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RapiClear 1.52

Human

1.Gulen MF et al. cGAS-STING drives ageing-related inflammation and neurodegeneration. Nature (2023). https://doi.org/10.1038/s41586-023-06373-1
2.Chung MH et al. Multimodal 3-D/2-D human islet and duct imaging in exocrine and endocrine lesion environment: associated pancreas tissue remodeling. Am J Physiol Endocrinol Metab (2022). https://doi.org/10.1152/ajpendo.00111.2022
3.Lynch B et al. A mechanistic view on the aging human skin through ex vivo layer-by-layer analysis of mechanics and microstructure of facial and mammary dermis. Sci Rep (2022). https://doi.org/10.1038/s41598-022-04767-1
4.Girardeau-Hubert S et al. Impact of microstructure on cell behavior and tissue mechanics in collagen and dermal decellularized extra-cellular matrices. Acta Biomater (2022). https://doi.org/10.1016/j.actbio.2022.02.035
5.Colom B et al. Mutant clones in normal epithelium outcompete and eliminate emerging tumours. Nature (2021). https://doi.org/10.1038/s41586-021-03965-7
6.Tien YW et al. Local islet remodelling associated with duct lesion-islet complex in adult human pancreas. Diabetologia (2021). https://doi.org/10.1007/s00125-021-05504-5
7.Louis F. et al. High-throughput drug screening models of mature adipose tissues which replicate the physiology of patients’ Body Mass Index (BMI). Bioact Mater (2021). https://doi.org/10.1016/j.bioactmat.2021.05.020
8.Ayala-Nunez NV et al. Zika virus enhances monocyte adhesion and transmigration favoring viral dissemination to neural cells. Nat Commun (2019). https://doi.org/10.1038/s41467-019-12408-x
9.Chien HJ et al. Human pancreatic afferent and efferent nerves: mapping and 3-D illustration of exocrine, endocrine, and adipose innervation. Am J Physiol Gastrointest Liver Physiol (2019). https://doi.org/10.1152/ajpgi.00116.2019
10.Shen CN et al. Lymphatic vessel remodeling and invasion in pancreatic cancer progression. EBioMedicine (2019). http://dx.doi.org/10.1016/j.ebiom.2019.08.044
11.Tan Y et al. 3-Dimensional Optical Clearing and Imaging of Pruritic Atopic Dermatitis and Psoriasis Skin Reveals Downregulation of Epidermal Innervation. J Invest Dermatol. (2018). http://dx.doi.org/10.1016/j.jid.2018.11.006
12.Tang SC et al. Human pancreatic neuro-insular network in health and fatty infiltration. Diabetologia. (2017). http://dx.doi.org/10.1007/s00125-017-4409-x

Organoids

1.Pikkupeura LM et al. Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation. Sci Adv (2023). https://doi.org/10.1126/sciadv.adf9460

2.Cossec JC et al. Transient suppression of SUMOylation in embryonic stem cells generates embryo-like structures. Cell Rep (2023). https://doi.org/10.1016/j.celrep.2023.112380

3.Kang SY et al. A Pillar and Perfusion Plate Platform for Robust Human Organoid Culture and Analysis. Adv Healthc Mater (2023). https://doi.org/10.1002/adhm.202302502

4.Beghin A et al. Automated high-speed 3D imaging of organoid cultures with multi-scale phenotypic quantification. Nat Methods (2022). https://doi.org/10.1038/s41592-022-01508-0

5.Ohira S et al. Efficient and simple genetic engineering of enteroids using mouse isolated crypts for investigating intestinal functions. Biochem Biophys Res Commun (2022). https://doi.org/10.1016/j.bbrc.2022.11.008

6.Sugimoto S et al. An organoid-based organ-repurposing approach to treat short bowel syndrome. Nature (2021). https://doi.org/10.1038/s41586-021-03247-2

7.Youk J et al. Three-Dimensional Human Alveolar Stem Cell Culture Models Reveal Infection Response to SARS-CoV-2. Cell Stem Cell (2021). https://doi.org/10.1016/j.stem.2020.10.004

Chip

1.Phouphetlinthong O et al. Protruding cantilever microelectrode array to monitor the inner electrical activity of cerebral organoids. Lab Chip (2023). https://doi.org/10.1039/d3lc00294b

2.Yamamoto K et al. Development of a human neuromuscular tissue-on-a-chip model on a 24-well-plate-format compartmentalized microfluidic device. Lab Chip (2021). https://doi.org/10.1039/d1lc00048a

Microscopy

1.Paul TC et al. Super-Resolution Imaging of Neuronal Structures with Structured Illumination Microscopy. Bioengineering (2023). https://doi.org/10.3390/bioengineering10091081

2.Johnson KA et al. Flexible Multiplane Structured Illumination Microscope with a Four-Camera Detector. Photonics (2022). https://doi.org/10.3390/photonics9070501

3.Borah BJ et al. Nyquist-exceeding high voxel rate acquisition in mesoscopic multiphoton microscopy for full-field submicron resolution resolvability. iScience (2021). https://doi.org/10.1016/j.isci.2021.103041

Tissue Engineering

1.Loffet EA et al. Elastic fibers define embryonic tissue stiffness to enable buckling morphogenesis of the small intestine. Biomaterials (2023). https://doi.org/10.1016/j.biomaterials.2023.122405

2.Zeinstra N et al. Stacking thick perfusable human microvascular grafts enables dense vascularity and rapid integration into infarcted rat hearts. Biomaterials (2023). https://doi.org/10.1016/j.biomaterials.2023.122250

3.Ching T et al. Biomimetic Vasculatures by 3D-Printed Porous Molds. Small (2022). https://doi.org/10.1002/smll.202203426

4.Kang DH et al. Engineered whole cut meat-like tissue by the assembly of cell fibers using tendon-gel integrated bioprinting. Nat Commun. (2021). https://doi.org/10.1038/s41467-021-25236-9

Mouse

1.Wong HY et al. Epidermal mutation accumulation in photodamaged skin is associated with skin cancer burden and can be targeted through ablative therapy. Adv Sci (2023). https://doi.org/10.1126/sciadv.adf2384

2.Hu CM et al. Oncogenic KRAS, Mucin 4, and Activin A-Mediated Fibroblast Activation Cooperate for Panin Initiation. Adv Sci (2023). https://doi.org/10.1002/advs.202301240

3.Mazzitelli JA et al. Skull bone marrow channels as immune gateways to the central nervous system. Nat Neurosci (2023). https://doi.org/10.1038/s41593-023-01487-1

4.Bordeu I et al. Inflationary theory of branching morphogenesis in the mouse salivary gland. Nat Commun (2023). https://doi.org/10.1038/s41467-023-39124-x

5.Cai X et al. Tenascin C+ papillary fibroblasts facilitate neuro-immune interaction in a mouse model of psoriasis. Nat Commun (2023). https://doi.org/10.1038/s41467-023-37798-x

6.Melgrati S et al. Atlas of the anatomical localization of atypical chemokine receptors in healthy mice. PLoS Biol (2023). https://doi.org/10.1371/journal.pbio.3002111

7.Worssam MD et al. Cellular mechanisms of oligoclonal vascular smooth muscle cell expansion in cardiovascular disease. Cardiovasc Res (2023). https://doi.org/10.1093/cvr/cvac138

8.Chatzeli L et al. A cellular hierarchy of Notch and Kras signaling controls cell fate specification in the developing mouse salivary gland. Dev Cell (2023). https://doi.org/10.1016/j.devcel.2022.12.009

9.Bayerl F et al. Guidelines for visualization and analysis of DC in tissues using multiparameter fluorescence microscopy imaging methods. Eur J Immunol (2023). https://doi.org/10.1002/eji.202249923

10.Itai N et al. Lymphangiogenesis and Lymphatic Zippering in Skin Associated with the Progression of Lymphedema. J Invest Dermatol (2023). https://doi.org/10.1016/j.jid.2023.08.014

11.Schmidt AJ et al. Skin Whole-Mount Immunofluorescent Staining Protocol, 3D Visualization, and Spatial Image Analysis. Curr Protoc (2023). https://doi.org/10.1002/cpz1.820

12.Schönherr-Hellec S et al. Implantation of engineered human microvasculature to study human infectious diseases in mouse models. iScience (2023). https://doi.org/10.1016/j.isci.2023.106286

13.Timin G et al. High-resolution confocal and light-sheet imaging of collagen 3D network architecture in very large samples. iScience (2023). https://doi.org/10.1016/j.isci.2023.106452

14.Caruso JA et al. Loss of PPARγ activity characterizes early protumorigenic stromal reprogramming and dictates the therapeutic window of opportunity. Proc Natl Acad Sci U S A (2023). https://doi.org/10.1073/pnas.2303774120

15.Nakamura S et al. Decreased Paneth cell α-defensins promote fibrosis in a choline-deficient L-amino acid-defined high-fat diet-induced mouse model of nonalcoholic steatohepatitis via disrupting intestinal microbiota. Sci Rep (2023). https://doi.org/10.1038/s41598-023-30997-y

16.Schnabellehner S et al. Penile cavernous sinusoids are Prox1-positive hybrid vessels. Vasc Biol (2023). https://doi.org/10.1530/VB-23-0014

17.Wang Y et al. The role of somatosensory innervation of adipose tissues. Nature (2022). https://doi.org/10.1038/s41586-022-05137-7

18.Mazzitelli JA et al. Cerebrospinal fluid regulates skull bone marrow niches via direct access through dural channels. Nat Neurosci (2022). https://doi.org/10.1038/s41593-022-01029-1

19.Sparano C et al. Embryonic and neonatal waves generate distinct populations of hepatic ILC1s. Sci Immunol (2022). https://doi.org/10.1126/sciimmunol.abo6641

20.Schloss MJ et al. B lymphocyte-derived acetylcholine limits steady-state and emergency hematopoiesis. Nat Immunol (2022). https://doi.org/10.1038/s41590-022-01165-7

21.Aouad P et al. Epithelial-mesenchymal plasticity determines estrogen receptor positive breast cancer dormancy and epithelial reconversion drives recurrence. Nat Commun (2022). https://doi.org/10.1038/s41467-022-32523-6

22.Barz MJ et al. B and T cell acute lymphoblastic leukemia evade chemotherapy at distinct sites in the bone marrow. Haematologica (2022). https://doi.org/10.3324/haematol.2021.280451

23.Fujita S et al. Quantitative Analysis of Sympathetic and Nociceptive Innervation Across Bone Marrow Regions in Mice. Exp Hematol (2022). https://doi.org/10.1016/j.exphem.2022.07.297

24.Worssam MD et al. Cellular mechanisms of oligoclonal vascular smooth muscle cell expansion in cardiovascular disease. Cardiovasc Res (2022). https://doi.org/10.1093/cvr/cvac138

25.Johnson KA et al. Flexible Multiplane Structured Illumination Microscope with a Four-Camera Detector. Photonics (2022). https://doi.org/10.3390/photonics9070501

26.Gillot L et al. Periostin in lymph node pre-metastatic niches governs lymphatic endothelial cell functions and metastatic colonization. Cell Mol Life Sci (2022). https://doi.org/10.1007/s00018-022-04262-w

27.Li W et al. Tracking Strain-Specific Morphogenesis and Angiogenesis of Murine Calvaria with Large-Scale Optoacoustic and Ultrasound Microscopy. J Bone Miner Res (2022). https://doi.org/10.1002/jbmr.4533

28.Miyachi K et al. UVA causes dysfunction of ETBR and BMPR2 in vascular endothelial cells, resulting in structural abnormalities of the skin capillaries. J Dermatol Sci (2022). https://doi.org/10.1016/j.jdermsci.2022.01.007

29.Fatehullah A et al. A tumour-resident Lgr5+ stem-cell-like pool drives the establishment and progression of advanced gastric cancers. Nat Cell Biol (2021). https://doi.org/10.1038/s41556-021-00793-9

30.Choi J et al. Release of Notch activity coordinated by IL-1β signalling confers differentiation plasticity of airway progenitors via Fosl2 during alveolar regeneration. Nat Cell Biol (2021). https://doi.org/10.1038/s41556-021-00742-6

31.Farrar EJ et al. OCT4-mediated inflammation induces cell reprogramming at the origin of cardiac valve development and calcification. Sci. Adv. (2021). https://doi.org/10.1126/sciadv.abf7910

32.Yip RKH et al. Mammary tumour cells remodel the bone marrow vascular microenvironment to support metastasis. Nat Commun. (2021). https://doi.org/10.1038/s41467-021-26556-6

33.Isringhausen S et al. Chronic viral infections persistently alter marrow stroma and impair hematopoietic stem cell fitness. J Exp Med (2021). https://doi.org/10.1084/jem.20192070

34.Succony L et al. Lrig1 expression identifies airway basal cells with high proliferative capacity and restricts lung squamous cell carcinoma growth. Eur Respir J (2021). https://doi.org/10.1183/13993003.00816-2020

35.Yum MK et al. Tracing oncogene-driven remodelling of the intestinal stem cell niche. Nature (2021). https://doi.org/10.1038/s41586-021-03605-0

36.McGinn J et al. A biomechanical switch regulates the transition towards homeostasis in oesophageal epithelium. Nat Cell Biol (2021). https://doi.org/10.1038/s41556-021-00679-w

37.Chen Q et al. Resident macrophages restrain pathological adipose tissue remodeling and protect vascular integrity in obese mice. EMBO Rep (2021). https://doi.org/10.15252/embr.202152835

38.Chen CC et al. Heterogeneity and neurovascular integration of intraportally transplanted islets revealed by 3-D mouse liver histology. Am J Physiol Endocrinol Metab (2021). http://dx.doi.org/10.1152/ajpendo.00605.2020

39.Tan SH et al. A constant pool of Lgr5 + intestinal stem cells is required for intestinal homeostasis. Cell Rep (2021). https://doi.org/10.1016/j.celrep.2020.108633

40.Hashimoto M et al. Autophagy is dispensable for the maintenance of hematopoietic stem cells in neonates. Blood Adv (2021). https://doi.org/10.1182/bloodadvances.2020002410

41.Suzuki K et al. Decrease of α-defensin impairs intestinal metabolite homeostasis via dysbiosis in mouse chronic social defeat stress model. Sci Rep (2021). https://doi.org/10.1038/s41598-021-89308-y

42.Thorsen AS et al. Heterogeneity in clone dynamics within and adjacent to intestinal tumours identified by Dre-mediated lineage tracing. Dis Model Mech (2021). https://doi.org/10.1242/dmm.046706

43.Uryga AK et al. Telomere damage promotes vascular smooth muscle cell senescence and immune cell recruitment after vessel injury. Commun Biol (2021). https://doi.org/10.1038/s42003-021-02123-z

44.Wong HY et al. Whole-mount staining coupled to a UV-inducible basal cell carcinoma murine model. STAR Protoc (2021). https://doi.org/10.1016/j.xpro.2021.100329

45.Yeo KP et al. Efficient aortic lymphatic drainage is necessary for atherosclerosis regression induced by ezetimibe. Sci Adv. (2020). https://doi.org/10.1126/sciadv.abc2697

46.Thorsen ASK et al. Heterogeneity in clone dynamics within and adjacent to intestinal tumours identified by Dre-mediated lineage tracing. Dis Model Mech. (2020). https://doi.org/10.1242/dmm.046706

47.Wong HY et al. Identification of CD137-Expressing B Cells in Multiple Sclerosis Which Secrete IL-6 Upon Engagement by CD137 Ligand. Front Immunol. (2020). https://doi.org/10.3389/fimmu.2020.571964

48.Mei YY et al. NMDA receptors sustain but do not initiate neuronal depolarization in spreading depolarization. Neurobiol Dis. (2020). https://doi.org/10.1016/j.nbd.2020.105071

49.Roy E et al. Regional Variation in Epidermal Susceptibility to UV-Induced Carcinogenesis Reflects Proliferative Activity of Epidermal Progenitors. Cell Rep. (2020). https://doi.org/10.1016/j.celrep.2020.107702

50.Sznurkowska MK et al. Tracing the cellular basis of islet specification in mouse pancreas. Nat Commun. (2020). https://doi.org/10.1038/s41467-020-18837-3

51.Koho SV et al. Two-photon image-scanning microscopy with SPAD array and blind image reconstruction. Biomed Opt Express (2020). https://doi.org/10.1364/BOE.374398

52.Deguchi T et al. Volumetric Lissajous confocal microscopy with tunable spatiotemporal resolution. Biomed Opt Express (2020). https://doi.org/10.1364/BOE.400777

53.Tan SH et al. AQP5 enriches for stem cells and cancer origins in the distal stomach. Nature (2020). https://doi.org/10.1038/s41586-020-1973-x

54.Zhang H et al. Nanosheet wrapping-assisted coverslip-free imaging for looking deeper into a tissue at high resolution. PLoS One (2020). https://doi.org/10.1371/journal.pone.0227650

55.Baccin C et al. Combined single-cell and spatial transcriptomics reveal the molecular, cellular and spatial bone marrow niche organization. Nat Cell Biol (2019). https://doi.org/10.1038/s41556-019-0439-6

56.Helbling PM et al. Global Transcriptomic Profiling of the Bone Marrow Stromal Microenvironment during Postnatal Development, Aging, and Inflammation. Cell Rep (2019). https://doi.org/10.1016/j.celrep.2019.11.004

57.Seishima R et al. Neonatal Wnt-dependent Lgr5 positive stem cells are essential for uterine gland development. Nat Commun (2019). https://doi.org/10.1038/s41467-019-13363-3

58.Han S et al. Defining the Identity and Dynamics of Adult Gastric Isthmus Stem Cells. Cell Stem Cell (2019). https://doi.org/10.1016/j.stem.2019.07.008

59.Agarwal P et al. Mesenchymal Niche-Specific Expression of Cxcl12 Controls Quiescence of Treatment-Resistant Leukemia Stem Cells. Cell Stem Cell (2019). https://doi.org/10.1016/j.stem.2019.02.018

60.Lopez-Millan B et al. NG2 antigen is a therapeutic target for MLL-rearranged B-cell acute lymphoblastic leukemia. Leukemia (2019). http://dx.doi.org/10.1038/s41375-018-0353-0

61.Gomariz A et al. Quantitative spatial analysis of haematopoiesis-regulating stromal cells in the bone marrow microenvironment by 3D microscopy. Nat Commun (2018). http://doi.org/10.1038/s41467-018-04770-z

62.Dobnikar L et al. Disease-relevant transcriptional signatures identified in individual smooth muscle cells from healthy mouse vessels. Nat Commun (2018). https://doi.org/10.1038/s41467-018-06891-x

63.Lenos KJ et al. Stem cell functionality is microenvironmentally defined during tumour expansion and therapy response in colon cancer. Nat Cell Biol (2018). https://doi.org/10.1038/s41556-018-0179-z

64.Sznurkowska MK et al. Defining Lineage Potential and Fate Behavior of Precursors during Pancreas Development. Dev Cell (2018). https://doi.org/10.1016/j.devcel.2018.06.028

65.Matsumoto A et al. Attenuated Activation of Homeostatic Glucocorticoid in Keratinocytes Induces Alloknesis via Aberrant Artemin Production. J Invest Dermatol (2018). https://doi.org/10.1016/j.jid.2018.02.010

66.Rulands S et al. Universality of clone dynamics during tissue development. Nature Physics (2018). http://dx.doi.org/10.1038/s41567-018-0055-6

67.Tang SC et al. Pancreatic neuro-insular network in young mice revealed by 3D panoramic histology. Diabetologia (2017). http://dx.doi.org/10.1007/s00125-017-4408-y 

68.Leushacke M et al. Lgr5-expressing chief cells drive epithelial regeneration and cancer in the oxyntic stomach. Nat Cell Biol (2017). http://dx.doi.org/10.1038/ncb3541

69.Chappell J et al. Extensive Proliferation of a Subset of Differentiated, Yet Plastic, Medial Vascular Smooth Muscle Cells Contribute to Neointimal Formation in Mouse Injury and Atherosclerosis Models. Circ Res (2016). http://dx.doi.org/10.1161/CIRCRESAHA.116.309799

70.Chien HJ et al. 3-D imaging of islets in obesity: formation of the islet-duct complex and neurovascular remodeling in young hyperphagic mice. Int J Obes (2016). http://dx.doi.org/10.1038/ijo.2015.224

71.Lin PY et al. PanIN-associated pericyte, glial, and islet remodeling in mice revealed by 3-D pancreatic duct lesion histology. Am J Physiol Gastrointest Liver Physiol (2016). http://dx.doi.org/10.1152/ajpgi.00071.2016

72.Patel J et al. Self-Renewal and High Proliferative Colony Forming Capacity of Late-Outgrowth Endothelial Progenitors is Regulated by Cyclin-Dependent Kinase Inhibitors Driven by Notch Signaling. Stem Cells (2016). http://dx.doi.org/10.1002/stem.2262

Zebrafish

1.Davis SPX et al. Convolutional neural networks for reconstruction of undersampled optical projection tomography data applied to in vivo imaging of zebrafish. J Biophotonics (2019). https://doi.org/10.1002/jbio.201900128

Chicken

1.Yoshihi K et al. Live imaging of avian epiblast and anterior mesendoderm grafting reveals the complexity of cell dynamics during early brain development. Development (2022). https://doi.org/10.1242/dev.199999

2.Iida H et al. Sox2 Gene Regulation via the D1 Enhancer in Embryonic Neural Tube and Neural Crest by the Combined Action of SOX2 and ZIC2. Genes Cells (2020). https://doi.org/10.1111/gtc.12753