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Article
| Open AccessLipofuscin-like autofluorescence within microglia and its impact on studying microglial engulfment
Microglia are brain macrophages that engulf and clear cellular material and protein aggregates. Here, the authors show that lipofuscin-like autofluorescence can confound microglial engulfment analyses, which they can resolve with a photobleaching protocol.
- Jacob M. Stillman
- , Francisco Mendes Lopes
- & Dorothy P. Schafer
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Article
| Open AccessNear-infrared-II photoacoustic imaging and photo-triggered synergistic treatment of thrombosis via fibrin-specific homopolymer nanoparticles
The near-infrared-II (NIR-II) window has shown great promise for in vivo imaging and therapy. Here, the authors integrate a homopolymer and thermo-sensitive nitric oxide prodrug into nanoparticles for long-wavelength NIR-II photoacoustic imaging and synergistic treatment in preclinical thrombosis models.
- Jianwen Song
- , Xiaoying Kang
- & Ji Qi
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Article
| Open AccessLactate biosensors for spectrally and spatially multiplexed fluorescence imaging
l-Lactate is increasingly recognized as a key metabolite and signalling molecule in mammals, but the methods to investigate it in vivo have been limited. Here, authors report a pair of improved biosensors—one green and one red—for visualizing l-lactate both inside and outside of cells.
- Yusuke Nasu
- , Abhi Aggarwal
- & Robert E. Campbell
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Article
| Open AccessVisualization of accessible cholesterol using a GRAM domain-based biosensor
Regulated cholesterol transport is essential for the maintenance of cellular cholesterol distribution and homeostasis, but tools to monitor this process are limited. Here, the authors develop a genetically encoded cholesterol biosensor and demonstrate its use for visualising cellular cholesterol distribution in various live cells in real time.
- Dylan Hong Zheng Koh
- , Tomoki Naito
- & Yasunori Saheki
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Article
| Open AccessSingle virus fingerprinting by widefield interferometric defocus-enhanced mid-infrared photothermal microscopy
The study of viruses relies on the detection of viral proteins or viral nucleic acids. Here, the authors present a widefield interferometric defocus-enhanced mid-infrared photothermal (WIDE-MIP) microscope for high-throughput fingerprinting of single viruses.
- Qing Xia
- , Zhongyue Guo
- & Ji-Xin Cheng
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Article
| Open AccessSonogenetic control of multiplexed genome regulation and base editing
Exogenous control of genes in vivo is important. Here the authors report a system that can be inducibly activated through thermal energy produced by ultrasound absorption and use this to control induction of gene activation and base editing: they apply this in cell lines and in a mouse model.
- Pei Liu
- , Josquin Foiret
- & Lei S. Qi
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Article
| Open AccessWidefield imaging of rapid pan-cortical voltage dynamics with an indicator evolved for one-photon microscopy
Genetically encoded voltage indicators need fast and large signals to allow widefield imaging of rapid neuronal activity. Here, the authors develop the indicator JEDI-1P and demonstrate pan-cortical voltage imaging and gamma-frequency tracking in awake mice in single trials.
- Xiaoyu Lu
- , Yunmiao Wang
- & François St-Pierre
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Article
| Open AccessLarge-scale recording of neuronal activity in freely-moving mice at cellular resolution
Single-cell resolution recording from behaving mice requires either head fixation or attachment of a miniaturized device which may alter behavior. Here, the authors present a new recording method without mechanical restrictions on mouse movement.
- Aniruddha Das
- , Sarah Holden
- & Hod Dana
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Article
| Open AccessBone disease imaging through the near-infrared-II window
Skeletal disorders are commonly diagnosed by X-ray imaging, but the radiation limits its use. Here, the authors show that intravital NIR-II bone imaging is effective in diagnosis of a series of common bone diseases non-invasively in mice.
- Chao Mi
- , Xun Zhang
- & Dayong Jin
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Article
| Open AccessFluorescent sensors for imaging of interstitial calcium
The study of interstitial calcium remains challenging due to scarce methodology. Here, authors present ultra-low affinity genetically encoded fluorescent biosensors for monitoring calcium in intercellular spaces in living tissues.
- Ariel A. Valiente-Gabioud
- , Inés Garteizgogeascoa Suñer
- & Oliver Griesbeck
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Article
| Open AccessBiomolecular condensates modulate membrane lipid packing and hydration
Nano-environmental probes and advance imaging microscopy provide deep insight into protein phase separation and the interaction of condensates with membranes, revealing that wetting by condensates can modulate membrane lipid packing and hydration.
- Agustín Mangiarotti
- , Macarena Siri
- & Rumiana Dimova
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Article
| Open AccessDeep learning-enabled realistic virtual histology with ultraviolet photoacoustic remote sensing microscopy
Oncologic tumour resection is not fully accurate. Here the authors report a label-free virtual histological imaging method based on a non-contact, reflection-mode ultraviolet photoacoustic remote sensing and scattering microscope, combined with unsupervised deep learning using a cycle-consistent GAN.
- Matthew T. Martell
- , Nathaniel J. M. Haven
- & Roger J. Zemp
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Article
| Open AccessSeasonal pigment fluctuation in diploid and polyploid Arabidopsis revealed by machine learning-based phenotyping method PlantServation
Long-term monitoring of plants in field fluctuating environments remains challenging. Here, the authors develop PlantServation, a machine learning-based phenotyping method, and estimate environmental and genotypic effects on the pigment anthocyanin content of diploid and polyploid Arabidopsis.
- Reiko Akiyama
- , Takao Goto
- & Kentaro K. Shimizu
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Article
| Open AccessLocating causal hubs of memory consolidation in spontaneous brain network in male mice
How long-lasting memory is formed remains incompletely understood. Here, using fMRI and hub silencing, the authors discovered causal network hubs that are instrumental in consolidating memory and contributing to network reorganization.
- Zengmin Li
- , Dilsher Athwal
- & Kai-Hsiang Chuang
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Article
| Open AccessTranscranial focused ultrasound-mediated neurochemical and functional connectivity changes in deep cortical regions in humans
The neural mechanisms underlying transcranial ultrasound stimulation (TUS) in humans are not well understood. Here, the authors show that theta-burst stimulation reduces gamma-aminobutyric acid (GABA) levels in the posterior cingulate cortex, as well as increasing functional connectivity in the anterior and posterior cingulate cortex.
- Siti N. Yaakub
- , Tristan A. White
- & Elsa F. Fouragnan
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Article
| Open AccessA photo-triggered self-accelerated nanoplatform for multifunctional image-guided combination cancer immunotherapy
Aggregation-induced emission luminogens (AIEgens) have shown high-performance as photosensitizers. Here the authors combine an AIEgen with paclitaxel-based hypoxia-responsive prodrug into nanoparticles for multifunctional image-guided photodynamic and immunotherapy in preclinical cancer models.
- Xiaoying Kang
- , Yuan Zhang
- & Ben Zhong Tang
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Article
| Open AccessSimultaneous magnetic resonance imaging of pH, perfusion and renal filtration using hyperpolarized 13C-labelled Z-OMPD
pH alterations are a hallmark of many pathologies including cancer and kidney disease. Here the authors describe [1,5- 13 C2]Z-OMPD as a probe for hyperpolarized 13C-MRI with good pH sensitivity and hyperpolarization properties which combined with tailored MRI protocols allow sub-minute imaging of pH, renal perfusion and filtration simultaneously.
- Martin Grashei
- , Pascal Wodtke
- & Franz Schilling
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Article
| Open AccessEngineered NIR-II fluorophores with ultralong-distance molecular packing for high-contrast deep lesion identification
To achieve high-contrast in fluorescence imaging of deep tissues is challenging. Here, the authors develop NIR-II fluorescent small molecules with high brightness and emission extending to 1900 nm, enabling in vivo imaging of deep tissues with enhanced signal-to-background ratios.
- Zhe Feng
- , Yuanyuan Li
- & Jun Qian
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Article
| Open AccessTIGIT can inhibit T cell activation via ligation-induced nanoclusters, independent of CD226 co-stimulation
CD226 provides a co-stimulatory signal to the T cell receptor during activation, and TIGIT is believed to inhibit this process by competing for the CD226 ligand CD155. Here authors show that ligand binding induces dense nanocluster formation by TIGIT which initiates intrinsic, CD226 independent inhibitory signals, proximal to T cell receptor signalling.
- Jonathan D. Worboys
- , Katherine N. Vowell
- & Daniel M. Davis
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Matters Arising
| Open AccessReply to: Fluid signal suppression characteristics of 3D-FLAIR with a T2 selective inversion pulse in the skull base
- Mehmet Sait Albayram
- , Garrett Smith
- & Onder Albayram
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Article
| Open AccessFluorescent protein lifetimes report densities and phases of nuclear condensates during embryonic stem-cell differentiation
Fluorescent proteins can report on many cellular variables. Here, authors develop a method for reporting high local densities, and use it to show that density distribution of heterochromatin in mouse embryonic stem cells are not in a liquid phase.
- Khalil Joron
- , Juliane Oliveira Viegas
- & Eitan Lerner
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Article
| Open AccessA mosaic adeno-associated virus vector as a versatile tool that exhibits high levels of transgene expression and neuron specificity in primate brain
Viral vectors with intense and long-lasting transgene expression are essential for manipulating and imaging of neuronal activity in the primate brain. Here, the authors created a mosaic vector composed of capsid proteins derived from AAV1 and AAV2 that exhibits improved transgene expression and neuronal specificity.
- Kei Kimura
- , Yuji Nagai
- & Masahiko Takada
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Article
| Open AccessNon-invasive electromechanical assessment during atrial fibrillation identifies underlying atrial myopathy alterations with early prognostic value
Electromechanical characterization during atrial fibrillation (AF) remains a significant gap in the understanding of AF-related atrial myopathy. Here, the authors use non-invasive atrial electromechanical assessment during AF to identify early remodeling changes associated with underlying myopathy, which in the clinic decrease the probability of acute and mid-term successful rhythm control.
- Daniel Enríquez-Vázquez
- , Jorge G. Quintanilla
- & David Filgueiras-Rama
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Article
| Open AccessRobust phenotyping of highly multiplexed tissue imaging data using pixel-level clustering
Multiplexed imaging studies are typically focused on cell-level phenotypes. Here, the authors propose Pixie, a cross-platform and open-source pipeline that achieves robust and quantitative annotation of both pixel-level and cell-level features in multiplexed imaging data.
- Candace C. Liu
- , Noah F. Greenwald
- & Michael Angelo
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Article
| Open AccessSelf-assembly of CIP4 drives actin-mediated asymmetric pit-closing in clathrin-mediated endocytosis
CIP4 drives an asymmetric closing process in clathrin-mediated endocytosis by LLPS-driven self assembly and stereospecific interaction with the curved membrane and actin-regulating proteins which generates an actin-rich microenvironment near the pit.
- Yiming Yu
- & Shige H. Yoshimura
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Article
| Open AccessHighly specific and non-invasive imaging of Piezo1-dependent activity across scales using GenEPi
Stretch-activated ion channel Piezo1 contribures to mechanotransduction in many tissues, but its output is mostly measured indirectly. Here, the authors introduce GenEPi, a fluorescent reporter for directly visualizing Piezo1 activation-dependent calcium influx.
- Sine Yaganoglu
- , Konstantinos Kalyviotis
- & Periklis Pantazis
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Article
| Open AccessBiodegradable polyphosphoester micelles act as both background-free 31P magnetic resonance imaging agents and drug nanocarriers
MRI agents can result in environmental pollution and organ accumulation. Here, the authors show that modifying the molecular structure of biodegradable polyphosphoesters and tailoring the polymers’ microstructure to adjust MRI relaxation times can overcome challenges in 31P MR imaging.
- Olga Koshkina
- , Timo Rheinberger
- & Frederik R. Wurm
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Article
| Open AccessDual-color DNA-PAINT single-particle tracking enables extended studies of membrane protein interactions
Single-particle tracking (SPT) has revolutionised studies of protein interactions but is often limited by photobleaching. Here, the authors evolve DNA-PAINT-SPT to enable simultaneous dual-colour detection for the quantification of protein dimerization and live cell membrane protein tracking.
- Christian Niederauer
- , Chikim Nguyen
- & Kristina A. Ganzinger
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Article
| Open AccessSpatial and functional arrangement of Ebola virus polymerase inside phase-separated viral factories
Here, the authors characterized the phase separation properties and internal structures of intracellular viral factories induced by Ebola virus and correlated these properties to important steps of viral biogenesis.
- Jingru Fang
- , Guillaume Castillon
- & Erica Ollmann Saphire
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Article
| Open AccessThree-dimensional images reveal the impact of the endosymbiont Midichloria mitochondrii on the host mitochondria
The mitochondrial symbiont, Candidatus Midichloria mitochondrii, exists in the hard tick Ixodus ricinus, the main vector for Lyme disease. Here, the authors use FIB-SEM to characterise mitochondrial morphology and bacterial interactions in the context of oocyte maturation and endosymbiosis.
- Zerrin Uzum
- , Dmitry Ershov
- & Fabrizia Stavru
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Article
| Open AccessLarge depth-of-field ultra-compact microscope by progressive optimization and deep learning
Traditional optical microscope, while bulky, often fails to deliver optimal performance. Here, the authors have engineered an integrated microscope of 0.15 cm3 in volume and a weight of 0.5 g, which outperforms a commercial microscope and can be seamlessly integrated with a smartphone.
- Yuanlong Zhang
- , Xiaofei Song
- & Qionghai Dai
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Article
| Open AccessExpanded vacuum-stable gels for multiplexed high-resolution spatial histopathology
Emerging high-plex imaging technologies are limited in resolving subcellular biomolecular features. Here, the authors propose a spatial histopathology tool that allows for high-plex protein staining and physical expansion, while retaining the lateral tissue expansion.
- Yunhao Bai
- , Bokai Zhu
- & Sizun Jiang
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Article
| Open AccessCucurbit[8]uril-based water-dispersible assemblies with enhanced optoacoustic performance for multispectral optoacoustic imaging
The applications of organic small-molecule contrast agents for multispectral optoacoustic imaging have been restrained by several challenges including relatively low extinction coefficient, poor water solubility and weak optoacoustic performance. Here, the authors address these limitations by constructing water-dispersible supramolecular optoacoustic assemblies based on cucurbit[8]uril.
- Yinglong Wu
- , Lihe Sun
- & Yanli Zhao
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Article
| Open AccessFast-exchanging spirocyclic rhodamine probes for aptamer-based super-resolution RNA imaging
Live-cell RNA imaging with high spatial and temporal resolution remains a major challenge. Here the authors design spirocyclic rhodamine probes that enable a fluorescent light-up aptamer system suitable for visualizing RNAs in live or fixed cells with two different super-resolution microscopy modalities SMLM and STED.
- Daniel Englert
- , Eva-Maria Burger
- & Murat Sunbul
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Article
| Open AccessAcute stress induces long-term metabolic, functional, and structural remodeling of the heart
Takotsubo disease, a stress induced cardiomyopathy mimicking acute coronary syndrome, increases the risk of heart failure and cardiac death. The authors show here that heart function and structure keep on deteriorating continuously after a single acute stress, this snowball effect being triggered by abnormalities incardiac metabolism.
- Thulaciga Yoganathan
- , Mailyn Perez-Liva
- & Bertrand Tavitian
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Article
| Open AccessDeep optoacoustic localization microangiography of ischemic stroke in mice
Optoacoustic super-resolution at millimeter-scale depths has been impeded by the strong background absorption from blood cells. Here, the authors use dichloromethane microdroplets with high optical absorption and demonstrate 3D microangiography of the mouse brain via optoacoustic localization.
- Xosé Luís Deán-Ben
- , Justine Robin
- & Daniel Razansky
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Article
| Open AccessRatiometric measurement of MAM Ca2+ dynamics using a modified CalfluxVTN
MAM Ca2+ dynamics play an important role in diverse biological processes, but directly and specifically measuring Ca2+ concentrations in this region is technically challenging. Here the authors report a MAM-specific BRET-based Ca2+ indicator called MAM-Calflux, which works as both a Ca2+ indicator and a structural marker due to its ratiometric nature.
- Eunbyul Cho
- , Youngsik Woo
- & Sang Ki Park
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Article
| Open AccessN-Acryloylindole-alkyne (NAIA) enables imaging and profiling new ligandable cysteines and oxidized thiols by chemoproteomics
Cysteine is a popular target of covalent drugs and can undergo redox modifications. Here, the authors developed cysteine probes, N-acryloylindole-alkynes, for imaging and chemoproteomics to study cysteine oxidation and to identify targetable hotspots by small molecule compounds.
- Tin-Yan Koo
- , Hinyuk Lai
- & Clive Yik-Sham Chung
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Article
| Open AccessA highly sensitive strategy for monitoring real-time proliferation of targeted cell types in vivo
Currently, tracking cell proliferation in vivo is hard. Here the authors report a method where the time series of proliferation of targeted cell types can be monitored in vivo in the same individuals, with no need for animal sacrifice: they use this to assess β-cell and hepatocyte proliferation in mice.
- Hiroto Sugawara
- , Junta Imai
- & Hideki Katagiri
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Article
| Open AccessAnalysis and modeling of cancer drug responses using cell cycle phase-specific rate effects
Understanding the impact of anti-cancer therapies on cell cycle progression could contribute to the discovery of effective therapeutic treatments. Here, the authors use genetically engineered breast cancer cell lines and computational models to analyse drug effects on specific cell cycle phases and identify effective combination treatments.
- Sean M. Gross
- , Farnaz Mohammadi
- & Laura M. Heiser
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Article
| Open AccessIntracranial electrophysiological and structural basis of BOLD functional connectivity in human brain white matter
Whether connectivity in white matter detected by functional MRI relates to underlying electrophysiological synchronization is unclear. Here, the authors show that blood-oxygenation-level-dependent (BOLD) functional connectivity and intracranial stereotactic-electroencephalography (SEEG) connectivity are correlated across a wide range of frequency bands.
- Yali Huang
- , Peng-Hu Wei
- & Guoguang Zhao
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Article
| Open AccessTransparent tissue in solid state for solvent-free and antifade 3D imaging
Current liquid-based optical clearing protocols can suffer from solvent evaporation and photobleaching. Here, the authors develop a solid high-refractive-index polymer to embed mouse and human tissues for clearing and antifade high-resolution 3D imaging.
- Fu-Ting Hsiao
- , Hung-Jen Chien
- & Shiue-Cheng Tang
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Article
| Open AccessEvaluation of therapeutic PD-1 antibodies by an advanced single-molecule imaging system detecting human PD-1 microclusters
Immune checkpoint inhibitors are now routinely used in cancer therapy, however, the dosage and integration into conventional cancer therapy is determined via empirical experience rather than mechanistic rationale. Here authors establish an advanced single-molecule imaging method, by with which they are directly monitoring and evaluating the effect of immune checkpoint inhibitors on T cell signaling.
- Wataru Nishi
- , Ei Wakamatsu
- & Tadashi Yokosuka
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Article
| Open AccessHierarchical fluctuation shapes a dynamic flow linked to states of consciousness
The neuroanatomical basis of consciousness is not fully understood. Here the authors show that a global state of consciousness might not depend on a specific brain region or location in Euclidean space; rather, it is linked to a low-dimensional dynamic pattern in topological space, as shown through the analysis of different experimental paradigms, imaging techniques, and species.
- Ang Li
- , Haiyang Liu
- & Bing Liu
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Article
| Open AccessParallel interrogation of the chalcogenide-based micro-ring sensor array for photoacoustic tomography
The authors report a highly sensitive chalcogenide-based micro-ring sensor array for photoacoustic tomography and develops a compatible parallel interrogation means by synthesizing a digital optical frequency comb. Imaging is demonstrated on fast-moving objects, leaf veins, and live zebrafish.
- Jingshun Pan
- , Qiang Li
- & Zhaohui Li
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Article
| Open AccessQuantitative structured illumination microscopy via a physical model-based background filtering algorithm reveals actin dynamics
Quantitative live-cell superresolution imaging that maintains the linearity of fluorescence signals remains difficult. Here, the authors propose a physical model-based background filtering method for 2D-SIM, which allows for quantitative imaging and high signal completeness.
- Yanquan Mo
- , Kunhao Wang
- & Liangyi Chen
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Article
| Open AccessWound infiltrating adipocytes are not myofibroblasts
Adipocyte plasticity during injury repair is debated. Here, the authors find that injury causes temporary adipocyte migration, but without lineage conversion to myofibroblasts. Distinct migration patterns, transcriptomics and ECM depositions indicate that adipocytes, unlike fibroblasts, do not contribute to fibrotic scars.
- Shruthi Kalgudde Gopal
- , Ruoxuan Dai
- & Yuval Rinkevich
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Article
| Open AccessNear-lifespan longitudinal tracking of brain microvascular morphology, topology, and flow in male mice
Brain vascular impairment may occur early in diseases such as Alzheimer’s disease. Here the authors longitudinally study brain vascular dynamics in mice using advanced optical coherence tomography and deep learning algorithms, which enables tracking of slow vascular decline in aging and models of disease.
- Konrad W. Walek
- , Sabina Stefan
- & Jonghwan Lee
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Article
| Open AccessUsing mass spectrometry imaging to map fluxes quantitatively in the tumor ecosystem
Isotopologue spectral analysis was originally designed to assess metabolic fluxes from bulk samples. Here, the authors adapted this approach to infer fluxes from discrete regions in tissue by using mass spectrometry imaging, showing increased fatty acid synthesis flux in brain tumors of mice.
- Michaela Schwaiger-Haber
- , Ethan Stancliffe
- & Gary J. Patti
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