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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Learning a Condensed Frame for Memory-Efficient Video Class-Incremental Learning

Recent incremental learning for action recognition usually stores representative videos to mitigate catastrophic forgetting. However, only a few bulky videos can be stored due to the limited memory. To address this problem, we propose FrameMaker, a memory-efficient video class-incremental learning approach that learns to produce a condensed frame for each selected video. Specifically, FrameMaker is mainly composed of two crucial components: Frame Condensing and Instance-Specific Prompt. The former is to reduce the memory cost by preserving only one condensed frame instead of the whole video, while the latter aims to compensate the lost spatio-temporal details in the Frame Condensing stage. By this means, FrameMaker enables a remarkable reduction in memory but keep enough information that can be applied to following incremental tasks. Experimental results on multiple challenging benchmarks, i.e., HMDB51, UCF101 and Something-Something V2, demonstrate that FrameMaker can achieve better performance to recent advanced methods while consuming only 20% memory. Additionally, under the same memory consumption conditions, FrameMaker significantly outperforms existing state-of-the-arts by a convincing margin.Comment: NeurIPS 202

Identification of immune infiltration and cuproptosis-related molecular clusters in tuberculosis

BackgroundTuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (Mtb) infection. Cuproptosis is a novel cell death mechanism correlated with various diseases. This study sought to elucidate the role of cuproptosis-related genes (CRGs) in TB.MethodsBased on the GSE83456 dataset, we analyzed the expression profiles of CRGs and immune cell infiltration in TB. Based on CRGs, the molecular clusters and related immune cell infiltration were explored using 92 TB samples. The Weighted Gene Co-expression Network Analysis (WGCNA) algorithm was utilized to identify the co-expression modules and cluster-specific differentially expressed genes. Subsequently, the optimal machine learning model was determined by comparing the performance of the random forest (RF), support vector machine (SVM), generalized linear model (GLM), and eXtreme Gradient Boosting (XGB). The predictive performance of the machine learning model was assessed by generating calibration curves and decision curve analysis and validated in an external dataset.Results11 CRGs were identified as differentially expressed cuproptosis genes. Significant differences in immune cells were observed in TB patients. Two cuproptosis-related molecular clusters expressed genes were identified. Distinct clusters were identified based on the differential expression of CRGs and immune cells. Besides, significant differences in biological functions and pathway activities were observed between the two clusters. A nomogram was generated to facilitate clinical implementation. Next, calibration curves were generated, and decision curve analysis was conducted to validate the accuracy of our model in predicting TB subtypes. XGB machine learning model yielded the best performance in distinguishing TB patients with different clusters. The top five genes from the XGB model were selected as predictor genes. The XGB model exhibited satisfactory performance during validation in an external dataset. Further analysis revealed that these five model-related genes were significantly associated with latent and active TB.ConclusionOur study provided hitherto undocumented evidence of the relationship between cuproptosis and TB and established an optimal machine learning model to evaluate the TB subtypes and latent and active TB patients

The epidemiology of Plasmodium vivax and Plasmodium falciparum malaria in China, 2004–2012: from intensified control to elimination

BACKGROUND In China, the national malaria elimination programme has been operating since 2010. This study aimed to explore the epidemiological changes in patterns of malaria in China from intensified control to elimination stages. METHODS Data on nationwide malaria cases from 2004 to 2012 were extracted from the Chinese national malaria surveillance system. The secular trend, gender and age features, seasonality, and spatial distribution by Plasmodium species were analysed. RESULTS In total, 238,443 malaria cases were reported, and the proportion of Plasmodium falciparum increased drastically from <10% before 2010 to 55.2% in 2012. From 2004 to 2006, malaria showed a significantly increasing trend and with the highest incidence peak in 2006 (4.6/100,000), while from 2007 onwards, malaria decreased sharply to only 0.18/100,000 in 2012. Males and young age groups became the predominantly affected population. The areas affected by Plasmodium vivax malaria shrunk, while areas affected by P. falciparum malaria expanded from 294 counties in 2004 to 600 counties in 2012. CONCLUSIONS This study demonstrated that malaria has decreased dramatically in the last five years, especially since the Chinese government launched a malaria elimination programme in 2010, and areas with reported falciparum malaria cases have expanded over recent years. These findings suggest that elimination efforts should be improved to meet these changes, so as to achieve the nationwide malaria elimination goal in China in 2020.This study was supported by grants from the Ministry of Science and Technology of China (2012ZX10004-201, 2012ZX10004-220) and the Ministry of Health of China (No. 201202006), and China UK Global Health Support Programme (grant no. GHSP-CS-OP1). S.I.H. is funded by a Senior Research Fellowship from the Wellcome Trust (#095066). S.I.H. also acknowledges funding support from the RAPIDD programme of the Science & Technology Directorate, Department of Homeland Security, and the Fogarty International Center, National Institutes of Health

Efficacy and Safety of Tribendimidine Against Clonorchis sinensis

In this randomized open-label trial, tribendimidine was shown to have an efficacy comparable to praziquantel for the treatment of Clonorchis sinensis infection. Patients treated with praziquantel experienced significantly more adverse events than tribendimidine recipient

Global epidemiology of clonorchiasis and its relation with cholangiocarcinoma

Human beings are infected through ingestion of raw or undercooked fish, which contains the metacercariae of liver flukes. This paper reviews the epidemiological status and characteristics of clonorchiasis at global level and the relationship between Clonorchis sinensis infection and cholangiocarcinoma (CCA). Liver flukes are a polyphyletic group of trematodes, including Clonorchis sinensis, Opisthorchis viverrini and Opisthorchis felineus. Cholangiocarcinoma (CCA) is a cancer of the bile ducts. The epidemiology of clonorchiasis is characterized by a rising trend in prevalence, variability among sex and age, as well as endemicity in different regions. Accurate evaluation of prevalence is necessary to promote adoption of suitable interventions

HDA18 Affects Cell Fate in Arabidopsis Root Epidermis via Histone Acetylation at Four Kinase Genes

The differentiation of hair (H) and non-hair (N) cells in the Arabidopsis thaliana root epidermis is dependent on positional relationships with underlying cortical cells. We previously found that histone acetylation relays positional information and that a mutant altered in the histone deacetylase gene family member HISTONE DEACETYLASE 18 (HDA18) exhibits altered H and N epidermal cell patterning. Here, we report that HDA18 has in vitro histone deacetylase activity and that both mutation and overexpression of HDA18 led to cells at the N position having H fate. The HDA18 protein physically interacted with histones related to a specific group of kinase genes, which are demonstrated in this study to be components of a positional information relay system. Both down- and upregulation of HDA18 increased transcription of the targeted kinase genes. Interestingly, the acetylation levels of histone 3 lysine 9 (H3K9), histone 3 lysine 14 (H3K14) and histone 3 lysine 18 (H3K18) at the kinase genes were differentially affected by down- or upregulation of HDA18, which explains why the transcription levels of the four HDA18-target kinase genes increased in all lines with altered HDA18 expression. Our results reveal the surprisingly complex mechanism by which HDA18 affects cellular patterning in Arabidopsis root epidermis

Biochemical characterization of an acetylesterase from Bacillus subtilis and its application for 7-aminocephalosporanic acid deacetylation

Deacetyl-7-aminocephalosporanic acid (D-7-ACA), which could be converted from 7-aminocephalosporanic acid (7-ACA), is a crucial starting material that is used for synthesizing industrial semisynthetic β-lactam antibiotics. Enzymes involved in the conversion from 7-ACA to D-7-ACA present critical resources in the pharmaceutical industry. In the present study, a putative acetylesterase, EstSJ, identified from Bacillus subtilis KATMIRA1933, was first heterologously expressed in Escherichia coli BL21(DE3) cells and biochemically characterized. EstSJ belongs to carbohydrate esterase family 12 and is active on short-chain acyl esters from p-NPC2 to p-NPC6. Multiple sequence alignments showed that EstSJ was also an SGNH family esterase with a typical GDS(X) motif at its N-terminal end and a catalytic triad composed of Ser186-Asp354-His357. The purified EstSJ displayed the highest specific activity of 1,783.52 U mg–1 at 30°C and pH 8.0, and was stable within the pH range of 5.0–11.0. EstSJ can deacetylate the C3′ acetyl group of 7-ACA to generate D-7-ACA, and the deacetylation activity was 4.50 U mg–1. Based on the structural and molecular docking with 7-ACA, the catalytic active sites (Ser186-Asp354-His357) together with four substrate-binding residues (Asn259, Arg295, Thr355, and Leu356) of EstSJ are revealed. This study provided a promising 7-ACA deacetylase candidate that could be applied to produce D-7-ACA from 7-ACA in the pharmaceutical industry

Disability Weight of Clonorchis sinensis Infection: Captured from Community Study and Model Simulation

Clonorchiasis is caused by eating incompletely cooked fishery product which carries the larval of Clonorchis sinensis. Millions of people are estimated to suffer in Southeast Asia. However, it is still among the most neglected tropical diseases due to the lack of clear evaluation, of which no disease burden available is one important reason. Our study is the first attempt to estimate the disability of C. sinensis infection, which reflects the average loss of life value due to some conditions and is crucial for calculating disease burden in terms of disability-adjusted life years (DALYs). After obtaining the probability and disability of single sequelae caused by C. sinensis infection through community investigation and literatures reviewing respectively, the overall disability was captured through model simulation. It was showed the overall disability of the male was higher than that of the female, positive correlation occurred between disability and infection intensity, and gallstone took the major attributable proportion. Thus, C. sinensis infection can cause apparent disability. The disability captured here may promote the further studies and benefit the final estimation of disease burden, which will promote health awareness and implementation of intervention