Letter from Swiss Consul General Shanghai to American, British, and Dutch Nationals in Peking.

Typewritten letter with seal of Representative of the Swiss Consul General, Peking. With envelope addressed to Rev. William A. Amrhein.https://digitalcommons.whitworth.edu/amrhein_corr/1002/thumbnail.jp

A two-parameter generalized Poisson model to improve the analysis of RNA-seq data

Deep sequencing of RNAs (RNA-seq) has been a useful tool to characterize and quantify transcriptomes. However, there are significant challenges in the analysis of RNA-seq data, such as how to separate signals from sequencing bias and how to perform reasonable normalization. Here, we focus on a fundamental question in RNA-seq analysis: the distribution of the position-level read counts. Specifically, we propose a two-parameter generalized Poisson (GP) model to the position-level read counts. We show that the GP model fits the data much better than the traditional Poisson model. Based on the GP model, we can better estimate gene or exon expression, perform a more reasonable normalization across different samples, and improve the identification of differentially expressed genes and the identification of differentially spliced exons. The usefulness of the GP model is demonstrated by applications to multiple RNA-seq data sets

Letter from Swiss Consul General Shanghai to American Catholic Missionaries in Peking.

Typewritten letter. Letterhead: Representative for Peking of the Swiss Consul General, Shanghai. With Envelope addressed to Rev. Leonard Amrhein.https://digitalcommons.whitworth.edu/amrhein_corr/1001/thumbnail.jp

Analytical models of probability distribution and excess noise factor of Solid State Photomultiplier signals with crosstalk

Silicon Photomultipliers (SiPM), also so-called Solid State Photomultipliers (SSPM), are based on Geiger mode avalanche breakdown limited by strong negative feedback. SSPM can detect and resolve single photons due to high gain and ultra-low excess noise of avalanche multiplication in this mode. Crosstalk and afterpulsing processes associated with the high gain introduce specific excess noise and deteriorate photon number resolution of the SSPM. Probabilistic features of these processes are widely studied because of its high importance for the SSPM design, characterization, optimization and application, but the process modeling is mostly based on Monte Carlo simulations and numerical methods. In this study, crosstalk is considered to be a branching Poisson process, and analytical models of probability distribution and excess noise factor (ENF) of SSPM signals based on the Borel distribution as an advance on the geometric distribution models are presented and discussed. The models are found to be in a good agreement with the experimental probability distributions for dark counts and a few photon spectrums in a wide range of fired pixels number as well as with observed super-linear behavior of crosstalk ENF.Comment: 10 pages, 2 tables, 3 figures, Reported at 6th International Conference on "New Developments In Photodetection - NDIP11

XVir: A Transformer-Based Architecture for Identifying Viral Reads from Cancer Samples

It is estimated that approximately 15% of cancers worldwide can be linked to viral infections. The viruses that can cause or increase the risk of cancer include human papillomavirus, hepatitis B and C viruses, Epstein-Barr virus, and human immunodeficiency virus, to name a few. The computational analysis of the massive amounts of tumor DNA data, whose collection is enabled by the recent advancements in sequencing technologies, have allowed studies of the potential association between cancers and viral pathogens. However, the high diversity of oncoviral families makes reliable detection of viral DNA difficult and thus, renders such analysis challenging. In this paper, we introduce XVir, a data pipeline that relies on a transformer-based deep learning architecture to reliably identify viral DNA present in human tumors. In particular, XVir is trained on genomic sequencing reads from viral and human genomes and may be used with tumor sequence information to find evidence of viral DNA in human cancers. Results on semi-experimental data demonstrate that XVir is capable of achieving high detection accuracy, generally outperforming state-of-the-art competing methods while being more compact and less computationally demanding.Comment: 8 page

Inception and evolution of financial reporting in the Protestant Episcopal Church in the United States of America

This research documents the emergence of accounting procedures and concepts in a centrally controlled not-for-profit organization during a period of change and consolidation. The evolution of accounting as prescribed by the General Canons is identified and its implementation throughout the church conferences is examined