Genome sequence and genetic linkage analysis of Shiitake mushroom _Lentinula edodes_

_Lentinula edodes_ (Shiitake/Xianggu) is an important cultivated mushroom. Understanding the genomics and functional genomics of _L. edodes_ allows us to improve its cultivation and quality. Genome sequence is a key to develop molecular genetic markers for breeding and genetic manipulation. We sequenced the genome of _L. edodes_ monokaryon L54A using Roche 454 and ABI SOLiD genome sequencing. Sequencing reads of about 1400Mb were de novo assembled into a 40.2 Mb genome sequence. We compiled the genome sequence into a searchable database with which we have been annotating the genes and analyzing the metabolic pathways. In addition, we have been using many molecular techniques to analyze genes differentially expressed during development. Gene ortholog groups of _L. edodes_ genome sequence compared across genomes of several fungi including mushrooms identified gene families unique to mushroom-forming fungi. We used a mapping population of haploid basidiospores of dikaryon L54 for genetic linkage analysis. High-quality variations such as single nucleotide polymorphisms, insertions, and deletions of the mapping population formed a high-density genetic linkage map. We compared the linkage map to the _L. edodes_ L54A genome sequence and located selected quantitative trait loci. The Shiitake community will benefit from these resources for genetic studies and breeding.
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Artificial Intelligence (AI) in Evidence-Based Approaches to Effectively Respond to Public Health Emergencies

Artificial intelligence (AI) techniques have been commonly used to track, predict early warning, forecast trends, and model and measure public health responses. Statistics have traditionally been used to track public health crises. AI-enabled methods, such as machine learning and deep learning–based models, have exploded in popularity recently, complementing statistical approaches. A wide range of medical fields have used various well-developed deep learning algorithms. Surveillance of public health emergencies is one region that has gained greatly from AI advancements in recent years. One of the examples of effectively reacting to public health emergencies is the need for developing AI evidence-based approaches to public health strategies for the scientific community’s response to the COVID-19 pandemic

Performance of screening tests for oesophageal squamous cell carcinoma: a systematic review and meta-analysis

Background and Aims: This systematic review and meta-analysis aims to compare the pooled diagnostic accuracy of the currently available esophageal squamous cell carcinoma (ESCC) screening tests. Methods: A comprehensive literature search of Embase and Medline (up to October 31, 2020) was performed to identify eligible studies. We pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), and diagnostic odds ratio (DOR) for ESCC screening tools using a bivariate random-effects model. The summary receiver operating characteristic (sROC) curves with area under the curve (AUC) were plotted for each screening test. Results: We included 161 studies conducted in 81 research articles involving 32,209 subjects. The pooled sensitivity, specificity, and AUC (95% CIs) of the major screening tools were: (1). Endoscopy (per-oral endoscopy): 0.94 (0.87-0.97), 0.92 (0.87-0.95), and 0.97 (0.96-0.99); (2) Endoscopy (transnasal endoscopy): 0.85 (0.70-0.93), 0.96 (0.91-0.98), and 0.97 (0.95, -0.98); (3). MicroRNA: 0.77 (0.75-0.80), 0.78 (0.75-0.80), and 0.85 (0.81-0.87); (4). Autoantibody: 0.45 (0.36-0.53), 0.91 (0.89-0.93), and 0.84 (0.81-0.87); and (5). Cytology: 0.82 (0.60-0.93), 0.97 (0.88-0.99), and 0.97 (0.95-0.98). There was high heterogeneity. Conclusions: The diagnostic accuracy seems comparable between Cytology and endoscopy, whilst autoantibody and microRNAs bear potential as future non-invasive screening tools for ESCC. To reduce ESCC-related death in the high-risk populations, it is important to develop a more accurate and less invasive screening test

Genotyping Performance Assessment of Whole Genome Amplified DNA with Respect to Multiplexing Level of Assay and Its Period of Storage

Whole genome amplification can faithfully amplify genomic DNA (gDNA) with minimal bias and substantial genome coverage. Whole genome amplified DNA (wgaDNA) has been tested to be workable for high-throughput genotyping arrays. However, issues about whether wgaDNA would decrease genotyping performance at increasing multiplexing levels and whether the storage period of wgaDNA would reduce genotyping performance have not been examined. Using the Sequenom MassARRAY iPLEX Gold assays, we investigated 174 single nucleotide polymorphisms for 3 groups of matched samples: group 1 of 20 gDNA samples, group 2 of 20 freshly prepared wgaDNA samples, and group 3 of 20 stored wgaDNA samples that had been kept frozen at −70°C for 18 months. MassARRAY is a medium-throughput genotyping platform with reaction chemistry different from those of high-throughput genotyping arrays. The results showed that genotyping performance (efficiency and accuracy) of freshly prepared wgaDNA was similar to that of gDNA at various multiplexing levels (17-plex, 21-plex, 28-plex and 36-plex) of the MassARRAY assays. However, compared with gDNA or freshly prepared wgaDNA, stored wgaDNA was found to give diminished genotyping performance (efficiency and accuracy) due to potentially inferior quality. Consequently, no matter whether gDNA or wgaDNA was used, better genotyping efficiency would tend to have better genotyping accuracy

PAX6 Haplotypes Are Associated with High Myopia in Han Chinese

Author name used in this publication: Maurice K. H. Yap2010-2011 > Academic research: refereed > Publication in refereed journalpublished_fina