Iron regulatory protein from the hard tick Haemaphysalis longicornis: characterization, function and assessment as a protective antigen.

BACKGROUND: Ticks are blood-feeding ectoparasites with different host specificities and are capable of pathogen transmission. Iron regulatory proteins (IRPs) play crucial roles in iron homeostasis in vertebrates. However, their functions in ticks remain poorly understood. The aim of the present study was to investigate the characteristics, functions, molecular mechanisms, and the vaccine efficacy of IRP in the hard tick Haemaphysalis longicornis. RESULTS: The full-length complementary DNA of IRP from Haemaphysalis longicornis (HlIRP) was 2973 bp, including a 2772 bp open reading frame. It is expressed throughout three developmental stages (larvae, nymphs, and adult females) and in various tissues (salivary glands, ovaries, midgut, and Malpighian tubules). Recombinant Haemaphysalis longicornis IRP (rHlIRP) was obtained via a prokaryotic expression system and exhibited aconitase, iron chelation, radical-scavenging, and hemolytic activities in vitro. RNA interference-mediated IRP knockdown reduced tick engorgement weight, ovary weight, egg mass weight, egg hatching rate, and ovary vitellin content, as well as prolonging the egg incubation period. Proteomics revealed that IRP may affect tick reproduction and development through proteasome pathway-associated, ribosomal, reproduction-related, and iron metabolism-related proteins. A trial on rabbits against adult Haemaphysalis longicornis infestation demonstrated that rHlIRP vaccine could significantly decrease engorged weight (by 10%), egg mass weight (by 16%) and eggs hatching rate (by 22%) of ticks. The overall immunization efficacy using rHlIRP against adult females was 41%. CONCLUSION: IRP could limit reproduction and development in Haemaphysalis longicornis, and HlIRP was confirmed as a candidate vaccine antigen to impair tick iron metabolism and protect the host against tick infestation. © 2024 Society of Chemical Industry.

Enhancing the quality of panel-based tumor mutation burden assessment: a comprehensive study of real-world and in-silico outcomes.

Targeted panel-based tumor mutation burden (TMB) assays are widely employed to guide immunotherapy for patients with solid tumors. However, the accuracy and consistency of this method can be compromised due to the variability in technical details across different laboratories, particularly in terms of panel size, somatic mutation detection and TMB calculation rules. Currently, systematic evaluations of the impact of these technical factors on existing assays and best practice recommendations remain lacking. We assessed the performance of 50 participating panel-based TMB assays involving 38 unique methods using cell line samples. In silico experiments utilizing TCGA MC3 datasets were performed to further dissect the impact of technical factors. Here we show that the panel sizes beyond 1.04 Mb and 389 genes are necessary for the basic discrete accuracy, as determined by over 40,000 synthetic panels. The somatic mutation detection should maintain a reciprocal gap of recall and precision less than 0.179 for reliable psTMB calculation results. The inclusion of synonymous, nonsense and hotspot mutations could enhance the accuracy of panel-based TMB assay. A 5% variant allele frequency cut-off is suitable for TMB assays using tumor samples with at least 20% tumor purity. In conclusion, this multicenter study elucidates the major technical factors as sources of variability in panel-based TMB assays and proposed comprehensive recommendations for the enhancement of accuracy and consistency. These findings will assist clinical laboratories in optimizing the methodological details through bioinformatic experiments to enhance the reliability of panel-based methods.

External quality assessment for detection of colorectal cancer by Septin9 DNA methylation in clinical laboratories.

BACKGROUND AND AIMS: The incidence and mortality rate of colorectal cancer (CRC) are increasing worldwide. Septin9 methylated (mSEPT9) DNA in circulation can be used as a non-invasive detection method to assist in the early diagnosis of CRC; however, the detection methods and procedures are complicated. This study aimed to evaluate the ability of clinical laboratories to detect Septin9 methylation in plasma cell-free DNA (cfDNA). MATERIALS AND METHODS: We prepared a sample panel consisting of positive and negative Septin9 methylation cells and CRC cells. Three positive samples with different methylation levels, one negative sample and one duplicate sample, two samples containing interference, three different CRC cell samples, and a fictitious case report were included. The panel was distributed to 59 laboratories for mSEPT9 analysis, result comparison, and scoring. RESULTS: The sample panel, validated by National Medical Products Administration (NMPA)-approved tests and targeted bisulfite sequencing, met expectations and could be used for external quality assessment (EQA). Among the 59 laboratories, 55 (93.22%) correctly reported the mSEPT9 results for all samples, while four (6.79%) reported 15 false negatives and were considered improvable. All false negatives originated from four laboratories using laboratory-developed tests (LDTs), with three failing to detect weakly positive samples, samples containing interference, and samples from different CRC cells, and one reported erroneous results on all positive samples. CONCLUSION: Our results illustrated that the detection of mSEPT9 in cfDNA is satisfactory in China. EQA is indispensable because it can help improve the diagnostic capability and quality management of the laboratories, and provide suggestions for the problems existing in mSEPT9 detection.

Health system-scale language models are all-purpose prediction engines.

Physicians make critical time-constrained decisions every day. Clinical predictive models can help physicians and administrators make decisions by forecasting clinical and operational events. Existing structured data-based clinical predictive models have limited use in everyday practice owing to complexity in data processing, as well as model development and deployment1-3. Here we show that unstructured clinical notes from the electronic health record can enable the training of clinical language models, which can be used as all-purpose clinical predictive engines with low-resistance development and deployment. Our approach leverages recent advances in natural language processing4,5 to train a large language model for medical language (NYUTron) and subsequently fine-tune it across a wide range of clinical and operational predictive tasks. We evaluated our approach within our health system for five such tasks: 30-day all-cause readmission prediction, in-hospital mortality prediction, comorbidity index prediction, length of stay prediction, and insurance denial prediction. We show that NYUTron has an area under the curve (AUC) of 78.7-94.9%, with an improvement of 5.36-14.7% in the AUC compared with traditional models. We additionally demonstrate the benefits of pretraining with clinical text, the potential for increasing generalizability to different sites through fine-tuning and the full deployment of our system in a prospective, single-arm trial. These results show the potential for using clinical language models in medicine to read alongside physicians and provide guidance at the point of care.

Consistency and reproducibility of large panel next-generation sequencing: Multi-laboratory assessment of somatic mutation detection on reference materials with mismatch repair and proofreading deficiency.

INTRODUCTION: Clinical precision oncology increasingly relies on accurate genome-wide profiling using large panel next generation sequencing; however, difficulties in accurate and consistent detection of somatic mutation from individual platforms and pipelines remain an open question. OBJECTIVES: To obtain paired tumor-normal reference materials that can be effectively constructed and interchangeable with clinical samples, and evaluate the performance of 56 panels under routine testing conditions based on the reference samples. METHODS: Genes involved in mismatch repair and DNA proofreading were knocked down using the CRISPR-Cas9 technology to accumulate somatic mutations in a defined GM12878 cell line. They were used as reference materials to comprehensively evaluate the reproducibility and accuracy of detection results of oncopanels and explore the potential influencing factors. RESULTS: In total, 14 paired tumor-normal reference DNA samples from engineered cell lines were prepared, and a reference dataset comprising 168 somatic mutations in a high-confidence region of 1.8 Mb were generated. For mutations with an allele frequency (AF) of more than 5% in reference samples, 56 panels collectively reported 1306 errors, including 729 false negatives (FNs), 179 false positives (FPs) and 398 reproducibility errors. The performance metric varied among panels with precision and recall ranging from 0.773 to 1 and 0.683 to 1, respectively. Incorrect and inadequate filtering accounted for a large proportion of false discovery (including FNs and FPs), while low-quality detection, cross-contamination and other sequencing errors during the wet bench process were other sources of FNs and FPs. In addition, low AF (<5%) considerably influenced the reproducibility and comparability among panels. CONCLUSIONS: This study provided an integrated practice for developing reference standard to assess oncopanels in detecting somatic mutations and quantitatively revealed the source of detection errors. It will promote optimization, validation, and quality control among laboratories with potential applicability in clinical use.

Assessment of China's contributions to the Regional Network for Asian Schistosomiasis and Other Helminth Zoonoses: a questionnaire survey.

BACKGROUND: The Regional Network for Asian Schistosomiasis and Other Helminth Zoonoses (RNAS+) was established in 1998, which has developed close partnerships with Asian countries endemic for schistosomiasis and other helminthiasis in Asia. RNAS+ has provided an ideal regional platform for policy-makers, practitioners and researchers on the prevention, control and research of parasitic diseases in Asian countries. China, one of the initiating countries, has provided significant technical and financial support to the regional network. However, its roles and contributions have not been explored so far. The purpose of this study was to assess China's contributions on the supporting of RNAS+ development. METHODS: An assessment research framework was developed to evaluate China's contributions to RNAS+ in four aspects, including capacity building, funding support, coordination, and cooperation. An anonymous web-based questionnaire was designed to acquire respondents' basic information, and information on China's contributions, challenges and recommendations for RNAS+development. Each participant scored from 0 to 10 to assess China's contribution: "0" represents no contribution, and "10" represents 100% contribution. Participants who included their e-mail address in the 2017-2019 RNAS+ annual workshops were invited to participate in the assessment. RESULTS: Of 71 participants enrolled, 41 responded to the survey. 37 (37/41, 90.24%) of them were from RNAS+ member countries, while the other 4 (4/41, 9.76%) were international observers. Most of the respondents (38/41, 92.68%) were familiar with RNAS+. Respondents reported that China's contributions mainly focused on improving capacity building, providing funding support, coordination responsibility, and joint application of cooperation programs on RNAS+ development. The average scores of China's contributions in the above four fields were 8.92, 8.64, 8.75, and 8.67, respectively, with an overall assessment score of 8.81 (10 for a maximum score). The challenge of RNAS+ included the lack of sustainable funding, skills, etc. and most participants expressed their continual need of China's support. CONCLUSIONS: This survey showed that China has played an important role in the development of RNAS+ since its establishment. This network-type organization for disease control and research can yet be regarded as a great potential pattern for China to enhance regional cooperation. These findings can be used to promote future cooperation between China and other RNAS+ member countries.

Economic cost analysis of malaria case management at the household level during the malaria elimination phase in The People's Republic of China.

BACKGROUND: In China, malaria has been posing a significant economic burden on households. To evaluate malaria economic burden in terms of both direct and indirect costs has its meaning in improving the effectiveness of malaria elimination program in China. METHODS: A number of study sites (eight counties in five provinces) were selected from the malaria endemic area in China, representing the different levels of malaria incidence, risk classification, economic development. A number of households with malaria cases (n = 923) were surveyed during the May to December in 2012 to collect information on malaria economic burden. Descriptive statistics were used to characterize the basic profiles of selected malaria cases in terms of their gender, age group, occupation and malaria type. The malaria economic costs were evaluated by direct and indirect costs. Comparisons were carried out by using the chi-square test (or Z-test) and the Mann-Whitney U test among malaria cases with reference to local/imported malaria patients, hospitalized/out patients, and treatment hospitals. RESULTS: The average cost of malaria per case was 1 691.23 CNY (direct cost was 735.41 CNY and indirect cost was 955.82 CNY), which accounted for 11.1 % of a household's total income. The average costs per case for local and imported malaria were 1 087.58 CNY and 4271.93 CNY, respectively. The average cost of a malaria patient being diagnosed and treated in a hospital at the county level or above (3 975.43 CNY) was 4.23 times higher than that of malaria patient being diagnosed and treated at a village or township hospital (938.80 CNY). CONCLUSION: This study found that malaria has been posing a significant economic burden on households in terms of direct and indirect costs. There is a need to improve the effectiveness of interventions in order to reduce the impact costs of malaria, especially of imported infections, in order to eliminate the disease in China.

Preparation for malaria resurgence in China: approach in risk assessment and rapid response.

With the shrinking of indigenous malaria cases and endemic areas in the People's Republic of China (P.R. China), imported malaria predominates over all reported cases accounting for more than 90% of the total. On the way to eliminate malaria, prompt detection and rapid response to the imported cases are crucial for the prevention of secondary transmission in previous endemic areas. Through a comprehensive literature review, this chapter aims to identify risk determinants of potential local transmission caused by the imported malaria cases and discusses gaps to be addressed to reach the elimination goal by 2020. Current main gaps with respect to dealing with potential malaria resurgence in P.R. China include lack of cross-sectoral cooperation, lack of rapid response and risk assessment, poor public awareness, and inadequate research and development in the national malaria elimination programme.

China-Africa cooperation initiatives in malaria control and elimination.

Malaria has affected human health globally with a significant burden of disease, and also has impeded social and economic development in the areas where it is present. In Africa, many countries have faced serious challenges in controlling malaria, in part due to major limitations in public health systems and primary health care infrastructure. Although China is a developing country, a set of control strategies and measures in different local settings have been implemented successfully by the National Malaria Control Programme over the last 60 years, with a low cost of investment. It is expected that Chinese experience may benefit malaria control in Africa. This review will address the importance and possibility of China-Africa collaboration in control of malaria in targeted African countries, as well as how to proceed toward the goal of elimination where this is technically feasible.

[The fundamental role of stage control technology on the detectability for Salmonella networking laboratory].

OBJECTIVE: To evaluated the fundamental role of stage control technology (SCT) on the detectability for Salmonella networking laboratories. METHODS: Appropriate Salmonella detection methods after key point control being evaluated, were establishment and optimized. Our training and evaluation networking laboratories participated in the World Health Organization-Global Salmonella Surveillance Project (WHO-GSS) and China-U.S. Collaborative Program on Emerging and Re-emerging infectious diseases Project (GFN) in Shanghai. Staff members from the Yunnan Yuxi city Center for Disease Control and Prevention were trained on Salmonella isolation from diarrhea specimens. Data on annual Salmonella positive rates was collected from the provincial-level monitoring sites to be part of the GSS and GFN projects from 2006 to 2012. RESULTS: The methodology was designed based on the conventional detection procedure of Salmonella which involved the processes as enrichment, isolation, species identification and sero-typing. These methods were simultaneously used to satisfy the sensitivity requirements on non-typhoid Salmonella detection for networking laboratories. Public Health Laboratories in Shanghai had developed from 5 in 2006 to 9 in 2011, and Clinical laboratories from 8 to 22. Number of clinical isolates, including typhoid and non-typhoid Salmonella increased from 196 in 2006 to 1442 in 2011. The positive rate of Salmonella isolated from the clinical diarrhea cases was 2.4% in Yuxi county, in 2012. At present, three other provincial monitoring sites were using the SBG technique as selectivity enrichment broth for Salmonella isolation, with Shanghai having the most stable positive baseline. CONCLUSION: The method of SCT was proved the premise of the network laboratory construction. Based on this, the improvement of precise phenotypic identification and molecular typing capabilities could reach the level equivalent to the national networking laboratory.

[Chinese version of SF-36 in the quality of life assessment among community-dwelling elders].

OBJECTIVE: To obtain scores in a community-dwelling population over 60 using the SF-36, to assess the reliability and validity of this general health questionnaire, and to analyze the difference in dimension scores among the elderly Chinese in Changsha. METHODS: We randomly selected 602 elders, aged 60 to 91 years, in multi-phases. All the subjects had resided in Changsha for at least one year. The reliability of the SF-36 was assessed by split-half reliability and Cronbach's alpha coefficient and the validity through factor analysis and correlation analysis, etc. The dimension scores of different people were obtained by analysis of variance and independent-samples t-test. RESULTS: The split-half reliability was 0.72 and the Cronbach's alpha coefficients of all the 8 dimensions were more than 0.8; the Pearson correlate coefficients of all the items to their dimensions were more than 0. 59. SF-36 contained 8 domains and 2 summary scales in the factor analysis. Health-related quality was different in different elders. CONCLUSION: The SF-36 is practical in studying the quality of life among community-dwelling elders.