High precision tracking analysis of cell position and motion fields using 3D U-net network models.

Cells are the basic units of biological organization, and the quantitative analysis of cellular states is an important topic in medicine and is valuable in revealing the complex mechanisms of microscopic world organisms. In order to better understand cell cycle changes as well as drug actions, we need to track cell migration and division. In this paper, we propose a novel engineering model for tracking cells using cell position and motion fields (CPMF). The training sample does not need to be manually annotated, and we modify and edit it against the ground truth using auxiliary tools. The core idea of the project is to combine detection and correlation, and the cell sequence samples are trained by a U-Net network model composed of 3D CNNs, which can track the migration, division, and entry and exit of cells in the field of view with high accuracy in all directions. The average detection accuracy of the cell coordinates is 98.38% and the average tracking accuracy is 98.70%.

H2S responsive PEGylated poly (lipoic acid) with ciprofloxacin for targeted therapy of Salmonella.

Targeted antibiotic delivery system would be an ideal solution for the treatment of enteropathogenic infections since it avoids the excessive usage of antibiotics clinically, which may lead to threat on public health and food safety. Salmonella spp. are Enteropathogens, but they are also robust H2S producers in the intestinal tracts of hosts. To this end, the PEGylated poly (α lipoic acid) (PEG-PALA) copolymer nanoparticles with hydrophilic exterior and hydrophobic interior were designated in this study to encapsulate the antibiotics and release them in response to H2S produced by Salmonella spp. The PEG-PALA nanoparticles demonstrated excellent stability in vitro and biocompatibility toward mammalian Caco-2 and 293 T cells. The release of ciprofloxacin from PEG-PALA nanoparticle was only 25.44 ± 0.57% and 26.98 ± 1.93% (w/w) in simulated gastric fluid (SGF) and simulated intestinal fluid (SIF) solutions without H2S stimulation. However, the release amounts of ciprofloxacin were up to 73.68 ± 1.63% (w/w) in the presence of 1 mM Na2S as H2S source. In the mouse infection model, PEG-PALA nanoparticles encapsulated with ciprofloxacin (PEG-PALA@CIP) reduced the Salmonella colonization in the heart, liver, spleen, lung, cecum, and faeces, prolonged ciprofloxacin persistence in the intestine while reducing its absorption into the blood. More importantly, these nanoparticles reduced 3.4-fold of Enterobacteriaceae levels and increased 1.5-fold of the Lactobacillaceae levels compared with the drug administered in the free form. Moreover, these nanoparticles resulted in only minimal signs of intestinal tract inflammation. The H2S-responsive antibiotic delivery systems reported in this study demonstrating a variety of advantages including protected the drug from deactivation by gastric and intestinal fluids, maintained a high concentration in the intestinal tract and maximally kept the gut microbiota homeostasis. As such, this targeted antibiotic delivery systems are for the encapsulation of antibiotics to target specific enteropathogens.

Molecular Epidemiology of Fosfomycin Resistant E. coli from a Pigeon Farm in China.

We determined the prevalence and molecular characteristics of fosfomycin-resistant Escherichia coli from a domestic pigeon farm. A total of 79 samples collected from pigeons and their surrounding environments were screened for the presence of fosfomycin resistant isolates and these included 49 E. coli isolates that displayed high-level resistance (MIC ≥ 256 mg L-1) and carried the fosA3 gene on plasmids with sizes ranging from 80 to 370 kb. MLST analysis of these fosA3-positive E. coli isolates indicated the presence of nine sequence types (ST6856, ST8804, ST457, ST746, ST533, ST165, ST2614, ST362 and ST8805) of which ST6856 was the most prevalent (24.5%, 12/49). PFGE combined with genomic context comparative analyses indicated that the fosA3 gene was spread by horizontal transfer as well as via clonal transmission between E. coli in the pigeon farm, and IS26 played an important role in fosA3 transmission. The high prevalence of fosA3 in the pigeon farm and the high similarity of the fosA3 genomic environment between E. coli isolates from humans and pigeons indicated that the pigeon farm served as a potential reservoir for human infections. The pigeon farm was found to be an important reservoir for the fosA3 gene and this should be further monitored.

AI-Blue-Carba: A Rapid and Improved Carbapenemase Producer Detection Assay Using Blue-Carba With Deep Learning.

A rapid and accurate detection of carbapenemase-producing Gram-negative bacteria (CPGNB) has an immediate demand in the clinic. Here, we developed and validated a method for rapid detection of CPGNB using Blue-Carba combined with deep learning (designated as AI-Blue-Carba). The optimum bacterial suspension concentration and detection wavelength were determined using a Multimode Plate Reader and integrated with deep learning modeling. We examined 160 carbapenemase-producing and non-carbapenemase-producing bacteria using the Blue-Carba test and a series of time and optical density values were obtained to build and validate the machine models. Subsequently, a simplified model was re-evaluated by descending the dataset from 13 time points to 2 time points. The best suitable bacterial concentration was determined to be 1.5 optical density (OD) and the optimum detection wavelength for AI-Blue-Carba was set as 615 nm. Among the 2 models (LRM and LSTM), the LSTM model generated the higher ROC-AUC value. Moreover, the simplified LSTM model trained by short time points (0-15 min) did not impair the accuracy of LSTM model. Compared with the traditional Blue-Carba, the AI-Blue-Carba method has a sensitivity of 95.3% and a specificity of 95.7% at 15 min, which is a rapid and accurate method to detect CPGNB.

Diversity of L1/L2 genes and molecular epidemiology of high-level carbapenem resistance Stenotrophomonas maltophilia isolates from animal production environment in China.

Stenotrophomonas maltophilia is emerging as a significant cause of human and animal disease worldwide. A total of 3400 samples were collected from animal farms and adjacent environments in China. The blaL1 and blaL2 genes were identified using whole genome sequence analyses and examined by phylogenetics. Isolates were also tested for susceptibility to 18 antibiotics. We isolated 118 strains of S. maltophilia from 3400 samples. The positive rates of blaL1 and blaL2 genes were 75% (89/118) and 22% (26/118) and we identified 11 L1 and 6 L2 amino acid sequence variants. S. maltophilia has at least two inducible ß-lactamases (L1 and L2) that can hydrolyze almost all classes of ß-lactams and these genes are suspected to confer carbapenem resistance. This represents a significant public health threat especially for hospitalized patients. We conducted a molecular surveillance study on the prevalence and characteristics of the blaL1 and blaL2 genes of S. maltophilia.

Raman and Visible-Near Infrared Spectra of Cu(InGa)Se2 Films.

Cu(InxGa1-x)Se2(CIGS) precursor films were prepared on ITO glass with potentiostatic electrodeposition. High quality CIGS films were obtained by selenization of the precursor films at high temperature in tubular furnace full of argon gas. X-ray diffraction (XRD), scanning electron microscopy (SEM) and UV-Vis-NIR spectroscopy were used to characterize the structure, morphology, composition and Vis-NIR absorption of CIGS films, respectively. XRD results show the selenized CIGS films have a preferential orientation (112) with average crystallite of 24.7 nm. Raman spectroscopy reveals that the CIGS films are pure quaternaryphases with chalcopyrite structure, and without binary or ternary phases in the films. Vis-NIR measurements determine that the bandgap of CIGS increases with the increase of Ga concentration in the film. When the Ga concentration is 5.41%, its bandgap is about 1.11 eV, and the calculated ratio of Ga to (Ga+In) is 16.3%, which is less than the ratio of Ga to (Ga+In), 21.4%, measured by SEM. This indicates that crystallinity of CIGS filmsneeds to be further improved. All the measurements demonstratethat optimum ITO/CIGS has a promising application in bifacial solar cells. In this paper, we provide a newmethodtoelectrodeposit low cost CIGS precursor films and a new method forselenization ofthe precursor films at high temperature. As a result, theuniform and compact CIGS films with good adhesion on ITO are successfully fabricated by these methods. The above characterization show that we have obtained CIGS films with high crystallinity, near stoichiometry, few impurity phases and superior light absorption. Electrodeposition, like magnetron sputtering, is very suitable for large-scale industrial production. The research work in this paper is therefore important and considerable to massive production of electrodeposition of CIGS films.

Raman and Visible-Near Infrared Spectra of Cu(InGa)Se2 Films.

Cu(InxGa1-x)Se2(CIGS) precursor films were prepared on ITO glass with potentiostatic electrodeposition. High quality CIGS films were obtained by selenization of the precursor films at high temperature in tubular furnace full of argon gas. X-ray diffraction (XRD), scanning electron microscopy (SEM) and UV-Vis-NIR spectroscopy were used to characterize the structure, morphology, composition and Vis-NIR absorption of CIGS films, respectively. XRD results show the selenized CIGS films have a preferential orientation (112) with average crystallite of 24.7 nm. Raman spectroscopy reveals that the CIGS films are pure quaternaryphases with chalcopyrite structure, and without binary or ternary phases in the films. Vis-NIR measurements determine that the bandgap of CIGS increases with the increase of Ga concentration in the film. When the Ga concentration is 5.41%, its bandgap is about 1.11 eV, and the calculated ratio of Ga to (Ga+In) is 16.3%, which is less than the ratio of Ga to (Ga+In), 21.4%, measured by SEM. This indicates that crystallinity of CIGS filmsneeds to be further improved. All the measurements demonstratethat optimum ITO/CIGS has a promising application in bifacial solar cells. In this paper, we provide a newmethodtoelectrodeposit low cost CIGS precursor films and a new method forselenization ofthe precursor films at high temperature. As a result, theuniform and compact CIGS films with good adhesion on ITO are successfully fabricated by these methods. The above characterization show that we have obtained CIGS films with high crystallinity, near stoichiometry, few impurity phases and superior light absorption. Electrodeposition, like magnetron sputtering, is very suitable for large-scale industrial production. The research work in this paper is therefore important and considerable to massive production of electrodeposition of CIGS films.