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Publication Open Access A compressed sensing framework for efficient dissection of neural circuits(Nature Publishing Group (NPG), 2019) Lee, Jeffrey B.; Yonar, Abdullah; Hallacy, Timothy; Shen, Ching-Han; Milloz, Josselin; Srinivasan, Jagan; Ramanathan, Sharad; Department of Physics; Kocabaş, Aşkın; Department of Physics; College of Sciences; 227753A fundamental question in neuroscience is how neural networks generate behavior. The lack of genetic tools and unique promoters to functionally manipulate specific neuronal subtypes makes it challenging to determine the roles of individual subtypes in behavior. We describe a compressed sensing-based framework in combination with non-specific genetic tools to infer candidate neurons controlling behaviors with fewer measurements than previously thought possible. We tested this framework by inferring interneuron subtypes regulating the speed of locomotion of the nematode Caenorhabditis elegans. We developed a real-time stabilization microscope for accurate long-term, high-magnification imaging and targeted perturbation of neural activity in freely moving animals to validate our inferences. We show that a circuit of three interconnected interneuron subtypes, RMG, AVB and SIA control different aspects of locomotion speed as the animal navigates its environment. Our work suggests that compressed sensing approaches can be used to identify key nodes in complex biological networks.Publication Open Access Applications of augmented reality in ophthalmology [invited](Optical Society of America (OSA), 2021) Artal, Pablo; Department of Physics; Department of Electrical and Electronics Engineering; Aydındoğan, Güneş; Kavaklı, Koray; Ürey, Hakan; Şahin, Afsun; Faculty Member; Faculty Member; Department of Physics; Department of Electrical and Electronics Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Sciences and Engineering; College of Engineering; School of Medicine; N/A; N/A; 8579; 171267Throughout the last decade, augmented reality (AR) head-mounted displays (HMDs) have gradually become a substantial part of modern life, with increasing applications ranging from gaming and driver assistance to medical training. Owing to the tremendous progress in miniaturized displays, cameras, and sensors, HMDs are now used for the diagnosis, treatment, and follow-up of several eye diseases. In this review, we discuss the current state-of-the-art as well as potential uses of AR in ophthalmology. This review includes the following topics: (i) underlying optical technologies, displays and trackers, holography, and adaptive optics; (ii) accommodation, 3D vision, and related problems such as presbyopia, amblyopia, strabismus, and refractive errors; (iii) AR technologies in lens and corneal disorders, in particular cataract and keratoconus; (iv) AR technologies in retinal disorders including age-related macular degeneration (AMD), glaucoma, color blindness, and vision simulators developed for other types of low-vision patients.Publication Open Access In vitro and in vivo biolasing of fluorescent proteins suspended in liquid microdroplet cavities(Royal Society of Chemistry (RSC), 2014) Jonas, Alexandr; Anand, Suman; McGloin, David; Department of Physics; Department of Chemistry; Bayraktar, Halil; Kiraz, Alper; Aas, Mehdi; Karadağ, Yasin; Manioğlu, Selen; Faculty Member; Faculty Member; PhD Student; Department of Physics; Department of Chemistry; College of Sciences; N/A; 22542; N/A; N/A; N/AFluorescent proteins are indispensable for selective, quantitative visualization of localization, dynamics, and interactions of key molecular constituents of live cells. Incorporation of fluorescent proteins into an optical cavity can lead to a significant increase in fluorescence signal levels due to stimulated emission and light amplification in the cavity, forming a laser with biological gain medium. Utilization of lasing emission from fluorescent biological molecules can then greatly enhance the performance of fluorescence-based biosensors benefiting from the high sensitivity of non-linear lasing processes to small perturbations in the cavity and the gain medium. Here we study optofluidic biolasers that exploit active liquid optical resonators formed by surface-supported aqueous microdroplets containing purified yellow fluorescent protein or a suspension of live E. coli bacterial cells expressing the fluorescent protein. We first demonstrate lasing in fluorescent protein solutions at concentrations as tow as 49 mu M. Subsequently, we show that a single fluorescent bacterial cell of micrometre size confined in a droplet-based cavity can serve as a laser gain medium. Aqueous droplet microcavities allow the maintenance of the bacterial cells under conditions compatible with unimpeded growth. Therefore, our results also suggest a direct route to microscopic sources of laser light with self-regenerating gain media.
Publication Metadata only Optofluidic FRET lasers using aqueous quantum dots as donors(Royal Soc Chemistry, 2016) Chen, Qiushu; Fan, Xudong; Department of Physics; Kiraz, Alper; Faculty Member; Department of Physics; College of Sciences; 22542An optofluidic FRET (fluorescence resonance energy transfer) laser is formed by putting FRET pairs inside a microcavity acting as a gain medium. This integration of an optofluidic laser and the FRET mechanism provides novel research frontiers, including sensitive biochemical analysis and novel photonic devices, such as on-chip coherent light sources and bio-tunable lasers. Here, we investigated an optofluidic FRET laser using quantum dots (QDs) as FRET donors. We achieved lasing from Cy5 as the acceptor in a QD-Cy5 pair upon excitation at 450 nm, where Cy5 has negligible absorption by itself. The threshold was approximately 14 mu J mm(-2). The demonstrated capability of QDs as donors in the FRET laser greatly improves the versatility of optofluidic laser operation due to the broad and large absorption cross section of the QDs in the blue and UV spectral regions. The excitation efficiency of the acceptor molecules through a FRET channel was also analyzed, showing that the energy transfer rate and the non-radiative Auger recombination rate of QDs play a significant role in FRET laser performance.Publication Metadata only Real time chemical and mechanical human motion monitoring with aerogel-based wearable sensors(Royal Soc Chemistry, 2020) Saraç, Feriha Eylem; Department of Electrical and Electronics Engineering; Department of Electrical and Electronics Engineering; N/A; Department of Physics; Department of Chemistry; Ergen, Onur; Çelik, Ecem; Ünal, Ahmet Hamdi; Erdolu, Mert Yusuf; Ünal, Uğur; Researcher; Faculty Member; PhD Student; Undergraduate Student; Undergraduate Student; Faculty Member; Department of Electrical and Electronics Engineering; Department of Physics; Department of Chemistry; College of Engineering; College of Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of Sciences; N/A; 272106; N/A; N/A; 42079Wearable bioelectronic systems are one of the most important tools for human health and motion monitoring. However, there is still a great challenge to fabricate high-performance flexible devices with a conformal integration of the human body and there is no single device that can collect and correlate data simultaneously from chemical and mechanical signals of the human body. We recently developed a new method to build aerogel-based strain and sweat sensors (aB-SSS) that can effectively extract real-time information by combining involuntary human motion and chemical signals due to their gradient functionalities. these sensors provide good mechanical integrity and allow high-density power generation during subtle human motion, Allowing sweat monitoring by measuring pH, ion concentration, perspiration rate,etc.