Kang Wu
@wukang.bsky.social
Maybe be passionate about bioinformatics, immunotherapy, and diagnosis, haha! Website https://iamhealthy.github.io/
TIL: a receptor could also be a ligand.
Researchers delineate how a membrane-bound receptor acts as a ligand for the immune inhibitory receptor LAIR-1, findings that may have implications for therapeutic strategies to regulate immune responses. #ScienceSignaling https://scim.ag/4iQ4oib
The scavenger receptor MARCO is a ligand for the immune inhibitory receptor LAIR-1 and regulates its function in cis
Inhibitory signaling by the receptor LAIR-1 in macrophages is suppressed in cis by a scavenger receptor.
scim.ag
December 11, 2025 at 2:26 AM
TIL: a receptor could also be a ligand.
- epithelial cells can be distinguished by positive staining of
various cytokeratins.
pubmed.ncbi.nlm.nih.gov/40980692/
various cytokeratins.
pubmed.ncbi.nlm.nih.gov/40980692/
An image analysis pipeline to quantify the spatial distribution of cell markers in stroma-rich tumors - PubMed
Aggressive cancers, such as pancreatic ductal adenocarcinoma (PDAC), are often characterized by a complex and desmoplastic tumor microenvironment, a stroma rich supportive connective tissue composed primarily of extracellular matrix (ECM) and non-cancerous cells. Desmoplasia, a dense deposition of s …
pubmed.ncbi.nlm.nih.gov
December 5, 2025 at 2:56 PM
- epithelial cells can be distinguished by positive staining of
various cytokeratins.
pubmed.ncbi.nlm.nih.gov/40980692/
various cytokeratins.
pubmed.ncbi.nlm.nih.gov/40980692/
This is how to use AI for preparing a scientific manuscript:
"Use of Large Language Models.
We used ChatGPT (OpenAI), model GPT-4o (version gpt-4o-2024-08-06 or gpt-4-turbo-2024-04-09), solely to improve grammar and language clarity during manuscript preparation. The prompt used was “Proofread.” "
"Use of Large Language Models.
We used ChatGPT (OpenAI), model GPT-4o (version gpt-4o-2024-08-06 or gpt-4-turbo-2024-04-09), solely to improve grammar and language clarity during manuscript preparation. The prompt used was “Proofread.” "
December 5, 2025 at 2:52 AM
This is how to use AI for preparing a scientific manuscript:
"Use of Large Language Models.
We used ChatGPT (OpenAI), model GPT-4o (version gpt-4o-2024-08-06 or gpt-4-turbo-2024-04-09), solely to improve grammar and language clarity during manuscript preparation. The prompt used was “Proofread.” "
"Use of Large Language Models.
We used ChatGPT (OpenAI), model GPT-4o (version gpt-4o-2024-08-06 or gpt-4-turbo-2024-04-09), solely to improve grammar and language clarity during manuscript preparation. The prompt used was “Proofread.” "
Chemicals widely used to mitigate endogenous autofluorescence are:
- copper sulfate (硫酸铜).
- ammonium chloride (氯化铵).
- Sudan Black B.
- sodium borohydride (钠硼氢化物).
"the chemical modification of the tissue can obscure true signals or compromise tissue integrity."
pubmed.ncbi.nlm.nih.gov/40961137/
- copper sulfate (硫酸铜).
- ammonium chloride (氯化铵).
- Sudan Black B.
- sodium borohydride (钠硼氢化物).
"the chemical modification of the tissue can obscure true signals or compromise tissue integrity."
pubmed.ncbi.nlm.nih.gov/40961137/
An open-source photobleacher for fluorescence imaging of large pigment-rich tissues - PubMed
Fluorescence imaging enables visualization of the specific molecules of interest with high contrast, and the use of multiple fluorophores in a single tissue sample allows visualization of complex relationships between biological molecules, cell types, and anatomy. The utility of fluorescence imaging …
pubmed.ncbi.nlm.nih.gov
December 3, 2025 at 8:13 AM
Chemicals widely used to mitigate endogenous autofluorescence are:
- copper sulfate (硫酸铜).
- ammonium chloride (氯化铵).
- Sudan Black B.
- sodium borohydride (钠硼氢化物).
"the chemical modification of the tissue can obscure true signals or compromise tissue integrity."
pubmed.ncbi.nlm.nih.gov/40961137/
- copper sulfate (硫酸铜).
- ammonium chloride (氯化铵).
- Sudan Black B.
- sodium borohydride (钠硼氢化物).
"the chemical modification of the tissue can obscure true signals or compromise tissue integrity."
pubmed.ncbi.nlm.nih.gov/40961137/
Some human endogenous pigments that interfere with fluorescence-based imaging:
- lipofuscin (脂褐质),
- nicotinamide adenine dinucleotide (NAD, 烟酰胺腺嘌呤二核苷酸),
- flavins (黄素),
- hemoglobin (血红蛋白) and its breakdown products,
- bisretinoids (双视黄醇类)
pubmed.ncbi.nlm.nih.gov/40961137/
- lipofuscin (脂褐质),
- nicotinamide adenine dinucleotide (NAD, 烟酰胺腺嘌呤二核苷酸),
- flavins (黄素),
- hemoglobin (血红蛋白) and its breakdown products,
- bisretinoids (双视黄醇类)
pubmed.ncbi.nlm.nih.gov/40961137/
An open-source photobleacher for fluorescence imaging of large pigment-rich tissues - PubMed
Fluorescence imaging enables visualization of the specific molecules of interest with high contrast, and the use of multiple fluorophores in a single tissue sample allows visualization of complex relationships between biological molecules, cell types, and anatomy. The utility of fluorescence imaging …
pubmed.ncbi.nlm.nih.gov
December 3, 2025 at 7:36 AM
Some human endogenous pigments that interfere with fluorescence-based imaging:
- lipofuscin (脂褐质),
- nicotinamide adenine dinucleotide (NAD, 烟酰胺腺嘌呤二核苷酸),
- flavins (黄素),
- hemoglobin (血红蛋白) and its breakdown products,
- bisretinoids (双视黄醇类)
pubmed.ncbi.nlm.nih.gov/40961137/
- lipofuscin (脂褐质),
- nicotinamide adenine dinucleotide (NAD, 烟酰胺腺嘌呤二核苷酸),
- flavins (黄素),
- hemoglobin (血红蛋白) and its breakdown products,
- bisretinoids (双视黄醇类)
pubmed.ncbi.nlm.nih.gov/40961137/
"... through experimental evolution over the course of 30 days, were able to vastly expand the host ranges of these phages to kill a broader range of clinical K. pneumoniae isolates including MDR (multi-drug resistant) and XDR (extensively-drug resistant) isolates."
www.nature.com/articles/s41...
www.nature.com/articles/s41...
November 26, 2025 at 7:35 AM
"... through experimental evolution over the course of 30 days, were able to vastly expand the host ranges of these phages to kill a broader range of clinical K. pneumoniae isolates including MDR (multi-drug resistant) and XDR (extensively-drug resistant) isolates."
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Small vesicles are everywhere, intracellular and extracellular.
Vesicles can be a mix from the host and (infected) pathogen.
Vesicles are a way for distant communication, besides via single molecules.
Communication might result in some outcomes (good or bad).
www.biorxiv.org/content/10.1...
Vesicles can be a mix from the host and (infected) pathogen.
Vesicles are a way for distant communication, besides via single molecules.
Communication might result in some outcomes (good or bad).
www.biorxiv.org/content/10.1...
November 21, 2025 at 2:53 AM
Small vesicles are everywhere, intracellular and extracellular.
Vesicles can be a mix from the host and (infected) pathogen.
Vesicles are a way for distant communication, besides via single molecules.
Communication might result in some outcomes (good or bad).
www.biorxiv.org/content/10.1...
Vesicles can be a mix from the host and (infected) pathogen.
Vesicles are a way for distant communication, besides via single molecules.
Communication might result in some outcomes (good or bad).
www.biorxiv.org/content/10.1...
November 10, 2025 at 1:00 AM
**Explaining Co-First Authorship**
- Common methods for determining the order of co-first authors include **alphabetical order, seniority, or even random selection like drawing straws**.
journals.asm.org/authorship
- Common methods for determining the order of co-first authors include **alphabetical order, seniority, or even random selection like drawing straws**.
journals.asm.org/authorship
Authorship
ASM Journals' Authorship Guidelines align with ICMJE standards, ensuring integrity and quality. Learn about qualifying as an author, responsibilities, approval process, resolving disputes, and more. D...
journals.asm.org
October 29, 2025 at 7:28 AM
**Explaining Co-First Authorship**
- Common methods for determining the order of co-first authors include **alphabetical order, seniority, or even random selection like drawing straws**.
journals.asm.org/authorship
- Common methods for determining the order of co-first authors include **alphabetical order, seniority, or even random selection like drawing straws**.
journals.asm.org/authorship
"The behavior is all the more impressive given that the rodents hunt at night, when they are effectively blind; the rats may rely on their whiskers to detect changes in air currents caused by the bats’ flapping wings."
Talk about an in-flight meal.
For the first time, researchers have captured rats hunting bats by grabbing them from the sky. Learn more: https://scim.ag/3Jqldmn
For the first time, researchers have captured rats hunting bats by grabbing them from the sky. Learn more: https://scim.ag/3Jqldmn
October 28, 2025 at 12:23 AM
"The behavior is all the more impressive given that the rodents hunt at night, when they are effectively blind; the rats may rely on their whiskers to detect changes in air currents caused by the bats’ flapping wings."
Reposted by Kang Wu
Talk about an in-flight meal.
For the first time, researchers have captured rats hunting bats by grabbing them from the sky. Learn more: https://scim.ag/3Jqldmn
For the first time, researchers have captured rats hunting bats by grabbing them from the sky. Learn more: https://scim.ag/3Jqldmn
October 27, 2025 at 10:31 PM
Talk about an in-flight meal.
For the first time, researchers have captured rats hunting bats by grabbing them from the sky. Learn more: https://scim.ag/3Jqldmn
For the first time, researchers have captured rats hunting bats by grabbing them from the sky. Learn more: https://scim.ag/3Jqldmn
“the first telomere-to-telomere (T2T) mouse genomes for two key inbred strains, C57BL/6J and CAST/EiJ.”
“add an additional 213 Mb of new sequence to the reference genome, which contains 517 protein-coding genes.”
“add an additional 213 Mb of new sequence to the reference genome, which contains 517 protein-coding genes.”
For over 20 years, the mouse model organism has helped scientists uncover the biology behind human health and disease.
But the mouse reference genomes still have missing pieces.
The first collection of telomere-to-telomere mouse genomes are now available for two key mouse strains.
🧬💻
But the mouse reference genomes still have missing pieces.
The first collection of telomere-to-telomere mouse genomes are now available for two key mouse strains.
🧬💻
October 27, 2025 at 12:29 PM
“the first telomere-to-telomere (T2T) mouse genomes for two key inbred strains, C57BL/6J and CAST/EiJ.”
“add an additional 213 Mb of new sequence to the reference genome, which contains 517 protein-coding genes.”
“add an additional 213 Mb of new sequence to the reference genome, which contains 517 protein-coding genes.”
- 16% of somatic variants occur in sequences absent from GRCh38
- Centromere kinetochore domains emerged as focal sites of structural, genetic, and epigenetic variation
www.biorxiv.org/content/10.1...
- Centromere kinetochore domains emerged as focal sites of structural, genetic, and epigenetic variation
www.biorxiv.org/content/10.1...
A telomere-to-telomere map of somatic mutation burden and functional impact in cancer
Oncogenesis involves widespread genetic and epigenetic alterations, yet the full spectrum of somatic variation genome-wide remains unresolved. We generated a near-telomere-to-telomere (T2T) diploid as...
www.biorxiv.org
October 14, 2025 at 3:55 AM
- 16% of somatic variants occur in sequences absent from GRCh38
- Centromere kinetochore domains emerged as focal sites of structural, genetic, and epigenetic variation
www.biorxiv.org/content/10.1...
- Centromere kinetochore domains emerged as focal sites of structural, genetic, and epigenetic variation
www.biorxiv.org/content/10.1...
- Are there individuals harboring **functionally** similar cGAS (mutations) to the one in naked mole-rats?
A cGAS-mediated mechanism in naked mole-rats potentiates DNA repair and delays aging | Science www.science.org/doi/10.1126/...
A cGAS-mediated mechanism in naked mole-rats potentiates DNA repair and delays aging | Science www.science.org/doi/10.1126/...
A cGAS-mediated mechanism in naked mole-rats potentiates DNA repair and delays aging
Efficient DNA repair might make possible the longevity of naked mole-rats. However, whether they have distinctive mechanisms to optimize functions of DNA repair suppressors is unclear. We find that na...
www.science.org
October 13, 2025 at 2:16 AM
- Are there individuals harboring **functionally** similar cGAS (mutations) to the one in naked mole-rats?
A cGAS-mediated mechanism in naked mole-rats potentiates DNA repair and delays aging | Science www.science.org/doi/10.1126/...
A cGAS-mediated mechanism in naked mole-rats potentiates DNA repair and delays aging | Science www.science.org/doi/10.1126/...
Serial sampling is a rational approach for monitoring (immuno)therapy.
e.g., for neoantigen-based immunotherapy, it may refine the neoantigens used.
But how to ensure the representativeness of dissected samples since a tumor is heterogeneous even within a single tumor locus?
e.g., for neoantigen-based immunotherapy, it may refine the neoantigens used.
But how to ensure the representativeness of dissected samples since a tumor is heterogeneous even within a single tumor locus?
Researchers have applied serial biopsies to safely monitor glioblastoma progression and responses to immunotherapy in two patients, capturing details that are invisible to standard-of-care MRI.
Learn more in #ScienceTranslationalMedicine: https://scim.ag/46Id31J
Learn more in #ScienceTranslationalMedicine: https://scim.ag/46Id31J
Now you see me; now you don’t
Multiomics on serial glioblastoma biopsies can enable differentiation of pseudoprogression from true tumor progression (see Ling et al.).
scim.ag
October 10, 2025 at 2:58 AM
Serial sampling is a rational approach for monitoring (immuno)therapy.
e.g., for neoantigen-based immunotherapy, it may refine the neoantigens used.
But how to ensure the representativeness of dissected samples since a tumor is heterogeneous even within a single tumor locus?
e.g., for neoantigen-based immunotherapy, it may refine the neoantigens used.
But how to ensure the representativeness of dissected samples since a tumor is heterogeneous even within a single tumor locus?
A big moment for TB vaccine research.
Clinical trial next.
Mining the CD4 antigen repertoire for next-generation tuberculosis vaccines: Cell www.cell.com/cell/fulltex...
Clinical trial next.
Mining the CD4 antigen repertoire for next-generation tuberculosis vaccines: Cell www.cell.com/cell/fulltex...
Mining the CD4 antigen repertoire for next-generation tuberculosis vaccines
Systematic antigen selection is an enduring challenge in tuberculosis (TB) vaccine
development. An antigen screen ranks protective CD4 T cell antigens and yields a novel
trivalent mRNA vaccine that pr...
www.cell.com
September 20, 2025 at 11:13 AM
A big moment for TB vaccine research.
Clinical trial next.
Mining the CD4 antigen repertoire for next-generation tuberculosis vaccines: Cell www.cell.com/cell/fulltex...
Clinical trial next.
Mining the CD4 antigen repertoire for next-generation tuberculosis vaccines: Cell www.cell.com/cell/fulltex...
“image analysis may be faster, more reproducible, and more quantitative than visual assessment.”
qupath.readthedocs.io/en/0.6/docs/...
qupath.readthedocs.io/en/0.6/docs/...
Measuring areas — QuPath 0.6.0 documentation
qupath.readthedocs.io
September 18, 2025 at 12:55 PM
“image analysis may be faster, more reproducible, and more quantitative than visual assessment.”
qupath.readthedocs.io/en/0.6/docs/...
qupath.readthedocs.io/en/0.6/docs/...
A good paper for knowing:
What mp-tNGS (multiplex-PCR targeted NGS) is.
What hc-tNGS (hybrid-capture targeted NGS) is.
www.thelancet.com/journals/ebi...
What mp-tNGS (multiplex-PCR targeted NGS) is.
What hc-tNGS (hybrid-capture targeted NGS) is.
www.thelancet.com/journals/ebi...
September 4, 2025 at 2:53 AM
A good paper for knowing:
What mp-tNGS (multiplex-PCR targeted NGS) is.
What hc-tNGS (hybrid-capture targeted NGS) is.
www.thelancet.com/journals/ebi...
What mp-tNGS (multiplex-PCR targeted NGS) is.
What hc-tNGS (hybrid-capture targeted NGS) is.
www.thelancet.com/journals/ebi...
Common pathogens infecting the urinary tract:
Escherichia coli
Proteus mirabilis
Streptococcus agalactiae
Klebsiella pneumoniae
Pseudomonas aeruginosa
Staphylococcus aureus
Enterococcus faecalis
Staphylococcus saprophyticus
Acinetobacter baumannii
Candida albicans
www.nature.com/articles/s41...
Escherichia coli
Proteus mirabilis
Streptococcus agalactiae
Klebsiella pneumoniae
Pseudomonas aeruginosa
Staphylococcus aureus
Enterococcus faecalis
Staphylococcus saprophyticus
Acinetobacter baumannii
Candida albicans
www.nature.com/articles/s41...
September 3, 2025 at 6:30 AM
Common pathogens infecting the urinary tract:
Escherichia coli
Proteus mirabilis
Streptococcus agalactiae
Klebsiella pneumoniae
Pseudomonas aeruginosa
Staphylococcus aureus
Enterococcus faecalis
Staphylococcus saprophyticus
Acinetobacter baumannii
Candida albicans
www.nature.com/articles/s41...
Escherichia coli
Proteus mirabilis
Streptococcus agalactiae
Klebsiella pneumoniae
Pseudomonas aeruginosa
Staphylococcus aureus
Enterococcus faecalis
Staphylococcus saprophyticus
Acinetobacter baumannii
Candida albicans
www.nature.com/articles/s41...
TIFF vs. OME-TIFF
===
"not all TIFFs are the same."
"the data in a TIFF file can be represented quite differently in terms of layout and compression."
"(TIFFs) file does not contain pyramidal layers"
===
"well-supported, open formats should generally be preferred (e.g. **OME-TIFF**)"
===
"not all TIFFs are the same."
"the data in a TIFF file can be represented quite differently in terms of layout and compression."
"(TIFFs) file does not contain pyramidal layers"
===
"well-supported, open formats should generally be preferred (e.g. **OME-TIFF**)"
September 1, 2025 at 12:24 PM
TIFF vs. OME-TIFF
===
"not all TIFFs are the same."
"the data in a TIFF file can be represented quite differently in terms of layout and compression."
"(TIFFs) file does not contain pyramidal layers"
===
"well-supported, open formats should generally be preferred (e.g. **OME-TIFF**)"
===
"not all TIFFs are the same."
"the data in a TIFF file can be represented quite differently in terms of layout and compression."
"(TIFFs) file does not contain pyramidal layers"
===
"well-supported, open formats should generally be preferred (e.g. **OME-TIFF**)"
Below is the principle (copied and edited from the original paper):
Given that RNA in FFPE samples is usually degraded and often highly fragmented due to the cross-linking effect of formaldehyde,
pubmed.ncbi.nlm.nih.gov/40882628/
Given that RNA in FFPE samples is usually degraded and often highly fragmented due to the cross-linking effect of formaldehyde,
pubmed.ncbi.nlm.nih.gov/40882628/
August 31, 2025 at 1:19 AM
Below is the principle (copied and edited from the original paper):
Given that RNA in FFPE samples is usually degraded and often highly fragmented due to the cross-linking effect of formaldehyde,
pubmed.ncbi.nlm.nih.gov/40882628/
Given that RNA in FFPE samples is usually degraded and often highly fragmented due to the cross-linking effect of formaldehyde,
pubmed.ncbi.nlm.nih.gov/40882628/
How about testing the impact of heatwave in experimental models, w/ or w/o a pathogen?
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Long-term impacts of heatwaves on accelerated ageing - Nature Climate Change
Ageing is linked to environmental factors. This study shows that although participants gradually adapted to heat over time, cumulative exposure to heatwaves had stable and adverse impacts on ageing, e...
www.nature.com
August 27, 2025 at 6:10 AM
How about testing the impact of heatwave in experimental models, w/ or w/o a pathogen?
www.nature.com/articles/s41...
www.nature.com/articles/s41...
From this image, at least we could know the general appearances of several important bacterial pathogens. 😁
www.mdpi.com/2076-393X/13...
www.mdpi.com/2076-393X/13...
August 24, 2025 at 9:16 AM
From this image, at least we could know the general appearances of several important bacterial pathogens. 😁
www.mdpi.com/2076-393X/13...
www.mdpi.com/2076-393X/13...
(i) genetic variation, (ii) individual-scale generation of additional genetic diversity solely in lymphocytes, and (iii) **collision** of these processes with a changing environment through life, triggering plastic responses that can have lasting effects.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
August 14, 2025 at 6:51 AM
(i) genetic variation, (ii) individual-scale generation of additional genetic diversity solely in lymphocytes, and (iii) **collision** of these processes with a changing environment through life, triggering plastic responses that can have lasting effects.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...