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A hypoxia-sensitive medullary nucleus modulates cerebral blood flow via a disynaptic pathway to cortex. bioRxiv. 2026 Feb 21. Chhabria K, Duckworth J, Yao P, Fassihi-Zakeri A, Kleinfeld D. PMID: 41757077; PMCID: PMC12934959.
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Microvascular architecture and physiological fluctuations constrain the control of cerebral microcirculation. Proc Natl Acad Sci U S A. 2026 Jan 20; 123(3):e2521872123. Ji X, Zhao Y, Bai L, Wang K, Kleinfeld D. PMID: 41538246; PMCID: PMC12818429.
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Glutamate indicators with increased sensitivity and tailored deactivation rates. Nat Methods. 2026 Feb; 23(2):417-425. Aggarwal A, Negrean A, Chen Y, Iyer R, Reep D, Liu A, Palutla A, Xie ME, MacLennan BJ, Hagihara KM, Kinsey LW, Sun JL, Yao P, Zheng J, Tsang A, Tsegaye G, Zhang Y, Patel RH, Arthur BJ, Hiblot J, Leippe P, Tarnawski M, Marvin JS, Vevea JD, Turaga SC, Tebo AG, Carandini M, Rossi LF, Kleinfeld D, Konnerth A, Svoboda K, Turner GC, Hasseman JP, Podgorski K. PMID: 41436654; PMCID: PMC12904790.
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Publisher Correction: A red fluorescent genetically encoded biosensor for in vivo imaging of extracellular l-lactate dynamics. Nat Commun. 2025 Dec 10; 16(1):11011. Kamijo Y, Mächler P, Ness N, Vu CQ, Kusakizako T, Mannuthodikayil J, Ku Z, Boisvert M, Grebenik E, Miyazaki I, Hashizume R, Sato H, Liu R, Hori Y, Tomita T, Katayama T, Furube A, Caraveo G, Paquet ME, Drobizhev M, Nureki O, Arai S, Brancaccio M, Campbell RE, Kleinfeld D, Nasu Y. PMID: 41372178; PMCID: PMC12695945.
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iGlucoSnFR2: A genetically encoded fluorescent sensor for measuring intracellular or extracellular glucose in vivo in mouse brain. Sci Adv. 2025 Nov 14; 11(46):eadz3889. Marvin JS, Mächler P, Meng C, Ates T, Patel RH, Adhikari R, Makurath MA, Ku Z, Feliciano D, Atasoy D, Cui G, Kleinfeld D, Brown TA. PMID: 41223288; PMCID: PMC12609159.
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A red fluorescent genetically encoded biosensor for in vivo imaging of extracellular L-lactate dynamics. Nat Commun. 2025 Oct 29; 16(1):9531. Kamijo Y, Mächler P, Ness N, Vu CQ, Kusakizako T, Mannuthodikayil J, Ku Z, Boisvert M, Grebenik E, Miyazaki I, Hashizume R, Sato H, Liu R, Hori Y, Tomita T, Katayama T, Furube A, Caraveo G, Paquet ME, Drobizhev M, Nureki O, Arai S, Brancaccio M, Campbell RE, Kleinfeld D, Nasu Y. PMID: 41162396; PMCID: PMC12572234.
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Defects, Parcellation, and Renormalized Negative Diffusivities in Nonhomogeneous Oscillatory Media. Phys Rev Lett. 2025 Oct 17; 135(16):168401. Sellier-Prono M, Cencini M, Kleinfeld D, Vergassola M. PMID: 41172177.
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Spatiotemporal focusing enables all-optical in situ histology of heterogeneous tissue. Nat Methods. 2025 Oct; 22(10):2205-2210. Ji X, Huang S, Friedman B, Kleinfeld D. PMID: 41044257.
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Spatiotemporal development of expanding bacterial colonies driven by emergent mechanical constraints and nutrient gradients. Nat Commun. 2025 May 26; 16(1):4878. Kannan H, Sun H, Warren M, Çaglar T, Yao P, Taylor BR, Sahu K, Ge D, Mori M, Kleinfeld D, Dong J, Li B, Hwa T. PMID: 40419492; PMCID: PMC12106844.
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Glutamate indicators with increased sensitivity and tailored deactivation rates. bioRxiv. 2025 Mar 31. Aggarwal A, Negrean A, Chen Y, Iyer R, Reep D, Liu A, Palutla A, Xie ME, MacLennan BJ, Hagihara KM, Kinsey LW, Sun JL, Yao P, Zheng J, Tsang A, Tsegaye G, Zhang Y, Patel RH, Arthur BJ, Hiblot J, Leippe P, Tarnawski M, Marvin JS, Vevea JD, Turaga SC, Tebo AG, Carandini M, Federico Rossi L, Kleinfeld D, Konnerth A, Svoboda K, Turner GC, Hasseman J, Podgorski K. PMID: 40196590; PMCID: PMC11974752.
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A brainstem map of orofacial rhythms. bioRxiv. 2025 Jan 27. Kaku H, Liu LD, Gao R, West S, Liao SM, Finkelstein A, Kleinfeld D, Thomas A, Tipparaju SL, Svoboda K, Li N. PMID: 39975015; PMCID: PMC11838403.
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Nobel honors for John Hopfield, who ushered attractor dynamics into neuroscience. Neuron. 2024 Dec 04; 112(23):3819-3822. Kleinfeld D. PMID: 39637837.
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Neurovascular Impulse Response Function (IRF) during spontaneous activity differentially reflects intrinsic neuromodulation across cortical regions. bioRxiv. 2024 Sep 15. Rauscher BC, Fomin-Thunemann N, Kura S, Doran PR, Perez PD, Kiliç K, Martin EA, Balog D, Chai NX, Froio FA, Bloniasz PF, Herrema KE, Tang R, Knudstrup SG, Garcia A, Jiang JX, Gavornik JP, Kleinfeld D, Hasselmo ME, Lewis LD, Sakadzic S, Tian L, Mishne G, Stephen EP, Thunemann M, Boas DA, Devor A. PMID: 40093105; PMCID: PMC11908222.
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CellBoost: A pipeline for machine assisted annotation in neuroanatomy. AI Open. 2024; 5:142-154. Qian K, Friedman B, Takatoh J, Groisman A, Wang F, Kleinfeld D, Freund Y. PMID: 40756693; PMCID: PMC12317837.
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Long-wavelength traveling waves of vasomotion modulate the perfusion of cortex. Neuron. 2024 Jul 17; 112(14):2349-2367.e8. Broggini T, Duckworth J, Ji X, Liu R, Xia X, Mächler P, Shaked I, Munting LP, Iyengar S, Kotlikoff M, van Veluw SJ, Vergassola M, Mishne G, Kleinfeld D. PMID: 38781972; PMCID: PMC11257831.
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CellBoost: A pipeline for machine assisted annotation in Neuroanatomy. bioRxiv. 2024 Jan 21. Qian K, Friedman B, Takatoh J, Wang F, Kleinfeld D, Freund Y. PMID: 38293051; PMCID: PMC10827062.
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Elephant trunks: Strength and dexterity from mini-fascicles. Curr Biol. 2023 11 20; 33(22):R1203-R1205. Olson W, Zhang L, O'Connor DH, Kleinfeld D. PMID: 37989101; PMCID: PMC11039408.
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Vagal sensory neurons mediate the Bezold-Jarisch reflex and induce syncope. Nature. 2023 11; 623(7986):387-396. Lovelace JW, Ma J, Yadav S, Chhabria K, Shen H, Pang Z, Qi T, Sehgal R, Zhang Y, Bali T, Vaissiere T, Tan S, Liu Y, Rumbaugh G, Ye L, Kleinfeld D, Stringer C, Augustine V. PMID: 37914931; PMCID: PMC10632149.
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Construction and use of an adaptive optics two-photon microscope with direct wavefront sensing. Nat Protoc. 2023 12; 18(12):3732-3766. Yao P, Liu R, Broggini T, Thunemann M, Kleinfeld D. PMID: 37914781; PMCID: PMC11033548.
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Low- and high-level coordination of orofacial motor actions. Curr Opin Neurobiol. 2023 12; 83:102784. Kleinfeld D, Deschênes M, Economo MN, Elbaz M, Golomb D, Liao SM, O'Connor DH, Wang F. PMID: 37757586; PMCID: PMC11034851.
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A lone spike in blood glucose can enhance the thrombo-inflammatory response in cortical venules. J Cereb Blood Flow Metab. 2024 02; 44(2):252-271. Shaked I, Foo C, Mächler P, Liu R, Cui Y, Ji X, Broggini T, Kaminski T, Suryakant Jadhav S, Sundd P, Firer M, Devor A, Friedman B, Kleinfeld D. PMID: 37737093; PMCID: PMC10993879.
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A brainstem circuit for the expression of defensive facial reactions in rat. Curr Biol. 2023 09 25; 33(18):4030-4035.e3. Callado Pérez A, Demers M, Fassihi A, Moore JD, Kleinfeld D, Deschênes M. PMID: 37703878; PMCID: PMC11034846.
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Interchangeable Role of Motor Cortex and Reafference for the Stable Execution of an Orofacial Action. J Neurosci. 2023 07 26; 43(30):5521-5536. Elbaz MA, Demers M, Kleinfeld D, Ethier C, Deschênes M. PMID: 37400255; PMCID: PMC10376937.
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Glutamate indicators with improved activation kinetics and localization for imaging synaptic transmission. Nat Methods. 2023 06; 20(6):925-934. Aggarwal A, Liu R, Chen Y, Ralowicz AJ, Bergerson SJ, Tomaska F, Mohar B, Hanson TL, Hasseman JP, Reep D, Tsegaye G, Yao P, Ji X, Kloos M, Walpita D, Patel R, Mohr MA, Tillberg PW, GENIE Project Team, Looger LL, Marvin JS, Hoppa MB, Konnerth A, Kleinfeld D, Schreiter ER, Podgorski K. PMID: 37142767; PMCID: PMC10250197.
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A change in behavioral state switches the pattern of motor output that underlies rhythmic head and orofacial movements. Curr Biol. 2023 05 22; 33(10):1951-1966.e6. Liao SM, Kleinfeld D. PMID: 37105167; PMCID: PMC10225163.
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Guide to the construction and use of an adaptive optics two-photon microscope with direct wavefront sensing. bioRxiv. 2023 Jan 24. Yao P, Liu R, Broginni T, Thunemann M, Kleinfeld D. PMID: 36747816; PMCID: PMC9900836.
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Correction: Assessment of single-vessel cerebral blood velocity by phase contrast fMRI. PLoS Biol. 2022 Dec; 20(12):e3001951. Chen X, Jiang Y, Choi S, Pohmann R, Scheffler K, Kleinfeld D, Yu X. PMID: 36577117; PMCID: PMC9797223.
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Theory of hierarchically organized neuronal oscillator dynamics that mediate rodent rhythmic whisking. Neuron. 2022 11 16; 110(22):3833-3851.e22. Golomb D, Moore JD, Fassihi A, Takatoh J, Prevosto V, Wang F, Kleinfeld D. PMID: 36113472; PMCID: PMC10248719.
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The whisking oscillator circuit. Nature. 2022 09; 609(7927):560-568. Takatoh J, Prevosto V, Thompson PM, Lu J, Chung L, Harrahill A, Li S, Zhao S, He Z, Golomb D, Kleinfeld D, Wang F. PMID: 36045290; PMCID: PMC10038238.
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Probing Neuropeptide Volume Transmission In Vivo by Simultaneous Near-Infrared Light-Triggered Release and Optical Sensing. Angew Chem Int Ed Engl. 2022 08 22; 61(34):e202206122. Xiong H, Lacin E, Ouyang H, Naik A, Xu X, Xie C, Youn J, Wilson BA, Kumar K, Kern T, Aisenberg E, Kircher D, Li X, Zasadzinski JA, Mateo C, Kleinfeld D, Hrabetova S, Slesinger PA, Qin Z. PMID: 35723610; PMCID: PMC9388559.
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A vibrissa pathway that activates the limbic system. Elife. 2022 02 10; 11. Elbaz M, Callado Perez A, Demers M, Zhao S, Foo C, Kleinfeld D, Deschenes M. PMID: 35142608; PMCID: PMC8830883.
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The Global Configuration of Visual Stimuli Alters Co-Fluctuations of Cross-Hemispheric Human Brain Activity. J Neurosci. 2021 11 24; 41(47):9756-9766. Nasr S, Kleinfeld D, Polimeni JR. PMID: 34663628; PMCID: PMC8612647.
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Contribution of animal models toward understanding resting state functional connectivity. Neuroimage. 2021 12 15; 245:118630. Pais-Roldán P, Mateo C, Pan WJ, Acland B, Kleinfeld D, Snyder LH, Yu X, Keilholz S. PMID: 34644593; PMCID: PMC9031339.
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Reversibly Modulating the Blood-Brain Barrier by Laser Stimulation of Molecular-Targeted Nanoparticles. Nano Lett. 2021 11 24; 21(22):9805-9815. Li X, Vemireddy V, Cai Q, Xiong H, Kang P, Li X, Giannotta M, Hayenga HN, Pan E, Sirsi SR, Mateo C, Kleinfeld D, Greene C, Campbell M, Dejana E, Bachoo R, Qin Z. PMID: 34516144; PMCID: PMC8616836.
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Assessment of single-vessel cerebral blood velocity by phase contrast fMRI. PLoS Biol. 2021 09; 19(9):e3000923. Chen X, Jiang Y, Choi S, Pohmann R, Scheffler K, Kleinfeld D, Yu X. PMID: 34499636; PMCID: PMC8454982.
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Reinforcement learning links spontaneous cortical dopamine impulses to reward. Curr Biol. 2021 09 27; 31(18):4111-4119.e4. Foo C, Lozada A, Aljadeff J, Li Y, Wang JW, Slesinger PA, Kleinfeld D. PMID: 34302743; PMCID: PMC8605927.
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PIP2 as the "coin of the realm" for neurovascular coupling. Proc Natl Acad Sci U S A. 2021 05 25; 118(21). Earley S, Kleinfeld D. PMID: 33952688; PMCID: PMC8166173.
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Abortive intussusceptive angiogenesis causes multi-cavernous vascular malformations. Elife. 2021 05 20; 10. Li W, Tran V, Shaked I, Xue B, Moore T, Lightle R, Kleinfeld D, Awad IA, Ginsberg MH. PMID: 34013885; PMCID: PMC8175082.
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Constructing an adult orofacial premotor atlas in Allen mouse CCF. Elife. 2021 04 27; 10. Takatoh J, Park JH, Lu J, Li S, Thompson PM, Han BX, Zhao S, Kleinfeld D, Friedman B, Wang F. PMID: 33904410; PMCID: PMC8137149.
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Endothelial struts enable the generation of large lumenized blood vessels de novo. Nat Cell Biol. 2021 04; 23(4):322-329. Weijts B, Shaked I, Ginsberg M, Kleinfeld D, Robin C, Traver D. PMID: 33837285; PMCID: PMC8500358.
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Mathematical synthesis of the cortical circulation for the whole mouse brain-part II: Microcirculatory closure. Microcirculation. 2021 07; 28(5):e12687. Hartung G, Badr S, Mihelic S, Dunn A, Cheng X, Kura S, Boas DA, Kleinfeld D, Alaraj A, Linninger AA. PMID: 33615601; PMCID: PMC8504684.
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Specific populations of basal ganglia output neurons target distinct brain stem areas while collateralizing throughout the diencephalon. Neuron. 2021 05 19; 109(10):1721-1738.e4. McElvain LE, Chen Y, Moore JD, Brigidi GS, Bloodgood BL, Lim BK, Costa RM, Kleinfeld D. PMID: 33823137; PMCID: PMC8169061.
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Brain microvasculature has a common topology with local differences in geometry that match metabolic load. Neuron. 2021 04 07; 109(7):1168-1187.e13. Ji X, Ferreira T, Friedman B, Liu R, Liechty H, Bas E, Chandrashekar J, Kleinfeld D. PMID: 33657412; PMCID: PMC8525211.
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A Suite of Neurophotonic Tools to Underpin the Contribution of Internal Brain States in fMRI. Curr Opin Biomed Eng. 2021 Jun; 18. Mächler P, Broggini T, Mateo C, Thunemann M, Fomin-Thunemann N, Doran PR, Sencan I, Kilic K, Desjardins M, Uhlirova H, Yaseen MA, Boas DA, Linninger AA, Vergassola M, Yu X, Lewis LD, Polimeni JR, Rosen BR, Sakadžic S, Buxton RB, Lauritzen M, Kleinfeld D, Devor A. PMID: 33959688; PMCID: PMC8095678.
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Voxelized simulation of cerebral oxygen perfusion elucidates hypoxia in aged mouse cortex. PLoS Comput Biol. 2021 01; 17(1):e1008584. Hartung G, Badr S, Moeini M, Lesage F, Kleinfeld D, Alaraj A, Linninger A. PMID: 33507970; PMCID: PMC7842915.
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Ultra-slow Oscillations in fMRI and Resting-State Connectivity: Neuronal and Vascular Contributions and Technical Confounds. Neuron. 2020 09 09; 107(5):782-804. Drew PJ, Mateo C, Turner KL, Yu X, Kleinfeld D. PMID: 32791040; PMCID: PMC7886622.
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Cerebrospinal fluid influx drives acute ischemic tissue swelling. Science. 2020 03 13; 367(6483). Mestre H, Du T, Sweeney AM, Liu G, Samson AJ, Peng W, Mortensen KN, Stæger FF, Bork PAR, Bashford L, Toro ER, Tithof J, Kelley DH, Thomas JH, Hjorth PG, Martens EA, Mehta RI, Solis O, Blinder P, Kleinfeld D, Hirase H, Mori Y, Nedergaard M. PMID: 32001524; PMCID: PMC7375109.
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Orofacial Movements Involve Parallel Corticobulbar Projections from Motor Cortex to Trigeminal Premotor Nuclei. Neuron. 2019 11 20; 104(4):765-780.e3. Mercer Lindsay N, Knutsen PM, Lozada AF, Gibbs D, Karten HJ, Kleinfeld D. PMID: 31587918; PMCID: PMC7962749.
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Can One Concurrently Record Electrical Spikes from Every Neuron in a Mammalian Brain? Neuron. 2019 09 25; 103(6):1005-1015. Kleinfeld D, Luan L, Mitra PP, Robinson JT, Sarpeshkar R, Shepard K, Xie C, Harris TD. PMID: 31495645; PMCID: PMC6763354.
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Direct wavefront sensing enables functional imaging of infragranular axons and spines. Nat Methods. 2019 07; 16(7):615-618. Liu R, Li Z, Marvin JS, Kleinfeld D. PMID: 31209383; PMCID: PMC6763395.
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Brain Capillary Networks Across Species: A few Simple Organizational Requirements Are Sufficient to Reproduce Both Structure and Function. Front Physiol. 2019; 10:233. Smith AF, Doyeux V, Berg M, Peyrounette M, Haft-Javaherian M, Larue AE, Slater JH, Lauwers F, Blinder P, Tsai P, Kleinfeld D, Schaffer CB, Nishimura N, Davit Y, Lorthois S. PMID: 30971935; PMCID: PMC6444172.
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An active texture-based digital atlas enables automated mapping of structures and markers across brains. Nat Methods. 2019 04; 16(4):341-350. Chen Y, McElvain LE, Tolpygo AS, Ferrante D, Friedman B, Mitra PP, Karten HJ, Freund Y, Kleinfeld D. PMID: 30858600; PMCID: PMC6736610.
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Awake Mouse Imaging: From Two-Photon Microscopy to Blood Oxygen Level-Dependent Functional Magnetic Resonance Imaging. Biol Psychiatry Cogn Neurosci Neuroimaging. 2019 06; 4(6):533-542. Desjardins M, Kiliç K, Thunemann M, Mateo C, Holland D, Ferri CGL, Cremonesi JA, Li B, Cheng Q, Weldy KL, Saisan PA, Kleinfeld D, Komiyama T, Liu TT, Bussell R, Wong EC, Scadeng M, Dunn AK, Boas DA, Sakadžic S, Mandeville JB, Buxton RB, Dale AM, Devor A. PMID: 30691968; PMCID: PMC6556427.
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Functional brain stem circuits for control of nose motion. J Neurophysiol. 2019 01 01; 121(1):205-217. Kurnikova A, Deschênes M, Kleinfeld D. PMID: 30461370; PMCID: PMC6383659.
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Simulations of blood as a suspension predicts a depth dependent hematocrit in the circulation throughout the cerebral cortex. PLoS Comput Biol. 2018 11; 14(11):e1006549. Hartung G, Vesel C, Morley R, Alaraj A, Sled J, Kleinfeld D, Linninger A. PMID: 30452440; PMCID: PMC6277127.
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Comparing two classes of biological distribution systems using network analysis. PLoS Comput Biol. 2018 09; 14(9):e1006428. Papadopoulos L, Blinder P, Ronellenfitsch H, Klimm F, Katifori E, Kleinfeld D, Bassett DS. PMID: 30192745; PMCID: PMC6145589.
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Ultra-Slow Single-Vessel BOLD and CBV-Based fMRI Spatiotemporal Dynamics and Their Correlation with Neuronal Intracellular Calcium Signals. Neuron. 2018 02 21; 97(4):925-939.e5. He Y, Wang M, Chen X, Pohmann R, Polimeni JR, Scheffler K, Rosen BR, Kleinfeld D, Yu X. PMID: 29398359; PMCID: PMC5845844.
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Entrainment of Arteriole Vasomotor Fluctuations by Neural Activity Is a Basis of Blood-Oxygenation-Level-Dependent "Resting-State" Connectivity. Neuron. 2017 Nov 15; 96(4):936-948.e3. Mateo C, Knutsen PM, Tsai PS, Shih AY, Kleinfeld D. PMID: 29107517; PMCID: PMC5851777.
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The impact of vessel size, orientation and intravascular contribution on the neurovascular fingerprint of BOLD bSSFP fMRI. Neuroimage. 2017 12; 163:13-23. Báez-Yánez MG, Ehses P, Mirkes C, Tsai PS, Kleinfeld D, Scheffler K. PMID: 28890417; PMCID: PMC5857886.
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Circuits in the rodent brainstem that control whisking in concert with other orofacial motor actions. Neuroscience. 2018 Jan 01; 368:152-170. McElvain LE, Friedman B, Karten HJ, Svoboda K, Wang F, Deschênes M, Kleinfeld D. PMID: 28843993; PMCID: PMC5849401.
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Parallel Inhibitory and Excitatory Trigemino-Facial Feedback Circuitry for Reflexive Vibrissa Movement. Neuron. 2017 08 02; 95(3):722-723. Bellavance MA, Takatoh J, Lu J, Demers M, Kleinfeld D, Wang F, Deschênes M. PMID: 28772127.
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Parallel Inhibitory and Excitatory Trigemino-Facial Feedback Circuitry for Reflexive Vibrissa Movement. Neuron. 2017 Aug 02; 95(3):673-682.e4. Bellavance MA, Takatoh J, Lu J, Demers M, Kleinfeld D, Wang F, Deschênes M. PMID: 28735746; PMCID: PMC5845798.
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Correction to 'Precision mapping of the vibrissa representation within murine primary somatosensory cortex'. Philos Trans R Soc Lond B Biol Sci. 2017 Apr 19; 372(1718). Knutsen PM, Mateo C, Kleinfeld D. PMID: 28242742; PMCID: PMC5332867.
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Coordination of Orofacial Motor Actions into Exploratory Behavior by Rat. Curr Biol. 2017 Mar 06; 27(5):688-696. Kurnikova A, Moore JD, Liao SM, Deschênes M, Kleinfeld D. PMID: 28216320; PMCID: PMC5653531.
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Depth-dependent flow and pressure characteristics in cortical microvascular networks. PLoS Comput Biol. 2017 02; 13(2):e1005392. Schmid F, Tsai PS, Kleinfeld D, Jenny P, Weber B. PMID: 28196095; PMCID: PMC5347440.
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The capillary bed offers the largest hemodynamic resistance to the cortical blood supply. J Cereb Blood Flow Metab. 2017 01; 37(1):52-68. Gould IG, Tsai P, Kleinfeld D, Linninger A. PMID: 27780904; PMCID: PMC5363755.
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The roadmap for estimation of cell-type-specific neuronal activity from non-invasive measurements. Philos Trans R Soc Lond B Biol Sci. 2016 10 05; 371(1705). Uhlirova H, Kiliç K, Tian P, Sakadžic S, Gagnon L, Thunemann M, Desjardins M, Saisan PA, Nizar K, Yaseen MA, Hagler DJ, Vandenberghe M, Djurovic S, Andreassen OA, Silva GA, Masliah E, Kleinfeld D, Vinogradov S, Buxton RB, Einevoll GT, Boas DA, Dale AM, Devor A. PMID: 27574309; PMCID: PMC5003857.
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Precision mapping of the vibrissa representation within murine primary somatosensory cortex. Philos Trans R Soc Lond B Biol Sci. 2016 10 05; 371(1705). Knutsen PM, Mateo C, Kleinfeld D. PMID: 27574305; PMCID: PMC5003853.
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Roger Tsien 1952-2016. Nat Neurosci. 2016 09 27; 19(10):1269-70. Kleinfeld D. PMID: 27669983.
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Analysis of Neuronal Spike Trains, Deconstructed. Neuron. 2016 07 20; 91(2):221-59. Aljadeff J, Lansdell BJ, Fairhall AL, Kleinfeld D. PMID: 27477016; PMCID: PMC4970242.
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Cell type specificity of neurovascular coupling in cerebral cortex. Elife. 2016 05 31; 5. Uhlirova H, Kiliç K, Tian P, Thunemann M, Desjardins M, Saisan PA, Sakadžic S, Ness TV, Mateo C, Cheng Q, Weldy KL, Razoux F, Vandenberghe M, Cremonesi JA, Ferri CG, Nizar K, Sridhar VB, Steed TC, Abashin M, Fainman Y, Masliah E, Djurovic S, Andreassen OA, Silva GA, Boas DA, Kleinfeld D, Buxton RB, Einevoll GT, Dale AM, Devor A. PMID: 27244241; PMCID: PMC4933561.
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Circuits in the Ventral Medulla That Phase-Lock Motoneurons for Coordinated Sniffing and Whisking. Neural Plast. 2016; 2016:7493048. Deschênes M, Kurnikova A, Elbaz M, Kleinfeld D. PMID: 27293905; PMCID: PMC4887653.
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Construction of Cell-based Neurotransmitter Fluorescent Engineered Reporters (CNiFERs) for Optical Detection of Neurotransmitters In Vivo. J Vis Exp. 2016 May 12; (111). Lacin E, Muller A, Fernando M, Kleinfeld D, Slesinger PA. PMID: 27214050; PMCID: PMC4939270.
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Inhibition, Not Excitation, Drives Rhythmic Whisking. Neuron. 2016 04 20; 90(2):374-87. Deschênes M, Takatoh J, Kurnikova A, Moore JD, Demers M, Elbaz M, Furuta T, Wang F, Kleinfeld D. PMID: 27041498; PMCID: PMC4929009.
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Neurovascular and Immuno-Imaging: From Mechanisms to Therapies. Proceedings of the Inaugural Symposium. Front Neurosci. 2016; 10:46. Akassoglou K, Agalliu D, Chang CJ, Davalos D, Grutzendler J, Hillman EM, Khakh BS, Kleinfeld D, McGavern DB, Nelson SJ, Zlokovic BV. PMID: 26941593; PMCID: PMC4761864.
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Whisking, Sniffing, and the Hippocampal θ-Rhythm: A Tale of Two Oscillators. PLoS Biol. 2016 Feb; 14(2):e1002385. Kleinfeld D, Deschênes M, Ulanovsky N. PMID: 26890361; PMCID: PMC4758648.
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Vibrissa Self-Motion and Touch Are Reliably Encoded along the Same Somatosensory Pathway from Brainstem through Thalamus. PLoS Biol. 2015; 13(9):e1002253. Moore JD, Mercer Lindsay N, Deschênes M, Kleinfeld D. PMID: 26393890; PMCID: PMC4579082.
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Ultra-large field-of-view two-photon microscopy. Opt Express. 2015 Jun 01; 23(11):13833-47. Tsai PS, Mateo C, Field JJ, Schaffer CB, Anderson ME, Kleinfeld D. PMID: 26072755; PMCID: PMC4523368.
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Juxtacellular Monitoring and Localization of Single Neurons within Sub-cortical Brain Structures of Alert, Head-restrained Rats. J Vis Exp. 2015 Apr 27; (98). Moore JD, Deschênes M, Kleinfeld D. PMID: 25938559; PMCID: PMC4541592.
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The Brainstem Oscillator for Whisking and the Case for Breathing as the Master Clock for Orofacial Motor Actions. Cold Spring Harb Symp Quant Biol. 2014; 79:29-39. Kleinfeld D, Moore JD, Wang F, Deschênes M. PMID: 25876629; PMCID: PMC4924579.
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Deflection of a vibrissa leads to a gradient of strain across mechanoreceptors in a mystacial follicle. J Neurophysiol. 2015 Jul; 114(1):138-45. Whiteley SJ, Knutsen PM, Matthews DW, Kleinfeld D. PMID: 25855692; PMCID: PMC4507969.
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Robust and fragile aspects of cortical blood flow in relation to the underlying angioarchitecture. Microcirculation. 2015 Apr; 22(3):204-218. Shih AY, Rühlmann C, Blinder P, Devor A, Drew PJ, Friedman B, Knutsen PM, Lyden PD, Mateo C, Mellander L, Nishimura N, Schaffer CB, Tsai PS, Kleinfeld D. PMID: 25705966; PMCID: PMC4393797.
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Fluorescently labeled peptide increases identification of degenerated facial nerve branches during surgery and improves functional outcome. PLoS One. 2015; 10(3):e0119600. Hussain T, Mastrodimos MB, Raju SC, Glasgow HL, Whitney M, Friedman B, Moore JD, Kleinfeld D, Steinbach P, Messer K, Pu M, Tsien RY, Nguyen QT. PMID: 25751149; PMCID: PMC4353702.
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Feedback in the brainstem: an excitatory disynaptic pathway for control of whisking. J Comp Neurol. 2015 Apr 15; 523(6):921-42. Matthews DW, Deschênes M, Furuta T, Moore JD, Wang F, Karten HJ, Kleinfeld D. PMID: 25503925; PMCID: PMC4329057.
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Monitoring Integrated Activity of Individual Neurons Using FRET-Based Voltage-Sensitive Dyes. Adv Exp Med Biol. 2015; 859:149-69. Briggman KL, Kristan WB, González JE, Kleinfeld D, Tsien RY. PMID: 26238052.
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The Musculature That Drives Active Touch by Vibrissae and Nose in Mice. Anat Rec (Hoboken). 2015 Jul; 298(7):1347-58. Haidarliu S, Kleinfeld D, Deschênes M, Ahissar E. PMID: 25408106; PMCID: PMC4930880.
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Cell-based reporters reveal in vivo dynamics of dopamine and norepinephrine release in murine cortex. Nat Methods. 2014 Dec; 11(12):1245-52. Muller A, Joseph V, Slesinger PA, Kleinfeld D. PMID: 25344639; PMCID: PMC4245316.
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Muscles involved in naris dilation and nose motion in rat. Anat Rec (Hoboken). 2015 Mar; 298(3):546-53. Deschênes M, Haidarliu S, Demers M, Moore J, Kleinfeld D, Ahissar E. PMID: 25257748; PMCID: PMC4929008.
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Activation and measurement of free whisking in the lightly anesthetized rodent. Nat Protoc. 2014 Aug; 9(8):1792-802. Moore JD, Deschênes M, Kurnikova A, Kleinfeld D. PMID: 24992095; PMCID: PMC4934662.
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How the brainstem controls orofacial behaviors comprised of rhythmic actions. Trends Neurosci. 2014 Jul; 37(7):370-80. Moore JD, Kleinfeld D, Wang F. PMID: 24890196; PMCID: PMC4100695.
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More than a rhythm of life: breathing as a binder of orofacial sensation. Nat Neurosci. 2014 May; 17(5):647-51. Kleinfeld D, Deschênes M, Wang F, Moore JD. PMID: 24762718; PMCID: PMC4140942.
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Spectral methods for functional brain imaging. Cold Spring Harb Protoc. 2014 Mar 01; 2014(3):248-62. Kleinfeld D, Mitra PP. PMID: 24591695.
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Optically induced occlusion of single blood vessels in rodent neocortex. Cold Spring Harb Protoc. 2013 Dec 01; 2013(12):1153-60. Shih AY, Nishimura N, Nguyen J, Friedman B, Lyden PD, Schaffer CB, Kleinfeld D. PMID: 24298038.
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Mediation of muscular control of rhinarial motility in rats by the nasal cartilaginous skeleton. Anat Rec (Hoboken). 2013 Dec; 296(12):1821-32. Haidarliu S, Kleinfeld D, Ahissar E. PMID: 24249396; PMCID: PMC4157211.
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The challenge of connecting the dots in the B.R.A.I.N. Neuron. 2013 Oct 16; 80(2):270-4. Devor A, Bandettini PA, Boas DA, Bower JM, Buxton RB, Cohen LB, Dale AM, Einevoll GT, Fox PT, Franceschini MA, Friston KJ, Fujimoto JG, Geyer MA, Greenberg JH, Halgren E, Hämäläinen MS, Helmchen F, Hyman BT, Jasanoff A, Jernigan TL, Judd LL, Kim SG, Kleinfeld D, Kopell NJ, Kutas M, Kwong KK, Larkum ME, Lo EH, Magistretti PJ, Mandeville JB, Masliah E, Mitra PP, Mobley WC, Moskowitz MA, Nimmerjahn A, Reynolds JH, Rosen BR, Salzberg BM, Schaffer CB, Silva GA, So PT, Spitzer NC, Tootell RB, Van Essen DC, Vanduffel W, Vinogradov SA, Wald LL, Wang LV, Weber B, Yodh AG. PMID: 24139032; PMCID: PMC3864648.
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All-optical osteotomy to create windows for transcranial imaging in mice. Opt Express. 2013 Oct 07; 21(20):23160-8. Jeong DC, Tsai PS, Kleinfeld D. PMID: 24104230; PMCID: PMC3971057.
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ReaChR: a red-shifted variant of channelrhodopsin enables deep transcranial optogenetic excitation. Nat Neurosci. 2013 Oct; 16(10):1499-508. Lin JY, Knutsen PM, Muller A, Kleinfeld D, Tsien RY. PMID: 23995068; PMCID: PMC3793847.
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Two-photon imaging of blood flow in the rat cortex. Cold Spring Harb Protoc. 2013 Aug 01; 2013(8):759-67. Driscoll JD, Shih AY, Drew PJ, Cauwenberghs G, Kleinfeld D. PMID: 23906919.
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The cortical angiome: an interconnected vascular network with noncolumnar patterns of blood flow. Nat Neurosci. 2013 Jul; 16(7):889-97. Blinder P, Tsai PS, Kaufhold JP, Knutsen PM, Suhl H, Kleinfeld D. PMID: 23749145; PMCID: PMC4141079.
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Hierarchy of orofacial rhythms revealed through whisking and breathing. Nature. 2013 May 09; 497(7448):205-10. Moore JD, Deschênes M, Furuta T, Huber D, Smear MC, Demers M, Kleinfeld D. PMID: 23624373; PMCID: PMC4159559.
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All-optical in situ histology of brain tissue with femtosecond laser pulses. Cold Spring Harb Protoc. 2013 Apr 01; 2013(4):327-34. Tsai PS, Blinder P, Squier JA, Kleinfeld D. PMID: 23547156.
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The smallest stroke: occlusion of one penetrating vessel leads to infarction and a cognitive deficit. Nat Neurosci. 2013 Jan; 16(1):55-63. Shih AY, Blinder P, Tsai PS, Friedman B, Stanley G, Lyden PD, Kleinfeld D. PMID: 23242312; PMCID: PMC3952571.
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Vectorization of optically sectioned brain microvasculature: learning aids completion of vascular graphs by connecting gaps and deleting open-ended segments. Med Image Anal. 2012 Aug; 16(6):1241-58. Kaufhold JP, Tsai PS, Blinder P, Kleinfeld D. PMID: 22854035; PMCID: PMC3443315.
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Dorsorostral snout muscles in the rat subserve coordinated movement for whisking and sniffing. Anat Rec (Hoboken). 2012 Jul; 295(7):1181-91. Haidarliu S, Golomb D, Kleinfeld D, Ahissar E. PMID: 22641389; PMCID: PMC4153473.
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A polished and reinforced thinned-skull window for long-term imaging of the mouse brain. J Vis Exp. 2012 Mar 07; (61). Shih AY, Mateo C, Drew PJ, Tsai PS, Kleinfeld D. PMID: 22433225; PMCID: PMC3460568.
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Interferometric detection of action potentials. Cold Spring Harb Protoc. 2012 Mar 01; 2012(3):307-11. LaPorta A, Kleinfeld D. PMID: 22383643.
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Two-photon microscopy as a tool to study blood flow and neurovascular coupling in the rodent brain. J Cereb Blood Flow Metab. 2012 Jul; 32(7):1277-309. Shih AY, Driscoll JD, Drew PJ, Nishimura N, Schaffer CB, Kleinfeld D. PMID: 22293983; PMCID: PMC3390800.
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Sniffing and whisking in rodents. Curr Opin Neurobiol. 2012 Apr; 22(2):243-50. Deschênes M, Moore J, Kleinfeld D. PMID: 22177596; PMCID: PMC4934665.
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Prospect for feedback guided surgery with ultra-short pulsed laser light. Curr Opin Neurobiol. 2012 Feb; 22(1):24-33. Jeong DC, Tsai PS, Kleinfeld D. PMID: 22088392; PMCID: PMC3763077.
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Large-scale automated histology in the pursuit of connectomes. J Neurosci. 2011 Nov 09; 31(45):16125-38. Kleinfeld D, Bharioke A, Blinder P, Bock DD, Briggman KL, Chklovskii DB, Denk W, Helmstaedter M, Kaufhold JP, Lee WC, Meyer HS, Micheva KD, Oberlaender M, Prohaska S, Reid RC, Smith SJ, Takemura S, Tsai PS, Sakmann B. PMID: 22072665; PMCID: PMC3758571.
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Neuronal basis for object location in the vibrissa scanning sensorimotor system. Neuron. 2011 Nov 03; 72(3):455-68. Kleinfeld D, Deschênes M. PMID: 22078505; PMCID: PMC3971931.
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Primary motor cortex reports efferent control of vibrissa motion on multiple timescales. Neuron. 2011 Oct 20; 72(2):344-56. Hill DN, Curtis JC, Moore JD, Kleinfeld D. PMID: 22017992; PMCID: PMC3717360.
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Quality metrics to accompany spike sorting of extracellular signals. J Neurosci. 2011 Jun 15; 31(24):8699-705. Hill DN, Mehta SB, Kleinfeld D. PMID: 21677152; PMCID: PMC3123734.
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Fluctuating and sensory-induced vasodynamics in rodent cortex extend arteriole capacity. Proc Natl Acad Sci U S A. 2011 May 17; 108(20):8473-8. Drew PJ, Shih AY, Kleinfeld D. PMID: 21536897; PMCID: PMC3100929.
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A guide to delineate the logic of neurovascular signaling in the brain. Front Neuroenergetics. 2011; 3:1. Kleinfeld D, Blinder P, Drew PJ, Driscoll JD, Muller A, Tsai PS, Shih AY. PMID: 21559095; PMCID: PMC3085135.
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Photon counting, censor corrections, and lifetime imaging for improved detection in two-photon microscopy. J Neurophysiol. 2011 Jun; 105(6):3106-13. Driscoll JD, Shih AY, Iyengar S, Field JJ, White GA, Squier JA, Cauwenberghs G, Kleinfeld D. PMID: 21471395; PMCID: PMC3118755.
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Characterizing ligand-gated ion channel receptors with genetically encoded Ca2++ sensors. PLoS One. 2011 Jan 28; 6(1):e16519. Yamauchi JG, Nemecz Á, Nguyen QT, Muller A, Schroeder LF, Talley TT, Lindstrom J, Kleinfeld D, Taylor P. PMID: 21305050; PMCID: PMC3030600.
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Spatio-temporally focused femtosecond laser pulses for nonreciprocal writing in optically transparent materials. Opt Express. 2010 Nov 22; 18(24):24673-8. Vitek DN, Block E, Bellouard Y, Adams DE, Backus S, Kleinfeld D, Durfee CG, Squier JA. PMID: 21164813; PMCID: PMC4157520.
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Differential Multiphoton Laser Scanning Microscopy. IEEE J Sel Top Quantum Electron. 2012 Jan-Feb; 18(1):14-28. Field JJ, Sheetz KE, Chandler EV, Hoover EE, Young MD, Ding SY, Sylvester AW, Kleinfeld D, Squier JA. PMID: 27390511; PMCID: PMC4932844.
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Chronic optical access through a polished and reinforced thinned skull. Nat Methods. 2010 Dec; 7(12):981-4. Drew PJ, Shih AY, Driscoll JD, Knutsen PM, Blinder P, Davalos D, Akassoglou K, Tsai PS, Kleinfeld D. PMID: 20966916; PMCID: PMC3204312.
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Temporally focused femtosecond laser pulses for low numerical aperture micromachining through optically transparent materials. Opt Express. 2010 Aug 16; 18(17):18086-94. Vitek DN, Adams DE, Johnson A, Tsai PS, Backus S, Durfee CG, Kleinfeld D, Squier JA. PMID: 20721196; PMCID: PMC3408926.
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Automatic identification of fluorescently labeled brain cells for rapid functional imaging. J Neurophysiol. 2010 Sep; 104(3):1803-11. Valmianski I, Shih AY, Driscoll JD, Matthews DW, Freund Y, Kleinfeld D. PMID: 20610792; PMCID: PMC2944673.
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Topological basis for the robust distribution of blood to rodent neocortex. Proc Natl Acad Sci U S A. 2010 Jul 13; 107(28):12670-5. Blinder P, Shih AY, Rafie C, Kleinfeld D. PMID: 20616030; PMCID: PMC2906564.
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Optimizing the fluorescent yield in two-photon laser scanning microscopy with dispersion compensation. Opt Express. 2010 Jun 21; 18(13):13661-72. Field JJ, Carriles R, Sheetz KE, Chandler EV, Hoover EE, Tillo SE, Hughes TE, Sylvester AW, Kleinfeld D, Squier JA. PMID: 20588500; PMCID: PMC4151303.
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An in vivo biosensor for neurotransmitter release and in situ receptor activity. Nat Neurosci. 2010 Jan; 13(1):127-132. Nguyen QT, Schroeder LF, Mank M, Muller A, Taylor P, Griesbeck O, Kleinfeld D. PMID: 20010818; PMCID: PMC3992257.
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Correlations of neuronal and microvascular densities in murine cortex revealed by direct counting and colocalization of nuclei and vessels. J Neurosci. 2009 Nov 18; 29(46):14553-70. Tsai PS, Kaufhold JP, Blinder P, Friedman B, Drew PJ, Karten HJ, Lyden PD, Kleinfeld D. PMID: 19923289; PMCID: PMC4972024.
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Enter the ratrix. Proc Natl Acad Sci U S A. 2009 Nov 17; 106(46):19209-10. Pesaran B, Kleinfeld D. PMID: 19906991; PMCID: PMC2780815.
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Severe blood-brain barrier disruption and surrounding tissue injury. Stroke. 2009 Dec; 40(12):e666-74. Chen B, Friedman B, Cheng Q, Tsai P, Schim E, Kleinfeld D, Lyden PD. PMID: 19893002; PMCID: PMC2819286.
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The glial cell response is an essential component of hypoxia-induced erythropoiesis in mice. J Clin Invest. 2009 Nov; 119(11):3373-83. Weidemann A, Kerdiles YM, Knaup KX, Rafie CA, Boutin AT, Stockmann C, Takeda N, Scadeng M, Shih AY, Haase VH, Simon MC, Kleinfeld D, Johnson RS. PMID: 19809162; PMCID: PMC2769183.
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Rapid determination of particle velocity from space-time images using the Radon transform. J Comput Neurosci. 2010 Aug; 29(1-2):5-11. Drew PJ, Blinder P, Cauwenberghs G, Shih AY, Kleinfeld D. PMID: 19459038; PMCID: PMC4962871.
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A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale. PLoS Comput Biol. 2009 Mar; 5(3):e1000334. Bohland JW, Wu C, Barbas H, Bokil H, Bota M, Breiter HC, Cline HT, Doyle JC, Freed PJ, Greenspan RJ, Haber SN, Hawrylycz M, Herrera DG, Hilgetag CC, Huang ZJ, Jones A, Jones EG, Karten HJ, Kleinfeld D, Kötter R, Lester HA, Lin JM, Mensh BD, Mikula S, Panksepp J, Price JL, Safdieh J, Saper CB, Schiff ND, Schmahmann JD, Stillman BW, Svoboda K, Swanson LW, Toga AW, Van Essen DC, Watson JD, Mitra PP. PMID: 19325892; PMCID: PMC2655718.
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Phase-to-rate transformations encode touch in cortical neurons of a scanning sensorimotor system. Nat Neurosci. 2009 Apr; 12(4):492-501. Curtis JC, Kleinfeld D. PMID: 19270688; PMCID: PMC2863011.
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Plasma-mediated ablation: an optical tool for submicrometer surgery on neuronal and vascular systems. Curr Opin Biotechnol. 2009 Feb; 20(1):90-9. Tsai PS, Blinder P, Migliori BJ, Neev J, Jin Y, Squier JA, Kleinfeld D. PMID: 19269159; PMCID: PMC3123732.
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Active dilation of penetrating arterioles restores red blood cell flux to penumbral neocortex after focal stroke. J Cereb Blood Flow Metab. 2009 Apr; 29(4):738-51. Shih AY, Friedman B, Drew PJ, Tsai PS, Lyden PD, Kleinfeld D. PMID: 19174826; PMCID: PMC2893883.
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Stimulus-induced changes in blood flow and 2-deoxyglucose uptake dissociate in ipsilateral somatosensory cortex. J Neurosci. 2008 Dec 31; 28(53):14347-57. Devor A, Hillman EM, Tian P, Waeber C, Teng IC, Ruvinskaya L, Shalinsky MH, Zhu H, Haslinger RH, Narayanan SN, Ulbert I, Dunn AK, Lo EH, Rosen BR, Dale AM, Kleinfeld D, Boas DA. PMID: 19118167; PMCID: PMC2655308.
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Advancing multifocal nonlinear microscopy: development and application of a novel multibeam Yb:KGd(WO4)2 oscillator. Opt Express. 2008 Oct 27; 16(22):17574-84. Sheetz KE, Hoover EE, Carriles R, Kleinfeld D, Squier JA. PMID: 18958037.
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Finding coherence in spontaneous oscillations. Nat Neurosci. 2008 Sep; 11(9):991-3. Drew PJ, Duyn JH, Golanov E, Kleinfeld D. PMID: 18725901.
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Texture coding in the rat whisker system: slip-stick versus differential resonance. PLoS Biol. 2008 Aug 26; 6(8):e215. Wolfe J, Hill DN, Pahlavan S, Drew PJ, Kleinfeld D, Feldman DE. PMID: 18752354; PMCID: PMC2525689.
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'Where' and 'what' in the whisker sensorimotor system. Nat Rev Neurosci. 2008 Aug; 9(8):601-12. Diamond ME, von Heimendahl M, Knutsen PM, Kleinfeld D, Ahissar E. PMID: 18641667.
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Biomechanics of the vibrissa motor plant in rat: rhythmic whisking consists of triphasic neuromuscular activity. J Neurosci. 2008 Mar 26; 28(13):3438-55. Hill DN, Bermejo R, Zeigler HP, Kleinfeld D. PMID: 18367610; PMCID: PMC6670594.
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Chapter 10. In vivo measurements of blood flow and glial cell function with two-photon laser-scanning microscopy. Methods Enzymol. 2008; 444:231-54. Helmchen F, Kleinfeld D. PMID: 19007667.
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Wilder Penfield in the age of YouTube: visualizing the sequential activation of sensorimotor areas across neocortex. Neuron. 2007 Dec 06; 56(5):760-2. Kleinfeld D, Waters J. PMID: 18054853.
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Suppressed neuronal activity and concurrent arteriolar vasoconstriction may explain negative blood oxygenation level-dependent signal. J Neurosci. 2007 Apr 18; 27(16):4452-9. Devor A, Tian P, Nishimura N, Teng IC, Hillman EM, Narayanan SN, Ulbert I, Boas DA, Kleinfeld D, Dale AM. PMID: 17442830; PMCID: PMC2680207.
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Active spatial perception in the vibrissa scanning sensorimotor system. PLoS Biol. 2007 Feb; 5(2):e15. Mehta SB, Whitmer D, Figueroa R, Williams BA, Kleinfeld D. PMID: 17227143; PMCID: PMC1769422.
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Large two-photon absorptivity of hemoglobin in the infrared range of 780-880 nm. J Chem Phys. 2007 Jan 14; 126(2):025102. Clay GO, Schaffer CB, Kleinfeld D. PMID: 17228976.
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Is there a common origin to surround-inhibition as seen through electrical activity versus hemodynamic changes? Focus on "Duration-dependent response in SI to vibrotactile stimulation in squirrel monkey". J Neurophysiol. 2007 Mar; 97(3):1880-2. Devor A, Trevelyan A, Kleinfeld D. PMID: 17215499.
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Penetrating arterioles are a bottleneck in the perfusion of neocortex. Proc Natl Acad Sci U S A. 2007 Jan 02; 104(1):365-70. Nishimura N, Schaffer CB, Friedman B, Lyden PD, Kleinfeld D. PMID: 17190804; PMCID: PMC1765467.
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Active sensation: insights from the rodent vibrissa sensorimotor system. Curr Opin Neurobiol. 2006 Aug; 16(4):435-44. Kleinfeld D, Ahissar E, Diamond ME. PMID: 16837190.
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Exploratory whisking by rat is not phase locked to the hippocampal theta rhythm. J Neurosci. 2006 Jun 14; 26(24):6518-22. Berg RW, Whitmer D, Kleinfeld D. PMID: 16775139; PMCID: PMC6674030.
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Seeing what the mouse sees with its vibrissae: a matter of behavioral state. Neuron. 2006 May 18; 50(4):524-6. Curtis JC, Kleinfeld D. PMID: 16701202; PMCID: PMC2863010.
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MPScope: a versatile software suite for multiphoton microscopy. J Neurosci Methods. 2006 Sep 30; 156(1-2):351-9. Nguyen QT, Tsai PS, Kleinfeld D. PMID: 16621010.
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Targeted insult to subsurface cortical blood vessels using ultrashort laser pulses: three models of stroke. Nat Methods. 2006 Feb; 3(2):99-108. Nishimura N, Schaffer CB, Friedman B, Tsai PS, Lyden PD, Kleinfeld D. PMID: 16432519.
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Science is an adventure, not a battle. Nature. 2006 Jan 05; 439(7072):18. Kleinfeld D. PMID: 16397477.
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Two-photon imaging of cortical surface microvessels reveals a robust redistribution in blood flow after vascular occlusion. PLoS Biol. 2006 Feb; 4(2):e22. Schaffer CB, Friedman B, Nishimura N, Schroeder LF, Tsai PS, Ebner FF, Lyden PD, Kleinfeld D. PMID: 16379497; PMCID: PMC1324794.
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Coding of stimulus frequency by latency in thalamic networks through the interplay of GABAB-mediated feedback and stimulus shape. J Neurophysiol. 2006 Mar; 95(3):1735-50. Golomb D, Ahissar E, Kleinfeld D. PMID: 16267113.
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From art to engineering? The rise of in vivo mammalian electrophysiology via genetically targeted labeling and nonlinear imaging. PLoS Biol. 2005 Oct; 3(10):e355. Kleinfeld D, Griesbeck O. PMID: 16207078; PMCID: PMC1250306.
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Activation of nucleus basalis facilitates cortical control of a brain stem motor program. J Neurophysiol. 2005 Jul; 94(1):699-711. Berg RW, Friedman B, Schroeder LF, Kleinfeld D. PMID: 15728764.
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Positive feedback in a brainstem tactile sensorimotor loop. Neuron. 2005 Feb 03; 45(3):447-57. Nguyen QT, Kleinfeld D. PMID: 15694330.
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Current flow in vibrissa motor cortex can phase-lock with exploratory rhythmic whisking in rat. J Neurophysiol. 2004 Sep; 92(3):1700-7. Ahrens KF, Kleinfeld D. PMID: 15331651.
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Developmental regulation of active and passive membrane properties in rat vibrissa motoneurones. J Physiol. 2004 Apr 01; 556(Pt 1):203-19. Nguyen QT, Wessel R, Kleinfeld D. PMID: 14766934; PMCID: PMC1664878.
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Frisking the whiskers: patterned sensory input in the rat vibrissa system. Neuron. 2004 Jan 22; 41(2):181-4. Mehta SB, Kleinfeld D. PMID: 14741099.
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Reversing cerebellar long-term depression. Proc Natl Acad Sci U S A. 2003 Dec 23; 100(26):15989-93. Lev-Ram V, Mehta SB, Kleinfeld D, Tsien RY. PMID: 14671315; PMCID: PMC307680.
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Imaging reveals synaptic targets of a swim-terminating neuron in the leech CNS. J Neurosci. 2003 Dec 10; 23(36):11402-10. Taylor AL, Cottrell GW, Kleinfeld D, Kristan WB. PMID: 14673004; PMCID: PMC6740517.
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Vibrissa movement elicited by rhythmic electrical microstimulation to motor cortex in the aroused rat mimics exploratory whisking. J Neurophysiol. 2003 Nov; 90(5):2950-63. Berg RW, Kleinfeld D. PMID: 12904336.
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All-optical histology using ultrashort laser pulses. Neuron. 2003 Jul 03; 39(1):27-41. Tsai PS, Friedman B, Ifarraguerri AI, Thompson BD, Lev-Ram V, Schaffer CB, Xiong Q, Tsien RY, Squier JA, Kleinfeld D. PMID: 12848930.
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Unilateral vibrissa contact: changes in amplitude but not timing of rhythmic whisking. Somatosens Mot Res. 2003; 20(2):163-9. Sachdev RN, Berg RW, Champney G, Kleinfeld D, Ebner FF. PMID: 12850826.
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Closed-loop neuronal computations: focus on vibrissa somatosensation in rat. Cereb Cortex. 2003 Jan; 13(1):53-62. Ahissar E, Kleinfeld D. PMID: 12466215.
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Rhythmic whisking by rat: retraction as well as protraction of the vibrissae is under active muscular control. J Neurophysiol. 2003 Jan; 89(1):104-17. Berg RW, Kleinfeld D. PMID: 12522163.
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Adaptive filtering of vibrissa input in motor cortex of rat. Neuron. 2002 Jun 13; 34(6):1021-34. Kleinfeld D, Sachdev RN, Merchant LM, Jarvis MR, Ebner FF. PMID: 12086648.
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Coherent electrical activity between vibrissa sensory areas of cerebellum and neocortex is enhanced during free whisking. J Neurophysiol. 2002 Apr; 87(4):2137-48. O'Connor SM, Berg RW, Kleinfeld D. PMID: 11929931.
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Cortical imaging through the intact mouse skull using two-photon excitation laser scanning microscopy. Microsc Res Tech. 2002 Feb 15; 56(4):304-5. Yoder EJ, Kleinfeld D. PMID: 11877806.
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Direct evidence for local oscillatory current sources and intracortical phase gradients in turtle visual cortex. Proc Natl Acad Sci U S A. 2000 Jan 18; 97(2):877-82. Prechtl JC, Bullock TH, Kleinfeld D. PMID: 10639173; PMCID: PMC15424.
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Dendritic Ca(2+)-activated K(+) conductances regulate electrical signal propagation in an invertebrate neuron. J Neurosci. 1999 Oct 01; 19(19):8319-26. Wessel R, Kristan WB, Kleinfeld D. PMID: 10493733; PMCID: PMC6783054.
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Supralinear summation of synaptic inputs by an invertebrate neuron: dendritic gain is mediated by an "inward rectifier" K(+) current. J Neurosci. 1999 Jul 15; 19(14):5875-88. Wessel R, Kristan WB, Kleinfeld D. PMID: 10407027; PMCID: PMC6783099.
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Identification of neural circuits by imaging coherent electrical activity with FRET-based dyes. Neuron. 1999 Jul; 23(3):449-59. Cacciatore TW, Brodfuehrer PD, Gonzalez JE, Jiang T, Adams SR, Tsien RY, Kristan WB, Kleinfeld D. PMID: 10433258.
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Anatomical loops and their electrical dynamics in relation to whisking by rat. Somatosens Mot Res. 1999; 16(2):69-88. Kleinfeld D, Berg RW, O'Connor SM. PMID: 10449057.
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Fluctuations and stimulus-induced changes in blood flow observed in individual capillaries in layers 2 through 4 of rat neocortex. Proc Natl Acad Sci U S A. 1998 Dec 22; 95(26):15741-6. Kleinfeld D, Mitra PP, Helmchen F, Denk W. PMID: 9861040; PMCID: PMC28114.
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Distributed representation of vibrissa movement in the upper layers of somatosensory cortex revealed with voltage-sensitive dyes. J Comp Neurol. 1996 Nov 04; 375(1):89-108. Kleinfeld D, Delaney KR. PMID: 8913895.
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Parenteral therapy for antibiotic-associated pseudomembranous colitis. J Infect Dis. 1988 Feb; 157(2):389. Kleinfeld DI, Sharpe RJ, Donta ST. PMID: 3335816.
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