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

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

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

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

Butelase 1 is an Asx-specific ligase enabling peptide macrocyclization and synthesis

Proteases are ubiquitous in nature, whereas naturally occurring peptide ligases, enzymes catalyzing the reverse reactions of proteases, are rare occurrences. Here we describe the discovery of butelase 1, to our knowledge the first asparagine/aspartate (Asx) peptide ligase to be reported. This highly efficient enzyme was isolated from Clitoria ternatea, a cyclic peptide-producing medicinal plant. Butelase 1 shares 71% sequence identity and the same catalytic triad with legumain proteases but does not hydrolyze the protease substrate of legumain. Instead, butelase 1 cyclizes various peptides of plant and animal origin with yields greater than 95%. With Kcat values of up to 17 s(-1) and catalytic efficiencies as high as 542,000 M(-1) s(-1), butelase 1 is the fastest peptide ligase known. Notably, butelase 1 also displays broad specificity for the N-terminal amino acids of the peptide substrate, thus providing a new tool for C terminus-specific intermolecular peptide ligations.Accepted versio