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Sharpening the tools for pericyte research.

Berthiaume AA, Shih AY.

Nat Neurosci. 2019 Jul;22(7):1041-1043. doi: 10.1038/s41593-019-0437-9. No abstract available.


Predicting the Binding of Fatty Acid Amide Hydrolase Inhibitors by Free Energy Perturbation.

Saha A, Shih AY, Mirzadegan T, Seierstad M.

J Chem Theory Comput. 2018 Nov 13;14(11):5815-5822. doi: 10.1021/acs.jctc.8b00672. Epub 2018 Oct 23.


Pericyte Structural Remodeling in Cerebrovascular Health and Homeostasis.

Berthiaume AA, Hartmann DA, Majesky MW, Bhat NR, Shih AY.

Front Aging Neurosci. 2018 Jul 17;10:210. doi: 10.3389/fnagi.2018.00210. eCollection 2018.


Rodent Models of Cerebral Microinfarct and Microhemorrhage.

Shih AY, Hyacinth HI, Hartmann DA, van Veluw SJ.

Stroke. 2018 Mar;49(3):803-810. doi: 10.1161/STROKEAHA.117.016995. Epub 2018 Feb 19. Review. No abstract available.


Dynamic Structural Differences between Human and Mouse STING Lead to Differing Sensitivity to DMXAA.

Shih AY, Damm-Ganamet KL, Mirzadegan T.

Biophys J. 2018 Jan 9;114(1):32-39. doi: 10.1016/j.bpj.2017.10.027.


Dynamic Remodeling of Pericytes In Vivo Maintains Capillary Coverage in the Adult Mouse Brain.

Berthiaume AA, Grant RI, McDowell KP, Underly RG, Hartmann DA, Levy M, Bhat NR, Shih AY.

Cell Rep. 2018 Jan 2;22(1):8-16. doi: 10.1016/j.celrep.2017.12.016.


Entrainment of Arteriole Vasomotor Fluctuations by Neural Activity Is a Basis of Blood-Oxygenation-Level-Dependent "Resting-State" Connectivity.

Mateo C, Knutsen PM, Tsai PS, Shih AY, Kleinfeld D.

Neuron. 2017 Nov 15;96(4):936-948.e3. doi: 10.1016/j.neuron.2017.10.012. Epub 2017 Oct 26.


Does pathology of small venules contribute to cerebral microinfarcts and dementia?

Hartmann DA, Hyacinth HI, Liao FF, Shih AY.

J Neurochem. 2018 Mar;144(5):517-526. doi: 10.1111/jnc.14228. Epub 2017 Nov 7. Review.


Organizational hierarchy and structural diversity of microvascular pericytes in adult mouse cortex.

Grant RI, Hartmann DA, Underly RG, Berthiaume AA, Bhat NR, Shih AY.

J Cereb Blood Flow Metab. 2019 Mar;39(3):411-425. doi: 10.1177/0271678X17732229. Epub 2017 Sep 21.


Higher prevalence of spontaneous cerebral vasculopathy and cerebral infarcts in a mouse model of sickle cell disease.

Hyacinth HI, Sugihara CL, Spencer TL, Archer DR, Shih AY.

J Cereb Blood Flow Metab. 2019 Feb;39(2):342-351. doi: 10.1177/0271678X17732275. Epub 2017 Sep 19.


Photothrombotic Induction of Capillary Ischemia in the Mouse Cortex during in vivo Two-photon Imaging.

Underly RG, Shih AY.

Bio Protoc. 2017 Jul 5;7(13). pii: e2378. doi: 10.21769/BioProtoc.2378.


Detection, risk factors, and functional consequences of cerebral microinfarcts.

van Veluw SJ, Shih AY, Smith EE, Chen C, Schneider JA, Wardlaw JM, Greenberg SM, Biessels GJ.

Lancet Neurol. 2017 Sep;16(9):730-740. doi: 10.1016/S1474-4422(17)30196-5. Epub 2017 Jul 14. Review.


Structural plasticity of the ventral stream and aphasia recovery.

McKinnon ET, Fridriksson J, Glenn GR, Jensen JH, Helpern JA, Basilakos A, Rorden C, Shih AY, Spampinato MV, Bonilha L.

Ann Neurol. 2017 Jul;82(1):147-151. doi: 10.1002/ana.24983.


Functional deficits induced by cortical microinfarcts.

Summers PM, Hartmann DA, Hui ES, Nie X, Deardorff RL, McKinnon ET, Helpern JA, Jensen JH, Shih AY.

J Cereb Blood Flow Metab. 2017 Nov;37(11):3599-3614. doi: 10.1177/0271678X16685573. Epub 2017 Jan 16.


Pericytes as Inducers of Rapid, Matrix Metalloproteinase-9-Dependent Capillary Damage during Ischemia.

Underly RG, Levy M, Hartmann DA, Grant RI, Watson AN, Shih AY.

J Neurosci. 2017 Jan 4;37(1):129-140. doi: 10.1523/JNEUROSCI.2891-16.2016.


Microvascular basis for growth of small infarcts following occlusion of single penetrating arterioles in mouse cortex.

Taylor ZJ, Hui ES, Watson AN, Nie X, Deardorff RL, Jensen JH, Helpern JA, Shih AY.

J Cereb Blood Flow Metab. 2016 Aug;36(8):1357-73. doi: 10.1177/0271678X15608388. Epub 2015 Oct 13.


Pericyte structure and distribution in the cerebral cortex revealed by high-resolution imaging of transgenic mice.

Hartmann DA, Underly RG, Grant RI, Watson AN, Lindner V, Shih AY.

Neurophotonics. 2015 Oct;2(4):041402. doi: 10.1117/1.NPh.2.4.041402. Epub 2015 May 27.


Robust and fragile aspects of cortical blood flow in relation to the underlying angioarchitecture.

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.

Microcirculation. 2015 Apr;22(3):204-218. doi: 10.1111/micc.12195. Review.


A murine toolbox for imaging the neurovascular unit.

Hartmann DA, Underly RG, Watson AN, Shih AY.

Microcirculation. 2015 Apr;22(3):168-82. doi: 10.1111/micc.12176. Review.


Modulation of the stemness and osteogenic differentiation of human mesenchymal stem cells by controlling RGD concentrations of poly(carboxybetaine) hydrogel.

Chien HW, Fu SW, Shih AY, Tsai WB.

Biotechnol J. 2014 Dec;9(12):1613-23. doi: 10.1002/biot.201300433. Epub 2014 Oct 31.


Optically induced occlusion of single blood vessels in rodent neocortex.

Shih AY, Nishimura N, Nguyen J, Friedman B, Lyden PD, Schaffer CB, Kleinfeld D.

Cold Spring Harb Protoc. 2013 Dec 1;2013(12):1153-60. doi: 10.1101/pdb.prot079509.


Targeted Occlusion of Individual Pial Vessels of Mouse Cortex.

Taylor ZJ, Shih AY.

Bio Protoc. 2013 Sep 5;3(17). pii: e897.


Hit-to-lead optimization and kinase selectivity of imidazo[1,2-a]quinoxalin-4-amine derived JNK1 inhibitors.

Li B, Cociorva OM, Nomanbhoy T, Weissig H, Li Q, Nakamura K, Liyanage M, Zhang MC, Shih AY, Aban A, Hu Y, Cajica J, Pham L, Kozarich JW, Shreder KR.

Bioorg Med Chem Lett. 2013 Sep 15;23(18):5217-22. doi: 10.1016/j.bmcl.2013.06.087. Epub 2013 Jul 8.


Two-photon imaging of blood flow in the rat cortex.

Driscoll JD, Shih AY, Drew PJ, Cauwenberghs G, Kleinfeld D.

Cold Spring Harb Protoc. 2013 Aug 1;2013(8):759-67. doi: 10.1101/pdb.prot076513.


Analysis of the structural and molecular basis of voltage-sensitive sodium channel inhibition by the spider toxin huwentoxin-IV (μ-TRTX-Hh2a).

Minassian NA, Gibbs A, Shih AY, Liu Y, Neff RA, Sutton SW, Mirzadegan T, Connor J, Fellows R, Husovsky M, Nelson S, Hunter MJ, Flinspach M, Wickenden AD.

J Biol Chem. 2013 Aug 2;288(31):22707-20. doi: 10.1074/jbc.M113.461392. Epub 2013 Jun 12.


A Pan-BCL2 inhibitor renders bone-marrow-resident human leukemia stem cells sensitive to tyrosine kinase inhibition.

Goff DJ, Court Recart A, Sadarangani A, Chun HJ, Barrett CL, Krajewska M, Leu H, Low-Marchelli J, Ma W, Shih AY, Wei J, Zhai D, Geron I, Pu M, Bao L, Chuang R, Balaian L, Gotlib J, Minden M, Martinelli G, Rusert J, Dao KH, Shazand K, Wentworth P, Smith KM, Jamieson CA, Morris SR, Messer K, Goldstein LS, Hudson TJ, Marra M, Frazer KA, Pellecchia M, Reed JC, Jamieson CH.

Cell Stem Cell. 2013 Mar 7;12(3):316-28. doi: 10.1016/j.stem.2012.12.011. Epub 2013 Jan 17.


The smallest stroke: occlusion of one penetrating vessel leads to infarction and a cognitive deficit.

Shih AY, Blinder P, Tsai PS, Friedman B, Stanley G, Lyden PD, Kleinfeld D.

Nat Neurosci. 2013 Jan;16(1):55-63. doi: 10.1038/nn.3278. Epub 2012 Dec 16.


Optical imaging of progenitor cell homing to patient-derived tumors.

Newton IG, Plaisted WC, Messina-Graham S, Abrahamsson Schairer AE, Shih AY, Snyder EY, Jamieson CH, Mattrey RF.

Contrast Media Mol Imaging. 2012 Nov-Dec;7(6):525-36. doi: 10.1002/cmmi.1485.


Identification of structural motifs critical for epstein-barr virus-induced molecule 2 function and homology modeling of the ligand docking site.

Zhang L, Shih AY, Yang XV, Kuei C, Wu J, Deng X, Mani NS, Mirzadegan T, Sun S, Lovenberg TW, Liu C.

Mol Pharmacol. 2012 Dec;82(6):1094-103. doi: 10.1124/mol.112.080275. Epub 2012 Aug 28.


Amyloid precursor protein (APP) regulates synaptic structure and function.

Tyan SH, Shih AY, Walsh JJ, Maruyama H, Sarsoza F, Ku L, Eggert S, Hof PR, Koo EH, Dickstein DL.

Mol Cell Neurosci. 2012 Aug;51(1-2):43-52. doi: 10.1016/j.mcn.2012.07.009. Epub 2012 Aug 3.


NOTCH1 signaling promotes human T-cell acute lymphoblastic leukemia initiating cell regeneration in supportive niches.

Ma W, Gutierrez A, Goff DJ, Geron I, Sadarangani A, Jamieson CA, Court AC, Shih AY, Jiang Q, Wu CC, Li K, Smith KM, Crews LA, Gibson NW, Deichaite I, Morris SR, Wei P, Carson DA, Look AT, Jamieson CH.

PLoS One. 2012;7(6):e39725. doi: 10.1371/journal.pone.0039725. Epub 2012 Jun 29.


A polished and reinforced thinned-skull window for long-term imaging of the mouse brain.

Shih AY, Mateo C, Drew PJ, Tsai PS, Kleinfeld D.

J Vis Exp. 2012 Mar 7;(61). pii: 3742. doi: 10.3791/3742.


Two-photon microscopy as a tool to study blood flow and neurovascular coupling in the rodent brain.

Shih AY, Driscoll JD, Drew PJ, Nishimura N, Schaffer CB, Kleinfeld D.

J Cereb Blood Flow Metab. 2012 Jul;32(7):1277-309. doi: 10.1038/jcbfm.2011.196. Epub 2012 Feb 1. Review. Erratum in: J Cereb Blood Flow Metab. 2013 Feb;33(2):319. Dosage error in article text.


Structural differences between soluble and membrane bound cytochrome P450s.

Denisov IG, Shih AY, Sligar SG.

J Inorg Biochem. 2012 Mar;108:150-8. doi: 10.1016/j.jinorgbio.2011.11.026. Epub 2011 Dec 14.


A guide to delineate the logic of neurovascular signaling in the brain.

Kleinfeld D, Blinder P, Drew PJ, Driscoll JD, Muller A, Tsai PS, Shih AY.

Front Neuroenergetics. 2011 Apr 25;3:1. doi: 10.3389/fnene.2011.00001. eCollection 2011.


Fluctuating and sensory-induced vasodynamics in rodent cortex extend arteriole capacity.

Drew PJ, Shih AY, Kleinfeld D.

Proc Natl Acad Sci U S A. 2011 May 17;108(20):8473-8. doi: 10.1073/pnas.1100428108. Epub 2011 May 2.


Photon counting, censor corrections, and lifetime imaging for improved detection in two-photon microscopy.

Driscoll JD, Shih AY, Iyengar S, Field JJ, White GA, Squier JA, Cauwenberghs G, Kleinfeld D.

J Neurophysiol. 2011 Jun;105(6):3106-13. doi: 10.1152/jn.00649.2010. Epub 2011 Apr 6.


Clinical predictors of frequent patient telephone calls in Parkinson's disease.

Liu AA, Boxhorn CE, Klufas MA, Christos PJ, Thorne JT, Shih AY, Tsankova NM, Dorfman BJ, Henchcliffe C, Piboolnurak P, Nirenberg MJ.

Parkinsonism Relat Disord. 2011 Feb;17(2):95-9. doi: 10.1016/j.parkreldis.2010.10.014. Epub 2010 Nov 27.


Chronic optical access through a polished and reinforced thinned skull.

Drew PJ, Shih AY, Driscoll JD, Knutsen PM, Blinder P, Davalos D, Akassoglou K, Tsai PS, Kleinfeld D.

Nat Methods. 2010 Dec;7(12):981-4. doi: 10.1038/nmeth.1530. Epub 2010 Oct 21.


Lipid-protein correlations in nanoscale phospholipid bilayers determined by solid-state nuclear magnetic resonance.

Kijac A, Shih AY, Nieuwkoop AJ, Schulten K, Sligar SG, Rienstra CM.

Biochemistry. 2010 Nov 2;49(43):9190-8. doi: 10.1021/bi1013722.


Topological basis for the robust distribution of blood to rodent neocortex.

Blinder P, Shih AY, Rafie C, Kleinfeld D.

Proc Natl Acad Sci U S A. 2010 Jul 13;107(28):12670-5. doi: 10.1073/pnas.1007239107. Epub 2010 Jun 28.


Automatic identification of fluorescently labeled brain cells for rapid functional imaging.

Valmianski I, Shih AY, Driscoll JD, Matthews DW, Freund Y, Kleinfeld D.

J Neurophysiol. 2010 Sep;104(3):1803-11. doi: 10.1152/jn.00484.2010. Epub 2010 Jul 7.


The glial cell response is an essential component of hypoxia-induced erythropoiesis in mice.

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.

J Clin Invest. 2009 Nov;119(11):3373-83. doi: 10.1172/JCI39378. Epub 2009 Oct 5.


Maturation of high-density lipoproteins.

Shih AY, Sligar SG, Schulten K.

J R Soc Interface. 2009 Oct 6;6(39):863-71. doi: 10.1098/rsif.2009.0173. Epub 2009 Jul 1.


Rapid determination of particle velocity from space-time images using the Radon transform.

Drew PJ, Blinder P, Cauwenberghs G, Shih AY, Kleinfeld D.

J Comput Neurosci. 2010 Aug;29(1-2):5-11. doi: 10.1007/s10827-009-0159-1. Epub 2009 May 21.


Acute vascular disruption and aquaporin 4 loss after stroke.

Friedman B, Schachtrup C, Tsai PS, Shih AY, Akassoglou K, Kleinfeld D, Lyden PD.

Stroke. 2009 Jun;40(6):2182-90. doi: 10.1161/STROKEAHA.108.523720. Epub 2009 Apr 16.


Active dilation of penetrating arterioles restores red blood cell flux to penumbral neocortex after focal stroke.

Shih AY, Friedman B, Drew PJ, Tsai PS, Lyden PD, Kleinfeld D.

J Cereb Blood Flow Metab. 2009 Apr;29(4):738-51. doi: 10.1038/jcbfm.2008.166. Epub 2009 Jan 28.


Molecular models need to be tested: the case of a solar flares discoidal HDL model.

Shih AY, Sligar SG, Schulten K.

Biophys J. 2008 Jun;94(12):L87-9. doi: 10.1529/biophysj.108.131581. Epub 2008 Mar 28.


Assembly of lipids and proteins into lipoprotein particles.

Shih AY, Arkhipov A, Freddolino PL, Sligar SG, Schulten K.

J Phys Chem B. 2007 Sep 27;111(38):11095-104. Epub 2007 Aug 14.


Disassembly of nanodiscs with cholate.

Shih AY, Freddolino PL, Sligar SG, Schulten K.

Nano Lett. 2007 Jun;7(6):1692-6. Epub 2007 May 16.


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