Search

The Hidden Markov Model (HMM) is a crucial probabilistic modeling technique for sequence data processing and statistical learning that has been extensively utilized in various engineering applications. Traditionally, the EM algorithm is employed to fit HMMs, but currently, academics and professionals exhibit augmenting enthusiasm in Bayesian inference. In the Bayesian context, Markov Chain Monte Carlo (MCMC) methods are commonly used for inferring HMMs, but they can be computationally demanding for high-dimensional covariate data. As a rapid substitute, variational approximation has become a noteworthy and effective approximate inference approach, particularly in recent years, for representation learning in deep generative models. However, there has been limited exploration of variational inference for HMMs with high-dimensional covariates. In this article, we develop a mean-field Variational Bayesian method with the double-exponential shrinkage prior to fit high-dimensional HMMs whose hidden states are of discrete types. The proposed method offers the advantage of fitting the model and investigating specific factors that impact the response variable changes simultaneously. In addition, since the proposed method is based on the Variational Bayesian framework, the proposed method can avoid huge memory and intensive computational cost typical of traditional Bayesian methods. In the simulation studies, we demonstrate that the proposed method can quickly and accurately estimate the posterior distributions of the parameters with good performance. We analyzed the Beijing Multi-Site Air-Quality data and predicted the PM2.5 values via the fitted HMMs.

Highlights circ_0025033 knockdown inhibited ovarian cancer malignant behaviors. circ_0025033 served as a hsa_miR-370-3p sponge. hsa_miR-370-3p targeted SLC1A5.

The construction of marine ranching is a concrete practice to fulfil the strategic objective of China’s maritime power. The shortage of funds has turned into an important issue to be resolved urgently in the modernization of marine ranching. This study constructs a supply chain system, involving a leading enterprise of marine ranching with short funds and a retailer, and introduces the government guidance fund to solve the issue of capital shortage. Then, we discuss the supply chain financing decision under two different power structure modes, and analyze the product environmental attribute (the product’s environmental friendliness and the environmental enrichment) and the guiding effect of government investment on the operation of different modes. The research shows that: (1) The wholesale price of products is mainly influenced by the dominant position of the marine ranching leading enterprise. Furthermore, the wholesale price and the marine ranching company’s profits increase with the growth of the product environmental attribute. (2) The retailer’s profit and the supply chain system’s profit are mainly affected by the dominant power of the retailer and are positively correlated with the product environmental attribute. In addition, the supply chain system’s overall profits are negatively related to the guiding effect of government investment.

Objectives: Klebsiella pneumoniae carbapenemase (KPC) has spread across the world. The present study focused on exploring the sequences of two new KPC-harbouring plasmids in K. pneumoniae. Methods: Eighteen KPC-harbouring K. pneumoniae isolates were collected from a tertiary teaching hospital in 2014 in Fujian, China, among which two new KPC-harbouring plasmids (pF77 and pF5) we identified. The characteristics of the plasmids and the isolates carrying them were investigated in detail. Results: The two KPC-harbouring plasmids (pF5 and pF77) carried the antimicrobial resistance genes blaKPC-2, blaCTX-M-65, blaSHV-12, catA2 and fosA3. Detailed sequence comparison revealed that the two plasmids might have evolved from recombination of the previously reported plasmids pKP1034 and pCT-KPC, which were considered to evolve from ancestor plasmids pHN7A8, pKPC-LK30 and pKPHS2. Plasmids pF5 and pF77 were non-conjugative and were mainly identified in sequence type 11 (ST11) K. pneumoniae isolates. Additionally, 4–55 core single nucleotide polymorphisms (SNPs) were identified in each pair of sequenced isolates that carried the identified plasmids. Conclusion: Plasmids pF5 and pF77 as well as the previously reported plasmids pKP1034 and pCT-KPC were all detected in 2013–2014 in South China and were carried by ST11 K. pneumoniae isolates. SNP analysis indicated high similarity of the sequenced isolates. Therefore, spread of the group of plasmids may be due to an outbreak of clonal dissemination of ST11 KPC-producing K. pneumoniae. This study also highlights the importance of plasmid analysis in the surveillance and control of antibiotic resistance spread in clinical isolates.

Purpose: Radiation-induced lung injury limits the implementation of radiotherapy plans and severely impairs the quality of life. Crocetin has the capability to protect against radiation. This study is aimed at estimate the preventive effect and mechanism of crocetin on acute radiation induced lung injury. Methods and Materials: In this study, we offer a strategy for radiation-induced lung injury by using crocetin, an extract of gardenia fruit. Histopathology, transcriptomics, flow cytometry, and other methods have served to examine the effect and mechanism of crocetin on acute radiation-induced lung injury. Results: Crocetin effectively alleviates radiation-induced alveolar wall thickening and alveolar destruction. The number of normal alveoli and lung structure of mice is well protected by the prevention of crocetin. It is found that crocetin inhibits necroptosis to achieve effective radioprotection by down regulating the Tnfrsf10b gene in vitro. Conclusion: Crocetin inhibits necroptosis through transcriptional regulation of the Tnfrsf10b gene, thereby preventing radiation-induced lung injury. This work may provide a new strategy for the prevention of lung radiation injury by the extract from Chinese herbal medicine.

Abstract. Background. Carbapenemase-producing Klebsiella pneumoniae (CP-Kp) poses distinct clinical challenges due to extensively drug resistant (XDR) phenotype, and sequence type (ST) 11 is the most dominant blaKPC-2-bearing CP-Kp clone in China. The purpose of this current retrospective study was to explore the genetic factors associated with the success of XDR CP-Kp ST11 strains circulated in the intensive care unit (ICU) of a Chinese tertiary hospital. Methods. Six ST11 XDR CP-Kp strains were identified between May and December 2014 and validated by minimum inhibitory concentration examination, polymerase chain reaction, and pyrosequencing. The six ST11 XDR CP-Kp, as well as three multi-drug resistant (MDR) and four susceptible strains, were sequenced using single-molecule real-time method. Comprehensively structural and functional analysis based on comparative genomics was performed to identify genomic characteristics of the XDR ST11 CP-Kp strains. Results. We found that ST11 XDR blaKPC-2-bearing CP-Kp strains isolated from inpatients spread in the ICU of the hospital. Functionally, genes associated with information storage and processing of the ST11 XDR CP-Kp strains were more abundant than those of MDR and susceptible strains, especially genes correlative with mobile genetic elements (MGEs) such as transposons and prophages. Structurally, eleven large-scale genetic regions taken for the unique genome in these ST11 XDR CP-Kp strains were identified as MGEs including transposons, integrons, prophages, genomic islands, and integrative and conjugative elements. Three of them were located on plasmids and eight on chromosomes; five of them were with antimicrobial resistance genes and eight with adaptation associated genes. Notably, a new blaKPC-2-bearing ΔΔTn1721-blaKPC-2 transposon, probably transposed and truncated from ΔTn1721-blaKPC-2 by IS903D and ISKpn8, was identified in all six ST11 XDR CP-Kp strains. Conclusion. Our findings suggested that together with clonal spread, MGEs identified uniquely in the ST11 XDR CP-Kp strains might contribute to their formidable adaptability, which facilitated their widespread dissemination in hospital.

Abstract Background Opportunistic pathogens are important for clinical practice as they often cause antibiotic-resistant infections. However, little is documented for many emerging opportunistic pathogens and their biological characteristics. Here, we isolated a strain of extended-spectrum β-lactamase-producing Enterobacteriaceae from a patient with a biliary tract infection. We explored the biological and genomic characteristics of this strain to provide new evidence and detailed information for opportunistic pathogens about the co-infection they may cause. Results The isolate grew very slowly but conferred strong protection for the co-infected cephalosporin-sensitive Klebsiella pneumoniae. As the initial laboratory testing failed to identify the taxonomy of the strain, great perplexity was caused in the etiological diagnosis and anti-infection treatment for the patient. Rigorous sequencing efforts achieved the complete genome sequence of the isolate which we designated as AF18. AF18 is phylogenetically close to a few strains isolated from soil, clinical sewage, and patients, forming a novel species together, while the taxonomic nomenclature of which is still under discussion. And this is the first report of human infection of this novel species. Like its relatives, AF18 harbors many genes related to cell mobility, various genes adaptive to both the natural environment and animal host, over 30 mobile genetic elements, and a plasmid bearing bla CTX-M-3 gene, indicating its ability to disseminate antimicrobial-resistant genes from the natural environment to patients. Transcriptome sequencing identified two sRNAs that critically regulate the growth rate of AF18, which could serve as targets for novel antimicrobial strategies. Conclusions Our findings imply that AF18 and its species are not only infection-relevant but also potential disseminators of antibiotic resistance genes, which highlights the need for continuous monitoring for this novel species and efforts to develop treatment strategies.

Tuning the mechanical properties of extracellular matrix is of great interest in tissue engineering but spatial control over stiffness in hydrogels has been demonstrated in two dimensions only. Here the authors developed a layer-by-layer printing technique which uses oxygen inhibition to control the heterogeneous stiffness in 3D printed structures.

Bacterial isolate X39 was isolated from a community-acquired pneumonia patient in Beijing, China. A phylogenetic tree based on rpoB genes and average nucleotide identity data confirmed that isolate X39 belonged to Klebsiella variicola. The genome of K. variicola X39 contained one circular chromosome and nine plasmids. Comparative genomic analyses with other K. variicola isolates revealed that K. variicola X39 contained the most unique genes. Of these unique genes, many were prophages and transposases. Many virulence factors were shared between K. variicola X39 and Klebsiella pneumoniae F1. The pathogenicity of K. variicola X39 was compared with that of K. pneumoniae F1 in an abdominal infection model. The results indicated that K. variicola X39 was less virulent than typical clinical K. pneumoniae F1. The genome of K. variicola X39 also contained some genes involved in plant colonization, nitrogen fixation, and defense against oxidative stress. GFP-labeled K. variicola X39 could colonize maize as an endophytic bacterium. We concluded that K. variicola X39 was a kingdom-crossing strain.

In this paper, we report a mid-wave infrared (MWIR) and long-wave infrared (LWIR) dual-band photodetector capable of voltage-controllable detection band selection. The voltage-tunable dual-band photodetector is based on the multiple stacks of sub-monolayer (SML) quantum dots (QDs) and self-assembled QDs. By changing the photodetector bias voltages, one can set the detection band to be MWIR, or LWIR or both with high photodetectivity and low crosstalk between the bands.

Background While global newborn hearing screening programmes (NHSP) are far from the optimal level, the combined hearing and genetic screening has emerged as an innovative approach of early healthcare interventions. There is a clear need for economic evaluation to establish whether newborn deafness gene screening (NDGS), currently mandated by many cities in China, is a good investment.Methods A decision-tree model was constructed to simulate a hypothetical 10-million Chinese newborn cohort over a lifetime with three strategies: (1) no screening, (2) NHSP (standard screening) and (3) NHSP+NDGS (combined screening). The presence of permanent congenital hearing loss (PCHL) and genetic mutation were assigned at birth and held constant for all strategies. Input parameters were obtained from the Cohort of Deafness-gene Screening study and literature review. The government contract price for genetic screening was US$77/child. Outcomes of interest included the number of early diagnosed PCHL, prelingual deafness, total deafness, special education referral, incremental cost-effectiveness ratio (ICER) and benefit–cost ratio (BCR).Results Both standard and combined screening strategies were more effective and more costly than ‘no screening’. Compared with standard screening, combined screening led to 9112 (28.0%) more PCHL cases early detected, avoiding 4071 (66.9%) prelingual deafness cases and 3977 (15.6%) special education referrals. The ICER and BCR for combined screening were US$ 4995/disability-adjusted life-year (95% uncertainty interval, 2963 to 9265) and 1.78 (1.19 to 2.39), from healthcare sector perspective. Combined screening would dominate standard screening from societal perspective. Moreover, it remained cost-effective even in pessimistic scenarios.Conclusions Our findings have particular implication for the ‘scale-up’ of genetic screening at the national level in China. The model may serve as a feasible example for hearing screening strategies in other countries, as well as genetic screening for other diseases.