Implementing a continuous quality-improvement framework for tuberculosis infection prevention and control in healthcare facilities in China, 2017-2019.

BACKGROUND: Tuberculosis (TB) infection prevention and control (IPC) in healthcare facilities is key to reducing transmission risk. A framework for systematically improving TB IPC through training and mentorship was implemented in 9 healthcare facilities in China from 2017 to 2019. METHODS: Facilities conducted standardized TB IPC assessments at baseline and quarterly thereafter for 18 months. Facility-based performance was assessed using quantifiable indicators for IPC core components and administrative, environmental, and respiratory protection controls, and as a composite of all control types We calculated the percentage changes in scores over time and differences by IPC control type and facility characteristics. RESULTS: Scores for IPC core components increased by 72% during follow-up when averaged across facilities. The percentage changes for administrative, environmental, and respiratory protection controls were 39%, 46%, and 30%, respectively. Composite scores were 45% higher after the intervention. Overall, scores increased most during the first 6 months. There was no association between IPC implementation and provincial economic development or volume of TB services. CONCLUSIONS: TB IPC policies and practices showed most improvement early during implementation and did not differ consistently by facility characteristics. The training component of the project helped increase the capacity of healthcare professionals to manage TB transmission risks. Lessons learned here will inform national TB IPC guidance.

Comparative genomics reveals insights into anuran genome size evolution.

BACKGROUND: Amphibians, particularly anurans, display an enormous variation in genome size. Due to the unavailability of whole genome datasets in the past, the genomic elements and evolutionary causes of anuran genome size variation are poorly understood. To address this, we analyzed whole-genome sequences of 14 anuran species ranging in size from 1.1 to 6.8 Gb. By annotating multiple genomic elements, we investigated the genomic correlates of anuran genome size variation and further examined whether the genome size relates to habitat types. RESULTS: Our results showed that intron expansions or contraction and Transposable Elements (TEs) diversity do not contribute significantly to genome size variation. However, the recent accumulation of transposable elements (TEs) and the lack of deletion of ancient TEs primarily accounted for the evolution of anuran genome sizes. Our study showed that the abundance and density of simple repeat sequences positively correlate with genome size. Ancestral state reconstruction revealed that genome size exhibits a taxon-specific pattern of evolution, with families Bufonidae and Pipidae experiencing extreme genome expansion and contraction events, respectively. Our result showed no relationship between genome size and habitat types, although large genome-sized species are predominantly found in humid habitats. CONCLUSIONS: Overall, our study identified the genomic element and their evolutionary dynamics accounting for anuran genome size variation, thus paving a path to a greater understanding of the size evolution of the genome in amphibians.

Nasopharyngeal Carcinoma Subtype Discovery via Immune Cell Scores from Tumor Microenvironment.

Background: Nasopharyngeal carcinoma (NPC) is one of the most prevalent cancers with a poor prognosis. Immunotherapy, especially immune checkpoint blockade (ICB), is becoming a potential therapeutic choice for NPC patients. Thus, the identification of patients who could benefit from immunotherapy is clinically significant. Methods: The NPC expression profiles from GSE102349 were used to calculate the cell scores of the tumor microenvironment (TME). The consensus clustering method was utilized to identify the potential molecular subtypes among NPC samples. The hub genes were selected from subtype-specific genes by bioinformatics analysis. Machine learning models, including random forest (RF) and support vector machine (SVM) algorithms, were constructed to predict the immune subtype. Results: In the present study, we identified two TME subtypes among NPC patients. Patients with the S1 subtype have higher levels of immune cells, immune checkpoint genes, and prognosis. Using expression data profiles of NPC patients, we constructed machine learning models for predicting TME subtypes of NPC patients. This model consists of 8 genes (LCK, CD247, FYN, ZAP70, SH2D1A, CD3D, CD3E, and CD3G). Among them, LCK, FYN, SH2D1A, and CD3D were associated with better prognoses. Among the two constructed models, SVM exhibited a higher area under curve (AUC) of 0.977, when compared with RF (AUC = 0.966). The web server based on the constructed machine learning models will contribute to the identification of NPC patients likely to benefit from ICB therapies. Conclusions: This study identified NPC subtypes and provided an accurate model to select individuals who are most likely to respond to ICB.

Identification of HPV16 E1 and E2-specific T cells in the oropharyngeal cancer tumor microenvironment.

BACKGROUND: High-risk human papillomavirus (HPV) is a primary cause of an increasing number of oropharyngeal squamous cell carcinomas (OPSCCs). The viral etiology of these cancers provides the opportunity for antigen-directed therapies that are restricted in scope compared with cancers without viral components. However, specific virally-encoded epitopes and their corresponding immune responses are not fully defined. METHODS: To understand the OPSCC immune landscape, we conducted a comprehensive single-cell analysis of HPV16+ and HPV33+ primary tumors and metastatic lymph nodes. We used single-cell analysis with encoded peptide-human leukocyte antigen (HLA) tetramers to analyze HPV16+ and HPV33+ OPSCC tumors, characterizing the ex vivo cellular responses to HPV-derived antigens presented in major Class I and Class II HLA alleles. RESULTS: We identified robust cytotoxic T-cell responses to HPV16 proteins E1 and E2 that were shared across multiple patients, particularly in HLA-A*01:01 and HLA-B*08:01. Responses to E2 were associated with loss of E2 expression in at least one tumor, indicating the functional capacity of these E2-recognizing T cells and many of these interactions validated in a functional assay. Conversely, cellular responses to E6 and E7 were limited in quantity and cytotoxic capacity, and tumor E6 and E7 expression persisted. CONCLUSIONS: These data highlight antigenicity beyond HPV16 E6 and E7 and nominate candidates for antigen-directed therapies.

Local characteristics of molecular epidemiolgy of Acinetobacter baumannii in Jilin province (northeast China).

A. Baumannii is an opportunistic nosocomial pathogen which has severe antibiotic resistance. However, the epidemiology is less clearly understood in Jilin province and China. Thus, 89 A. baumannii isolates from a single hospital in Jilin province between 2013-2017 were performed by MLST. In order to better understanding of the epidemiology of Jilin isolates, Chinese strains originated from other domestic regions and worldwide isolates in MLST database were analyzed by silico phylogenetic tools together. A total of 22 STs in Jilin were identified, and 10 STs were found to be novel. The top three predominant sequence types are ST195 (n = 34, 38.2%), ST208 (n = 14, 15.7%) and ST540 (n = 13, 14.6%). ST369 is predicted to be group founder and ST195, ST540 are subgroup founders of the majority STs in Jilin Province. Some newly discovered singletons showed close relationship with strains from other countries, which suggest that nation-cross transmission is one of important origin of Jilin strains. The majority of Jilin STs showed clonality and close relationship with the majorities from other regions of China. But occupation of individual STs in Jilin were different from that of other domestic regions. The aggregation trend and genetic relationship proved that predominant Jilin STs continue to mutate during transmission. Drug resistance facilitated transmission of Jilin A.baumannii isolates because more than 94% of isolates are resistant to at least one carbapenem and the STs with strong resistance to carbapenems usually has more isolates. In conclusion, high diversity and different occupation of STs, and occupation of novel STs proved that epidemiology of A. baumannii in Jilin has special regional characteristics, and drug resistance facilitated transmission of domestic strains and foreign strains.

Characterization and genomic analysis of JC01, a novel bacteriophage infecting Cronobacter sakazakii.

The lytic bacteriophage JC01 was isolated using a strain of Cronobacter sakazakii previously isolated from powdered infant formula (PIF). The complete genome sequence of phage JC01 was determined. The double-stranded DNA genome of phage JC01 is composed of 61,736 bp with a G + C content of 58.9%, and it contains 76 putative open reading frames (ORFs) without any tRNA genes. The predicted ORFs were classified into functional groups, including DNA manipulation, transcription, phage packaging, phage structure, host lysis, and hypothetical proteins. Based on overall nucleotide sequence comparisons, calculation of phage intergenomic similarities, and phylogenetic analysis, JC01 appears to be a novel bacteriophage infecting C. sakazakii.

The highest-elevation frog provides insights into mechanisms and evolution of defenses against high UV radiation.

Defense against ultraviolet (UV) radiation exposure is essential for survival, especially in high-elevation species. Although some specific genes involved in UV response have been reported, the full view of UV defense mechanisms remains largely unexplored. Herein, we used integrated approaches to analyze UV responses in the highest-elevation frog, Nanorana parkeri. We show less damage and more efficient antioxidant activity in skin of this frog than those of its lower-elevation relatives after UV exposure. We also reveal genes related to UV defense and a corresponding temporal expression pattern in N. parkeri. Genomic and metabolomic analysis along with large-scale transcriptomic profiling revealed a time-dependent coordinated defense mechanism in N. parkeri. We also identified several microRNAs that play important regulatory roles, especially in decreasing the expression levels of cell cycle genes. Moreover, multiple defense genes (i.e., TYR for melanogenesis) exhibit positive selection with function-enhancing substitutions. Thus, both expression shifts and gene mutations contribute to UV adaptation in N. parkeri. Our work demonstrates a genetic framework for evolution of UV defense in a natural environment.

CircSOX9 acts as a molecular sponge of miR-485-3p to promote the progression of nasopharyngeal carcinoma.

Circular RNA (circRNA) plays a vital role in the occurrence and development of nasopharyngeal carcinoma (NPC). However, the role of certain specific circRNAs in NPC are still unknown. In this study, collect tumor samples and adjacent normal tissues from clinical NPC patients and detect the expression of circSOX9 by qRT-PCR. Use nucleoplasmic separation analysis, RNase R digestion assay and FISH to detect the characteristics of circSOX9. After knocking down circSOX9, clone formation experiment and transwell assay were used to detect the proliferation and invasion ability of nasopharyngeal carcinoma cells HONE1 and CNE2, and western blot was used to further detect the level of epithelial-mesenchymal transition (EMT). Use the database to screen for possible downstream target genes and verify them with dual-luciferase experiments. Bioinformatics analysis showed that circSOX9 was significantly up-regulated in NPC, and its expression level was positively correlated with the malignant progression of cancer. Data from function gain or loss studies showed that decrease of circSOX9 inhibited the invasion and proliferation of HONE1 and CNE2 cell lines. Further analysis proved that miR-485-3p was the downstream target of circSOX9. The luciferase test showed that by acting as a molecular sponge of miR-485-3p, circSOX9 promotes the proliferation and invasion of NPC cells, while miR-485-3p can target the expression of SOX9. In conclusion, circSOX9 acts as an oncogene in the progression of NPC through miR-485-3p/SOX9, indicating that circSOX9 can be used as a potential therapeutic target and predictive marker for nasopharyngeal carcinoma.

Expression Plasticity of Transposable Elements Is Highly Associated with Organismal Re-adaptation to Ancestral Environments.

Understanding the roles of phenotypic plasticity in adaptive evolution has gained recognition for decades. Studies involving multiple taxa have shown that gene expression plasticity serves as "long-term memory" to facilitate re-adaptations to ancestral environments. Nevertheless, the general pattern and the underlying genetic basis of expression plasticity remain unclear. The transposable elements (TEs) play crucial roles in gene expression regulation and are widely distributed within the genome. Given this, we re-analyzed the transcriptomic data of chicken (Gallus gallus) generated from a reciprocal transplant experiment to examine whether expression shifts of TEs are involved in the re-adaptation process. Similar to the protein-coding genes, the plastic changes of TEs overwhelmingly exceed the genetic changes in the re-adaptation process. Further, the associated TEs co-expressed with diverse genes to perform a regulatory activity. Thus, our study supports the general function of phenotypic plasticity in adaptive evolution, and suggests a regulatory functions of TEs in this process.

New Target of Oxidative Stress Regulation in Cochleae: Alternative Splicing of the p62/Sqstm1 Gene.

We investigated oxidative stress and antioxidant response in the p62/Sqstm1-Keap1-Nrf2 pathway in C57BL/6 mice cochleae during age-related hearing loss (ARHL) and noise-induced hearing loss (NIHL), and the function of full-length and variant p62 in the regulation of Nrf2 activation. Groups of young (2 months), old (13-14 months), control, and acoustic trauma (AT) mice were examined cochlear damage and oxidative stress as follows: auditory brainstem response and hair cell counts; malondialdehyde (MDA) levels measured by assay kit and 7,8-dihydro-8-oxoguanine (8-oxoG) detected by immunohistochemistry. Full-length and variant p62 were examined for expression in cochleae, hippocampus (HIP), and auditory cortex (AC) using immunoblotting. Keap1-Nrf2 pathway activation was based on immunoblotting of nuclear Nrf2 and quantitative real-time PCR of Nrf2 target genes HO-1/NQO-1. The oxidative function of full-length and variant p62 was examined in HEI-OC-1 cells by flow cytometry. The results showed hearing loss, and cochlear hair cell loss was associated with MDA accumulation and 8-oxoG expression during ARHL and NIHL. Nrf2 showed no obvious changes in nuclear protein. Expression levels mRNA for HO-1 and NQO1 were lower in old mice and mildly greater in AT Mice. The expression of p62 splicing variant lacking the Keap1-interacting region was greater than full-length p62 in cochleae. However, the expression of p62 splicing variant was lesser than full-length p62 in HIP and AC. For HEI-OC-1 cells, overexpression of full-length p62 decreased ROS levels induced by H2O2. Oxidative stress is closely related to ARHL and NIHL. Changing the ratio of full-length to variant p62 protein expression may be a new target to reduce the level of oxidative stress in cochleae.

A randomised controlled study on the effects of hernial sac stump fenestration on ultrasound seroma prevention in laparoscopic Type III inguinal hernia repair.

BACKGROUND: The incidence of ultrasound seromas has significantly increased after large hernial sac surgery. Several methods are available for preventing ultrasound seromas, but the clinical results are poor. It has also been demonstrated that hernial sac stump fenestration during laparoscopic incisional hernia repair surgery can significantly decrease the incidence of ultrasound seromas. MATERIALS AND METHODS: Ninety patients aged 18-75 years who were treated in our hospital for primary Type III indirect inguinal hernia from March 2017 to March 2018 were randomised to a preventive fenestration group and a control group. All patients underwent transabdominal preperitoneal repair. The number of ultrasound seromas in the inguinal regions and ultrasound seroma volume on day 6 and months 1 and 3 after surgery in the two groups were compared. The secondary outcomes included length of surgery, urinary retention, acute pain, chronic pain, length of hospitalisation, recurrence rate and other complications. RESULTS: There were no significant differences in demographic characteristics. Ultrasound seroma incidence and ultrasound seroma volume on day 6 and months 1 and 3 after surgery were significantly lower in the preventive fenestration group than that in the control group. There were no significant differences in the length of hospitalisation or incidence of acute pain or urinary retention between the two groups. CONCLUSIONS: Hernial sac stump fenestration after hernial sac transection in inguinal hernia repair surgery is a simple method that can effectively reduce post-operative ultrasound seromas.

Cross-Layer-Aided Opportunistic Routing for Sparse Underwater Wireless Sensor Networks.

Underwater wireless sensor networks (UWSNs) have emerged as a promising technology to monitor and explore the oceans instead of traditional undersea wireline instruments. Traditional routing protocols are inefficient for UWSNs due to the specific nature of the underwater environment. In contrast, Opportunistic Routing (OR) protocols establish an online route for each transmission, which can well adapt with time-varying underwater channel. Cross-layer design is an effective approach to combine the metrics from different layers to optimize an OR routing in UWSNs. However, typical cross-layer OR routing protocols that are designed for UWSNs suffer from congestion problem at high traffic loads. In this paper, a Cross-Layer-Aided Opportunistic Routing Protocol (CLOR) is proposed to reduce the congestion in multi-hop sparse UWSNs. The CLOR consists of a negotiation phase and transmission phase. In the negotiation phase, the cross-layer information in fuzzy logic is utilized to attain an optimal forwarder node. In the transmission phase, to improve the transmission performance, a burst transmission strategy with network coding is exploited. Finally, we perform simulations of the proposed CLOR protocol in a specific sea region. Simulation results show that CLOR significantly improves the network performances at various traffic rates compared to existing protocols.

Preliminary Exploration of Setting the Disease Severity Score in the Nutritional Risk Screening of Patients with Severe Novel Coronavirus Pneumonia by Applying NRS2002.

OBJECTIVE: This study was designed to explore the impact of different scoring settings of disease severity on the accuracy of screening by NRS2002. METHODS: Patients with severe COVID-19 who were admitted to our hospital from January 26, 2020, to March 16, 2020, were enrolled in this study. The basic data, the scores of the NRS2002 score sheet, and the serum prealbumin (PAB) level when these patients were admitted were collected, and the reflection of NRS2002 scores under different disease severity score settings to abnormal patients was analyzed. RESULTS: 1. When the severity of the disease was set to 0 points, four of the six hospitalized patients with PAB levels below the lower normal limit were not screened out; 2. When the severity was set to 1 point, two patients with COVID-19 who developed to a severe stage during the treatment process were screened out, but three of the six hospitalized patients with PAB levels below the lower normal limit at admission were not screened out; 3. When the severity of the disease of a patient with severe COVID-19 and fever scored 2 points, and that of a patient without fever scored 1 point, two patients with COVID-19 who developed to the severe stage during the treatment process were screened out, and six patients who were hospitalized with PAB levels below the lower normal limit at admission were also screened out. CONCLUSION: When the severe degree of patients with COVID-19 and fever is rated as 2 points, and that of the patients without fever is rated as 1 point, it can more accurately reflect the severity degree of patients with undernourishment.

The Value of Nutritional Status in the Prognostic Analysis of Patients with AIDS-Related Lymphoma.

OBJECTIVE: Many studies have suggested that indexes of nutritional status, such as body mass index (BMI), serum albumin (ALB), serum pre-albumin (PA), and hemoglobin, may be used as risk factors for the prognosis of HIV or lymphoma. Therefore, this study aimed to retrospectively analyze and explore the value of nutritional status in the prognostic assessment of patients with AIDS-related lymphoma (ARL). METHODS: In this retrospective study, the clinical data of 69 patients with ARL were collected. All patients had a definite diagnosis of non-Hodgkin lymphoma by pathological examination and met the requirements of the Hematopoietic and Lymphocytic Tissue Tumor Classification (2016) established by the World Health Organization. Patients who did not receive standard chemotherapy, those with incomplete medical records, and those with an unclear pathological diagnosis were excluded. The patients were divided into two groups (survival and death) according to the prognostic outcome, and their clinical characteristics and prognoses were discussed by relevant statistical methods. RESULTS: During the three-year follow-up period, 20 (28.99%) patients died, and 49 (71.01%) survived. The one-year cumulative survival rate was 78.26%. A univariate analysis found that the prognosis was associated with the International Prognostic Index (IPI) score, BMI, ALB, PA, and CD4 T lymphocyte count. The Cox risk proportional regression analysis showed that the IPI score, BMI, and PA were the independent risk factors for survival; their combination had a greater ability to forecast the clinical outcome (area under the curve = 0.874, P < 0.001). CONCLUSION: In this study, at the time of the visit, the patients with ARL tended to be in the advanced stages of disease and, therefore, at high risk of mortality. Therefore, their nutritional status might be of great value to the prognostic assessment. The combination of BMI, PA, and IPI scores could be used for risk stratification and better screening of high-risk patients.

Expression of α2-Na/K-ATPase in C57BL/6J Mice Inner Ear and Its Relationship with Age-related Hearing Loss.

K+ cycling in the cochlea is critical to maintain hearing. Many sodium-potassium pumps are proved to participate in K+ cycling, such as Na/K-ATPase. The α2-Na/K-ATPase is an important isoform of Na/K-ATPase. The expression of α2-Na/K-ATPase in the cochlea is not clear. In this study, we used C57BL/6 mice as a model of presbycusis and implemented immunohistochemistry staining and quantitative real time-PCR, and the α2-Na/K-ATPase expression pattern was confirmed in the inner ear. It was found α2-Na/K-ATPase was expressed widely in cochlea and its mRNA and protein expression was gradually reduced with aging (4-, 14-, 26- and 48-weeks old mice). We suspected that, the down-regulation of α2-Na/K-ATPase expression might be associated with the remodeling of K+ cycling, degeneration of morphological structure and decrease of hearing function in aging C57 mice. In conclusion, we speculated that the reduction of α2-Na/K-ATPase might play an important role in the pathogenesis of age-related hearing loss.

Characterization and Genomic Analysis of Escherichia coli O157:H7 Bacteriophage FEC14, a New Member of Genus Kuttervirus.

Escherichia coli O157:H7 is an important foodborne pathogen that has become a major worldwide factor affecting the public safety of food. Bacteriophage has gradually attracted attention because of its ability to kill specific pathogens. In this study, a lytic phage of E. coli O157:H7, named FEC14, was isolated from hospital sewage. Transmission electron microscopy analysis showed that phage FEC14 had an isometric head 80 ± 5 nm in diameter and a contractile tail whose terminal spikes present an umbrella-like structure. Phage FEC14 revealed 158,639 bp double-stranded DNA, with the G+C content of 44.6%, 209 ORFs and four tRNAs. Genome DNA of FEC14 could not be digested by some endonucleases. Many of the features of phage FEC14 are very similar to those of the newly classified genus "Kuttervirus", including morphology, genome size and organization, etc. Phage FEC14 is proposed to be a new isolate of genus "Kuttervirus" within the family Ackermannviridae, moreover, the endonuclease resistance of phage FEC14, has priority over other genera of bacteriophages for its use in biocontrol of foodborne pathogens.

Zbtb20 Restrains CD8 T Cell Immunometabolism and Restricts Memory Differentiation and Antitumor Immunity.

CD8 T cell differentiation is orchestrated by dynamic metabolic changes that direct activation, proliferation, cytotoxic function, and epigenetic changes. We report that the BTB-ZF family transcriptional repressor Zbtb20 negatively regulates CD8 T cell metabolism and memory differentiation in mice. Effector and memory CD8 T cells with conditional Zbtb20 deficiency displayed enhanced mitochondrial and glycolytic metabolism, and memory CD8 T cells had enhanced spare respiratory capacity. Furthermore, Zbtb20-deficient CD8 T cells displayed increased flexibility in the use of mitochondrial fuel sources. Phenotypic and transcriptional skewing toward the memory fate was observed during the CD8 T cell response to Listeria monocytogenes Memory cells mounted larger secondary responses and conferred better protection following tumor challenge. These data suggest that inactivation of Zbtb20 may offer an approach to enhance metabolic activity and flexibility and improve memory CD8 T cell differentiation, useful attributes for T cells used in adoptive immunotherapy.

Feature Classification Method of Resting-State EEG Signals From Amnestic Mild Cognitive Impairment With Type 2 Diabetes Mellitus Based on Multi-View Convolutional Neural Network.

The convolutional neural network (CNN) model is an active research topic in the field of EEG signals analysis. However, the classification effect of CNN on EEG signals of amnestic mild cognitive impairment (aMCI) with type 2 diabetes mellitus (T2DM) is not ideal. Even if EEG signals are transformed into multispectral images that are more closely matched with the model, the best classification performance can not be achieved. Therefore, to improve the performance of CNN toward EEG multispectral image classification, a multi-view convolutional neural network (MVCNN) classification model based on inceptionV1 is designed in this study. This model mainly improves and optimizes the convolutional layers and stochastic gradient descent (SGD) in the convolutional architecture model. Firstly, based on the discreteness of EEG multispectral image features, the multi-view convolutional layer structure was proposed. Then the learning rate change function of the SGD was optimized to increase the classification performance. The multi-view convolutional nerve was used in an EEG multispectral classification task involving 19 aMCI with T2DM and 20 normal controls. The results showed that compared with the traditional classification models, MVCNN had a better stability and accuracy. Therefore, MVCNN could be used as an effective feature classification method for aMCI with T2DM.

Perspectives on studying molecular adaptations of amphibians in the genomic era.

Understanding the genetic mechanisms underlying particular adaptations/phenotypes of organisms is one of the core issues of evolutionary biology. The use of genomic data has greatly advanced our understandings on this issue, as well as other aspects of evolutionary biology, including molecular adaptation, speciation, and even conservation of endangered species. Despite the well-recognized advantages, usages of genomic data are still limited to non-mammal vertebrate groups, partly due to the difficulties in assembling large or highly heterozygous genomes. Although this is particularly the case for amphibians, nonetheless, several comparative and population genomic analyses have shed lights into the speciation and adaptation processes of amphibians in a complex landscape, giving a promising hope for a wider application of genomics in the previously believed challenging groups of organisms. At the same time, these pioneer studies also allow us to realize numerous challenges in studying the molecular adaptations and/or phenotypic evolutionary mechanisms of amphibians. In this review, we first summarize the recent progresses in the study of adaptive evolution of amphibians based on genomic data, and then we give perspectives regarding how to effectively identify key pathways underlying the evolution of complex traits in the genomic era, as well as directions for future research.