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    "title": "1. 基本信息/background",
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    "text": "The right three images were prepared using QuPath v0.6.0.\n\n\n\n\n1. 基本信息/background\n姓名/name：吴康/Kang Wu（husband, dad, Ph.D）\n邮箱/e-mail：wu__kang@126.com\nORCID：0000-0002-9024-795X\n个人网页/website：https://iamhealthy.github.io/\n\n\n2. 教育/education\n\n\n2007-09 ~ 2012-07，上海交通大学，生物化学与分子生物学(博士)\n\n\n2007-09 ~ 2012-07，Biochemistry and Molecular Biology (Ph.D), Shanghai Jiao Tong University\n\n\n2001-09 ~ 2007-07，西北农林科技大学，生物技术(本硕连读)\n\n\n2001-09 ~ 2007-07，Biotechnology (joint program of bachelor and master), Northwest A&F University\n\n\n\n\n3. 工作/experience\n\n3.4 2022-07 ~ 2026-03，上海锐赛循益生物技术有限公司，科创中心(高级开发总监)\n\n\n肿瘤分子诊断产品开发(相关专利申请号：202410274764.3、202410372505.4)。\n\n\n基于NGS的诊断技术和产品开发(相关专利授权公告号：CN117343999B、CN117701691B)。\n\n\nDCs疫苗临床试验和应用支持、间充质干细胞外泌体临床试验和应用支持。\n\n\n肿瘤panel NGS数据的生信分析，发现基因/蛋白突变以指导临床个体化用药。\n\n\n临床相关数据的生信分析和支持。\n\n\n\n\n3.3 2021-08 ~ 2022-06，杭州杰毅生物技术有限公司，创新应用研究院(医学科学家)\n\n\n基于公司的mNGS产品和临床医生/科室开展合作项目，参与并指导相关项目书撰写、项目推进、项目结题(比如数据整理、分析，SCI文章撰写)。\n\n\n\n\n3.2 2021-06 ~ 2021-08，上海派森诺生物科技有限公司，研发中心(研发项目经理)\n\n\n负责在公司建立metagenomic next-generation sequencing (mNGS)诊断技术。短暂的3个月工作期间，带领3个人的团队建立了该技术的实验部分，及生信分析的框架。\n\n\n\n\n3.1 2012-07 ~ 2021-06，复旦大学附属上海市公共卫生临床中心，科学研究部(助理研究员)\n\n\n宿主(志愿者外周血、吞噬细胞)对于结核分枝杆菌的(全基因组)转录应答和生信分析(相关专利授权公告号：CN104182654B)。\n\n\n牛分枝杆菌卡介苗(结核疫苗)的基因重组改造，及在小鼠的免疫保护研究(相关专利授权公告号：CN111979162B、CN106148258B)。\n\n\n白血病发病机理探索(分子和细胞层面)(相关专利授权公告号：CN103740760B)。\n\n\n\n\n\n4. 💩期刊论文/journal articles\n\n4.1 (并列)一作/(co-)1st author SCI (# co-first author，*corresponding author)\n\n\nXu JC#, Wu K#, Ma RQ, Li JH, Tao J, Hu ZD, Fan XY*. Establishment of an in vitro model of monocyte-like THP-1 cells for trained immunity induced by bacillus Calmette-Guérin. BMC Microbiol. 2024;24:130. (IF: 4.2)\n\n\nShi JC#, Wu WJ#, Wu K#, Ni CR, He GQ, Zheng SL, Cheng F, Yi YX, Ren RT*, Jiang XG*. The diagnosis of leptospirosis complicated by pulmonary tuberculosis complemented by metagenomic next-generation sequencing: a case report. Front Cell Infect Microbiol. 2022;12:922996. (Case report). (IF: 5.7)\n\n\nLiu C#, Wu K#, Sun TY, Chen B, Yi YX, Ren RT*, Xie LX*, Xiao K*. Effect of invasive mechanical ventilation on the diversity of the pulmonary microbiota. Crit Care. 2022;26:252. (Review). (IF: 15.1)\n\n\nWu K, Yan B, Douglas BL, Li T*, Fan XY*. Tailored co-localization analysis of intracellular microbes and punctum-distributed phagosome-lysosome pathway proteins using ImageJ plugin EzColocalization. Sci Rep. 2021;11:1096. (IF: 4.996)\n\n\nWu K, Li M, Chen ZY, Douglas BL*, Fan XY*. Probe signal values in mRNA arrays imply an excessive involvement of neutrophil FCGR1 in tuberculosis. Front Med. 2020;7:19. (IF: 5.091)\n\n\nPei ZL#, Wu K#, Li ZH#, Li CQ#, Zeng L, Li F, Pei N, Liu HM, Zhang SL, Song YZ, Zhang XY, Xu JQ, Fan XY*, Wang J*. Pharmacologic ascorbate as a pro-drug for hydrogen peroxide release to kill mycobacteria. Biomed Pharmacother. 2019;109:2119-2127. (IF: 4.545)\n\n\nWu K#, Wong KW#, Deng WL, Zhang H, Li J, Lowrie DB*, Fan XY*. The numerical predominance and large transcriptome differences of neutrophils in peripheral blood together inevitably account for a reported pulmonary tuberculosis signature. Int J Genomics. 2017;2017:5830971. (IF: 1.904)\n\n\nWu K#, Zhao XJ#, Wong KW, Fan XY*. Comparison of plasmid DNA versus PCR amplified gene of insert DNA for nucleofection in Kasumi-1 cells. Cytotechnology. 2015;67(2):275-283. (IF: 1.864)\n\n\nWu K, Fang H, Lyu LD, Lowrie DB, Wong KW*, Fan XY*. A derived network-based interferon-related signature of human macrophages responding to Mycobacterium tuberculosis. Biomed Res Int. 2014;2014:713071. (IF: 1.579)\n\n\nMa H#, Wu K#, Liu F Yang H, Kang H, Chen NN, Yuan Q, Zhou WJ, Fan XY*. Dose of incorporated immunodominant antigen in recombinant BCG impacts modestly on Th1 immune response and protective efficiency against Mycobacterium tuberculosis in mice. J Immunol Res. 2014;2014:196124. (IF: 2.934)\n\n\nJin W#, Wu K#, Li YZ# Yang WT, Zou B, Zhang F, Zhang J*, Wang KK*. AML1-ETO targets and suppresses cathepsin G, a serine protease, which is able to degrade AML1-ETO in t(8;21) acute myeloid leukemia. Oncogene. 2013;32(15):1978-1987. (IF: 8.559)\n\n\nWu K#, Dong DD#, Fang H#, Levillain F#, Jin W, Mei J, Gicquel B, Du Y, Wang K, Gao Q, Neyrolles O*, Zhang J*. An interferon-related signature in the transcriptional core response of human macrophages to Mycobacterium tuberculosis infection. PLoS One. 2012;7(6):e38367. (IF: 3.730)\n\n\n亦可通过My Bibliography (NCBI)查看如上列表。\n\n\n\n\n4.2 (并列)一作中文/(co-)1st author Chinese (# co-first author，*corresponding author)\n\n\n吴康#、屈蓉#、王刚、薛清华、吕建新、Douglas B. Lowrie、范小勇*。基于常规引物靶向结核分枝杆菌II型分枝杆菌散在重复单位的恒温扩增。复旦学报(医学版)。2020;47:799-808。\n\n\n\n\n4.3 一个有意思的文稿/one interesting draft\n\n\n吴康。《红楼梦》中的疑似活动性结核病患者。知乎。2020。\n\n\n\n\n4.4 非(并列)一作文章/non-(co-)1st articles (# co-first author，*corresponding author)\n\n\nHuang Z#, Huang H#, Hu J, Xia L, Liu XH, Qu R, Huang XL, Yang Y, Wu K, Ma RQ, Xu JC, Chen ZY, Wu YH, Yang J, Fang Y, Zeng JF, Lai WH, Sui GD, Sha W, Xiong YH, Lu SH*, Fan XY*. A novel quantitative urine LAM strip for point-of-care tuberculosis diagnosis in non-HIV adults. J Infect. 2023;S0163-4453(23)00586-8. (Letter).\n\n\nHuang H#, Qu R#, Wu K, Xu JC, Li JH, Lu SH, Sui GD, Fan XY*. Proteinase K-pretreated ConA-based ELISA assay: a novel urine LAM detection strategy for TB diagnosis. Front Microbiol. 2023;14:1236599.\n\n\n屈蓉、吴康、吴娟、范小勇、吕建新*。结核分枝杆菌早期分泌蛋白MPT64的原核表达及其在结核病血清学诊断上的初步应用。中国生物制品学杂志。2021:34(05):566-570。\n\n\nZhao HM#, Du R#, Li CL, Ji P, Li HC, Wu K, Hu ZD, Lu SH, Douglas BL, Fan XY*. Differential T cell responses against DosR-associated antigen Rv2028c in BCG-vaccinated populations with tuberculosis infection. J Infect. 2019;78(4):275-280.\n\n\nHu ZD#, Wong KW#, Zhao HM, Wen HL, Ji P, Ma H, Wu K, Lu SH, Li F, Li ZM, Shu T, Xu JQ, Douglas BL, Fan XY*. Sendai virus mucosal vaccination establishes lung-resident memory CD8 T cell immunity and boosts BCG-primed protection against TB in mice. Mol Ther. 2017;25(5):1222-1233.\n\n\nWen HL, Li CL, Li G, Lu YH, Li HC, Li T, Zhao HM, Wu K, Douglas BL, Lv JX, Lu SH*, Fan XY*. Involvement of methylated HBHA expressed from Mycobacterium smegmatis in an IFN-γ release assay to aid discrimination between latent infection and active tuberculosis in BCG-vaccinated populations. Eur J Clin Microbiol Infect Dis. 2017;36(8):1415-1423.\n\n\nLi G#, Li F#, Zhao HM, Wen HL, Li HC, Li CL, Ji P, Xu P, Wu K, Hu ZD, Lu SH, Douglas BL, Lv JX*, Fan XY*. Evaluation of a new IFN-γ release assay for rapid diagnosis of active tuberculosis in a high-incidence setting. Front Cell Infect Microbiol. 2017;7:117.\n\n\n李春玲、吴康、范小勇*。氧化应激与结核病。生命科学。2017;29(11):1108-1112。(综述)。\n\n\n问寒利、李海聪、李根、赵慧敏、施理敏、韩伟靖、吴康、范小勇*。结核分枝杆菌肝素结合血凝黏附素的原核表达及其在结核病血清学诊断中的应用。中国生物制品学杂志。2016;29(05):497-502。\n\n\nChen L, Guo S, Wu LX, Fan XY, Ma H, Wu K, Wu J, Zhang JH*. IL-17A Autoantibody Induced by Recombinant Mycobacterium smegmatis Expressing Ag85A-IL-17A Fusion Protein. Appl Biochem Biotechnol. 2015; 176(7):2018-2026.\n\n\n吉萍、范小勇*、吴康、卢水华。结核分枝杆菌潜伏性感染相关抗原的研究进展。中华微生物学和免疫学杂志。2015;35(1):59-64。(综述)。\n\n\nKang H, Yuan Q, Ma H, Hu ZD, Han DP, Wu K, Douglas BL, Fan XY*. Enhanced protective efficacy against Mycobacterium tuberculosis afforded by BCG prime-DNA boost regimen in an early challenge mouse model is associated with increased splenic interleukin-2-producing CD4 T-cell frequency post-vaccination. Immunology. 2014;143(4):661-669.\n\n\n\n\n4.5 放弃发表的一作文章/1st author articles abandoned for publication (# co-first author，*corresponding author)\n\n\nWu K, Douglas BL*, Fan XY*. Fever of unknown origin and incipient tuberculosis. Un-published. Drafted in 2020. (Letter).\n\n\nWu K, Douglas BL, Wong KW*, Fan XY*. Re-analysis of the transcriptome data of host Macrophages in response to Mycobacterium tuberculosis infection by weighted gene co-expression network analysis. Un-published. Drafted in 2014.\n\n\n\n\n4.6 被致谢的文章/acknowledged articles(# co-first author，*corresponding author)\n\n\nCheng XB#, Chai RR#, Zhang T#, Chen YJ, Fan FQ, Ye YF, Jin GQ, Li TT, Wang H, Ding JW, Zheng M, Han YH, Tang QZ, Song ZQ, Ji YQ, Song WW, Luo WF*, Kang Y*. A novel methylation-detection panel for HPV associated high-grade squamous intraepithelial lesion and cervical cancer screening. Sci Rep. 2024;14(1):25556. “In particular, we acknowledge Dr. Wu Kang for giving professional advice on this article.”\n\n\n\n\n\n5. 💩专利/patents\n\n\n张腾、吴康、纪逸群、东亚娟、钟军、罗卫峰、范小勇、赵建华。一种改变不同核酸靶标相对PCR扩增速度的方法。发明专利。申请号：202410372505.4。申请日期：2024.03.29。_该专利在2024.06.18被驳回。本人自认为该专利有有趣的发现，即通过具体实验证实了带有通用引物序列的靶标特异引物对的qPCR扩增性能更好（扩增体系亦包括通用引物对。相比于未带通用引物序列的靶标特异引物对的qPCR），进而能够较好实现改变不同核酸靶标的相对PCR扩增速度的目的。\n\n\n吴康、张腾、纪逸群、钟军、罗卫峰、范小勇、赵建华。一种通过预先PCR改变不同核酸靶标相对扩增速度的方法。发明专利。申请号：202410274764.3。申请日期：2024.03.11。\n\n\n吴康、赵建华、张腾、范小勇、罗卫峰、东亚娟、纪逸群。基于人基因组扩增子的illumina测序文库构建的引物组合。发明专利。授权公告号：CN117701691B。申请日期：2024.02.01。\n\n\n吴康、东亚娟、张腾、范小勇、罗卫峰、赵建华、纪逸群。基于左侧探针退火和右侧探针退火延伸的核酸扩增方法。发明专利。授权公告号：CN117343999B。申请日期：2023.12.05。\n\n\n范小勇、吴康、罗道良。基于常规引物的针对串联重复序列的恒温扩增体系、扩增方法及常规引物对。发明专利。授权公告号：CN111269969B；申请日期：2020.03.06。\n\n\n范小勇、吴康、罗道良。重组卡介苗菌株、其制备方法和用途。发明专利。授权公告号：CN111979162B；申请日期：2019.05.22。\n\n\n范小勇、吕亮东、赵国屏、马辉、吴康。mazG基因缺失的抗结核重组卡介苗。发明专利。授权公告号：CN106148258B；申请日期：2015.04.20。\n\n\n吴康、黄家颖、范小勇。基于蛋白-蛋白相互作用网络的基因集鉴定方法。发明专利。授权公告号：CN104182654B；申请日期：2014.07.30。\n\n\n吴康、范小勇、黄家颖、赵旭杰。PCR扩增基因核转悬浮动物细胞的方法。发明专利。授权公告号：CN103740760B；申请日期：2014.01.09。专利权终止日期：2024.01.09。\n\n\n\n\n6. 💩科研项目/scientific projects\n\n\n\n\n\n\n\n\n\n\n\n\n序号\n项目类型\n项目名称\n项目号\n负责人\n期限\n经费额(万)\n\n\n\n\n5\n舟山市普陀区一般科技计划项目\n基于靶向高通量测序的膀胱癌和泌尿感染集成诊断的技术和产品研发\n2023YB003\n吴康\n2023/01-2025/06\n12\n\n\n4\n上海市科委医学引导\n结核分枝杆菌DosR抗原在结核病免疫鉴别诊断及临床预后中的应用研究\n18411970700\n吴康\n2018/09-2021/09\n20\n\n\n3\n国家重点研发计划\n种畜场牛结核和布鲁氏菌病综合防控与净化技术集成与示范–>课题2：牛结核诊断技术集成与净化示范–>子课题3：基于微流控芯片的牛结核抗原快速检测产品的研发\n2018YFD0500900\n吴康(子课题3)\n2018/06-2021/09\n47/1263\n\n\n2\n国自然青年\n结核分枝杆菌胞内表达上调分泌性基因集的T细胞抗原筛选及其免疫保护功能鉴定\n81301407\n吴康\n2014/01-2016/12\n23\n\n\n1\n上海市科委青年\nActA促进分枝杆菌自噬逃逸并提高卡介苗MHC I类抗原呈递的研究\n12ZR1448200\n吴康\n2012/10-2015/09\n10\n\n\n\n\n\n7. 💩人才项目/talent projects\n\n\n\n\n\n\n\n\n\n\n\n序号\n项目名称\n项目号\n负责人\n期限\n经费额(万)\n\n\n\n\n1\n舟山市“舟创未来”海纳计划创新长期人才 II 类\n【2023】第 1 批-08\n吴康\n2024/04-2029/04\n30"
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    "text": "A1: You can check out this website: International Committee on Taxonomy of Viruses: ICTV."
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    "text": "A1: You can check out this website: International Committee on Taxonomy of Viruses: ICTV."
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    "title": "The biological-relevant questions",
    "section": "Q2: How to define a successful pathogen?",
    "text": "Q2: How to define a successful pathogen?\nA2:\n\nAlthough the definition of a successful pathogen can be uncertain and controversial, in recent years, this term has been used to define those microorganisms that manage to establish a successful relationship with their host, which guarantees its transmissibility and its permanence on Earth. Thus, the ability of a microorganism to rapidly adapt to changes in the microenvironment through the deployment of specialized strategies, and survive within its host despite the deadly attack of the innate and adaptive immune response seems to be the key leading to evolutionary success.\n\n\nC. glabrata (光滑念珠菌，真菌) is a successful pathogen and an artist manipulating the immune response like M. tuberculosis (结核分枝杆菌，细菌).\n\nMicrobiol Res. 2022. PMID: 35430489\nThen, how to define a successful person?"
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    "title": "The biological-relevant questions",
    "section": "Q3: How long can Mycobacterium tuberculosis “hold its breath”?",
    "text": "Q3: How long can Mycobacterium tuberculosis “hold its breath”?\nA3:\n\nFor example, Corper and Cohn, showed that sealed Mtb cultures held at 37°C for 12-30 years yielded viable bacilli in their anaerobic sediments.\n\nAm J Respir Crit Care Med. 2022. PMID: 35442854"
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    "title": "The biological-relevant questions",
    "section": "Q4: How long ago was the first case of tuberculosis (TB) discovered?",
    "text": "Q4: How long ago was the first case of tuberculosis (TB) discovered?\nA4:\n\nTuberculosis has been a scourge of humanity for millennia: the oldest known cases are in a pair of 9,000-year-old skeletons.\n\nNature. 2022. PMID: 35534687"
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    "href": "nutrition/To-present_bio-miscellany_Q-and-A/index.html#q5-what-are-the-historical-vaccination-policies-for-the-bcg-tuberculosis-vaccine-in-various-countries",
    "title": "The biological-relevant questions",
    "section": "Q5: What are the historical vaccination policies for the BCG tuberculosis vaccine in various countries?",
    "text": "Q5: What are the historical vaccination policies for the BCG tuberculosis vaccine in various countries?\nA5: Visit THE BCG WORLD ATLAS.\nPLoS Med. 2011. PMID: 21445325"
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    "title": "The biological-relevant questions",
    "section": "Q6: What are the differences between QuPath and ImageJ (in brief)?",
    "text": "Q6: What are the differences between QuPath and ImageJ (in brief)?\nA6:\n\nThere’s a lot that QuPath can do that ImageJ can’t, especially when it comes to working with whole slide images and object classification. But it works the other way too: there’s also a lot that’s possible with ImageJ, but which isn’t possible with QuPath alone.\n\n\nFortunately, you don’t have to choose one or the other. They are both open and can be used together.\n\nQuPath"
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    "title": "The biological-relevant questions",
    "section": "Q7: How do we know we can trust the bioimage analysis results?",
    "text": "Q7: How do we know we can trust the bioimage analysis results?\nA7:\n\nExcellent question - stay skeptical!\n\n\nImage analysis lets you generate numbers, but these can be sensitive to how precisely you do the analysis (with or without machine learning). QuPath gives you the tools to make the measurements and to visualize them, but the meaning and validation is up to the user.\n\n\nThis is why image analysis results (from any software) should be carefully validated and treated with caution. Doing this is challenging because the ‘truth’ can be hard to define. One way is to compare with expert evaluation. Another (in some cases) is to use clinical outcome. Both these have limitations; validation is almost always hard – but crucial.\n\n\nThere is also the possibility of bugs in any software. If you find any discrepancies, please report them so they can be investigated and fixed if necessary.\n\nQuPath"
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    "title": "The biological-relevant questions",
    "section": "Q8: What is the relationship between image analysis & objectivity?",
    "text": "Q8: What is the relationship between image analysis & objectivity?\nA8:\n\nOne of the claimed advantages of image analysis over visual assessment is that it is objective.\n\n\nI hope this tutorials helps demonstrate why this is completely wrong!\n\n\nEven for this very simple example, we need to make decisions:\n\n\n\nAt what resolution will we perform our detection?\nWhat should be included in the tissue? Do we want areas of fat or not?\nHow to we define our stain colors?\nWhat thresholds do we use?\n\n\n\nAll of these can impact the results. Different people may (subjectively) make different decisions, and the results of their analysis will differ accordingly.\n\n\nQuPath does not answer these questions for you, but gives you the tools for you to construct your own analysis pipelines.\n\n\nHowever, while it is important to be aware that image analysis is not objective, this does not make it useless. Used cautiously – and with careful validation – image analysis may be faster, more reproducible, and more quantitative than visual assessment.\n\nQuPath"
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    "section": "Q9: How are the Nobel Prize laureates selected?",
    "text": "Q9: How are the Nobel Prize laureates selected?\nA9:\n\nThousands of members of academies, university professors, scientists, previous laureates, members of parliamentary assemblies and others, submit nominations for the Nobel Prizes every year. These nominators have been chosen to ensure that as many countries and universities as possible are represented over time. After a long selection process, the Nobel Prize awarding institutions finally make their choice and announce them in October.\n\nThe Nobel Prize in X"
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    "section": "Q10: What endogenous molecules in human tissue could exhibit autofluorescence?",
    "text": "Q10: What endogenous molecules in human tissue could exhibit autofluorescence?\nA10:\nSome human endogenous pigments that might exhibit fluorescence and thus might interfere with fluorescence-based imaging:\n\nlipofuscin (脂褐质).\nnicotinamide adenine dinucleotide (NAD, 烟酰胺腺嘌呤二核苷酸).\nflavins (黄素).\nhemoglobin (血红蛋白) and its breakdown products.\nbisretinoids (双视黄醇类).\n\nProc Natl Acad Sci U S A. 2025. PMID: 40961137"
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    "section": "Q11: What chemical agents are widely exployed to mitigate the issue of autofluorescence?",
    "text": "Q11: What chemical agents are widely exployed to mitigate the issue of autofluorescence?\nA11:\n\nAmong the chemicals used are copper sulfate (硫酸铜), ammonium chloride (氯化铵), Sudan Black B (苏丹黑B), and sodium borohydride (钠硼氢化物)…the chemical modification of the tissue can obscure true signals or compromise tissue integrity.\n\nProc Natl Acad Sci U S A. 2025. PMID: 40961137"
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    "section": "Q12: What is photobleaching?",
    "text": "Q12: What is photobleaching?\nA12:\n\nPhotobleaching is an irreversible process in which fluorophores, upon repeated absorption of excitation photons, undergo chemical modifications that result in a permanent loss of their fluorescence.\n\nProc Natl Acad Sci U S A. 2025. PMID: 40961137"
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    "title": "The biological-relevant questions",
    "section": "Q13: For general microscopy image analysis, what software platforms are available?",
    "text": "Q13: For general microscopy image analysis, what software platforms are available?\nA13:\n\nSeveral software platforms support general microscopy image analysis - including open-source tools such as QuPath, CellProfiler, Fiji, and Napari, as well as commercial packages like HALO (Indica Labs, Albuquerque, NM, United States) and Visiopharm (Hørsholm, Denmark).\n\nFront Bioinform. 2025. PMID: 40980692"
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    "title": "The biological-relevant questions",
    "section": "Q14: What is clonal hematopoiesis of indeterminate potential (CHIP)?",
    "text": "Q14: What is clonal hematopoiesis of indeterminate potential (CHIP)?\nA14:\n\nCHIP is the presence of a clonally expanded hematopoietic stem cell caused by a leukemogenic mutation in individuals without evidence of hematologic malignancy, dysplasia, or cytopenia.\n\n\nCHIP is associated with a 0.5-1.0% risk per year of leukemia. Remarkably, it confers a two-fold increase in cardiovascular risk independent of traditional risk factors.\n\n\nRoughly 80% of patients with CHIP have mutations in epigenetic regulators DNMT3A, TET2, ASXL1, DNA damage repair genes PPM1D, TP53, the regulatory tyrosine kinase JAK2, or mRNA spliceosome components SF3B1, and SRSF2.\n\nJ Mol Cell Cardiol. 2021. PMID: 34298011"
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    "text": "Note\n\n\n\nThe image/logo of this post was created following https://bsky.app/profile/piterpasma.nl/post/3mijvxe54622w."
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    "text": "2026-05\n\nThe grid package provides the underlying graphics system upon which ggplot2 is built. It’s one of two quite different drawing systems that are included in base R: base graphics and grid.\n\nggplot2: Elegant Graphics for Data Analysis\n\nI must mention here that tinyplot has made base R graphics great again since 2024, and kudos to its authors.\n\nYihui Xie/谢益辉"
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    "section": "2026-04",
    "text": "2026-04\n\nPositron is a “batteries-included” fork of VS Code by Posit PBC.\n\nGrant McDermott\n\nFiji is a “batteries-included” distribution of ImageJ.\n\nFiji\n\nOur best and our worst chaotically intertwining.\n\nLauren Harper\n\nPerson A (perhaps a PI or team leader …): No, I have no technical ability.\n\n\nPerson B (perhaps bigger boss …): So what are you being paid for?\n\n\nPerson A: The confidence that I have in my taste, and my ability to express what I feel.\n\nFrom Bluesky"
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    "section": "2026-03",
    "text": "2026-03\n\nIf you kill Americans, if you threaten Americans anywhere on earth, well will hunt you down without apology and without hesitation, and we will kill you.\n\n美国第29任国防部长Peter Brian Hegseth\n\n明犯强汉者，虽远必诛。\n\n西汉名将陈汤\n\nYou don’t need to go viral. You just need to keep showing up and sharing what you know. Consistently. For years.\n\nMing Tommy Tang\n\nFor me at least, I find trial and error in a state of desperation and frustration to be the best (only?) way to pick up many important new skills.\n\nPeter Bankhead\n\nChina is ruled by engineers, whereas the United States is ruled by lawyers.\n\nNature"
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    "section": "2026-02",
    "text": "2026-02\n\n… articulate something I’ve been thinking about for a while but have struggled putting into workds …\n\nStephen D. Turner"
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    "section": "2026-01",
    "text": "2026-01\n\n…贴在了独木寺的院门上，一边是：气度殊高，居天以上。一边是：光芒微吐，助月之明。\n\n《消息》17 独木寺，贾平凹"
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    "text": "I treat it as a book (mainly in Chinese/中文)."
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    "text": "The right three images were prepared using QuPath v0.6.0.\n\n\n\nPhone: +86-15821314790\nEmail_1: wu__kang@126.com\nEmail_2: wukangx9@gmail.com\nEmail_3: 15821314790@126.com\nWechat: +86-15821314790, or scan the following QR code:\n\n\n\nAcknowledgements\nThis website was primarily developed based on the guidelines from the Creating your personal website using Quarto."
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    "text": "1️⃣After my Ph.D.👨🏻‍🎓in Shanghai Jiao Tong U., I became a Research Assistant at Shanghai Public Health Clinical Center (affiliated with Fudan U.), focusing on TB immunology, vaccine development, and a little bit of bioinformatics (R) (2012 - 2021).\n2️⃣Then after leaving academia, I have continued to pursue🕵🏻advancements in omics-, cell-, and BioImageAnalysis-relevant technologies, particularly in therapeutic and diagnostic applications (freelance now).\n3️⃣I am self-taught in R, and …🚶🏻‍➡️."
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    "text": "The biological-relevant questions\n\n\n\nMiscellany\n\n\n\nThe routine questions I don’t know and the answers\n\n\n\nKang Wu\n\n\nFeb 8, 2026\n\n\n\n\n\n\n\n\n\n\n\n\n\nSome good sentences in biology\n\n\n\nsentences\n\n\n\nCompletely personal opinion\n\n\n\nKang Wu\n\n\nApr 22, 2026\n\n\n\n\n\n\n\n\n\n\n\n\n\nSome good sentences beyond biology\n\n\n\nsentences\n\n\n\nCompletely personal opinion\n\n\n\nKang Wu\n\n\nMay 18, 2026\n\n\n\n\n\n\n\n\n\n\n\n\n\nBOOK：【生物】信息、科技、和图像分析（2）\n\n\n\nservices and knowledge\n\n\n\nMainly scientific and technical\n\n\n\nKang Wu\n\n\nMar 21, 2026\n\n\n\n\n\n\n\n\n\n\n\n\n\nBOOK：【生物】信息、科技、和图像分析（1）\n\n\n\nservices and knowledge\n\n\n\nMainly scientific and technical\n\n\n\nKang Wu\n\n\nMar 21, 2026\n\n\n\n\n\n\nNo matching items"
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    "text": "Note\n\n\n\nThe moka-pot-coffee image is from https://bsky.app/profile/nrennie.bsky.social/post/3mjukrwxyxs2y"
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    "text": "2025-07\n\nAntibody function is governed not only by antigen specificity, conferred by the antigen-binding (Fab) domain to neutralize pathogens but also by the antibody constant (Fc) domain, which recruits complement and engages Fc receptors (FcRs) on the surface of immune cells.\n\nImmunity. 2025. PMID: 40449485\n\nAny given MHC molecule can bind numerous different peptides, and some peptide can bind to several different MHC molecules. Because of this broad specificity, the binding between a peptide and an MHC molecule is often referred to as “promiscuous”.\n\nKuby immunology 2018 p533\n\n…studies use a cross-validation approach, in which one chunk of a data set is reserved for training and another for testing. This can lead to issues such as overfitting, meaning that an algorithm performs well on data similar to the information that the model has encountered before but does poorly on disparate data. “The problem with cross-validation is that it tends to provide fairly optimistic results,” Madabhushi explains. “The cleanest and best way to validate these models is through external, independent validation, where the external test set is separate and distinct from the training set and ideally from a separate institution.”\n\nNature. 2025. PMID: 40410341\n\nTrained immunity in alveolar macrophages can lead to damaging lung inflammation, confirming the importance of context in this phenomenon.\n\neLife. 2025. doi: 10.7554/eLife.107787\n\nWhether it’s a sales skill, writing skill, musical talent, preaching ability, inventiveness, food production, cleaning, or childcare, these are all value-creation skills. Few people possess all these skills, and no one is the world’s best at all of them. That’s why most people specialize and outsource the rest.\n\nIsrael Kloss on LinkedIn\n\nActually you have 22 pairs of chromosomes numbered 1 through 22, and if you’re a woman, you have a pair of X chromosomes, for a total of 23 pairs. If you’re a man, you have one X and one Y chromosome instead of two X’s, so the 23rd “pair” isn’t technically a pair at all, even though some parts of Y are identical to some parts of X.\n\nSteven Salzberg on Substack\n\nIt is important to be aware that most common image/photo editing software applications don’t care about preserving pixel values. Only the appearance really matters. Therefore if you adjust the brightness/contrast of an image in such software you can easily make the image unsuitable for later quantitative analysis by compromising the data.\n\n\nIn practice, magnification is then not terribly meaningful: the pixel size is the crucial value needed to make measurements in physical units, and to compare the resolution across images.\n\nQuPath\n\nWriting compels us to think — not in the chaotic, non-linear way our minds typically wander, but in a structured, intentional manner.\n\nNature Reviews Bioengineering\n\nIn QuPath, as in life, it is neither easy nor wise to rewrite history.\n\nQuPath\n\nI am a strong believer that depth of data can be just as powerful as scale of data. Deep analysis of small groups of humans, and even individuals, can lead to novel biological insights and principles.\n\nAnsu Satpathy on X\n\nEnergy and initiative matter more than talent.\n\nMing Tommy Tang on BlueSky"
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    "text": "2025-08\n\nQuanlity before quantity.\n\nMing Tommy Tang on BlueSky\n\nThe testis is known for its immune-privileged status, maintained by the blood–testis barrier, which prevents autoimmune reactions against spermatogenic cells.\n\nMed Sci (Basel). 2025. PMID: 40843751\n\n… doesn’t yet have the thick skin to shrug off the hostility.\n\nRoy Perlis on LinkedIn\n\nGood ideas come from having lots of experience. And experience comes from having lots of bad ideas.\n\nItai Yanai on BlueSky"
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    "text": "2025-09\n\nthe rapid growth and accumulation of sequence data have outpaced efficient analysis capabilities.\n\nbioRxiv. 2025\n\nClear lines of logical argument, precise definitions, often can only be composed in writing. Paper and pencil (or the word processor) are extensions of our brains.\n\nWolfgang Huber on BlueSky\n\n… image analysis may be faster, more reproducible, and more quantitative than visual assessment.\n\nQuPath\n\n… story-telling is easier than science.\n\nMing Tommy Tang on BlueSky\n\nAs far as the computer is concerned, each pixel is really just a number and the full image is a 2D matrix of these numbers: the pixel values … In science, the pixel values are crucial - how they are displayed is not.\n\nQuPath"
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    "text": "2025-10\n\nUC wins 5 Nobel Prizes in 3 days — and sets a new world record.\n\nUNIVERSIDAD DE CALIFORNIA\n\nGreat to know that we are not alone in this effort.\n\nJoseph Arboleda-Velasquez on LinkedIn\n\nThe naked mole-rat/裸鼹鼠 (Heterocephalus glaber) is an extraordinarily long-lived rodent with a maximum life span of ∼37 years.\n\nScience. 2025. DOI: 10.1126/science.adp5056\n\nThe naked mole rat (Heterocephalus glaber) is the longest-lived rodent, with a maximum life span of nearly 40 years.\n\nScience. 2025. DOI: 10.1126/science.aeb6125\n\nWe complement each other very much.\n\nPeter Howitt, laureate of 2025 Nobel Prize in Economics Sciences, on X\n\nThe more variability you capture in the training data, the more accurate the classifier will be.\n\nMicroscopeRA on forum.image.sc\n\nAt more than 200 years, the maximum lifespan of the bowhead whale exceeds that of all other mammals.\n\nNature. 2025"
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    "text": "2025-11\n\n… in most cases you’ll have to train the projects on multiple images, representative of the whole dataset.\n\nforum.image.sc\n\n… skepticism belongs in science - particularly in image analysis - and it’s always worth testing things from multiple angles, just in case.\n\nIntroduction to Bioimage Analysis\n\nThe first thing you need to figure out is why the intensity changes across images. Is it something real about the biology, or inconsistent staining, or changing acquisition protocols? Also, is it that some images, as a whole, are brighter than others, or are there regional changes throughout a slide?\n\nSara McArdle\n\n… commercial kits available for quenching AF (autofluorescence) … Good quality sections with clean staining and well-scanned images is by far the most immportant part of image analysis.\n\nChris Starling\n\nConsider that perhaps intensity based gating (even with correction) is not going to get you there… probability based object classifier, or Deep Learning based phenotyping … can take into account more than just intensity (eg. textural features, patterning, puncta, polarisation), and in fact be more robust against changes field-to-field and image-to-image… be comfortable with an error rate (however small). Given the complexity of multiplexed tissue image analysis, there will be errors.\n\nDavid Mason\n\n… image analysis is not for perfectionist or you’ll never ended: just be rigorous with good controls.\n\nA colleague of Nicolas Goudin"
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    "text": "2025-12\n\n… if the function of two gene products completely overlaps then, throughout the course of evolution, one of the genes will likely accumulate mutations to the point of loss-of-function.\n\n\nM. tuberculosis genome retains redundant functions at multiple levels that allow the bacilli to adapt to extremely heterogeneous environments in the human host.\n\nPLoS Pathog. 2025. PMID: 41348814\n\nWhen working with an image in ImageJ, I almost always have at least one duplicate lingering around for when things inevitably go wrong.\n\nIntroduction to Bioimage Analysis\n\nR is widely used in statistical computing, data analysis, and bioinformatics. A key contributor to its success in bioinformatics and computational biology is the open-source project Bioconductor.\n\nbioRxiv. 2025. doi: https://doi.org/10.64898/2025.12.22.695980\n\nAlmost all interesting image analysis involves filtering in some way at some stage.\n\nIntroduction to Bioimage Analysis"
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    "text": "2026-01\n\nThe Greenland shark is the longest-living vertebrate on Earth, with an estimated lifespan of up to 400 years.\n\nNat Commun. 2026. PMID: 41491153\n\nI think that’s where QuPath has the most value: not trying to do everything for everyone, but trying to do some things well … and expand its horizons over time.\n\nPete Bankhead"
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    "text": "2026-03\n\narXiv, the granddaddy of preprints servers.\n\nBlueSky\n\nYou can publish a paper with wrong data. You can’t make a working drug with a wrong experiment.\n\nMing Tommy Tang"
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