Baseline CD4 Cell Counts of Newly Diagnosed HIV Cases in China: 2006–2012

Background: Late diagnosis of HIV infection is common. We aim to assess the proportion of newly diagnosed HIV cases receiving timely baseline CD4 count testing and the associated factors in China. Methods: Data were extracted from the Chinese HIV/AIDS Comprehensive Response Information Management System. Adult patients over 15 years old who had been newly diagnosed with HIV infection in China between 2006 and 2012 were identified. The study cohort comprised individuals who had a measured baseline CD4 count. Results: Among 388,496 newly identified HIV cases, the median baseline CD4 count was 294 cells/µl (IQR: 130–454), and over half (N = 130,442, 58.8%) were less than 350 cells/µl. The median baseline CD4 count increased from 221 (IQR: 63–410) in 2006 to 314 (IQR: 159–460) in 2012. A slight majority of patients (N = 221,980, 57.1%) received baseline CD4 count testing within 6 months of diagnosis. The proportion of individuals who received timely baseline CD4 count testing increased significantly from 20.0% in 2006 to 76.9% in 2012. Factors associated with failing to receiving timely CD4 count testing were: being male (OR: 1.17, 95% CI: 1.15–1.19), age 55 years or older (OR:1.03, 95% CI: 1.00–1.06), educational attainment of primary school education or below (OR: 1.30, 95% CI: 1.28–1.32), infection with HIV through injection drug use (OR: 2.07, 95% CI: 2.02–2.12) or sexual contact and injection drug use (OR: 1.87, 95% CI: 1.76–1.99), diagnosis in a hospital (OR: 1.91, 95% CI: 1.88–1.95) or in a detention center (OR: 1.75, 95% CI: 1.70–1.80), and employment as a migrant worker (OR:1.55, 95% CI:1.53–1.58). Conclusion: The proportion of newly identified HIV patients receiving timely baseline CD4 testing has increased significantly in China from 2006–2012. Continued effort is needed for further promotion of early HIV diagnosis and timely baseline CD4 cell count testing

Relationship between histone demethylase LSD family and development and prognosis of gastric cancer

Objectiveto elucidate the correlation between histone demethylase and gastric cancerResearch objecthistone demethylase and gastric cancerResultsAs one of the important regulatory mechanisms in molecular biology and epigenetics, histone modification plays an important role in gastric cancer including downstream gene expression regulation and epigenetics effect. Both histone methyltransferase and histone demethylases are involved in the formation and maintaining different of histone methylation status, which in turn through a variety of vital molecules and signaling pathways involved in the recognition of histone methylation modification caused by the downstream biological process, eventually participate in the regulation of chromatin function, and with a variety of important physiological activities, especially closely related to the occurrence of gastric cancer and embryonic development.ConclusionThis paper intends to review the research progress in this field from the aspects of histone methylation modification and the protein structure, catalytic mechanism and biological function of the important histone demethylases LSD1 and LSD2, in order to provide the theoretical reference for further understanding and exploration of histone demethylases in development and prognosis of gastric cancer

The Performance of Pleural Fluid T-SPOT.TB Assay for Diagnosing Tuberculous Pleurisy in China: A Two-Center Prospective Cohort Study

The performance of T-SPOT.TB (T-SPOT) assay in diagnosing pleural tuberculosis (plTB) is inconsistent. In this study, we compared the performance of peripheral blood (PB) and pleural fluid (PF) T-SPOT assay in diagnosing plTB. Between July 2017 and March 2018, 218 and 210 suspected plTB patients were prospectively enrolled from Wuhan (training) and Guangzhou (validation) cohort, respectively. PB T-SPOT, PF T-SPOT, and other conventional tests were simultaneously performed. Our data showed the performance of PB T-SPOT in diagnosing plTB was limited, especially with low sensitivity. However, the results of early secreted antigenic target 6 (ESAT-6) and culture filtrate protein 10 (CFP-10) in PF T-SPOT were significantly increased compared with those in PB T-SPOT in plTB patients. If using 76 as the cutoff value of MAX (the larger of ESAT-6 and CFP-10) in Wuhan cohort, the sensitivity and specificity of PF T-SPOT to diagnose plTB were 89.76 and 96.70%, respectively. The diagnostic accuracy of PF T-SPOT was better than other routine tests such as pathogen detection methods and biochemical markers. The diagnostic accuracy of PF T-SPOT in Guangzhou cohort was similar to that in Wuhan cohort, with a sensitivity and specificity of 91.07 and 94.90%, respectively. Furthermore, CD4+ T cells were more activated in PF compared with PB, and the frequency of mycobacterium tuberculosis-specific CD4+ T cells in PF was significantly higher than that in PB in plTB patients. In conclusion, the performance of PF T-SPOT is obviously better than PB T-SPOT or other laboratory tests, which suggests that PF T-SPOT assay has been of great value in the diagnosis of pleural tuberculosis

Systematic evaluation of chromosome conformation capture assays [preprint]

Chromosome conformation capture (3C)-based assays are used to map chromatin interactions genome-wide. Quantitative analyses of chromatin interaction maps can lead to insights into the spatial organization of chromosomes and the mechanisms by which they fold. A number of protocols such as in situ Hi-C and Micro-C are now widely used and these differ in key experimental parameters including cross-linking chemistry and chromatin fragmentation strategy. To understand how the choice of experimental protocol determines the ability to detect and quantify aspects of chromosome folding we have performed a systematic evaluation of experimental parameters of 3C-based protocols. We find that different protocols capture different 3D genome features with different efficiencies. First, the use of cross-linkers such as DSG in addition to formaldehyde improves signal-to-noise allowing detection of thousands of additional loops and strengthens the compartment signal. Second, fragmenting chromatin to the level of nucleosomes using MNase allows detection of more loops. On the other hand, protocols that generate larger multi-kb fragments produce stronger compartmentalization signals. We confirmed our results for multiple cell types and cell cycle stages. We find that cell type-specific quantitative differences in chromosome folding are not detected or underestimated by some protocols. Based on these insights we developed Hi-C 3.0, a single protocol that can be used to both efficiently detect chromatin loops and to quantify compartmentalization. Finally, this study produced ultra-deeply sequenced reference interaction maps using conventional Hi-C, Micro-C and Hi-C 3.0 for commonly used cell lines in the 4D Nucleome Project

Identification of ZDHHC14 as a novel human tumour suppressor gene

Genomic changes affecting tumour suppressor genes are fundamental to cancer. We applied SNP array analysis to a panel of testicular germ cell tumours to search for novel tumour suppressor genes and identified a frequent small deletion on 6q25.3 affecting just one gene, ZDHHC14. The expression of ZDHHC14, a putative protein palmitoyltransferase with unknown cellular function, was decreased at both RNA and protein levels in testicular germ cell tumours. ZDHHC14 expression was also significantly decreased in a panel of prostate cancer samples and cell lines. In addition to our findings of genetic and protein expression changes in clinical samples, inducible overexpression of ZDHHC14 led to reduced cell viability and increased apoptosis through the classic caspase-dependent apoptotic pathway and heterozygous knockout of ZDHHC14 decreased cell colony formation ability. Finally, we confirmed our in vitro findings of the tumour suppressor role of ZDHHC14 in a mouse xenograft model, showing that overexpression of ZDHHC14 inhibits tumourigenesis. Thus, we have identified a novel tumour suppressor gene that is commonly down-regulated in testicular germ cell tumours and prostate cancer, as well as given insight into the cellular functional role of ZDHHC14, a potential protein palmitoyltransferase that may play a key protective role in cancer

The Algorithm of Link Prediction on Social Network

At present, most link prediction algorithms are based on the similarity between two entities. Social network topology information is one of the main sources to design the similarity function between entities. But the existing link prediction algorithms do not apply the network topology information sufficiently. For lack of traditional link prediction algorithms, we propose two improved algorithms: CNGF algorithm based on local information and KatzGF algorithm based on global information network. For the defect of the stationary of social network, we also provide the link prediction algorithm based on nodes multiple attributes information. Finally, we verified these algorithms on DBLP data set, and the experimental results show that the performance of the improved algorithm is superior to that of the traditional link prediction algorithm

Epidemiology of Clostridium difficile infection in hospitalized adults and the first isolation of C. difficile PCR ribotype 027 in central China

Abstract Background Clostridium difficile infection (CDI) is an emerging healthcare problem in the world. The purpose of this study was to perform a systematic epidemiological research of CDI in Tongji hospital, the central of China. Methods Stool samples from hospitalized adults suspected of CDI were enrolled. The diagnosis of CDI were based on the combination of clinical symptoms and laboratory results. Clinical features of CDI and non-CDI patients were compared by appropriate statistical tests to determine the risk factors of CDI. Multilocus sequence typing (MLST) was employed for molecular epidemiological analysis. Susceptibility testing and relevant antimicrobial agent resistance genes were performed as well. Results From June 2016 to September 2017, 839 hospitalized adults were enrolled. Among them, 107 (12.8%, 107/839) patients were C. difficile culture positive, and 73 (8.7%, 73/839) were infected with toxigenic C. difficile (TCD), with tcdA + tcdB+ strains accounting for 90.4% (66/73) and tcdA-tcdB+ for 9.6% (7/73). Meanwhile, two TCD strains were binary toxin positive and one of them was finally identified as CD027. Severe symptoms were observed in these two cases. Multivariate analysis indicated antibiotic exposure (p = 0.001, OR = 5.035) and kidney disease (p = 0.015, OR = 8.329) significantly increased the risk of CDI. Phylogenetic tree analysis demonstrated 21 different STs, including one new ST (ST467); and the most dominant type was ST54 (35.6%, 26/73). Multidrug-resistant (MDR) TCD were 53.4% (39/73); resistance to ciprofloxacin, erythromycin, and clindamycin were > 50%. Other antibiotics showed relative efficiency and all strains were susceptible to metronidazole and vancomycin. All moxifloxacin-resistant isolates carried a mutation in GyrA (Thr82 → Ile), with one both having mutation in GyrB (Ser366 → Ala). Conclusions Knowledge of epidemiological information for CDI is limited in China. Our finding indicated tcdA + tcdB+ C. difficile strains were the dominant for CDI in our hospital. Significant risk factors for CDI in our setting appeared to be antibiotic exposure and kidney disease. Metronidazole and vancomycin were still effective for CDI. Although no outbreak was observed, the first isolation of CD027 in center China implied the potential spread of this hypervirulent clone. Further studies are needed to enhance our understanding of the epidemiology of CDI in China

Impact of Parent Satisfaction toward the Quality of After School Programs on Their Conative Behaviors: A Path Analysis

During school years, children are directly and indirectly exposed to physical and psychosocial challenges that are literally precursors of success and risk. Ideally, children should not be left to face these auspicious developments alone. They depend on adults to carefully guide the process of maturation. Given the importance of these formative years, it is striking that organized adult responses to serve the needs of children all-too-often are inadequate. This is acutely evidenced during the hours after the close of school. A growing number of children are left alone after-school and without care. An estimated seven million school-aged children are “latchkey kids” who have no supervision for an extended period of time each day. A majority of these latchkey children, about 55%, usually come from households with two working parents or a single parent. Children who are exposed to inadequate or non-existent care are more susceptible to the influence of others than those who attend structured and supervised care. Violent crimes committed by youth are the highest during after-school hours. Nonetheless, children who are provided with care are frequently involved in activities that are unstructured, poorly supervised, and non-productive. It is apparently necessary to provide well-organized, enrichment programs to youth, especially during the after-school hours from 3:00 to 6:00 p.m. A great need exists for after-school activities that provide appropriate youth supervision and involvement. Academic literature supports that children and parents are well served by carefully organized and supervised youth programs during after-school hours. These programs can extend social, educational, and recreational activities for children, while protecting them from unhealthy environments. The growing community interests in after-school programs have been due to the following four public beliefs: (a) public spaces such as streets and playgrounds are no longer safe for children, (b) it is stressful and unproductive for children to be left on their own during after-school hours, (c) many children need additional time and individual attention for academic works beyond regular schools can provide, and (d) economically disadvantaged children need opportunities for developmentally enriching activities. Although the nature and curriculum of after-school programs are often heterogeneous, consensus usually exists in key program objectives. After-school curriculums generally center on one or more of the following four components: (a) academic enhancement, (b) personal skill development, (c) community involvement, and (d) enrichment activities. Most of youth sport and recreation programs take place during the after school hours, which would fall under enrichment activities. To achieve these program objectives, it is critical to have quality program curriculum, organization, implementation, supervision, facility, and evaluation. Good quality programs can assist students in their schooling and help them avoid high risk and unsupervised situations. Quality programs would attract and maintain participants to continuously participate in the program. Parents, therefore, can choose to continue working during after school hours with a sense of security and well-being about the care and enhanced learning opportunities available to their children. This is especially important for families headed by single parents — a fast growing segment of our communities. To enhance the effectiveness of program management, program evaluation plays an important role in providing information for curriculum and activity adjustment, reallocation of funding, improvement of facility, staff development, decision-making, and accountability. Previous evaluation studies have primarily focused on program participants and program teachers. Nevertheless, parent observations and their opinions of program quality would also be fundamental for recognizing the merits, weaknesses, and future directions of programs. Numerous researchers have indicated that parental involvement in the education of their children is an important aspect of effective education programs from the elementary through high school years. Parental influences significantly impact children’s participation in exercise, games, and sports. Parents positively or negatively influence children’s motivation levels as they engage in activities and play a significant role in children’s engagement in a variety of learning, sporting, and other activities. The purpose of this study was to examine the relationships between parent satisfaction toward the quality of after school enrichment programs and intentions for program re-enrollment and referral. A total of 8,136 parents of students enrolled at 268 after programs responded to a survey in three language versions: English, Spanish, and Haitian Creole. Of the respondents, a majority responded to the English version (89.4%), and the Spanish and Creole versions accounted for 9.7% and 0.8%, respectively. The survey form included three sections: (a) the Parent Scale for Enrichment Program (PSEP; Zhang, Lam, Smith, Fleming, & Connaughton, 2005) that had a total of 23 items in a Likert 5-point scale under four factors (Program Management – 6 items, Program Offering – 6 items, Program Assurance – 4 items, and Program Effect - 7items); (b) criterion variables including two variables (intention to re-enroll child(ren) in the after school program and intention to refer the program to others); and (c) background variables for sample description purpose. These parents had one or more children in the after school program (M = 1.45, SD = 0.72), with one child being the majority (i.e., 66.0%). In terms of ethnic background, parents were primarily of African American and Hispanic background, accounting for over 75% respondents. Their households had two to eight people (M = 4.32, SD = 1.36), with a majority of them having a household income less than $40,000 (i.e., 85%). This percentage was consistent with the portion of students receiving free or reduced lunch at school. Over 80% families had resided in the current community for over three years; however, close to 20% were new to the community, suggesting the possibility of a mobile population segment. Zero-order correlations among the four PSEP factors and the two criterion variables were calculated and tested. All the PSEP factors were found to be significantly (p \u3c .01) related to the two criterion variables, namely, re-enrollment and referral intentions. These findings indicate that satisfied parents in the areas of Program Management, Program Offering, Program Effect, and Program Assurance were likely to re-enroll their children in the after school program and refer the program to others. To further examine the predictability of the PSEP factors (i.e., Program Management, Program Offering, Program Assurance, and Program Effect) to program re-enrollment and referral intentions, a path analysis was conducted by adopting the maximum likelihood estimate. The path analysis consisted of three regressions, with direct effects on Re-enrollment and Referral in the last two regressions and indirect effects assessed in the first regression. In the first regression, Program Effect was regressed on the three control variables: Program Offering, Program Management, and Program Assurance. In the second regression, Re-enrollment was regressed on both Program Effect and three control variables. In the final regression, Referral was regressed on both Program Effect and three control variables. The values of Goodness-of-Fit indices suggested the resulted model fit the data well (χ2 (2) = 8.1, p \u3c .05, CFI = 1.0, TLI = .998, RMSEA = .018, and SRMR = .003). All three control variables were significantly (p \u3c .05) predictive of Program Effect. In predicting Re-enrollment and Referral, the direct effect of Program Effect was significant (β = .21 and β = .16 respectively, both p \u3c .001), where both direct and indirect effects of Program Assurance and Program Management were significant, and Program Offering was found to have only indirect effect mediated by Program Effect. The regression with all variables entered predicting re-enrollment directly and indirectly explained a total of 31.8% variance, and the regression with all variables entered predicting referral directly and indirectly explained a total of 35.6% variance. In summary, all four PSEP factors were found to be important and relevant factors affecting parents’ decision to re-enroll their children in the after school program and refer the program to other parents. These findings indicated that the PSEP factors were primary considerations by parents when making a decision to re-enroll their child(ren) into after school programs and conduct program referrals; thus, they should be highly considered by the program administrations when planning and managing after school programs