Low-intensity pulsed ultrasound-mediated nose-to-brain co-delivery of β-blockers and aPD-L1 enhances glioblastoma immunotherapy.

Code ↔ Paper

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

The 2 matches

[1] § Methods › Transcriptome sequencing (RNA-Seq) ↔ src/options.h, lines 286–387 · score 0.59 · quality score, quality filtering, insert, adapter, trimming, sequencing
[2] § Methods › Transcriptome sequencing (RNA-Seq) ↔ src/main.cpp, lines 64–105 · score 0.54 · quality filtering, quality score, accuracy, discarding, trimming, Seq

Paper

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The authors' code

C/C++ header · 389 lines · 8.8 KB · MIT · 1 match

#ifndef OPTIONS_H
#define OPTIONS_H
#include <stdio.h>
#include <stdlib.h>
#include <string>
#include <vector>
#include <map>
using namespace std;
#define UMI_LOC_NONE 0
#define UMI_LOC_INDEX1 1
#define UMI_LOC_INDEX2 2
#define UMI_LOC_READ1 3
#define UMI_LOC_READ2 4
#define UMI_LOC_PER_INDEX 5
#define UMI_LOC_PER_READ 6
class MergeOptions {
public:
MergeOptions() {
enabled = false;
includeUnmerged = false;
}
public:
bool enabled;
bool includeUnmerged;
string out;
};
class DuplicationOptions {
public:
DuplicationOptions() {
enabled = true;
histSize = 32;
dedup = false;
accuracyLevel = 1;
}
public:
bool enabled;
int histSize;
bool dedup;
int accuracyLevel;
};
class IndexFilterOptions {
public:
IndexFilterOptions() {
enabled = false;
threshold = 0;
}
public:
vector<string> blacklist1;
vector<string> blacklist2;
bool enabled;
int threshold;
};
class LowComplexityFilterOptions {
public:
LowComplexityFilterOptions() {
enabled = false;
threshold = 0.3;
}
public:
bool enabled;
double threshold;
};
class OverrepresentedSequenceAnasysOptions {
public:
OverrepresentedSequenceAnasysOptions() {
enabled = false;
sampling = 20;
}
public:
bool enabled;
int sampling;
};
class PolyGTrimmerOptions {
public:
PolyGTrimmerOptions() {
enabled = false;
minLen = 10;
}
public:
bool enabled;
int minLen;
};
class PolyXTrimmerOptions {
public:
PolyXTrimmerOptions() {
enabled = false;
minLen = 10;
}
public:
bool enabled;
int minLen;
};
class UMIOptions {
public:
UMIOptions() {
enabled = false;
location = UMI_LOC_NONE;
length = 0;
skip = 0;
delimiter= ":";
}
public:
bool enabled;
int location;
int length;
int skip;
string prefix;
string separator;
string delimiter;
};
class CorrectionOptions {
public:
CorrectionOptions() {
enabled = false;
}
public:
bool enabled;
};
class QualityCutOptions {
public:
QualityCutOptions() {
enabledFront = false;
enabledTail = false;
enabledRight = false;
windowSizeShared = 4;
qualityShared = 20;
windowSizeFront = windowSizeShared;
qualityFront = qualityShared;
windowSizeTail = windowSizeShared;
qualityTail = qualityShared;
windowSizeRight = windowSizeShared;
qualityRight = qualityShared;
}
public:
// enable 5' cutting by quality
bool enabledFront;
// enable 3' cutting by quality
bool enabledTail;
// enable agressive cutting mode
bool enabledRight;
// the sliding window size
int windowSizeShared;
// the mean quality requirement
int qualityShared;
// the sliding window size for cutting by quality in 5'
int windowSizeFront;
// the mean quality requirement for cutting by quality in 5'
int qualityFront;
// the sliding window size for cutting by quality in 3'
int windowSizeTail;
// the mean quality requirement for cutting by quality in 3'
int qualityTail;
// the sliding window size for cutting by quality in aggressive mode
int windowSizeRight;
// the mean quality requirement for cutting by quality in aggressive mode
int qualityRight;
};
class SplitOptions {
public:
SplitOptions() {
enabled = false;
needEvaluation = false;
number = 0;
size = 0;
digits = 4;
byFileNumber = false;
byFileLines = false;
}
public:
bool enabled;
// number of files
int number;
// lines of each file
long size;
// digits number of file name prefix, for example 0001 means 4 digits
int digits;
// need evaluation?
bool needEvaluation;
bool byFileNumber;
bool byFileLines;
};
class AdapterOptions {
public:
AdapterOptions() {
enabled = true;
hasSeqR1 = false;
hasSeqR2 = false;
detectAdapterForPE = false;
allowGapOverlapTrimming = false;
dimerMaxLen = 2;
}
public:
bool enabled;
string sequence;
string sequenceR2;
string detectedAdapter1;
string detectedAdapter2;
vector<string> seqsInFasta;
string fastaFile;
bool hasSeqR1;
bool hasSeqR2;
bool hasFasta;
bool detectAdapterForPE;
bool allowGapOverlapTrimming;
int dimerMaxLen;
};
class TrimmingOptions {
public:
TrimmingOptions() {
front1 = 0;
tail1 = 0;
front2 = 0;
tail2 = 0;
maxLen1 = 0;
maxLen2 = 0;
}
public:
// trimming first cycles for read1
int front1;
// trimming last cycles for read1
int tail1;
// trimming first cycles for read2
int front2;
// trimming last cycles for read2
int tail2;
// max length of read1
int maxLen1;
// max length of read2
int maxLen2;
};
class QualityFilteringOptions {
public:
QualityFilteringOptions() {
enabled = true;
// '0' = Q15
qualifiedQual = '0';
unqualifiedPercentLimit = 40;
nBaseLimit = 5;
}
public:
// quality filter enabled
bool enabled;
// if a base's quality phred score < qualifiedPhred, then it's considered as a low_qual_base
char qualifiedQual;
// if low_qual_base_num > lowQualLimit, then discard this read
int unqualifiedPercentLimit;
// if n_base_number > nBaseLimit, then discard this read
int nBaseLimit;
// if average qual score < avgQualReq, then discard this read
int avgQualReq;
};
class ReadLengthFilteringOptions {
public:
ReadLengthFilteringOptions() {
enabled = false;
requiredLength = 15;
maxLength = 0;
}
public:
// length filter enabled
bool enabled;
// if read_length < requiredLength, then this read is discard
int requiredLength;
// length limit, 0 for no limitation
int maxLength;
};
class Options{
public:
Options();
void init();
bool isPaired();
bool validate();
bool adapterCuttingEnabled();
bool polyXTrimmingEnabled();
string getAdapter1();
string getAdapter2();
void initIndexFiltering(string blacklistFile1, string blacklistFile2, int threshold = 0);
vector<string> makeListFromFileByLine(string filename);
bool shallDetectAdapter(bool isR2 = false);
void loadFastaAdapters();
public:
// file name of read1 input
string in1;
// file name of read2 input
string in2;
// file name of read1 output
string out1;
// file name of read2 output
string out2;
// file name of unpaired read1 output
string unpaired1;
// file name of unpaired read2 output
string unpaired2;
// file name of failed reads output
string failedOut;
// json file
string overlappedOut;
// json file
string jsonFile;
// html file
string htmlFile;
// html report title
string reportTitle;
// compression level
int compression;
// the input file is using phred64 quality scoring
bool phred64;
// do not rewrite existing files
bool dontOverwrite;
// read STDIN
bool inputFromSTDIN;
// write STDOUT
bool outputToSTDOUT;
// the input R1 file is interleaved
bool interleavedInput;
// only process first N reads
int readsToProcess;
// fix the MGI ID tailing issue
bool fixMGI;
// worker thread number
int thread;
// trimming options
TrimmingOptions trim;
// quality filtering options
QualityFilteringOptions qualfilter;
// length filtering options
ReadLengthFilteringOptions lengthFilter;
// adapter options
AdapterOptions adapter;
// multiple file splitting options
SplitOptions split;
// options for quality cutting
QualityCutOptions qualityCut;
// options for base correction
CorrectionOptions correction;
// options for UMI
UMIOptions umi;
// 3' end polyG trimming, default for Illumina NextSeq/NovaSeq
PolyGTrimmerOptions polyGTrim;
// 3' end polyX trimming
PolyXTrimmerOptions polyXTrim;
// for overrepresentation analysis
OverrepresentedSequenceAnasysOptions overRepAnalysis;
map<string, long> overRepSeqs1;
map<string, long> overRepSeqs2;
int seqLen1;
int seqLen2;
// low complexity filtering
LowComplexityFilterOptions complexityFilter;
// black lists for filtering by index
IndexFilterOptions indexFilter;
// options for duplication profiling
DuplicationOptions duplicate;
// max value of insert size
int insertSizeMax;
// overlap analysis threshold
int overlapRequire;
int overlapDiffLimit;
int overlapDiffPercentLimit;
// output debug information
bool verbose;
// merge options
MergeOptions merge;
// the buffer size for writer
size_t writerBufferSize;
};
#endif

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

Overview

Authors: Lei Dong^1,2, Zhengcheng Yun², Lin Gao², Yue Li³, Ying Zhou⁴, Yini Zhu⁴, Meng Li⁵, Leqian Ying¹, Xuhong Yang², Jiangtao Yue², Xueqing Yong⁶, Wanqing Cheng², Jia Miao², Nuo Xu², Xinyu Zhang², Hui Yang⁷, Tingting Liu⁸, Gaolin Liang⁹, Shenghong Ju², Haijun Zhang¹, Jinbing Xie²

ORCID iDs: Lei Dong, Yue Li, Yini Zhu, Xuhong Yang, Jia Miao, Gaolin Liang, Shenghong Ju, Haijun Zhang, Jinbing Xie

Institutions: Zhongda Hospital Southeast University (China); Southeast University (China); University of Macau (Macao SAR China); Zhengzhou University (China); State Key Laboratory of Digital Medical Engineering (China)

Journal: Nature communications, volume 17, issue 1, article 9254

Dates: received 16 October 2025; accepted 15 July 2026; published online 30 July 2026

Type: Research article · Language: English

License: CC BY

Identifiers: DOI 10.1038/s41467-026-76103-4 · PMID 42669690 · PMCID PMC13526793 · OpenAlex W7171789952

Open access: gold, a free copy (OpenAlex)

Status: code verified

Categories: other (modality), human (organism), mouse (organism), other condition (population)

Methods: Statistics, Evoked potentials

Keywords: Nanoparticles, Permeation and transport, Neurophysiology, Targeted therapies

MeSH: Adrenergic beta-Antagonists*, Brain Neoplasms*, Glioblastoma*, Immunotherapy*, Administration, Intranasal, Animals, Blood-Brain Barrier, Brain, Carvedilol, Cell Line, Tumor, Drug Delivery Systems, Female, Humans, Mice, Nasal Mucosa, T-Lymphocytes, Ultrasonic Waves (* major topic)

Topic: Ultrasound and Hyperthermia Applications (Biomedical Engineering, Engineering), according to OpenAlex

Funding: National Natural Science Foundation of China (National Science Foundation of China) (82372023, 82402355, 82172010)

Citations: not cited yet (Europe PMC); 57 references in the paper

Abstract

Intranasal delivery offers a direct route to the brain, circumventing the blood-brain barrier (BBB) and minimizing systemic toxicity. However, its efficiency is mainly limited by the nasal mucosal barrier (NMB). Here, low-intensity pulsed ultrasound (LIPUS) without depending on the microbubbles (MBs) to amplify energy, is directly used to reversibly open the NMB by disrupting tight junction proteins. A bionic nanovesicle (iRGD-anti-programmed cell death ligand 1 (aPD-L1) & carvedilol (β-blocker) @ macrophage-derived extracellular vesicles, iMPC) is designed to co-deliver carvedilol for β-receptor blockade to reduce T-cell exhaustion, and aPD-L1 to enhance T-cell anti-tumor activity in orthotopic glioblastoma (GBM) mice during the two-hour window for NMB opening. Consequently, compared to free aPD-L1, up to a 33.38-fold increase of aPD-L1 in the GBM region is obtained with LIPUS-mediated intranasal delivery of iMPC. Reactivating T cells significantly enhances immunotherapy, leading to a 40% tumor reduction, extended survival, and long-term immune memory in orthotopic GBM mice. Overall, the LIPUS-mediated NMB opening strategy notably enhances nose-to-brain drug delivery efficiency, offering a promising platform for treating brain diseases.

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

Repository

Its files are read in the Code ↔ Paper reader above, with 2 matches 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, “Transcriptome sequencing (RNA-Seq)”

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, 1 match
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, 1 match
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
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

The paper's code and data availability statement is in the Data section.

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;
2 matches between paragraphs of the paper and lines of the code (method lexical-v1);
neither the text of the paper nor the code itself.

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

Data

Datasets cited

ngdc.cncb.ac.cn/gsa/browse, at ngdc.cncb.ac.cn; found in “Data availability”

Data availability

The data that support the findings of this study are available in the supplementary material of this article. Source data are provided with this paper. All raw sequencing data generated in this study have been deposited in the Genome Sequence Archive for Human (GSA-Human,) database under accession code CRA031945 (https://ngdc.cncb.ac.cn/gsa/browse/CRA031945). Source data are provided with this paper.

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

Versions

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

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 21 authors, 4 keywords, 17 MeSH terms, 1 funder, 57 references.

Cite

This paper

Dong, L., Yun, Z., Gao, L., Li, Y., Zhou, Y., Zhu, Y., Li, M., Ying, L., Yang, X., Yue, J., Yong, X., Cheng, W., Miao, J., Xu, N., Zhang, X., Yang, H., Liu, T., Liang, G., Ju, S., . . . Xie, J. (2026). Low-intensity pulsed ultrasound-mediated nose-to-brain co-delivery of β-blockers and aPD-L1 enhances glioblastoma immunotherapy. Nature communications, 17(1), 9254. https://doi.org/10.1038/s41467-026-76103-4

BibTeX

@article{dong2026low, author = {Dong, Lei and Yun, Zhengcheng and Gao, Lin and Li, Yue and Zhou, Ying and Zhu, Yini and Li, Meng and Ying, Leqian and Yang, Xuhong and Yue, Jiangtao and Yong, Xueqing and Cheng, Wanqing and Miao, Jia and Xu, Nuo and Zhang, Xinyu and Yang, Hui and Liu, Tingting and Liang, Gaolin and Ju, Shenghong and Zhang, Haijun and Xie, Jinbing}, title = {{Low-intensity pulsed ultrasound-mediated nose-to-brain co-delivery of β-blockers and aPD-L1 enhances glioblastoma immunotherapy}}, journal = {Nature communications}, year = {2026}, month = jul, volume = {17}, number = {1}, pages = {9254}, publisher = {Nature Publishing Group}, issn = {2041-1723}, doi = {10.1038/s41467-026-76103-4}, url = {https://doi.org/10.1038/s41467-026-76103-4}, pmid = {42669690}, pmcid = {PMC13526793} }

RIS

TY - JOUR AU - Dong, Lei AU - Yun, Zhengcheng AU - Gao, Lin AU - Li, Yue AU - Zhou, Ying AU - Zhu, Yini AU - Li, Meng AU - Ying, Leqian AU - Yang, Xuhong AU - Yue, Jiangtao AU - Yong, Xueqing AU - Cheng, Wanqing AU - Miao, Jia AU - Xu, Nuo AU - Zhang, Xinyu AU - Yang, Hui AU - Liu, Tingting AU - Liang, Gaolin AU - Ju, Shenghong AU - Zhang, Haijun AU - Xie, Jinbing TI - Low-intensity pulsed ultrasound-mediated nose-to-brain co-delivery of β-blockers and aPD-L1 enhances glioblastoma immunotherapy T2 - Nature communications J2 - Nat Commun PY - 2026 DA - 2026/07/30 VL - 17 IS - 1 SP - 9254 SN - 2041-1723 PB - Nature Publishing Group DO - 10.1038/s41467-026-76103-4 UR - https://doi.org/10.1038/s41467-026-76103-4 LA - en ER -

CSL-JSON

{ "id": "10.1038/s41467-026-76103-4", "type": "article-journal", "title": "Low-intensity pulsed ultrasound-mediated nose-to-brain co-delivery of β-blockers and aPD-L1 enhances glioblastoma immunotherapy", "container-title": "Nature communications", "author": [ { "family": "Dong", "given": "Lei" }, { "family": "Yun", "given": "Zhengcheng" }, { "family": "Gao", "given": "Lin" }, { "family": "Li", "given": "Yue" }, { "family": "Zhou", "given": "Ying" }, { "family": "Zhu", "given": "Yini" }, { "family": "Li", "given": "Meng" }, { "family": "Ying", "given": "Leqian" }, { "family": "Yang", "given": "Xuhong" }, { "family": "Yue", "given": "Jiangtao" }, { "family": "Yong", "given": "Xueqing" }, { "family": "Cheng", "given": "Wanqing" }, { "family": "Miao", "given": "Jia" }, { "family": "Xu", "given": "Nuo" }, { "family": "Zhang", "given": "Xinyu" }, { "family": "Yang", "given": "Hui" }, { "family": "Liu", "given": "Tingting" }, { "family": "Liang", "given": "Gaolin" }, { "family": "Ju", "given": "Shenghong" }, { "family": "Zhang", "given": "Haijun" }, { "family": "Xie", "given": "Jinbing" } ], "container-title-short": "Nat Commun", "volume": "17", "issue": "1", "page": "9254", "DOI": "10.1038/s41467-026-76103-4", "PMID": "42669690", "PMCID": "PMC13526793", "ISSN": "2041-1723", "publisher": "Nature Publishing Group", "URL": "https://doi.org/10.1038/s41467-026-76103-4", "language": "en", "issued": { "date-parts": [ [ 2026, 7, 30 ] ] } }

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