Endothelial UNC5B regulates blood‑retinal barrier homeostasis.

Code ↔ Paper

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

The 1 match · it ties a paragraph to a whole file, not to given lines: a weak match, whose lines are not tinted

[1] § Materials and methods › Bulk RNA sequencing analysis ↔ src/simd.h, the whole file · a weak match · score 0.56 · quality threshold, low quality, Phred, fastp, sequencing, filtering

Paper

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The paper is loaded by your browser, with JavaScript: read it at doi.org or on Europe PMC.

The authors' code

C/C++ header · 38 lines · 1.4 KB · MIT · 1 match

#ifndef FASTP_SIMD_H
#define FASTP_SIMD_H
#include <cstddef>
namespace fastp_simd {
// Count quality metrics for a read in one pass.
// qualstr/seqstr: quality and sequence strings of length len.
// qualThreshold: phred+33 encoded quality threshold for "low quality".
// Outputs: lowQualNum, nBaseNum, totalQual (sum of qual-33 values).
void countQualityMetrics(const char* qualstr, const char* seqstr, int len,
char qualThreshold, int& lowQualNum, int& nBaseNum,
int& totalQual);
// Reverse complement a DNA sequence.
// src: input sequence of length len.
// dst: output buffer of at least len bytes (must NOT alias src).
void reverseComplement(const char* src, char* dst, int len);
// Count adjacent-base differences for low complexity filter.
// Returns the number of positions where data[i] != data[i+1].
int countAdjacentDiffs(const char* data, int len);
// Count mismatches between two byte strings.
// Returns the number of positions where a[i] != b[i], up to len bytes.
int countMismatches(const char* a, const char* b, int len);
// Count mismatches with early exit.
// Returns mismatch count if <= limit, or a value > limit if exceeded.
int countMismatchesBounded(const char* a, const char* b, int len, int limit);
// Run all SIMD unit tests. Returns true if all pass.
bool testSimd();
} // namespace fastp_simd
#endif // FASTP_SIMD_H

simd.h at commit 8a2397b, under MIT · at the source

Overview

Authors: Yujia Yao¹, Suyu Wang¹, Jiajun Li¹, Qianzi Jin¹, Ziyi Chen¹, Qin Jiang¹, Keran Li¹

ORCID iDs: Ziyi Chen

Department of Ophthalmology, The Affiliated Eye Hospital, Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China

Institutions: Nanjing Medical University (China)

Journal: International journal of molecular medicine, volume 57, issue 4, article 100

Dates: received 23 September 2025; accepted 14 January 2026; published online 20 February 2026; in print April 2026

Type: Research article · Language: English

License: CC BY-NC-ND

Identifiers: DOI 10.3892/ijmm.2026.5771 · PMID 41789631 · PMCID PMC12948558 · OpenAlex W7130653316

Open access: hybrid, a free copy (OpenAlex)

Status: code verified

Categories: histology / microscopy (modality), human (organism), mouse (organism), other condition (population), cellular / molecular (subfield)

Methods: Statistics, Smoothing, state filtering, decompositions, Connectivity, Physiology & signal measures

Keywords: unc-5 netrin receptor B, netrin-1, blood-retinal barrier, neurovascular unit, diabetic retinopathy, retinal vein occlusion, endothelial cells, pericytes, Hippo signaling pathway, extracellular matrix

MeSH: Blood-Retinal Barrier*, Endothelial Cells*, Homeostasis*, Netrin Receptors*, Animals, Apoptosis, Diabetic Retinopathy, Humans, Male, Mice, Mice, Inbred C57BL, Netrin-1, Pericytes (* major topic)

Topic: Axon Guidance and Neuronal Signaling (Cellular and Molecular Neuroscience, Neuroscience), according to OpenAlex

Citations: not cited yet (Europe PMC); 72 references in the paper

Abstract

The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.

Repository

Its files are read in the Code ↔ Paper reader above, with 1 match between paragraphs and lines of code.

OpenGene/fastp

License: MIT

State: the link answers, verified on 27 September 2026

Evidence: files inventoried

Commit: 8a2397b6628ae14127efdb7566f67fc05f9aea56, 10 September 2026

Languages: C/C++ (34), C++ (29), Shell (2), Python (1)

Size: 73 files, 66 scripts

Software Heritage: not archived

Found in: the text, “Bulk RNA sequencing analysis”

Holds: README, license file, continuous integration

Not found: CITATION.cff, environment file, tests, documentation

Availability: 1 check, the latest on 27 September 2026: the link answers

27 September 2026: the link answers

68 files

parallel.py, Python, 592 lines
scripts/bench_e2e.sh, Shell, 238 lines
scripts/test_issue_697_stdout_merge.sh, Shell, 28 lines
src/adaptertrimmer.cpp, C++, 185 lines
src/adaptertrimmer.h, C/C++, 27 lines
src/basecorrector.cpp, C++, 107 lines
src/basecorrector.h, C/C++, 24 lines
src/bgzf.h, C/C++, 243 lines
src/cmdline.h, C/C++, 809 lines
src/common.h, C/C++, 67 lines
src/duplicate.cpp, C++, 169 lines
src/duplicate.h, C/C++, 42 lines
src/evaluator.cpp, C++, 633 lines
src/evaluator.h, C/C++, 38 lines
src/fastareader.cpp, C++, 120 lines
src/fastareader.h, C/C++, 66 lines
src/fastqreader.cpp, C++, 460 lines
src/fastqreader.h, C/C++, 106 lines
src/filter.cpp, C++, 264 lines
src/filter.h, C/C++, 32 lines
src/filterresult.cpp, C++, 474 lines
src/filterresult.h, C/C++, 82 lines
src/htmlreporter.cpp, C++, 629 lines
src/htmlreporter.h, C/C++, 51 lines
src/jsonreporter.cpp, C++, 172 lines
src/jsonreporter.h, C/C++, 37 lines
src/knownadapters.h, C/C++, 251 lines
src/main.cpp, C++, 522 lines
src/matcher.cpp, C++, 101 lines
src/matcher.h, C/C++, 22 lines
src/nucleotidetree.cpp, C++, 104 lines
src/nucleotidetree.h, C/C++, 40 lines
src/options.cpp, C++, 525 lines
src/options.h, C/C++, 389 lines
src/overlapanalysis.cpp, C++, 210 lines
src/overlapanalysis.h, C/C++, 38 lines
src/peprocessor.cpp, C++, 1,090 lines
src/peprocessor.h, C/C++, 75 lines
src/polyx.cpp, C++, 130 lines
src/polyx.h, C/C++, 28 lines
src/processor.cpp, C++, 23 lines
src/processor.h, C/C++, 22 lines
src/read.cpp, C++, 301 lines
src/read.h, C/C++, 73 lines
src/readpool.cpp, C++, 75 lines
src/readpool.h, C/C++, 38 lines
src/seprocessor.cpp, C++, 488 lines
src/seprocessor.h, C/C++, 59 lines
src/sequence.cpp, C++, 54 lines
src/sequence.h, C/C++, 29 lines
src/simd.cpp, C++, 568 lines
src/simd.h, C/C++, 38 lines, 1 match
src/singleproducersingleconsumerlist.h, C/C++, 178 lines
src/stats.cpp, C++, 982 lines
src/stats.h, C/C++, 109 lines
src/threadconfig.cpp, C++, 161 lines
src/threadconfig.h, C/C++, 71 lines
src/umiprocessor.cpp, C++, 88 lines
src/umiprocessor.h, C/C++, 25 lines
src/unittest.cpp, C++, 39 lines
src/unittest.h, C/C++, 17 lines
src/util.h, C/C++, 293 lines
src/writer.cpp, C++, 154 lines
src/writer.h, C/C++, 73 lines
src/writerthread.cpp, C++, 214 lines
src/writerthread.h, C/C++, 68 lines
LICENSE, License, 21 lines
README.md, Text, 558 lines

At the source: github.com/OpenGene/fastp

Tracing map

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

What the map holds:

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

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

Data

Datasets cited

geo:GSE178121, at NCBI GEO; found in the text, “Bioinformatics analysis revealed downregulated…”

Data availability statement

The paper has a data availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:

no repository, dataset or request procedure was recognized in it

Read it in the paper: doi.org/10.3892/ijmm.2026.5771.

Versions

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

Version 1, 30 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 7 authors, 10 keywords, 13 MeSH terms, 71 references.

Cite

This paper

Yao, Y., Wang, S., Li, J., Jin, Q., Chen, Z., Jiang, Q., & Li, K. (2026). Endothelial UNC5B regulates blood‑retinal barrier homeostasis. International journal of molecular medicine, 57(4), 100. https://doi.org/10.3892/ijmm.2026.5771

BibTeX

@article{yao2026endothelial, author = {Yao, Yujia and Wang, Suyu and Li, Jiajun and Jin, Qianzi and Chen, Ziyi and Jiang, Qin and Li, Keran}, title = {{Endothelial UNC5B regulates blood‑retinal barrier homeostasis}}, journal = {International journal of molecular medicine}, year = {2026}, month = mar, volume = {57}, number = {4}, pages = {100}, publisher = {Spandidos Publications}, issn = {1107-3756}, doi = {10.3892/ijmm.2026.5771}, url = {https://doi.org/10.3892/ijmm.2026.5771}, pmid = {41789631}, pmcid = {PMC12948558} }

RIS

TY - JOUR AU - Yao, Yujia AU - Wang, Suyu AU - Li, Jiajun AU - Jin, Qianzi AU - Chen, Ziyi AU - Jiang, Qin AU - Li, Keran TI - Endothelial UNC5B regulates blood‑retinal barrier homeostasis T2 - International journal of molecular medicine J2 - Int J Mol Med PY - 2026 DA - 2026/03/06 VL - 57 IS - 4 SP - 100 SN - 1107-3756 PB - Spandidos Publications DO - 10.3892/ijmm.2026.5771 UR - https://doi.org/10.3892/ijmm.2026.5771 LA - en ER -

CSL-JSON

{ "id": "10.3892/ijmm.2026.5771", "type": "article-journal", "title": "Endothelial UNC5B regulates blood‑retinal barrier homeostasis", "container-title": "International journal of molecular medicine", "author": [ { "family": "Yao", "given": "Yujia" }, { "family": "Wang", "given": "Suyu" }, { "family": "Li", "given": "Jiajun" }, { "family": "Jin", "given": "Qianzi" }, { "family": "Chen", "given": "Ziyi" }, { "family": "Jiang", "given": "Qin" }, { "family": "Li", "given": "Keran" } ], "container-title-short": "Int J Mol Med", "volume": "57", "issue": "4", "page": "100", "DOI": "10.3892/ijmm.2026.5771", "PMID": "41789631", "PMCID": "PMC12948558", "ISSN": "1107-3756", "publisher": "Spandidos Publications", "URL": "https://doi.org/10.3892/ijmm.2026.5771", "language": "en", "issued": { "date-parts": [ [ 2026, 3, 6 ] ] } }

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