Early-detection and classification of live bacteria using time-lapse coherent imaging and deep learning

We present a computational live bacteria detection system that periodically captures coherent microscopy images of bacterial growth inside a 60 mm diameter agar-plate and analyzes these time-lapsed holograms using deep neural networks for rapid detection of bacterial growth and classification of the corresponding species. The performance of our system was demonstrated by rapid detection of Escherichia coli and total coliform bacteria (i.e., Klebsiella aerogenes and Klebsiella pneumoniae subsp. pneumoniae) in water samples. These results were confirmed against gold-standard culture-based results, shortening the detection time of bacterial growth by >12 h as compared to the Environmental Protection Agency (EPA)-approved analytical methods. Our experiments further confirmed that this method successfully detects 90% of bacterial colonies within 7-10 h (and >95% within 12 h) with a precision of 99.2-100%, and correctly identifies their species in 7.6-12 h with 80% accuracy. Using pre-incubation of samples in growth media, our system achieved a limit of detection (LOD) of ~1 colony forming unit (CFU)/L within 9 h of total test time. This computational bacteria detection and classification platform is highly cost-effective (~$0.6 per test) and high-throughput with a scanning speed of 24 cm2/min over the entire plate surface, making it highly suitable for integration with the existing analytical methods currently used for bacteria detection on agar plates. Powered by deep learning, this automated and cost-effective live bacteria detection platform can be transformative for a wide range of applications in microbiology by significantly reducing the detection time, also automating the identification of colonies, without labeling or the need for an expert.Comment: 24 pages, 6 figure

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Design and synthesis of cysteine-rich peptides

My thesis focuses on the methodology and application of novel synthetic strategies for high-throughput preparation of the cyclic cysteine-rich peptides with therapeutic potential. Cyclic cysteine-rich peptides are macrocyclic peptides with intramolecular disulfide bonds. The end-to-end cyclic backbone together with multiple disulfide bonds provides conformational constraints to enhance the structural stability. My strategy involves synthesizing these peptides by chemical approaches using solid-phase peptide synthesis. A new cyclization method was developed employing an N-S acyl shift mechanism to mimic the natural production of peptide bonds. The oxidative folding process is also optimized by introducing organic solvents. With the novel cyclization and the organic folding strategy in a one-pot manner, I have successfully prepared cyclic cysteine-rich peptides in a shorter reaction time with an improved yield than with conventional methods. They could be used as a simple and high-throughput synthetic platform to prepare cyclic cysteine-rich peptides. In addition, the substrate specificity of a novel transpeptidase named butelase 1 was also investigated for ligation and cyclization reactions. With high efficiency and broad substrate specificity, it would be exploited as a novel chemoselective approach for peptide and protein engineering. For applications, the cyclic peptide sunflower trypsin inhibitor-1 which possesses a cyclic backbone is modified by a grafting approach with bioactive peptides while retaining the cyclic peptide scaffold. New analogs with improved stability and new functions were developed as a proof-of-concept to advance the development of potential peptide biologics.DOCTOR OF PHILOSOPHY (SBS

Studies on the Failure Modes of Stationary VRLA Batteries

研究了由于水损耗、热失控而引起固定型阀控式铅酸蓄电池失效的原因．认为通过提高电池内部氧再复合效率、采用合适的电池槽盖材料及减少正极板腐蚀，可解决水损耗问题；热失控问题可通过改善电池外部条件解决．In order to improve the reliability and the quality of stationary valve regulated lead acid (VRLA) batteries, the failure modes of the stationary VRLA batteries which caused by the water loss and the thermal runaway are studied. The water loss may be solved by increasing the Oxygen recombination efficiency, choosing the suitable grid material and the additives of megative paste, decreasing the corrosion of the positive plates. The thermal runaway may be solved by decreasing the inner ohmic resistance of VRLA batteries, improving the outside condition of batteries such as putting into the absorbing heat material between the abtteries etc..作者联系地址：杭州南都电源有限公司Author's Address: Hangzhou Narada Battery Co., LTD., Zhejiang 31001

Grouting mechanism and experimental study of goaf considering filtration effect.

The filtration effect significantly affects the gangue slurry velocity and concentration, making it difficult to evaluate the gangue slurry diffusion range. Based on the Darcy seepage law, a seepage theoretical calculation model is established considering the filtration time and space effect. And the "water-cement ratio change matrix" in the seepage process of coal gangue slurry is deduced, revealing the basic mechanism of the porous media filtration effect, and the water-cement ratio gradually increases in the seepage process of gangue slurry. The visual test platform for slurry diffusion in goaf was independently developed for testing. The active heating optical fiber method (AHFO) was used to monitor the flow and diffusion of coal gangue slurry in the collapse zone of goaf, and the gravity gradient and water cement ratio of slurry in goaf were measured. The law of particle sedimentation in the gangue slurry flow process under the filtration effect was revealed, and engineering verification was carried out. The results show that the average slope of the gangue slurry in the gangue accumulation is 6.34%, and the overall flow law of the gangue slurry in the goaf is the first longitudinal expansion and then transverse diffusion. The water-cement ratio near the grouting mouth is smaller than the initial water-cement ratio, the near-end water-cement ratio is smaller, and the far-end water-cement ratio is larger. During on-site filling, the accumulated grouting volume of a single hole is 700 m3, and the gangue slurry diffusion distance is greater than 45m, indicating that the gangue slurry has good fluidity

Matematični model in analiza toplotnih lastnosti sten letalske kabine pod tlakom

In the present paper, we investigate the heat transfer through the multilayer wall of aircraft cabins, as this process influences the comfortable conditions created for most passengers and crew members. The numerical modelling results and calculation of a multilayer wall with a hat-stringer in aircraft design are presented. The thermal characteristics evaluation and their relationship with the design parameters were made. The effect of the air layer size on the overall thermal resistance of the multilayer wall, taking into account the geometrical dimensions and properties of the surfaces, was studied. The relative temperature field in the insulation layer, which crosses the hat-stringer elements of the fuselage frame, is calculated. It is shown that the insufficient thickness of the layer of thermal insulation material in the zone of the hat-stringer at low temperatures leads to a significant deterioration in the multilayer wall characteristics, which can worsen the microclimatic conditions inside the aircraft cabin

A thioethylalkylamido (TEA) thioester surrogate in the synthesis of a cyclic peptide via a tandem acyl shift

The cyclic cystine-knot peptide, kalata B1, was synthesized by employing a novel Fmoc-compatible thioethylalkylamido (TEA) thioester surrogate via an N–S acyl shift followed by a thiol-thioester exchange reaction. TEA thioester surrogate is cost-effective, conveniently prepared in one-step with starting materials, readily available from commercial sources, and highly efficient in preparing peptide thioesters

Dynamic difference and characterization of reservoir fluid in continental rift basins

In order to establish the relationship between hydrocarbon characteristic variations and dynamic environments, the differences of hydrocarbon geochemical characteristics of reservoirs in various pressure systems (overpressure zone, transitional pressure zone and normal pressure zone) were studied. The Dongying and Zhanhua sags in the Jiyang Depression of the Bohai Bay Basin were taken as examples in this paper, the variations of sterane isomerization parameter, sterane light/heavy ratio with depth were revealed. The transition from overpressure charging to normal pressure driving was clarified. The typical profiles of the Boxing (single pressure structure) and Bonan (composite pressure structure) sub-sags in the Dongying and Zhanhua sags, respectively, were selected for the differential analyses of geochemical parameters and corresponding dynamic conditions in various belts. The variations of the geochemical parameters showed high correlations to overpressure driving and buoyancy driving. The development ranges of abnormal pressure during reservoir formation were studied as well, which are much larger than the present abnormal pressure distribution ranges. Especially in the step-fault zone belt, historic overpressure had greatly extended outwards. According to the geochemical characterization of dynamic conditions, the reservoir formation systems and hydrocarbon supply ranges were described in detail

Selective bi-directional amide bond cleavage of N-methylcysteinyl peptide

A selective bi-directional peptide bond cleavage mediated by N-methylcysteine (MeCys) in Xaa-MeCys-Yaa peptides (Xaa and Yaa, non-cysteine residues) leading to thioesters and thiolactones is described. Rate and product analyses showed that an Nα-amide bond cleavage occurred at the Xaa-MeCys bond by an N–S acyl shift to generate an Xaa-S-(MeCys-Yaa) thioester at pH 1–5, whereas under strongly acidic conditions of H0 = –5, the MeCys-Yaa bond underwent a Cα-amide bond cleavage via an oxazolone intermediate, which was trapped by thiocresol (TC) as an Xaa-MeCys-TC thioester. This thioester was then transformed into an Xaa-MeCys-β-thiolactone at pH 4–5. Replacing MeCys by a Cys residue did not result in significant bi-directional peptide bond cleavage, which suggests that N-methylation in a MeCys residue is important for the N–S acyl shift reaction and formation of oxazolone. The isomerization of amides and thioesters was successfully used to prepare cyclic peptides