Yinhai Wang | PubMed Health

PubMed2024

A statistical simulation model to guide the choices of analytical methods in arrayed CRISPR screen experiments.

An arrayed CRISPR screen is a high-throughput functional genomic screening method, which typically uses 384 well plates and has different gene knockouts in different wells. Despite various computational workflows, there is currently no systematic way to find what is a good workflow for arrayed CRISPR screening data analysis. To guide this choice, we developed a statistical simulation model that mimics the data generating process of arrayed CRISPR screening experiments. Our model is flexible and can simulate effects on phenotypic readouts of various experimental factors, such as the effect size of gene editing, as well as biological and technical variations. With two examples, we showed that the simulation model can assist making principled choice of normalization and hit calling method for the arrayed CRISPR data analysis. This simulation model is implemented in an R package and can be downloaded from Github.

CRISPR-Cas Systems↗

PubMed2004

Estimating the risk of collisions between bicycles and motor vehicles at signalized intersections.

Collisions between bicycles and motor vehicles have caused severe life and property losses in many countries. The majority of bicycle-motor vehicle (BMV) accidents occur at intersections. In order to reduce the number of BMV accidents at intersections, a substantial understanding of the causal factors for the collisions is required. In this study, intersection BMV accidents were classified into three types based on the movements of the involved motor vehicles and bicycles. The three BMV accident classifications were through motor vehicle related collisions, left-turn motor vehicle related collisions, and right-turn motor vehicle related collisions. A methodology for estimating these BMV accident risks was developed based on probability theory. A significant difference between this proposed methodology and most current approaches is that the proposed approach explicitly relates the risk of each specific BMV accident type to its related flows. The methodology was demonstrated using a 4-year (1992-1995) data set collected from 115 signalized intersections in the Tokyo Metropolitan area. This data set contains BMV accident data, bicycle flow data, motor vehicle flow data, traffic control data, and geometric data for each intersection approach. For each BMV risk model, an independent explanatory variable set was chosen according to the characteristics of the accident type. Three negative binomial regression models (one corresponding to each BMV accident type) were estimated using the maximum likelihood method. The coefficient value and its significance level were estimated for each selected variable. The negative binomial dispersion parameters for all the three models were significant at 0.01 levels. This supported the choice of the negative binomial regression over the Poisson regression for the quantitative analyses in this study.

Accidents, Traffic↗

PubMed2002

Rational growth of Bi2S3 nanotubes from quasi-two-dimensional precursors.

Synthesis of Bi2S3 nanotubes from rolling of the quasi-two-dimensional (2-D) layered precursor represents new progress in the synthetic approach and adds new members to the present inorganic fullerene family. These nanotubes display multiwalled structures that resemble that of a multiwalled carbon nanotube. The successful synthesis of Bi2S3 nanotubes highlights the feasibility of inorganic fullerene-like structures from other chemicals that possess layered crystalline structures, not only the well-known 2-D family, but possibly also those quasi-2-D members.

Journal Article↗