Timothy J. Gardner's research while affiliated with University of Oregon and other places

... [201][202][203][204] The generally studied silicate materials is the ORMOCER ® (Organic Modified Ceramic), which has been applied in numerous photonic applications, and also as a scaffold for cell growth and biomolecule immobilization applications. [205][206][207][208][209] Combining silicon alkoxides with monomers and other metal alkoxides makes the modification of the material properties possible for specific TPL applications, such as the silicon-zirconium hybrid SZ2080™, which is a transparent, biocompatible, and mechanically stable hybrid that can be used for complex 3D structures without shrinkage ( Figure 3f). [119,[210][211][212][213][214][215][216] So far, different variants of silicon-zirconium composites have been investigated. ...

... 48 Researchers have used PAFs to cluster vocalisations of zebra finches (Taeniopygia 49 guttata) [18], baboons (Papio ursinus) [19], bottlenose dolphins (Tursiops 50 truncatus) [20], gibbons (Hylobates funereus) [21], and mice (Mus musculus) [22,23]. 51 For instance, Elie et al. [18] used 22 PAFs extracted using the Biosound package [24] to 52 cluster zebra finch (Taeniopygia guttata) vocalisations, Sainburg et al. [25] used 18 53 features from the same package to visualise and cluster vocalisations from 20 species, 54 Clink and Klinck [21] used Mel Frequency Cepstral Coefficients (MFCCs) to cluster 55 gibbon (Hylobates funereus) calls by individual, and Van Segbroeck et al. [22] used a 56 gammatone filterbank to cluster mice (Mus musculus) vocalisations. Alternatively, to 57 capture spectro-temporal variations, the concatenation of consecutive spectrogram 58 frames can be used [25,26]. ...

... However, it is still unclear how various neurotransmitters, hormones and neurotrophins regulate songbird singing behavior through related neural pathways. Optogenetics, chemogenetics and other targeted neural pathway manipulation techniques can be a key link between behavior and neural activity (Singh Alvarado et al., 2021). In the meantime, the related cell types and gene expression patterns of birds and mammals were compared by single-cell sequencing technology to reveal their evolutionary analogy (Colquitt et al., 2021). ...

... While cellular-resolution devices typically offer small fields of view (FOVs) covering less than one vertebra, large-FOV microscopes ('macroscopes') provide limited spatiotemporal resolution, sensitivity and contrast or are incompatible with use in freely moving mice 2,5,6 . Wearable widefield macroscopes with millimeter-sized FOVs have recently been developed [7][8][9][10] . Still, none offer the combined cellular resolution, frame rates, sensitivity and weights necessary for spinal cord imaging in mice. ...

... Fixed and sectioned tissues, rather than entire brains, still dominate studies of zebra finch song system projections. Though not a new technique in itself, organotypic brain slices have been recently used to image the finch brain at a higher resolution, including functional imaging using calcium sensors (Shen et al., 2017). The use of brain slices allows better access to tissues for specific labeling of structures and may prove useful for introducing other biosensors or looking at glial function. ...

... The same tools can be applied to differentiating between individuals in the same recording environment (e.g., Adi et al., 2010;Mielke and Zuberbühler, 2013). Most recent approaches rely on deep neural networks to detect vocalizations in noisy environments (e.g., Stowell et al., 2019;Cohen et al., 2020a). Current neural networks generally rely on some combination of convolutional filters in the temporal-frequency space of spectrograms (Convolutional Neural Networks or CNNs, Figure 3B) and temporal-recurrence (Recurrent Neural Networks, or RNNs, Figure 3C). ...

... Time-points at Days 1, 3, and 7 were considered sufficient given the regenerative capacity of musculoskeletal tissues and the decreased time-to-stability this imparts for implantable devices. [27][28][29][30] The rat was placed into a clear chamber and allowed to move freely. Video with simultaneous recording shows that movement of the implanted muscle group was associated with increased signal (Video S1, Supporting Information). ...

... No other mammalian species produce vocalizations that are as richly structured as human language. Many songbird species could produce songs that have complex syntax with syllable sequences following certain rules [1][2][3][4], which are flexible in different contexts [5]. Therefore, songbirds have been widely studied as an animal model to investigate the evolution and neural mechanisms of complex vocal sequencing [6,7]. ...

... A number of recording channels can be increased using hundreds of splayed microfibers, each following a path of least resistance through tissue. 356 More recently, a proof-of-principle demonstration of deep brain imaging has been achieved by scanning the excitation beam through an implanted multimodal optical fiber to form an image (Sec. 4.4). ...

... In addition to improvements in materials for SLA, there are also great opportunities in the customization of 3D printers. In a system similar to a two-photon DLW system, Pearre et al. (122) used resonant mirrors to speed up printing but maintain 1-µm resolution. This printer was capable of creating approximately 400 × 400 x 400 µm 3 cubes in 25 s. ...