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

Results from unannounced visits to check compliance with smoke-free regulations in three types of indoor places in Beijing

Background Beijing Tobocco control regulation come into force in 2015. According to the regulation, all indoor areas are smoke free. To assess compliance with the Beijing Regulations, identify weaknesses and problems, and provide scientific evidence for policy making by the government and other authorities. Methods on site, unannounced visits. We conducted unannounced visits to a sample of 821 places in three types of places across the sixteen districts of Beijing, including medical and health facilities (including health and family planning commissions, CDCs, health inspection institutes and a variety of hospitals), colleges (including vocational schools) and taxis (including Shouqi Group vehicles booked online). Results Among medical and health facilities, all posted smoke-free signage, and no cigarette end or smoking paraphernalia was found indoors, except in private hospitals, community health service centers and few maternal and child care centers. Among colleges, 96.9% of them posted smoke-free signage, cigarette end was found indoors in 9.9% of colleges, smell of smoking was detected indoors in 1.9% of colleges, and ashtray was found indoors in 0.6% of colleges. Among taxies, 6% of drivers of online booked vehicles permit passengers to smoke inside their car, and no smell of smoking, container of cigarette ends/ashes, or driver smoking was detected in these online booked vehicles. Among the conventional cruising taxis, 48.4% of taxi drivers permit passengers to smoke inside their car, smell of smoking was found in 9.6% of taxies, and 1.6% of taxi drivers smoke in their car. Conclusions Smoking in violation of the Regulations is serious in the taxi sector, and targeted stronger supervision and administration are needed

Deformation Response Research of the Existing Subway Tunnel Impacted by Adjacent Foundation Pit Excavation

The excavation of foundation pits is one of the most important factors causing changes to the initial stress state of its surrounding soil, thus affecting the safety of nearby existing subway tunnels. In order to study the deformation in metro lines induced by adjacent foundation pit excavation, a three-dimensional model based on an actual engineering case was established, and the deformation regulations of the retaining wall, surrounding soil, and tunnels were investigated, which also validated the model’s feasibility. Additionally, the deformation and strain response of the subway tunnel under different selection parameters of the enclosing structure and soil were studied. The results showed that, after the foundation pit excavation, the soil inside the pit underwent an uplift, the surrounding soil outside of the pit showed vertical settlement, and the retaining wall created a deformation towards the interior of the pit. Mechanical parameters of plate elements have a small influence on the deformation of metro lines. Axial strain and maximum displacement of the subway tunnel increase with the increase in the soil’s Poisson’s ratio, and on the contrary, they decrease with the increase in the m-value and G0,ref. The maximum responses of the subway tunnel came from changes to G0,ref and υ. These analysis results can be used for the safety evaluation of subway tunnel operation, design, and construction in other similar engineering settings

Experimental Study on Mechanical Properties of Cement-Solidified Remolded Soil Reinforces by Polyvinyl Alcohol Fiber

As a reusable resource, remolded soils are often not utilized on a large scale due to their high water content and low bearing capacity. By using polyvinyl alcohol fiber (PVA) as reinforcing material and cement as cementing material, the remolded soil was improved into a usable consolidated remolded soil, and the effects of different fiber content, fiber length modulus, and conservation age on the static and dynamic characteristics of the consolidated remolded soil were investigated by conducting triaxial consolidated undrained shear tests and dynamic triaxial tests on the consolidated remolded soil. The results show that the use of PVA fiber reinforced cement can effectively improve the shear strength and dynamic strength of the remolded soil and reduce the water content of the remolded soil; the best effect on the static strength of the remolded soil was achieved when 0.1% of PVA fibers with a length of 6 mm were incorporated into the specimens at a conservation age of 28 d; the best effect on the dynamic strength of the remolded soil was achieved when 0.3% of PVA fibers with a length of 12 mm were incorporated into the specimens at a conservation age of 7 d

The performance of a new local false discovery rate method on tests of association between coronary artery disease (CAD) and genome-wide genetic variants

The maximum entropy (ME) method is a recently-developed approach for estimating localfalse discovery rates (LFDR) that incorporates external information allowing assignment ofa subset of tests to a category with a different prior probability of following the null hypothesis.Using this ME method, we have reanalyzed the findings from a recent large genomewideassociation study of coronary artery disease (CAD), incorporating biologic annotations.Our revised LFDR estimates show many large reductions in LFDR, particularly among the genetic variants belonging to annotation categories that were known to be of particular interest for CAD. However, among SNPs with rare minor allele frequencies, the reductions in LFDR were modest in size

Allelic and haplotypic polymorphisms and paternal genetic analysis of Chinese Shaanxi Han population utilizing a multiplex Y-STR set

Background The analysis of Y chromosomal genetic markers is of great significance in human genetic fields related to male individuals. The Han nationality is the most populous ethnic group. It is critical to investigate the Y-chromosome short tandem repeat (Y-STR) genetic informativeness of Han nationalities in different Chinese regions in order to gain a comprehensive understanding of their paternal genetic relationships and origin. Aim To assess the allelic and haplotypic polymorphisms of the novel AGCU Y SUPP STR amplification system containing seven Y-STRs in the maximal dataset of the Y-STR Haplotype Reference Database (YHRD) and 17 newly included Y-STRs, and explore the genetic relationships among the Shaanxi Han population and 12 reference populations from China. Subjects and methods A total sample of 220 Han male subjects were obtained from the Shaanxi Province, China, and genotyped by the novel AGCU Y SUPP STR amplification system. Multiplex population genetic analyses derived from the same 16 Y-STR loci were carried out among the Shaanxi Han population and 12 reference populations from China. Results The gene diversities (GD) ranged from the maximum value of 0.9609 (DYS385a,b) to the minimum value of 0.5441 (DYS531). Besides, 217 distinct haplotypes were detected wholly in 220 individuals, of which 214 (98.62%) were exclusive. The entire haplotype diversity (HD) and discrimination capacity (DC) were 0.9999 and 0.9864, respectively, while the haplotype match probability (HMP) was 0.0045. Among the reference populations, the obtained results of population genetic analyses revealed that the Shaanxi Han population had the largest genetic distance with the Guangxi Yao group, but the smallest genetic distance with the Hunan Tujia group. Conclusions These Y-STR loci in the AGCU Y SUPP STR amplification system were of high genetic polymorphisms and the amplification system could be used as a prospective complementary tool for forensic application and paternal genetics in the Shaanxi Han population

MtDNA polymorphism analyses in the Chinese Mongolian group: Efficiency evaluation and further matrilineal genetic structure exploration

Abstract Background Profiling of mitochondrial DNA is surely to provide valuable investigative clues for forensic cases involving highly degraded specimens or complex maternal lineage kinship determination. But traditionally used hypervariable region sequencing of mitochondrial DNA is less frequently suggested by the forensic community for insufficient informativeness. Genome‐wide sequencing of mitochondrial DNA can provide considerable amount of variant information but can be high cost at the same time. Methods Efficiency of the 60 mitochondrial DNA polymorphic sites dispersing across the control region and coding region of mitochondrial DNA genome was evaluated with 106 Mongolians recruited from the Xinjiang Uyghur Autonomous Region, China, and allele‐specific PCR technique was employed for mitochondrial DNA typing. Results Altogether 58 haplotypes were observed and the haplotypic diversity, discrimination power and random match probability were calculated to be 0.981, 0.972, and 0.028, respectively. Mitochondrial DNA haplogroup affiliation exhibited an exceeding percentage (12.26%) of west Eurasian lineage (H haplogroup) in the studied Mongolian group, which needed to be further verified with more samples. Furthermore, the genetic relationships between the Xinjiang Mongolian group and the comparison populations were also investigated and the genetic affinity was discovered between the Xinjiang Mongolian group and the Xinjiang Kazak group in this study. Conclusion It was indicated that the panel was potentially enough to be used as a supplementary tool for forensic applications. And the matrilineal genetic structure analyses based on mitochondrial DNA variants in the Xinjiang Mongolian group could be helpful for subsequent anthropological studies

Genetic polymorphism and relationship analyses of standard poodle and bichon frise groups based on 19 short tandem repeat loci

Context: As the increasing number of pet canines, the identification of canine has attracted much attentions in the forensic field, however, the genetic diversities of pet canines still remained unknown. Aims: To explore genetic polymorphisms of 19 short tandem repeat (STR) loci and genetic relationships between the two studied canine groups and reference group. Subjects and Methods: In the present study, genetic polymorphisms of 19 STR loci and a sex-linked zinc finger locus were analyzed in a total of 594 canines in Standard Poodle and Bichon Frise groups from China. Results: A total of 166, 159 alleles were observed in the Standard Poodle, Bichon Frise groups with the corresponding allelic frequencies ranging from 0.0030–0.6108 to 0.0012–0.6148, respectively. The combined discrimination power and probability of exclusion of 19 STR loci in Standard Poodle and Bichon Frise groups were 0.9999999999999497, 0.999962884; and 0.99999999999999995, 0.999965955, respectively. Furthermore, the genetic distances between the two canine groups and Labrador retriever group were calculated, and the results indicated that Standard Poodle and Bichon Frise groups showed a closer genetic relationship, while the two canine groups had distant genetic relationships with Labrador retriever group. The result of population genetic structure revealed that genetic component distributions in the three canine groups were different. The predicted accuracies of the constructed random forest prediction model for three validation sets (25% individuals randomly selected from three populations with 808 individuals) were higher than 0.9, especially for the individuals in validation set from the Bichon Frise group is 1. Conclusions: The 19 STR loci could be used for individual identification, canine breed identification and paternity testing in the two canine groups