Effective data reduction algorithm for topological data analysis

One of the most interesting tools that have recently entered the data science toolbox is topological data analysis (TDA). With the explosion of available data sizes and dimensions, identifying and extracting the underlying structure of a given dataset is a fundamental challenge in data science, and TDA provides a methodology for analyzing the shape of a dataset using tools and prospects from algebraic topology. However, the computational complexity makes it quickly infeasible to process large datasets, especially those with high dimensions. Here, we introduce a preprocessing strategy called the Characteristic Lattice Algorithm (CLA), which allows users to reduce the size of a given dataset as desired while maintaining geometric and topological features in order to make the computation of TDA feasible or to shorten its computation time. In addition, we derive a stability theorem and an upper bound of the barcode errors for CLA based on the bottleneck distance.Comment: 13 pages, 10 figures, 2 table

Toward Green Synthesis of Graphene Oxide Using Recycled Sulfuric Acid via Couette-Taylor Flow

Developing eco-friendly and cost-effective processes for the synthesis of graphene oxide (GO) is essential for its widespread industrial applications. In this work, we propose a green synthesis technique for GO production using recycled sulfuric acid and filter-processed oxidized natural graphite obtained from a Couette-Taylor flow reactor. The viscosity of reactant mixtures processed from Couette-Taylor flow was considerably lower (???200 cP at 25 ??C) than that of those from Hummers' method, which enabled the simple filtration process. The filtered sulfuric acid can be recycled and reused for the repetitive GO synthesis with negligible differences in the as-synthesized GO qualities. This removal of sulfuric acid has great potential in lowering the overall GO production cost as the amount of water required during the fabrication process, which takes a great portion of the total production cost, can be dramatically reduced after such acid filtration. The proposed eco-friendly GO fabrication process is expected to promote the commercial application of graphene materials into industry shortly

Kernel excess mass test for multimodality

In this paper we propose a new statistical procedure for testing the multimodality of an underlying distribution. Peter Hall developed an innovative idea of calibrating the null distribution for the excess mass test statistic using the empirical distribution function. We find that the qualitative characteristics of a smooth underlying distribution function on the number of modes is barely preserved in the excess mass functional by the non-smooth empirical distribution function. Instead of the empirical distribution function, we propose to use a kernel distribution function estimator. We derive the limiting distribution of the resulting test statistic under strong unimodality, based on which we apply the calibration idea to the proposed test statistic to obtain a cut-off value. Our numerical study suggests that the calibrated kernel excess mass test has greater power than other existing methods. We also illustrate the use of the proposed method in a case study in astronomy which supports an assumption on a physical property of minor planets in the solar system.OAIID:RECH_ACHV_DSTSH_NO:T201816872RECH_ACHV_FG:RR00200001ADJUST_YN:EMP_ID:A079053CITE_RATE:.385DEPT_NM:통계학과EMAIL:[email protected]_YN:YY

Optical coherence tomography of the Tokay gecko (Gekko gecko) eye

Objective To provide images of the anterior and posterior structures of the gecko eye using spectral domain optical coherence tomography (SD-OCT). Animals and procedures Eight ophthalmologically normal Tokay geckos (Gekko gecko) were used. The nose-cloaca distance and body weight were measured for each gecko. Tomographic images were obtained using SD-OCT without the use of anesthetic or mydriatic agents. The central corneal thickness (CCT), the anterior chamber depth (ACD), and the length of the conus papillaris (CP) were manually measured using OCT images. The thickness of the retinal nerve fiber layer (RNFL) around the CP and the retinal thickness in all four quadrants (superior, nasal, inferior, and temporal areas) were automatically measured using the OCT software program. Results The mean values of the nose-cloaca distance and body weight were 13.8 +/- 0.9 cm and 41.3 +/- 9.0 g, respectively. The mean values of CCT, ACD, and CP length were 177.6 +/- 20.9 mu m, 1205.0 +/- 79.9 mu m, and 1546.4 +/- 208.8 mu m, respectively. The mean value of RNFL thickness was 52.0 +/- 8.2 mu m, and the superior region was the thickest. The mean value of total retinal thickness was 202.5 +/- 9.4 mu m, and the temporal region was the thickest. Conclusions Tomographic images of the anterior and posterior segments of the living gecko eye could be obtained using the OCT unit. Multiple retinal layers and anatomical features of the CP were identified.N

Ultrasound biomicroscopic study of the effects of topical latanoprost on the anterior segment and ciliary body thickness in dogs

Objective The goal of this study was to evaluate the effects of topical latanoprost on the anterior segment and ciliary body using ultrasound biomicroscopy (UBM) in dogs. Animals studied This study included six eyes of six clinically normal beagles. Procedures UBM scans were performed on six sedated dogs before and 2 h after topical latanoprost instillation. From the next day on, latanoprost was topically applied twice daily for 7 days. After 1 week of instillation, the UBM scans were repeated. The ciliary body thickness (CBT) and the anterior segment parameters, including the iridocorneal angle (ICA), the width of the ciliary cleft (CC) entry, the length of the CC, and the width of the mid-CC, were measured. Results The topical latanoprost decreased the ICA and CC entry width and increased the mid-CC width without any significant alterations in the CC length. There were time-dependent alterations in the CBT: a reduction in the CBT after 2 h of instillation and rebound thickening after 1 week of instillation. Conclusions The topical latanoprost widened the ciliary cleft despite the narrowing of the ICA and CC entry. Time-dependent alterations in the CBT were demonstrated by the UBM and might be a reflection of the mechanism of the uveoscleral outflow enhancement induced by the topical latanoprost.N

GATA1 deletion in human pluripotent stem cells increases differentiation yield and maturity of neutrophils.

Human pluripotent stem cell (hPSC)-derived tissues can be used to model diseases in cell types that are challenging to harvest and study at-scale, such as neutrophils. Neutrophil dysregulation, specifically neutrophil extracellular trap (NET) formation, plays a critical role in the prognosis and progression of multiple diseases, including COVID-19. While hPSCs can generate limitless neutrophils (iNeutrophils) to study these processes, current differentiation protocols generate heterogeneous cultures of granulocytes and precursors. Here, we describe a method to improve iNeutrophil differentiations through the deletion of GATA1. GATA1 knockout (KO) iNeutrophils are nearly identical to primary neutrophils in form and function. Unlike wild-type iNeutrophils, GATA1 KO iNeutrophils generate NETs in response to the physiologic stimulant lipopolysaccharide, suggesting they are a more accurate model when performing NET inhibitor screens. Furthermore, through deletion of CYBB, we demonstrate that GATA1 KO iNeutrophils are a powerful tool in determining involvement of a given protein in NET formation

Efficient production of retinol in Yarrowia lipolytica by increasing stability using antioxidant and detergent extraction

© 2022 International Metabolic Engineering SocietyThe demand for bio-based retinol (vitamin A) is currently increasing, however its instability represents a major bottleneck in microbial production. Here, we developed an efficient method to selectively produce retinol in Yarrowia lipolytica. The β-carotene 15,15′-dioxygenase (BCO) cleaves β-carotene into retinal, which is reduced to retinol by retinol dehydrogenase (RDH). Therefore, to produce retinol, we first generated β-carotene-producing strain based on a high-lipid-producer via overexpressing genes including heterologous β-carotene biosynthetic genes, GGS1F43I mutant of endogenous geranylgeranyl pyrophosphate synthase isolated by directed evolution, and FAD1 encoding flavin adenine dinucleotide synthetase, while deleting several genes previously known to be beneficial for carotenoid production. To produce retinol, 11 copies of BCO gene from marine bacterium 66A03 (Mb.Blh) were integrated into the rDNA sites of the β-carotene overproducer. The resulting strain produced more retinol than retinal, suggesting strong endogenous promiscuous RDH activity in Y. lipolytica. The introduction of Mb.Blh led to a considerable reduction in β-carotene level, but less than 5% of the consumed β-carotene could be detected in the form of retinal or retinol, implying severe degradation of the produced retinoids. However, addition of the antioxidant butylated hydroxytoluene (BHT) led to a >20-fold increase in retinol production, suggesting oxidative damage is the main cause of intracellular retinol degradation. Overexpression of GSH2 encoding glutathione synthetase further improved retinol production. Raman imaging revealed co-localization of retinol with lipid droplets, and extraction of retinol using Tween 80 was effective in improving retinol production. By combining BHT treatment and extraction using Tween 80, the final strain CJ2104 produced 4.86 g/L retinol and 0.26 g/L retinal in fed-batch fermentation in a 5-L bioreactor, which is the highest retinol production titer ever reported. This study demonstrates that Y. lipolytica is a suitable host for the industrial production of bio-based retinol.N