundant microbial reads in myeloid cells undergoing proinflammatory transcriptional alterations | Robinson, W.; Stone, J. K.; Schischlik, F.; Gasmi, B.; Kelly, M. C.; Seibert, C.; Dadkhah, K.; Gertz, E. M.; Lee, J. S.; Zhu, K.; Ma, L.; Wang, X. W.; Sahinalp, C.; Patro, R.; Leiserson, M. D.; Harris, C. C.; Schäffer, A. A.; Ruppin, E. | Eytan Ruppin | Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute | 2023-04-28T00:00:00 | 3 | new results | cc0 | cancer biology | https://www.biorxiv.org/content/early/2023/04/28/2020.05.14.096230.source.xml | The study of the tumor microbiome has been garnering increased attention. We developed a computational pipeline (CSI-Microbes) for identifying microbial reads from single-cell RNA sequencing (scRNA-seq) data. Using a series of controlled experiments and analyses, we performed the first systematic evaluation of the effi... | NA | biorxiv |
10.1101/2020.05.15.097907 | HerpesDRG: a comprehensive resource for human herpesvirus antiviral drug resistance genotyping | Charles, O. J.; Venturini, C.; Goldstein, R. A.; Breuer, J. | Judith Breuer | University College London | 2023-10-24T00:00:00 | 2 | new results | cc_by_nc_nd | bioinformatics | https://www.biorxiv.org/content/early/2023/10/24/2020.05.15.097907.source.xml | The prevention and treatment of many herpesvirus associated diseases is based on the utilization of antiviral therapies, however therapeutic success is limited by the development of drug resistance. A comprehensive point of truth of resistance conferring mutations has been missing but would be important to aid the deve... | NA | biorxiv |
10.1101/2020.05.20.106930 | WITHDRAWN: Complement C3-dependent glutamatergic synapse elimination in the developing hippocampus is region- and synapse-specific | Salter, E. W.; Lei, G.; Choi, S.-L.; Ralph, L. T.; Zhang, L.; Jin, F.; Kadia, A.; Wang, J.; Georgiou, J.; Collingridge, G. L. | Graham L Collingridge | Lunenfeld-Tanenbaum Research Institute/University of Toronto/University of Bristol/TANZ Centre for Research in Neurodegenerative Diseases | 2023-09-26T00:00:00 | 2 | withdrawn | cc_by | neuroscience | https://www.biorxiv.org/content/early/2023/09/26/2020.05.20.106930.source.xml | Withdrawal statementThe authors have withdrawn their manuscript owing to the results of this pre-print being based on experiments performed prior to COVID-19 shutdowns, which required a near complete culling of the mouse colony. Upon re-initiating the colony, the phenotype outlined in the pre-print could no longer be o... | NA | biorxiv |
10.1101/2020.05.25.114959 | Improvements in task performance after practice are associated with scale-free dynamics of brain activity | Kardan, O.; Stier, A. J.; Layden, E. A.; Choe, K. W.; Lyu, M.; Zhang, X.; Beilock, S. L.; Rosenberg, M. D.; Berman, M. G. | Omid Kardan | University of Chicago | 2023-04-04T00:00:00 | 2 | new results | cc_by_nc_nd | neuroscience | https://www.biorxiv.org/content/early/2023/04/04/2020.05.25.114959.source.xml | Although practicing a task generally benefits later performance on that same task, there are individual differences in practice effects. One avenue to model such differences comes from research showing that brain networks extract functional advantages from operating in the vicinity of criticality, a state in which brai... | 10.1162/netn_a_00319 | biorxiv |
10.1101/2020.05.26.104687 | Pictorial balance is a bottom-up aesthetic property mediated by eye movements. A model of a primitive visual operating system explains balance and visual properties of pictures | Corwin, D. M. | David M Corwin | David Corwin MD | 2023-08-22T00:00:00 | 18 | new results | cc_by | neuroscience | https://www.biorxiv.org/content/early/2023/08/22/2020.05.26.104687.source.xml | Pictorial balance has been used to explain why some paintings evoke feelings of unity and harmony. This study shows how it is calculated and proposes an evolutionary reason for its existence. The concept of pictorial balance as a center of mass effect, i.e. the feeling that somehow a person on the left seems to be bala... | NA | biorxiv |
10.1101/2020.05.26.104687 | Pictorial balance is a bottom-up aesthetic property mediated by eye movements. A model of a primitive visual operating system explains balance and visual properties of pictures | Corwin, D. M. | David M Corwin | David Corwin MD | 2024-04-18T00:00:00 | 19 | new results | cc_by | neuroscience | https://www.biorxiv.org/content/early/2024/04/18/2020.05.26.104687.source.xml | Pictorial balance has been used to explain why some paintings evoke feelings of unity and harmony. This study shows how it is calculated and proposes an evolutionary reason for its existence. The concept of pictorial balance as a center of mass effect, i.e. the feeling that somehow a person on the left seems to be bala... | NA | biorxiv |
10.1101/2020.05.26.104687 | Pictorial balance is a bottom-up neuro-aesthetic property mediating attention and eye movements. A model of a primitive visual operating system explains the property of balance and some visual properties of pictures | Corwin, D. M. | David M Corwin | David Corwin MD | 2024-08-26T00:00:00 | 20 | new results | cc_by | neuroscience | https://www.biorxiv.org/content/early/2024/08/26/2020.05.26.104687.source.xml | Pictorial balance has been used to explain why some paintings evoke feelings of unity and harmony. This study shows how it is calculated and proposes an evolutionary reason for its existence. The concept of pictorial balance as a center of mass effect, i.e. the feeling that somehow a person on the left seems to be bala... | NA | biorxiv |
End of preview.
Biorxiv Abstracts from the our ICML 2025 paper "Private federated learning using preference-optimized synthetic data"
- Paper: https://arxiv.org/abs/2504.16438
- We collected biorxiv abstracts using biorxiv public API under permitted licenses[1]
- This dataset is intended to evaluate federated learning algorithms.There are 57k clients (i.e. abstracts) for date range 2023-04-01 to 2024-08-31. Since there are more speeches that are later added, there will be more clients as we increase the date range.
- Hugging Face repo: https://huggingface.co/datasets/hazylavender/biorxiv-abstract
- Github: https://github.com/hazylavender/fl_llm_benchmark_dataset
Dataset statistics
(cutoff 2024-08-31)
- Number of abstracts: 57k
- Token distribution (by nltk tokenizer)
Citation
If you found our datasets useful for your work, please consider citing our paper:
@misc{hou2025privatefederatedlearningusing,
title={Private Federated Learning using Preference-Optimized Synthetic Data},
author={Charlie Hou and Mei-Yu Wang and Yige Zhu and Daniel Lazar and Giulia Fanti},
year={2025},
eprint={2504.16438},
archivePrefix={arXiv},
primaryClass={cs.LG},
url={https://arxiv.org/abs/2504.16438},
}
[1] The dataset we collected are under 'cc_by_nc_nd', 'cc_by_nd', 'cc_by_nc', 'cc_by', 'cc0' licenses. Source: https://www.biorxiv.org/about/FAQ
- Downloads last month
- 111