@article{li_moatti_zhang_ghashghaei_greenbaum_2022, title={Deep learning-based autofocus method enhances image quality in light-sheet fluorescence microscopy: publishers note (vol 12, pg 5214, 2021)}, volume={13}, ISSN={["2156-7085"]}, DOI={10.1364/BOE.450829}, abstractNote={[This corrects the article on p. 5214 in vol. 12, PMID: 34513252.].}, number={1}, journal={BIOMEDICAL OPTICS EXPRESS}, author={LI, Chen and Moatti, Adele and Zhang, Xuying and Ghashghaei, H. Troy and Greenbaum, Alon}, year={2022}, month={Jan}, pages={373–373} }
 @article{popowski_moatti_scull_silkstone_lutz_lópez de juan abad_george_belcher_zhu_mei_et al._2022, title={Inhalable dry powder mRNA vaccines based on extracellular vesicles}, volume={5}, ISSN={2590-2385}, url={http://dx.doi.org/10.1016/j.matt.2022.06.012}, DOI={10.1016/j.matt.2022.06.012}, abstractNote={Respiratory diseases are a global burden, with millions of deaths attributed to pulmonary illnesses and dysfunctions. Therapeutics have been developed, but they present major limitations regarding pulmonary bioavailability and product stability. To circumvent such limitations, we developed room-temperature-stable inhalable lung-derived extracellular vesicles or exosomes (Lung-Exos) as mRNA and protein drug carriers. Compared with standard synthetic nanoparticle liposomes (Lipos), Lung-Exos exhibited superior distribution to the bronchioles and parenchyma and are deliverable to the lungs of rodents and nonhuman primates (NHPs) by dry powder inhalation. In a vaccine application, severe acute respiratory coronavirus 2 (SARS-CoV-2) spike (S) protein encoding mRNA-loaded Lung-Exos (S-Exos) elicited greater immunoglobulin G (IgG) and secretory IgA (SIgA) responses than its loaded liposome (S-Lipo) counterpart. Importantly, S-Exos remained functional at room-temperature storage for one month. Our results suggest that extracellular vesicles can serve as an inhaled mRNA drug-delivery system that is superior to synthetic liposomes.}, number={9}, journal={Matter}, publisher={Elsevier BV}, author={Popowski, Kristen D. and Moatti, Adele and Scull, Grant and Silkstone, Dylan and Lutz, Halle and López de Juan Abad, Blanca and George, Arianna and Belcher, Elizabeth and Zhu, Dashuai and Mei, Xuan and et al.}, year={2022}, month={Sep}, pages={2960–2974} }
 @article{moatti_li_sivadanam_cai_ranta_piedrahita_cheng_ligler_greenbaum_2022, title={Ontogeny of cellular organization and LGR5 expression in porcine cochlea revealed using tissue clearing and 3D imaging}, volume={25}, ISSN={["2589-0042"]}, DOI={10.1016/j.isci.2022.104695}, abstractNote={•Porcine cochlear cartography unveiled via tissue clearing and light-sheet microscopy•The porcine cochlea development rate and characteristics found to be similar to humans•The LGR5 expression in the cochlear cells in pigs was different from that in mice•The porcine cochlea showed increased relevance compared to the murine model for translational research Over 11% of the world’s population experience hearing loss. Although there are promising studies to restore hearing in rodent models, the size, ontogeny, genetics, and frequency range of hearing of most rodents’ cochlea do not match that of humans. The porcine cochlea can bridge this gap as it shares many anatomical, physiological, and genetic similarities with its human counterpart. Here, we provide a detailed methodology to process and image the porcine cochlea in 3D using tissue clearing and light-sheet microscopy. The resulting 3D images can be employed to compare cochleae across different ages and conditions, investigate the ontogeny of cochlear cytoarchitecture, and produce quantitative expression maps of LGR5, a marker of cochlear progenitors in mice. These data reveal that hair cell organization, inner ear morphology, cellular cartography in the organ of Corti, and spatiotemporal expression of LGR5 are dynamic over developmental stages in a pattern not previously documented. Over 11% of the world’s population experience hearing loss. Although there are promising studies to restore hearing in rodent models, the size, ontogeny, genetics, and frequency range of hearing of most rodents’ cochlea do not match that of humans. The porcine cochlea can bridge this gap as it shares many anatomical, physiological, and genetic similarities with its human counterpart. Here, we provide a detailed methodology to process and image the porcine cochlea in 3D using tissue clearing and light-sheet microscopy. The resulting 3D images can be employed to compare cochleae across different ages and conditions, investigate the ontogeny of cochlear cytoarchitecture, and produce quantitative expression maps of LGR5, a marker of cochlear progenitors in mice. These data reveal that hair cell organization, inner ear morphology, cellular cartography in the organ of Corti, and spatiotemporal expression of LGR5 are dynamic over developmental stages in a pattern not previously documented. Normal adult human hearing covers a broad frequency range (20 Hz–20k Hz) that spans deep bass to high whistling sounds (Burns et al., 1992Burns E.M. Arehart K.H. Campbell S.L. Prevalence of spontaneous otoacoustic emissions in neonates.J. Acoust. Soc. Am. 1992; 91: 1571-1575https://doi.org/10.1121/1.402438Crossref PubMed Scopus (133) Google Scholar; Purves et al., 2001Purves D. Augustine G.J. Fitzpatrick D. Katz L.C. LaMantia A.-S. McNamara J.O. Williams S.M. The Audible spectrum.in: Neuroscience. Second edition. Sinauer Associates, 2001Google Scholar). The loss of hearing at low frequency (<3,000 Hz) affects the perception of low-pitched and deeper sounds important for sound localization, while people who suffer from high-frequency hearing loss (3,000–8,000 Hz) are unable to hear high-pitched sounds such as consonants (Hornsby and Ricketts, 2006Hornsby B.W.Y. Ricketts T.A. The effects of hearing loss on the contribution of high- and low-frequency speech information to speech understanding. II. Sloping hearing loss.J. Acoust. Soc. Am. 2006; 119: 1752-1763https://doi.org/10.1121/1.2161432Crossref PubMed Scopus (63) Google Scholar). Most rodent models that are used to study hearing loss have rather different frequency ranges from humans. An animal model that matches the human organ’s size and frequency range could guide novel treatment plans in relation to therapeutic dosage, diffusion, targetability, and efficiency. The similarity in size also facilitates the analysis of conductive hearing loss where the size and structure of the middle ear is a critical factor (Kim and Koo, 2015Kim J. Koo M. Mass and stiffness impact on the middle ear and the cochlear partition.J Audiol Otol. 2015; 19: 1-6https://doi.org/10.7874/jao.2015.19.1.1Crossref PubMed Scopus (20) Google Scholar). The porcine model can address the above gaps. In general, the pig is an attractive translational mammalian model owing to its similarity with humans in terms of size, physiology, developmental stages, and disease progression (Lunney, 2007Lunney J.K. Advances in swine biomedical model genomics.Int. J. Biol. Sci. 2007; 3: 179-184https://doi.org/10.7150/ijbs.3.179Crossref PubMed Scopus (413) Google Scholar). The porcine model, in terms of genome evolution rate, can be positioned between non-human primates and rodents, a comparison that extends to the inner ear (Hosoya et al., 2016Hosoya M. Fujioka M. Ogawa K. Okano H. Distinct expression patterns of causative genes responsible for hereditary progressive hearing loss in non-human primate cochlea.Sci. Rep. 2016; 6: 22250https://doi.org/10.1038/srep22250Crossref PubMed Scopus (37) Google Scholar). In addition, porcine gene-editing tools and somatic cell nuclear transfer (SCNT) are thoroughly developed (Dai et al., 2002Dai Y. Vaught T.D. Boone J. Chen S.-H. Phelps C.J. Ball S. Monahan J.A. Jobst P.M. McCreath K.J. Lamborn A.E. et al.Targeted disruption of the α1, 3-galactosyltransferase gene in cloned pigs.Nat. Biotechnol. 2002; 20: 251-255https://doi.org/10.1038/nbt0302-251Crossref PubMed Scopus (618) Google Scholar; Zhao et al., 2019Zhao J. Lai L. Ji W. Zhou Q. Genome editing in large animals: current status and future prospects.Natl. Sci. Rev. 2019; 6: 402-420https://doi.org/10.1093/nsr/nwz013Crossref PubMed Scopus (42) Google Scholar). This is a considerable advantage as hearing loss research has benefited tremendously from the generation of gene-edited animal models (Farooq et al., 2020Farooq R. Hussain K. Tariq M. Farooq A. Mustafa M. CRISPR/Cas9: targeted genome editing for the treatment of hereditary hearing loss.J. Appl. Genet. 2020; 61: 51-65https://doi.org/10.1007/s13353-019-00535-6Crossref PubMed Scopus (10) Google Scholar; Zou et al., 2015Zou B. Mittal R. Grati M. Lu Z. Shu Y. Tao Y. Feng Y. Xie D. Kong W. Yang S. et al.The application of genome editing in studying hearing loss.Hear. Res. 2015; 327: 102-108https://doi.org/10.1016/j.heares.2015.04.016Crossref PubMed Scopus (40) Google Scholar). In comparison with non-human primates, the pig is easier to breed and handle, and its use as an animal model has fewer ethical concerns. Specifically, the pig is suitable for auditory research given its morphology, size, and hearing range. The pig, like humans and unlike most rodents, can hear at birth and has a hearing range (42 Hz–40 kHz) that overlaps better with humans (20–20 kHz) (Heffner and Heffner, 1990Heffner R.S. Heffner H.E. Hearing in domestic pigs (Sus scrofa) and goats (Capra hircus).Hear. Res. 1990; 48: 231-240https://doi.org/10.1016/0378-5955(90)90063-uCrossref PubMed Scopus (0) Google Scholar). The low frequency (42 Hz) is closer to that of humans (20 Hz) than for mice (∼2000 Hz), Mongolian gerbils (100 Hz), or even chinchillas (50 Hz) (Engel, 2008Engel J. Gerbils can tune in.J. Physiol. 2008; 586: 919https://doi.org/10.1113/jphysiol.2007.150409Crossref PubMed Scopus (4) Google Scholar; Heffner and Heffner, 1990Heffner R.S. Heffner H.E. Hearing in domestic pigs (Sus scrofa) and goats (Capra hircus).Hear. Res. 1990; 48: 231-240https://doi.org/10.1016/0378-5955(90)90063-uCrossref PubMed Scopus (0) Google Scholar, Heffner and Heffner, 2007Heffner H.E. Heffner R.S. Hearing ranges of laboratory animals.J. Am. Assoc. Lab. Anim. Sci. 2007; 46: 20-22PubMed Google Scholar; Purves et al., 2001Purves D. Augustine G.J. Fitzpatrick D. Katz L.C. LaMantia A.-S. McNamara J.O. Williams S.M. The Audible spectrum.in: Neuroscience. Second edition. Sinauer Associates, 2001Google Scholar; Ryan, 1976aRyan A. Hearing sensitivity of the Mongolian gerbil, Meriones unguiculatis.J. Acoust. Soc. Am. 1976; 59: 1222https://doi.org/10.1121/1.380961Crossref PubMed Scopus (262) Google Scholar; Trevino et al., 2019Trevino M. Lobarinas E. Maulden A.C. Heinz M.G. The chinchilla animal model for hearing science and noise-induced hearing loss.J. Acoust. Soc. Am. 2019; 146: 3710-3732https://doi.org/10.1121/1.5132950Crossref PubMed Scopus (24) Google Scholar). Previous studies reported that the anatomy of the porcine middle ear is very similar to that of humans (Gurr et al., 2009Gurr A. Kevenhörster K. Stark T. Pearson M. Dazert S. The common pig: a possible model for teaching ear surgery.Eur. Arch. Oto-Rhino-Laryngol. 2009; 267: 213-217https://doi.org/10.1007/s00405-009-1040-6Crossref PubMed Scopus (29) Google Scholar). Additionally, the morphology of the cochlear hair cells, their organization and distribution (Guo et al., 2015Guo W. Yi H. Ren L. Chen L. Zhao L. Sun W. Yang S.-M. The morphology and electrophysiology of the cochlea of the miniature pig.Anat. Rec. 2015; 298: 494-500https://doi.org/10.1002/ar.23095Crossref Scopus (30) Google Scholar), and the maturity of the porcine auditory system at birth (Lovell and Harper, 2007Lovell J.M. Harper G.M. The morphology of the inner ear from the domestic pig (Sus scrofa).J. Microsc. 2007; 228: 345-357https://doi.org/10.1111/j.1365-2818.2007.01852.xCrossref PubMed Scopus (16) Google Scholar) are similar to humans. The porcine model could be an excellent model system both for genetic and noise-induced hearing loss. For example, several recent reports used transgenic porcine models to study deafness and explore the applicability of gene therapy for rare genetic diseases that cause hearing loss—e.g., Waardenburg syndrome (Guo and Yang, 2015Guo W. Yang S.m. Advantages of a miniature pig model in research on human hereditary hearing loss.J. Otolaryngol. 2015; 10: 105-107https://doi.org/10.1016/j.joto.2015.11.001Crossref Scopus (8) Google Scholar; Hai et al., 2017Hai T. Guo W. Yao J. Cao C. Luo A. Qi M. Wang X. Wang X. Huang J. Zhang Y. et al.Creation of miniature pig model of human Waardenburg syndrome type 2A by ENU mutagenesis.Hum. Genet. 2017; 136: 1463-1475https://doi.org/10.1007/s00439-017-1851-2Crossref PubMed Scopus (23) Google Scholar; Xu et al., 2020Xu C. Ren W. Zhang Y. Zheng F. Zhao H. Shang H. Guo W. Yang S. KIT gene mutation causes deafness and hypopigmentation in Bama miniature pigs.Am. J. Transl. Res. 2020; 12: 5095-5107PubMed Google Scholar). Measurements of behavior and physiological responses (i.e., auditory brainstem responses) to sounds have been established in wild-type pigs, thus providing a crucial step for creating a noise-induced hearing loss model (Anderson et al., 2019Anderson N.C. Thomovsky S.A. Lucas J.R. Kushiro-Banker T. Radcliffe J.S. Stewart K.R. Lay Jr., D.C. Auditory brainstem responses in weaning pigs and three ages of sows1.Transl. Animal Sci. 2019; 3: 1416-1422https://doi.org/10.1093/tas/txz123Crossref PubMed Scopus (1) Google Scholar; Heffner and Heffner, 1990Heffner R.S. Heffner H.E. Hearing in domestic pigs (Sus scrofa) and goats (Capra hircus).Hear. Res. 1990; 48: 231-240https://doi.org/10.1016/0378-5955(90)90063-uCrossref PubMed Scopus (0) Google Scholar; Kristensen and Gimsing, 1988Kristensen S. Gimsing S. Brief communication: occupational hearing impairment in pig breeders.Scand. Audiol. 1988; 17: 191-192https://doi.org/10.3109/01050398809042192Crossref PubMed Scopus (12) Google Scholar). However, there is still a significant gap to connect these in-vivo measurements and rough anatomical and mechanical studies to molecular and cellular phenomena in the porcine cochlea. The gap arises as the porcine cochlea (like human cochlea) is buried in a massive temporal bone, and it is challenging to process it for histological analysis (Knoll et al., 2019Knoll R.M. Reinshagen K.L. Barber S.R. Ghanad I. Swanson R. Smith D.H. Abdullah K.G. Jung D.H. Remenschneider A.K. Kozin E.D. High resolution computed tomography atlas of the porcine temporal bone and skull base: anatomical correlates for traumatic brain injury research.J. Neurotrauma. 2019; 36: 1029-1039https://doi.org/10.1089/neu.2018.5808Crossref PubMed Scopus (2) Google Scholar; Montgomery and Cox, 2016Montgomery S.C. Cox B.C. Whole mount dissection and immunofluorescence of the adult mouse cochlea.JoVE. 2016; 53561https://doi.org/10.3791/53561Crossref Scopus (51) Google Scholar). The benefit of using 3D imaging such as light-sheet fluorescent microscopy (LSFM) and synchrotron radiation phase-contrast imaging has been shown previously in imaging cochlea (Hutson et al., 2021Hutson K.A. Pulver S.H. Ariel P. Naso C. Fitzpatrick D.C. Light sheet microscopy of the gerbil cochlea.J. Comp. Neurol. 2021; 529: 757-785https://doi.org/10.1002/cne.24977Crossref PubMed Scopus (10) Google Scholar; Keppeler et al., 2021Keppeler D. Kampshoff C.A. Thirumalai A. Duque-Afonso C.J. Schaeper J.J. Quilitz T. Töpperwien M. Vogl C. Hessler R. Meyer A. et al.Multiscale photonic imaging of the native and implanted cochlea.Proc. Natl. Acad. Sci. USA. 2021; 118e2014472118https://doi.org/10.1073/pnas.2014472118Crossref PubMed Scopus (3) Google Scholar; Kopecky et al., 2012Kopecky B. Johnson S. Schmitz H. Santi P. Fritzsch B. Scanning thin-sheet laser imaging microscopy elucidates details on mouse ear development.Dev. Dynam. 2012; 241: 465-480https://doi.org/10.1002/dvdy.23736Crossref PubMed Scopus (27) Google Scholar; Li et al., 2021bLi H. Helpard L. Ekeroot J. Rohani S.A. Zhu N. Rask-Andersen H. Ladak H.M. Agrawal S. Three-dimensional tonotopic mapping of the human cochlea based on synchrotron radiation phase-contrast imaging.Sci. Rep. 2021; 11: 4437https://doi.org/10.1038/s41598-021-83225-wCrossref PubMed Scopus (13) Google Scholar). Some of these seminal studies show LSFM images of the mouse, gerbil, and marmoset, which are considerably smaller than the human and porcine cochlea. We have introduced a methodology to image the porcine cochlea in 3D using tissue clearing and custom light-sheet microscopy (Moatti et al., 2020Moatti A. Cai Y. Li C. Sattler T. Edwards L. Piedrahita J. Ligler F.S. Greenbaum A. Three-dimensional imaging of intact porcine cochlea using tissue clearing and custom-built light-sheet microscopy.Biomed. Opt. Express. 2020; 11: 6181https://doi.org/10.1364/BOE.402991Crossref PubMed Scopus (10) Google Scholar). This method maintains, with high fidelity, the 3D structure of the cochlea that is important to its proper function. Here we also expand this methodology for 3D histology, and we investigate the ontogeny of the porcine cochlea with respect to characteristics such as basilar membrane length and hair cell count. We have also utilized the transgenic pig model in which histone 2B (H2B)-green fluorescent protein (GFP) expresses under the control of leucine-rich repeat-containing G protein-coupled receptor 5 (LGR5) promotor (LGR5-H2B-GFP) (Polkoff et al., 2020Polkoff K.M. Chung J. Simpson S.G. Gleason K. Piedrahita J.A. In vitro validation of transgene expression in gene-edited pigs using CRISPR transcriptional activators.CRISPR J. 2020; 3: 409-418https://doi.org/10.1089/crispr.2020.0037Crossref PubMed Scopus (2) Google Scholar). Evidence from murine studies suggests that the LGR5+ supporting cells could be progenitors of hair cells and that expansion of LGR5+ cells could trigger the regeneration of hair cells in mice (Cox et al., 2014Cox B.C. Chai R. Lenoir A. Liu Z. Zhang L. Nguyen D.-H. Chalasani K. Steigelman K.A. Fang J. Cheng A.G. Zuo J. Spontaneous hair cell regeneration in the neonatal mouse cochlea in vivo.Development. 2014; 141: 816-829https://doi.org/10.1242/dev.103036Crossref PubMed Scopus (192) Google Scholar; Lenz et al., 2019Lenz D.R. Gunewardene N. Abdul-Aziz D.E. Wang Q. Gibson T.M. Edge A.S.B. Applications of Lgr5-positive cochlear progenitors (LCPs) to the study of hair cell differentiation.Front. Cell Dev. Biol. 2019; 7: 14https://doi.org/10.3389/fcell.2019.00014Crossref PubMed Scopus (16) Google Scholar; McLean et al., 2017McLean W.J. Yin X. Lu L. Lenz D.R. McLean D. Langer R. Karp J.M. Edge A.S. Clonal expansion of Lgr5-positive cells from mammalian cochlea and high-purity generation of sensory hair cells.Cell Rep. 2017; 18: 1917-1929https://doi.org/10.1016/j.celrep.2017.01.066Abstract Full Text Full Text PDF PubMed Scopus (102) Google Scholar; Shi et al., 2012Shi F. Kempfle J.S. Edge A.S.B. Wnt-responsive Lgr5-expressing stem cells are hair cell progenitors in the cochlea.J. Neurosci. 2012; 32: 9639-9648https://doi.org/10.1523/JNEUROSCI.1064-12.2012Crossref PubMed Scopus (176) Google Scholar; Wang et al., 2015Wang T. Chai R. Kim G.S. Pham N. Jansson L. Nguyen D.-H. Kuo B. May L.A. Zuo J. Cunningham L.L. Cheng A.G. Lgr5+ cells regenerate hair cells via proliferation and direct transdifferentiation in damaged neonatal mouse utricle.Nat. Commun. 2015; 6: 6613https://doi.org/10.1038/ncomms7613Crossref PubMed Scopus (111) Google Scholar). However, the spontaneous regeneration capability of LGR5+ cells seems to disappear after the first postnatal week (Lenz et al., 2019Lenz D.R. Gunewardene N. Abdul-Aziz D.E. Wang Q. Gibson T.M. Edge A.S.B. Applications of Lgr5-positive cochlear progenitors (LCPs) to the study of hair cell differentiation.Front. Cell Dev. Biol. 2019; 7: 14https://doi.org/10.3389/fcell.2019.00014Crossref PubMed Scopus (16) Google Scholar; McLean et al., 2017McLean W.J. Yin X. Lu L. Lenz D.R. McLean D. Langer R. Karp J.M. Edge A.S. Clonal expansion of Lgr5-positive cells from mammalian cochlea and high-purity generation of sensory hair cells.Cell Rep. 2017; 18: 1917-1929https://doi.org/10.1016/j.celrep.2017.01.066Abstract Full Text Full Text PDF PubMed Scopus (102) Google Scholar), which corresponds to the maturation of the cochlea in mice. Here, we seek to generate a clear LGR5 expression map in a porcine model which could be used as a guide to evaluating the regeneration potential of LGR5+ supporting cells after birth. It is important to consider that, unlike many other antibodies that we have previously tested, commercial anti-LGR5 antibodies are not reactive with porcine stem cells or with human stem cells (Tan et al., 2020Tan S.H. Swathi Y. Tan S. Goh J. Seishima R. Murakami K. Oshima M. Tsuji T. Phuah P. Tan L.T. et al.AQP5 enriches for stem cells and cancer origins in the distal stomach.Nature. 2020; 578: 437-443https://doi.org/10.1038/s41586-020-1973-xCrossref PubMed Scopus (43) Google Scholar); therefore, the utilization of the transgenic pig was paramount to unlock the expression patterns of these important LGR5+ cells. To characterize cellular LGR5+ expression and to set the foundation for a comprehensive quantitative cochlea reference atlas, we used the 3D histology method mentioned above to reconstruct a 3D frequency map of the porcine cochlea. From this map, we could easily register (i.e., transforming different datasets into one coordinate system) and compare cochleae across different ages, as well as generate a quantitative spatiotemporal map of LGR5 in supporting cells. Together with past porcine auditory studies, this work establishes the pig as an excellent large animal model for understanding hearing impairment, mapping cochlea development, and exploring regenerative medical therapies before translation into humans. Clearing, labeling, and imaging the mature cochleae of pigs required resection from the surrounding bone and an optimized tissue-clearing protocol. The BoneClear process was used to render the tissue transparent (Wang et al., 2019Wang Q. Liu K. Yang L. Wang H. Yang J. BoneClear: whole-tissue immunolabeling of the intact mouse bones for 3D imaging of neural anatomy and pathology.Cell Res. 2019; 29: 870-872https://doi.org/10.1038/s41422-019-0217-9Crossref PubMed Scopus (11) Google Scholar), and the 3D volume of the specimen was imaged using a custom adaptive light-sheet microscope, as described in our previous works (Li et al., 2021aLi C. Li C. Zhang X. Troy Ghashghaei H. Greenbaum A. Zhang X. Ghashghaei H.T. Ghashghaei H.T. Greenabum A. Greenabum A. et al.Deep learning-based autofocus method enhances image quality in light-sheet fluorescence microscopy.Biomed. Opt. Express. 2021; 12: 5214https://doi.org/10.1364/BOE.427099Crossref PubMed Scopus (9) Google Scholar; Moatti et al., 2020Moatti A. Cai Y. Li C. Sattler T. Edwards L. Piedrahita J. Ligler F.S. Greenbaum A. Three-dimensional imaging of intact porcine cochlea using tissue clearing and custom-built light-sheet microscopy.Biomed. Opt. Express. 2020; 11: 6181https://doi.org/10.1364/BOE.402991Crossref PubMed Scopus (10) Google Scholar). The custom adaptive light-sheet microscope can provide excellent optical sectioning capabilities while maintaining a fast acquisition rate (Santi et al., 2009Santi P.A. Johnson S.B. Hillenbrand M. Grandpre P.Z. Glass T.J. Leger J.R. Thin-sheet laser imaging microscopy for optical sectioning of thick tissues.Biotechniques. 2009; 46: 287-294https://doi.org/10.2144/000113087Crossref PubMed Scopus (92) Google Scholar). The resulting 3D images were processed using the data analysis pipeline that is depicted in Figure 1A . Figure 1B shows representative images of a postnatal day 0 (P0) cochlea before and after clearing, and it is evident that the sample was transparent after the clearing process. Figure 1C shows an example of a 3D image of a mature P120 cochlea acquired with our adaptive custom-built light-sheet microscope, and after digitally extracting the organ of Corti (OC). Radial view and zoomed-in images are shown in Figure 1D. The digital extraction removed considerable background noise and facilitated the quantitative analysis. In every sample that we imaged, hair cells were stained for MYO7a to provide a reference for the orientation and location of structures along the organ of Corti. The autofluorescence of the tissue also revealed important structural landmarks such as the tunnel of Corti, the tectorial membrane, and in some cases the neuronal cell bodies of the spiral ganglion. The 3D rendering of samples facilitated the extraction of invaluable information regarding the porcine cochlea, including measurements of the length of the spiral, length and count of hair cells, the 3D location of the cells with respect to each other, the estimated 3D-location map based on the Greenwood equation (Greenwood, 1990Greenwood D.D. A cochlear frequency-position function for several species--29 years later.J. Acoust. Soc. Am. 1990; 87: 2592-2605https://doi.org/10.1121/1.399052Crossref PubMed Scopus (1488) Google Scholar), and more. The estimated 3D frequency map enabled us to register cochleae that were extracted from different animals and across different ages. In general, the frequency map correlated the position of the hair cells within the organ of Corti to a specific auditory frequency responsivity. To extract the frequency map, we traced the 3D spiral trajectory indicated by the rows of both the inner and outer hair cells and recorded the trajectory coordinates from the apex to the base. Then, using the Greenwood equation (Greenwood, 1990Greenwood D.D. A cochlear frequency-position function for several species--29 years later.J. Acoust. Soc. Am. 1990; 87: 2592-2605https://doi.org/10.1121/1.399052Crossref PubMed Scopus (1488) Google Scholar), the estimated 3D frequency map of the cochlea was extracted as shown in Figure 1E. We used the experimental auditory brainstem response to find low- and high-frequency limits (Heffner and Heffner, 1990Heffner R.S. Heffner H.E. Hearing in domestic pigs (Sus scrofa) and goats (Capra hircus).Hear. Res. 1990; 48: 231-240https://doi.org/10.1016/0378-5955(90)90063-uCrossref PubMed Scopus (0) Google Scholar). The estimated frequency map can be used as a global coordinate system to compare cochlear cytoarchitecture and protein expression across different ages and animals, for instance, LGR5 expression in the porcine supporting cells (Figure 1E). Using the technology described in Figure 1 and intending to use the pig as a large animal model for hearing research, we first established the developmental timeline of the porcine cochlea in comparison to humans and other established animal models. For this purpose, we examined the cochlear structure at six different time points (embryonic day 38 (E38), E53, E80, E115/Postnatal day 0 (P0), P60, and P120; Figure 2). In E38 embryos (out of 115 gestation days), the otic capsule had already formed, and the three turns of the cochlea were clearly observed (Figure 2A). In E53, the cochlear duct had lengthened, and the apical, middle, and basal turns were recognized (Figure 2B). The formation of the scala vestibuli and scala tympani, however, was incomplete; these structures were visible in the basal turn, but not in the apical or middle turn. The Reissner’s membrane (RM) in the basal turn had begun to form. In the scala media, the sensory epithelium formation was still immature (Figure S1A). This stage resembles E15.5 in mice (Kopecky et al., 2012Kopecky B. Johnson S. Schmitz H. Santi P. Fritzsch B. Scanning thin-sheet laser imaging microscopy elucidates details on mouse ear development.Dev. Dynam. 2012; 241: 465-480https://doi.org/10.1002/dvdy.23736Crossref PubMed Scopus (27) Google Scholar). In the human fetal cochlea, the anatomical maturation of the scala tympani and scala vestibuli occurs up to gestation week 17 (GW17) (Kim et al., 2011Kim J.H. Rodríguez-Vázquez J.F. Verdugo-López S. Cho K.H. Murakami G. Cho B.H. Early fetal development of the human cochlea.Anat. Rec. 2011; 294: 996-1002https://doi.org/10.1002/ar.21387Crossref Scopus (14) Google Scholar; Locher et al., 2013Locher H. Frijns J.H. van Iperen L. de Groot J.C. Huisman M.A. Chuva de Sousa Lopes S.M. Neurosensory development and cell fate determination in the human cochlea.Neural Dev. 2013; 8: 20https://doi.org/10.1186/1749-8104-8-20Crossref PubMed Scopus (51) Google Scholar), and by GW20, the stria vascularis has developed. In E80 embryos of the pig, like GW20 in humans, P9 in mice, and P12 in rats (Kim et al., 2011Kim J.H. Rodríguez-Vázquez J.F. Verdugo-López S. Cho K.H. Murakami G. Cho B.H. Early fetal development of the human cochlea.Anat. Rec. 2011; 294: 996-1002https://doi.org/10.1002/ar.21387Crossref Scopus (14) Google Scholar; Locher et al., 2013Locher H. Frijns J.H. van Iperen L. de Groot J.C. Huisman M.A. Chuva de Sousa Lopes S.M. Neurosensory development and cell fate determination in the human cochlea.Neural Dev. 2013; 8: 20https://doi.org/10.1186/1749-8104-8-20Crossref PubMed Scopus (51) Google Scholar; Roth and Bruns, 1992Roth B. Bruns V. Postnatal development of the rat organ of Corti.Anat. Embryol. 1992; 185: 571-581https://doi.org/10.1007/BF00185616Crossref PubMed Scopus (94) Google Scholar), the cochlear duct was well developed, comprising 3.5 turns (Figure 2C); the scala vestibuli, scala tympani, and scala media were fully developed, as pointed out by arrows in Figure 2C. In the scala media, the sensory epithelium, the organ of Corti, and stria vascularis (StV) formation appeared more mature (Figure 2C). However, we identified that the height and width of the tunnel of Corti (TC) at E80 were significantly smaller than in older cochlea using a two-way ANOVA (Figure S1B). In the lesser epithelial ridge (LER), outer sulcus cells, Claudius cells, and HS were well-formed at this stage (Figures 2C and S1C). However, in the greater epithelial ridge (GER) on the neural side, cells only partially regressed and still developing into inner sulcus cells in the apex. This is in accordance with what has been reported before with cochlea maturation from base to apex (Rubel, 1984Rubel E.W. Ontogeny of auditory system function.Annu. Rev. Physiol. 1984; 46: 213-229https://doi.org/10.1146/annurev.ph.46.030184.001241Crossref PubMed Google Scholar). At postnatal day 0, the cochlear formation was completed (Figure 2D), including full regression of Kölliker’s organ and increased height and width of the TC that was not observed for E80 (Figures 2D and S1B). In a mature cochlea (Figures 2D–2F; P0, P60, and P120, respectively), we observed the stria vascularis comprising all three layers: marginal cells, intermediate cells, and basal cells (Figure S1D). The equivalent gestation period of the pig in comparison to a human, a common marmoset, and a mouse is also provided in Figure 2G (Basch et al., 2016Basch M.L. Brown II, R.M. Jen H.-I. Groves A.K. Where hearing starts: the development of the mammalian cochlea.J. Anat. 2016; 228: 233-254https://doi.org/10.1111/joa.12314Crossref PubMed Scopus (71) Google Scholar; Hosoya et al., 2021Hosoya M. Fujioka M. Murayama A.Y. Okano H. Ogawa K. The common marmoset as suitable nonhuman alternative for the analysis of primate cochlear development.FEBS J. 2021; 288: 325-353https://doi.org/10.1111/febs.15341Crossref PubMed Scopus (8) Google Scholar; Igarashi and Ishii, 1980Igarashi Y. Ishii T. Embryonic development of the human organ of Corti: electron microscopic study.Int. J. Pediatr. Otorhinolaryngol. 1980; 2: 51-62https://doi.org/10.1016/0165-5876(80)90028-2Crossref PubMed Scopus (27) Google Scholar; Kim et al., 2011Kim J.H. Rodríguez-Vázquez J.F. Verdugo-López S. Cho K.H. Murakami G. Cho B.H. Early fetal development of the human cochlea.Anat. Rec. 2011; 294: 996-1002https://doi.org/10.1002/ar.21387Crossref Scopus (14) Google Scholar; Locher et al., 2013Locher H. Frijns J.H. van Iperen L. de Groot J.C. Huisman M.A. Chuva de Sousa Lopes S.M. Neurosensory development and cell fate determination in the human cochlea.Neural Dev. 2013; 8: 20https://doi.org/10.1186/1749-8104-8-20Crossref PubMed Scopus (51) Google Scholar; Cantos et al., 2000Cantos R. Cole L.K. Acampora D. Simeone A. Wu D.K. Patterning of the mammalian cochlea.Proc. Natl. Acad. Sci. USA. 2000; 97: 11707-11713https://doi.org/10.1073/pnas.97.22.11707Crossref PubMed Scopus (104) Google Scholar; Roccio and Edge, 2019Roccio M. Edge A. Inner ear organoids: new tools to understand neurosensory cell development, d}, number={8}, journal={ISCIENCE}, author={Moatti, Adele and Li, Chen and Sivadanam, Sasank and Cai, Yuheng and Ranta, James and Piedrahita, Jorge A. and Cheng, Alan G. and Ligler, Frances S. and Greenbaum, Alon}, year={2022}, month={Aug} }
 @article{moatti_mineo-foley_gupta_sachan_narayan_2022, title={Spin Engineering of VO2 Phase Transitions and Removal of Structural Transition}, volume={14}, ISSN={["1944-8252"]}, url={https://doi.org/10.1021/acsami.1c24978}, DOI={10.1021/acsami.1c24978}, abstractNote={Vanadium dioxide undergoes a metal-to-insulator transition, where the energy of electron-electron, electron-lattice, spin-spin, and spin-lattice interactions are of the same order of magnitude. This leads to the coexistence of electronic and structural transitions in VO2 that limit the lifetime and speed of VO2-based devices. However, the closeness of interaction energy of lattice-electron-spin can be turned into an opportunity to induce some transitions while pinning others via external stimuli. That is, the contribution of spin, charge, orbital, and lattice degrees of freedom can be manipulated. In this study, spin engineering has been exploited to affect the spin-related interactions in VO2 by introducing a ferromagnetic Ni layer. The coercivity in the Ni layer is engineered by controlling the shape anisotropy via kinetics of growth. Using spin engineering, the structural pinning of the monoclinic M2 phase of VO2 is successfully achieved, while the electronic and magnetic transitions take place.}, number={10}, journal={ACS APPLIED MATERIALS & INTERFACES}, publisher={American Chemical Society (ACS)}, author={Moatti, Adele and Mineo-Foley, Gabrielle and Gupta, Siddharth and Sachan, Ritesh and Narayan, Jay}, year={2022}, month={Mar}, pages={12883–12892} }
 @article{li_moatti_zhang_ghashghaei_greenabum_2021, title={Deep learning-based autofocus method enhances image quality in light-sheet fluorescence microscopy}, volume={12}, ISSN={["2156-7085"]}, url={http://dx.doi.org/10.1364/boe.427099}, DOI={10.1364/BOE.427099}, abstractNote={Light-sheet fluorescence microscopy (LSFM) is a minimally invasive and high throughput imaging technique ideal for capturing large volumes of tissue with sub-cellular resolution. A fundamental requirement for LSFM is a seamless overlap of the light-sheet that excites a selective plane in the specimen, with the focal plane of the objective lens. However, spatial heterogeneity in the refractive index of the specimen often results in violation of this requirement when imaging deep in the tissue. To address this issue, autofocus methods are commonly used to refocus the focal plane of the objective-lens on the light-sheet. Yet, autofocus techniques are slow since they require capturing a stack of images and tend to fail in the presence of spherical aberrations that dominate volume imaging. To address these issues, we present a deep learning-based autofocus framework that can estimate the position of the objective-lens focal plane relative to the light-sheet, based on two defocused images. This approach outperforms or provides comparable results with the best traditional autofocus method on small and large image patches respectively. When the trained network is integrated with a custom-built LSFM, a certainty measure is used to further refine the network's prediction. The network performance is demonstrated in real-time on cleared genetically labeled mouse forebrain and pig cochleae samples. Our study provides a framework that could improve light-sheet microscopy and its application toward imaging large 3D specimens with high spatial resolution.}, number={8}, journal={BIOMEDICAL OPTICS EXPRESS}, publisher={The Optical Society}, author={Li, Chen and Moatti, Adele and Zhang, Xuying and Ghashghaei, H. Troy and Greenabum, Alon}, year={2021}, month={Aug}, pages={5214–5226} }
 @article{carter_popowski_cheng_greenbaum_ligler_moatti_2021, title={Enhancement of Bone Regeneration Through the Converse Piezoelectric Effect, A Novel Approach for Applying Mechanical Stimulation}, volume={9}, ISSN={["2576-3113"]}, url={https://doi.org/10.1089/bioe.2021.0019}, DOI={10.1089/bioe.2021.0019}, abstractNote={Serious bone injuries have devastating effects on the lives of patients including limiting working ability and high cost. Orthopedic implants can aid in healing injuries to an extent that exceeds the natural regenerative capabilities of bone to repair fractures or large bone defects. Autografts and allografts are the standard implants used, but disadvantages such as donor site complications, a limited quantity of transplantable bone, and high costs have led to an increased demand for synthetic bone graft substitutes. However, replicating the complex physiological properties of biological bone, much less recapitulating its complex tissue functions, is challenging. Extensive efforts to design biocompatible implants that mimic the natural healing processes in bone have led to the investigation of piezoelectric smart materials because the bone has natural piezoelectric properties. Piezoelectric materials facilitate bone regeneration either by accumulating electric charge in response to mechanical stress, which mimics bioelectric signals through the direct piezoelectric effect or by providing mechanical stimulation in response to electrical stimulation through the converse piezoelectric effect. Although both effects are beneficial, the converse piezoelectric effect can address bone atrophy from stress shielding and immobility by improving the mechanical response of a healing defect. Mechanical stimulation has a positive impact on bone regeneration by activating cellular pathways that increase bone formation and decrease bone resorption. This review will highlight the potential of the converse piezoelectric effect to enhance bone regeneration by discussing the activation of beneficial cellular pathways, the properties of piezoelectric biomaterials, and the potential for the more effective administration of the converse piezoelectric effect using wireless control.}, journal={BIOELECTRICITY}, publisher={Mary Ann Liebert Inc}, author={Carter, Amber and Popowski, Kristen and Cheng, Ke and Greenbaum, Alon and Ligler, Frances S. and Moatti, Adele}, year={2021}, month={Sep} }
 @article{moatti_sachan_narayan_2020, title={Mechanism of strain relaxation: key to control of structural and electronic transitions in VO2 thin-films}, url={https://doi.org/10.1080/21663831.2019.1681030}, DOI={10.1080/21663831.2019.1681030}, abstractNote={VO2 is a smart transition-metal oxide, which exhibits a tetragonal-to-monoclinic phase transition at ∼ 68°C. We report a case where both tetragonal and monoclinic phases exist in relaxed and strain...}, journal={Materials Research Letters}, author={Moatti, Adele and Sachan, Ritesh and Narayan, Jagdish}, year={2020}, month={Jan} }
 @article{moatti_cai_li_sattler_edwards_piedrahita_ligler_greenbaum_2020, title={Three-dimensional imaging of intact porcine cochlea using tissue clearing and custom-built light-sheet microscopy}, volume={11}, ISSN={["2156-7085"]}, url={http://dx.doi.org/10.1364/boe.402991}, DOI={10.1364/BOE.402991}, abstractNote={Hearing loss is a prevalent disorder that affects people of all ages. On top of the existing hearing aids and cochlear implants, there is a growing effort to regenerate functional tissues and restore hearing. However, studying and evaluating these regenerative medicine approaches in a big animal model (e.g. pigs) whose anatomy, physiology, and organ size are similar to a human is challenging. In big animal models, the cochlea is bulky, intricate, and veiled in a dense and craggy otic capsule. These facts complicate 3D microscopic analysis that is vital in the cochlea, where structure-function relation is time and again manifested. To allow 3D imaging of an intact cochlea of newborn and juvenile pigs with a volume up to ∼ 250 mm 3 , we adapted the BoneClear tissue clearing technique, which renders the bone transparent. The transparent cochleae were then imaged with cellular resolution and in a timely fashion, which prevented bubble formation and tissue degradation, using an adaptive custom-built light-sheet fluorescence microscope. The adaptive light-sheet microscope compensated for deflections of the illumination beam by changing the angles of the beam and translating the detection objective while acquiring images. Using this combination of techniques, macroscopic and microscopic properties of the cochlea were extracted, including the density of hair cells, frequency maps, and lower frequency limits. Consequently, the proposed platform could support the growing effort to regenerate cochlear tissues and assist with basic research to advance cures for hearing impairments.}, number={11}, journal={BIOMEDICAL OPTICS EXPRESS}, publisher={The Optical Society}, author={Moatti, Adele and Cai, Yuheng and Li, Chen and Sattler, Tyler and Edwards, Laura and Piedrahita, Jorge and Ligler, Frances S. and Greenbaum, Alon}, year={2020}, month={Nov}, pages={6181–6196} }
 @article{moatti_sachan_narayan_2020, title={Volatile and non-volatile behavior of metal–insulator transition in VO2 through oxygen vacancies tunability for memory applications}, url={https://doi.org/10.1063/5.0006671}, DOI={10.1063/5.0006671}, abstractNote={Vanadium dioxide can be utilized as a Mott memory, where “0” and “1” states can be defined by insulator and metal states, respectively. In stoichiometric VO2, voltage or joule heating can trigger the transition and activate the volatile behavior. As a result, there is a constant need for such a stimulus to preserve the “1” state. If oxygen vacancies are introduced to the system while maintaining the crystal structure of the VO2 phase, the state “1” can be obtained/written permanently. That is, there is no need for external stimuli to read and recall the data. Here, we have shown the reversibility of the behavior and structure of the VO2 when oxygen vacancies are introduced to and removed from the system. The structure and relaxation mechanism are discussed, as well. This research paves the way for the nonvolatile application of VO2 in neuromorphic devices.}, journal={Journal of Applied Physics}, author={Moatti, Adele and Sachan, Ritesh and Narayan, Jagdish}, year={2020}, month={Jul} }
 @article{moatti_sachan_kumar_narayan_2019, title={Catalyst-assisted epitaxial growth of ferromagnetic TiO2/TiN nanowires}, volume={167}, ISSN={1359-6454}, url={http://dx.doi.org/10.1016/J.ACTAMAT.2019.01.052}, DOI={10.1016/j.actamat.2019.01.052}, abstractNote={Abstract We report a novel method of growth for single-crystalline TiO2/TiN nanowires through oxidation of epitaxial TiN nanowires on Si-SiO2 (amorphous) and c-sapphire (crystalline) as practical substrates. We propose that the laser ablated Ti and N diffuse into molten Au to form TiN nanodots where the growth rate of nanowires is directly proportional to the laser ablation flux due to high diffusion in molten Au. The TiN nanowires were grown by Pulsed Laser Deposition method using Au as a catalyst. The TiN nanowires were then oxidized to create TiO2/TiN core-shell nanowires. The growth of TiO2 (rutile) occurs by domain matching epitaxy paradigm in such a way that (002) planes of the TiO2 match with (200) plane of TiN, where the TiO2 thickness can be tuned by adjustment of oxidation time and temperature. This design provides a core-shell structure of TiO2/TiN nanowires integrated with silicon and sapphire substrates. The Rutile TiO2 nanowires show ferromagnetic behavior, while the as-grown TiN exhibits diamagnetic behavior. The SEM, TEM, and EBSD are used to characterize the microstructure and atomic alignments of TiO2 nanowires. The simple method of oxidation combined with tunable magnetic properties provides benefits to many smart applications where the magnetic field can be used as an external stimulation.}, journal={Acta Materialia}, publisher={Elsevier BV}, author={Moatti, A. and Sachan, R. and Kumar, D. and Narayan, J.}, year={2019}, month={Apr}, pages={112–120} }
 @article{moatti_sachan_cooper_narayan_2019, title={Electrical Transition in Isostructural VO2 Thin-Film Heterostructures}, volume={9}, ISSN={2045-2322}, url={http://dx.doi.org/10.1038/S41598-019-39529-Z}, DOI={10.1038/s41598-019-39529-z}, abstractNote={Abstract Control over the concurrent occurrence of structural (monoclinic to tetragonal) and electrical (insulator to the conductor) transitions presents a formidable challenge for VO 2 -based thin film devices. Speed, lifetime, and reliability of these devices can be significantly improved by utilizing solely electrical transition while eliminating structural transition. We design a novel strain-stabilized isostructural VO 2 epitaxial thin-film system where the electrical transition occurs without any observable structural transition. The thin-film heterostructures with a completely relaxed NiO buffer layer have been synthesized allowing complete control over strains in VO 2 films. The strain trapping in VO 2 thin films occurs below a critical thickness by arresting the formation of misfit dislocations. We discover the structural pinning of the monoclinic phase in (10 ± 1 nm) epitaxial VO 2 films due to bandgap changes throughout the whole temperature regime as the insulator-to-metal transition occurs. Using density functional theory, we calculate that the strain in monoclinic structure reduces the difference between long and short V-V bond-lengths (Δ V − V ) in monoclinic structures which leads to a systematic decrease in the electronic bandgap of VO 2 . This decrease in bandgap is additionally attributed to ferromagnetic ordering in the monoclinic phase to facilitate a Mott insulator without going through the structural transition.}, number={1}, journal={Scientific Reports}, publisher={Springer Science and Business Media LLC}, author={Moatti, Adele and Sachan, Ritesh and Cooper, Valentino R and Narayan, Jagdish}, year={2019}, month={Feb} }
 @article{sachan_hachtel_bhaumik_moatti_prater_idrobo_narayan_2019, title={Emergence of shallow energy levels in B-doped Q-carbon: A high-temperature superconductor}, volume={174}, url={https://doi.org/10.1016/j.actamat.2019.05.013}, DOI={10.1016/j.actamat.2019.05.013}, abstractNote={Abstract We report the spectroscopic demonstration of the shallow-level energy states in the recently discovered B-doped Q-carbon Bardeen-Cooper-Schrieffer (BCS) high-temperature superconductor. The Q-carbon is synthesized by ultrafast melting and quenching, allowing for high B-doping concentrations which increase the superconducting transition temperature (Tc) to 36 K (compared to 4 K for B-doped diamond). The increase in Tc is attributed to the increased density of energy states near the Fermi level in B-doped Q-carbon, which give rise to superconducting states via strong electron-phonon coupling below Tc. These shallow-level energy states, however, are challenging to map due to limited spatial and energy resolution. Here, we use ultrahigh energy resolution monochromated electron energy-loss spectroscopy (EELS), to detect and visualize the newly formed shallow-level energy states (vibrational modes) near the Fermi level (ranging 30–100 meV) of the B-doped Q-carbon. With this study, we establish the significance of high-resolution EELS in understanding the superconducting behavior of BCS superconducting C-based materials, which demonstrate a phenomenal enhancement in the presence of shallow-level energy states.}, journal={Acta Materialia}, publisher={Elsevier BV}, author={Sachan, Ritesh and Hachtel, Jordan A. and Bhaumik, Anagh and Moatti, Adele and Prater, John and Idrobo, Juan Carlos and Narayan, Jagdish}, year={2019}, month={Aug}, pages={153–159} }
 @article{gupta_moatti_bhaumik_sachan_narayan_2019, title={Room-temperature ferromagnetism in epitaxial titanium nitride thin films}, volume={166}, ISSN={1359-6454}, url={http://dx.doi.org/10.1016/J.ACTAMAT.2018.12.041}, DOI={10.1016/j.actamat.2018.12.041}, abstractNote={Abstract Localized charge injection by formation of vacancies provides an attractive platform for the development of multifunctional nanomaterials with direct implications in spintronics. However, further progress in spintronics critically depends on a deeper understanding of polaronic interactions between the localized charge states. This report is focused on TiN metallic system, which exhibits Pauli paramagnetism due to the absence of unpaired localized spin states. Here, nitrogen vacancies (VN) are used as a variable to tune the magnetic properties of epitaxial TiN thin films by thermal annealing in high-vacuum and N2 environment. Systematic introduction of VN generates robust magnetic ordering in vacuum-annealed TiN1-x films, with Curie temperature (TC) ∼700 K, and saturation magnetization (Ms) at absolute zero of 13.6 emu g−1. The signature spin-glass behavior below the irreversibility temperature (Tir ∼40 K) indicates the Ruderman-Kittel-Kasuya-Yosida (RKKY) coupling interactions between the unpaired localized spin-states. Through spatially resolved electron energy-loss spectroscopy, we have determined the generation of unpaired localized spins at Ti+2 polarons with ∼12 ± 2 at.% VN in TiN1-x films. Such a large concentration of VN results in increased spin stiffness and high TC. These findings open a definitive pathway for tuning the magnetic nature of metallic materials for spintronic applications.}, journal={Acta Materialia}, publisher={Elsevier BV}, author={Gupta, Siddharth and Moatti, Adele and Bhaumik, Anagh and Sachan, Ritesh and Narayan, Jagdish}, year={2019}, month={Mar}, pages={221–230} }
 @article{moatti_sachan_prater_narayan_2018, title={An optimized sample preparation approach for atomic resolution in situ studies of thin films}, volume={81}, ISSN={1059-910X 1097-0029}, url={http://dx.doi.org/10.1002/JEMT.23130}, DOI={10.1002/jemt.23130}, abstractNote={This work provides the details of a simple and reliable method with less damage to prepare electron transparent samples for in situ studies in scanning/transmission electron microscopy. In this study, we use epitaxial VO2 thin films grown on c-Al2O3 by pulsed laser deposition, which have a monoclinic–rutile transition at ~68°C. We employ an approach combining conventional mechanical wedge-polishing and Focused Ion beam to prepare the electron transparent samples of epitaxial VO2 thin films. The samples are first mechanically wedge-polished and ion-milled to be electron transparent. Subsequently, the thin region of VO2 films are separated from the rest of the polished sample using a focused ion beam and transferred to the in situ electron microscopy test stage. As a critical step, carbon nanotubes are used as connectors to the manipulator needle for a soft transfer process. This is done to avoid shattering of the brittle substrate film on the in situ sample support stage during the transfer process. We finally present the atomically resolved structural transition in VO2 films using this technique. This approach significantly increases the success rate of high-quality sample preparation with less damage for in situ studies of thin films and reduces the cost and instrumental/user errors associated with other techniques. The present work highlights a novel, simple, reliable approach with reduced damage to make electron transparent samples for atomic-scale insights of temperature-dependent transitions in epitaxial thin film heterostructures using in situ TEM studies.}, number={11}, journal={Microscopy Research and Technique}, publisher={Wiley}, author={Moatti, Adele and Sachan, Ritesh and Prater, John and Narayan, Jagdish}, year={2018}, month={Oct}, pages={1250–1256} }
 @article{moatti_narayan_2018, title={High-quality TiN/AlN thin film heterostructures on c-sapphire}, volume={145}, ISSN={["1873-2453"]}, url={https://doi.org/10.1016/j.actamat.2017.11.044}, DOI={10.1016/j.actamat.2017.11.044}, abstractNote={We have developed TiN/AlN/c-sapphire epitaxial heterostructures and compared it with TiN/c-sapphire epitaxial heterostructures, needed for GaN-based LEDs and lasers. AlN is used as a buffer layer to provide a high misfit strain and facilitate the 2D growth on sapphire. The large misfit strain between sapphire and AlN makes this substrate a great candidate for GaN-based devices because it guarantees a full relaxation of AlN thin films through domain matching epitaxy paradigm. TiN can also act as an excellent contact and bottom electrode for Ⅲ-Ⅴ nitrides. Also, the introduction of TiN as a buffer layer decreases the critical thickness beyond which dislocations can grow in GaN thin films due to higher misfit strain compared to sapphire, which also improves the quality of potential GaN thin films. The selected-area-electron-diffraction patterns, scanning transmission electron microscopy, and transmission Kikuchi diffractions along with atomic arrangement simulations revealed that films are epitaxial with the following relationships: TiN<101>‖AlN[1¯21¯0]‖sapphire[011¯0] (in-plane), and TiN<111>‖AlN[0001]‖sapphire[0001] (out-of-plane). This is equivalent to a 30° rotation of Al basal plane in AlN with respect to that in sapphire. In TiN/c-sapphire epitaxial platforms, there is a 30° rotation: TiN<101>‖sapphire[011¯0] (in-plane), and TiN<111>‖sapphire[0001] (out-of-plane). It is shown that these heterostructures are fully relaxed in terms of misfit strains and only thermal strain stays as unrelaxed. The domain matching epitaxy paradigm is used to rationalize the epitaxial growth. The details of dislocations nucleation and glide in these heterostructures were studied and the results also discussed to elucidate the mechanism of strain relaxation.}, journal={ACTA MATERIALIA}, publisher={Elsevier BV}, author={Moatti, A. and Narayan, J.}, year={2018}, month={Feb}, pages={134–141} }
 @article{jaipan_nannuri_mucha_singh_xu_moatti_narayan_fialkova_kotoka_yarmolenko_et al._2018, title={Influence of Gold Catalyst on the Growth o Titanium Nitride Nanowires}, volume={7}, ISSN={["2169-4303"]}, DOI={10.1166/mat.2018.1571}, number={5}, journal={MATERIALS FOCUS}, author={Jaipan, Panupong and Nannuri, Chandra and Mucha, Nikhil Reddy and Singh, Mayur P. and Xu, Zhigang and Moatti, Adele and Narayan, Jay and Fialkova, Svitlana and Kotoka, Ruben and Yarmolenko, Sergey and et al.}, year={2018}, month={Oct}, pages={720–725} }
 @article{moatti_sachan_gupta_narayan_2018, title={Vacancy-Driven Robust Metallicity of Structurally Pinned Monoclinic Epitaxial VO2 Thin Films}, volume={11}, ISSN={1944-8244 1944-8252}, url={http://dx.doi.org/10.1021/ACSAMI.8B17879}, DOI={10.1021/acsami.8b17879}, abstractNote={Vanadium dioxide (VO2) is a strongly correlated material with 3d electrons, which exhibits temperature-driven insulator-to-metal transition with a concurrent change in the crystal symmetry. Interestingly, even modest changes in stoichiometry-induced orbital occupancy dramatically affect the electrical conductivity of the system. Here, we report a successful transformation of epitaxial monoclinic VO2 thin films from a conventionally insulating to permanently metallic behavior by manipulating the electron correlations. These ultrathin (∼10 nm) epitaxial VO2 films were grown on NiO(111)/Al2O3(0001) pseudomorphically, where the large misfit between NiO and Al2O3 were fully relaxed by domain-matching epitaxy. Complete conversion from an insulator to permanent metallic phase is achieved through injecting oxygen vacancies ( x ∼ 0.20 ± 0.02) into the VO2- x system via annealing under high vacuum (∼5 × 10-7 Torr) and increased temperature (450 °C). Systematic introduction of oxygen vacancies partially converts V4+ to V3+ and generates unpaired electron charges which result in the emergence of donor states near the Fermi level. Through the detailed study of the vibrational modes by Raman spectroscopy, hardening of the V-V vibrational modes and stabilization of V-V dimers are observed in vacuum-annealed VO2 films, providing conclusive evidence for stabilization of a monoclinic phase. This ultimately leads to convenient free-electron transport through the oxygen-deficient VO2- x thin films, resulting in metallic characteristics at room temperature. With these results, we propose a defect engineering pathway through the control of oxygen vacancies to tune electrical and optical properties in epitaxial monoclinic VO2.}, number={3}, journal={ACS Applied Materials & Interfaces}, publisher={American Chemical Society (ACS)}, author={Moatti, Adele and Sachan, Ritesh and Gupta, Siddharth and Narayan, Jagdish}, year={2018}, month={Dec}, pages={3547–3554} }
 @article{moatti_sachan_prater_narayan_2017, title={Control of Structural and Electrical Transitions of VO2 Thin Films}, volume={9}, ISSN={["1944-8252"]}, url={https://doi.org/10.1021/acsami.7b05620}, DOI={10.1021/acsami.7b05620}, abstractNote={Unstrained and defect-free VO2 single crystals undergo structural (from high-temperature tetragonal to low-temperature monoclinic phase) and electronic phase transitions simultaneously. In thin films, however, in the presence of unrelaxed strains and defects, structural (Peierls) and electronic (Mott) transitions are affected differently, and are separated. In this paper, we have studied the temperature dependence of structural and electrical transitions in epitaxially grown vanadium dioxide films on (0001) sapphire substrates. These results are discussed using a combined kinetics and thermodynamics approach, where the velocity of phase transformation is controlled largely by kinetics, and the formation of intermediate phases is governed by thermodynamic considerations. We have grown (020) VO2 on (0001) sapphire with two (001) and (100) in-plane orientations rotated by 122°. The (100)-oriented crystallites are fully relaxed by the paradigm of domain-matching epitaxy, whereas (001) crystallites are not relaxed and exhibit the formation of a few atomic layers of thin interfacial V2O3. We have studied the structural (Peierls) transition by temperature-dependent in situ X-ray diffraction measurements, and electronic (Mott) transition by electrical resistance measurements. A delay of 3 °C is found between the onset of structural (76 °C) and electrical (73 °C) transitions in the heating cycle. This temporal lag in the transition is attributed to the residual strain existing in the VO2 crystallites. With this study, we suggest that the control of structural and electrical transitions is possible by varying the transition activation barrier for atomic jumps through the strain engineering.}, number={28}, journal={ACS APPLIED MATERIALS & INTERFACES}, publisher={American Chemical Society (ACS)}, author={Moatti, Adele and Sachan, Ritesh and Prater, John and Narayan, Jay}, year={2017}, month={Jul}, pages={24298–24307} }
 @article{moatti_bayati_narayan_2016, title={Epitaxial growth of rutile TiO2 thin films by oxidation of TiN/Si{100} heterostructure}, volume={103}, ISSN={["1873-2453"]}, url={https://doi.org/10.1016/j.actamat.2015.10.022}, DOI={10.1016/j.actamat.2015.10.022}, abstractNote={Abstract We have integrated epitaxial TiO 2 on a TiN/Si(100) platform through oxidation of TiN. The oxidation of TiN(100)/Si(100) results in the formation of an epitaxial rutile-TiO 2 (r-TiO 2 ) with a [110] out-of-plane orientation. We have studied in detail the r-TiO 2 epitaxy and the epitaxial relationship is determined to be TiO 2 (1 1 ¯ 0)||TiN(100) and TiO 2 (110)||TiN(110). We rationalized this epitaxy using the domain matching epitaxy paradigm. Below the r-TiO 2 epitaxial layer, we observed cuboids, which are mostly voids. We described the mechanism of oxidation where Ti out diffusion during oxidation leads to collapse of the nitrogen octahedron. This collapse makes neighboring Ti bonds weaker, promoting these Ti atoms to diffuse out next. Thus, cuboids filled with atomic nitrogen are formed, which then form N 2 gas. The N 2 pressure in these cuboids was estimated to be as high as 359 MPa, assuming all N 2 is retained in the cuboids. This pressure can exceed the fracture stress of TiO 2 and leads to rupture of thin TiO 2 surface, which has been observed under certain conditions.}, journal={ACTA MATERIALIA}, publisher={Elsevier BV}, author={Moatti, A. and Bayati, R. and Narayan, J.}, year={2016}, month={Jan}, pages={502–511} }
 @article{moatti_bayati_singamaneni_narayan_2016, title={Epitaxial integration of TiO2 with Si(100) through a novel approach of oxidation of TiN/Si(100) epitaxial heterostructure}, volume={1}, ISSN={["2059-8521"]}, DOI={10.1557/adv.2016.463}, number={37}, journal={MRS ADVANCES}, author={Moatti, A. and Bayati, R. and Singamaneni, S. and Narayan, J.}, year={2016}, pages={2629–2634} }
 @article{moatti_bayati_singamaneni_narayan_2016, title={Thin film bi-epitaxy and transition characteristics of TiO2/TiN buffered VO2 on Si(100) substrates}, volume={1}, ISSN={["2059-8521"]}, DOI={10.1557/adv.2016.544}, abstractNote={Bi-epitaxial VO2 thin films with [011] out-of-plane orientation were integrated with Si(100) substrates through TiO2/TiN buffer layers. At the first step, TiN is grown epitaxially on Si(100), where a cube-on-cube epitaxy is achieved. Then, TiN was oxidized in-situ ending up having epitaxial r-TiO2. Finally, VO2 was deposited on top of TiO2. The alignment across the interfaces was stablished as VO2(011)║TiO2(110)║TiN(100)║Si(100) and VO2(110) /VO2(010)║TiO2(011)║TiN(112)║Si(112). The inter-planar spacing of VO2(010) and TiO2(011) equal to 2.26 and 2.50 A, respectively. This results in a 9.78% tensile misfit strain in VO2(010) lattice which relaxes through 9/10 alteration domains with a frequency factor of 0.5, according to the domain matching epitaxy paradigm. Also, the inter-planar spacing of VO2(011) and TiO2(011) equals to 3.19 and 2.50 A, respectively. This results in a 27.6% compressive misfit strain in VO2(011) lattice which relaxes through 3/4 alteration domains with a frequency factor of 0.57. We studied semiconductor to metal transition characteristics of VO2/TiO2/TiN/Si heterostructures and established a correlation between intrinsic defects and magnetic properties.}, number={37}, journal={MRS ADVANCES}, author={Moatti, Adele and Bayati, Reza and Singamaneni, Srinivasa Rao and Narayan, Jagdish}, year={2016}, pages={2635–2640} }