Assessment of a diverse panel of transmitted/founder HIV-1 infectious molecular clones in a luciferase based CD8 T-cell mediated viral inhibition assay.

Introduction: Immunological protection against human immunodeficiency virus-1 (HIV-1) infection is likely to require both humoral and cell-mediated immune responses, the latter involving cytotoxic CD8 T-cells. Characterisation of CD8 T-cell mediated direct anti-viral activity would provide understanding of potential correlates of immune protection and identification of critical epitopes associated with HIV-1 control. Methods: The present report describes a functional viral inhibition assay (VIA) to assess CD8 T-cell-mediated inhibition of replication of a large and diverse panel of 45 HIV-1 infectious molecular clones (IMC) engineered with a Renilla reniformis luciferase reporter gene (LucR), referred to as IMC-LucR. HIV-1 IMC replication in CD4 T-cells and CD8 T-cell mediated inhibition was characterised in both ART naive subjects living with HIV-1 covering a broad human leukocyte antigen (HLA) distribution and compared with uninfected subjects. Results & discussion: CD4 and CD8 T-cell lines were established from subjects vaccinated with a candidate HIV-1 vaccine and provided standard positive controls for both assay quality control and facilitating training and technology transfer. The assay was successfully established across 3 clinical research centres in Kenya, Uganda and the United Kingdom and shown to be reproducible. This IMC-LucR VIA enables characterisation of functional CD8 T-cell responses providing a tool for rational T-cell immunogen design of HIV-1 vaccine candidates and evaluation of vaccine-induced T-cell responses in HIV-1 clinical trials.

Cognitive Function Assessment and Prediction for Subjective Cognitive Decline and Mild Cognitive Impairment.

Alzheimer's disease (AD) is a progressive and irreversible neurodegenerative dementia. Recent studies found that subjective cognitive decline (SCD) may be the early clinical precursor that precedes mild cognitive impairment (MCI) for AD. SCD subjects with normal cognition may already have some medial temporal lobe atrophy. Although brain changes by AD have been widely studied in the literature, it is still challenging to investigate the anatomical subtle changes in SCD. This paper proposes a machine learning framework by combination of sparse coding and random forest (RF) to identify the informative imaging biomarkers for assessment and prediction of cognitive functions and their changes in individuals with MCI, SCD and normal control (NC) using magnetic resonance imaging (MRI). First, we compute the volumes from both the regions of interest from whole brain and the subregions of hippocampus and amygdala as the features of structural MRIs. Then, sparse coding is applied to identify the relevant features. Finally, the proximity-based RF is used to combine three sets of volumetric features and establish a regression model for predicting clinical scores. Our method has double feature selections to better explore the relevant features for prediction and is evaluated with the T1-weighted structural MR images from 36 MCI, 112 SCD, 78 NC subjects. The results demonstrate the effectiveness of proposed method. In addition to hippocampus and amygdala, we also found that the fimbria, basal nucleus and cortical nucleus subregions are more important than other regions for prediction of Mini-Mental State Examination (MMSE) and Montreal Cognitive Assessment (MoCA) scores and their changes.

Rapid and economical drug resistance profiling with Nanopore MinION for clinical specimens with low bacillary burden of Mycobacterium tuberculosis.

OBJECTIVE: We designed and tested a Nanopore sequencing panel for direct tuberculosis drug resistance profiling. The panel targeted 10 resistance-associated loci. We assessed the feasibility of amplifying and sequencing these loci from 23 clinical specimens with low bacillary burden. RESULTS: At least 8 loci were successfully amplified from the majority for predicting first- and second-line drug resistance (14/23, 60.87%), and the 12 specimens yielding all 10 targets were sequenced with Nanopore MinION and Illumina MiSeq. MinION sequencing data was corrected by Nanopolish and recurrent variants were filtered. A total of 67,082 bases across all consensus sequences were analyzed, with 67,019 bases called by both MinION and MiSeq as wildtype. For the 41 single nucleotide variants (SNVs) called by MiSeq with 100% variant allelic frequency (VAF), 39 (95.1%) were called by MinION. For the 22 mixed bases called by MiSeq, a SNV with the highest VAF (70%) was called by MinION. With short assay time, reasonable reagent cost as well as continuously improving sequencing chemistry and signal correction pipelines, this Nanopore method can be a viable option for direct tuberculosis drug resistance profiling in the near future.

[Assessment of schistosomiasis transmission risk after flood damage in Wuhan City].

OBJECTIVE: To assess the schistosomiasis transmission risk after flood damage in Wuhan City. METHODS: Schistosomiasis epidemic villages in Wuhan City were selected by using probability proportional to size sampling (PPS). The field investigations of Oncomelania hupensis snails, the activity of people and cattle on marshland, water infectivity of schistosome, reservoir host infection and wild feces contamination were conducted. I-III levels of risk environments were assessed and treated with appropriate measures. RESULTS: A total of 90 schistosomiasis epidemic villages and 170 environments were monitored. Totally 9 811 snails were dissected but no Schistosoma japonicum infected snails were found. There were significant decreases in the density of snails and the survival rate of living snails after the flood (χ2 = 102.517, t = 4.724, both P < 0.01). Totally 289 pieces of wild feces were captured, and no eggs of S. japonicum were detected. A total of 11 surveillance and forecast sites were detected on water systems, and 221 sentinel mice were placed. After breeding, 219 sentinel mice survived (99.10%), and no schistosome infection was detected. In addition, 1 720 mouse traps were placed in 3 survey sites, and 66 Apodemus agrarius were captured, and no schistosome-infected ones were found. All of the environments were assessed as Grade III. Meanwhile, 5 key schistosomiasis control areas were determined, and no emergency happened after the implementation of comprehensive control interventions. CONCLUSIONS: The risk of schistosomiasis transmission remains low in Wuhan City after the flood, but the potential epidemic risk cannot be ignored.

Impact of an antimicrobial stewardship program on the use of carbapenems in a tertiary women's and children's hospital, Singapore.

OBJECTIVES: Antimicrobial stewardship programs (ASPs) promote the judicious use of antimicrobials by limiting inappropriate use. This article evaluates the impact of a prospective-audit-and-feedback ASP implementation on the appropriate utilization of carbapenems in a tertiary pediatrics and obstetrics/gynecology hospital in Singapore (KKH) after the establishment of an ASP in July 2011. METHODS: This was a prospective, single-center, pre-post intervention study designed to analyze the appropriate prescribing of carbapenems pre-ASP (October 2009 to June 2011) and post-ASP (July 2011 to December 2013). Utilization of carbapenems was evaluated by daily defined doses (DDDs), days of therapy (DOTs), prescriptions, as well as cost per 100 patient-days pre-ASP and post-ASP using a segmented regression of interrupted time series analysis. RESULTS: Of 404 prescriptions for carbapenems reviewed post-ASP, 70.3% were appropriate compared with those prescribed pre-ASP (55.9%; p=0.027). Reasons for inappropriate prescribing included inappropriate choice (36.1%) and duration (31.3%). A total of 61.2% of the interventions (213 of 348) were accepted. For pediatrics, there was a significant decrease in DDDs per 100 patient-days by 55.6% from a baseline of 0.9-0.4 (p=0.013) post-ASP and a reduction in DOTs per 100 patient-days by 46.7% from a baseline of 1.5-0.8 (p=0.06) post-ASP without significant changes in prescription rates. Pediatrics utilization cost increased from a pre-ASP mean of $175 per 100 patient-days to a peak of $238 (p<0.001) and decreased significantly post-ASP to a mean of $149 (p=0.01). For obstetrics/gynecology, there were no significant changes in DDDs (0.3 vs 0.3, p=0.99), DOTs (0.2 vs 0.3, p=0.36), prescriptions (0.03 vs 0.04, p=0.38), or cost ($45 vs $52, p=0.63) per 100 patient-days pre- versus post-ASP. CONCLUSIONS: ASPs improved the appropriateness of carbapenems prescribing overall and reduced utilization in pediatrics. Identification of areas of inappropriate prescribing will be valuable in guiding future ASP efforts.

Responses, actions and health-promoting behavior among rural Taiwanese women with abnormal Papanicolaou test.

OBJECTIVES: The incidence and mortality rate of cervical cancer in Taiwan are higher than in other developed countries. This study aimed to explore women's responses and actions after receiving their test reports and their practice of health-promoting behaviors. DESIGN: This study employed a cross-sectional descriptive design. SAMPLE: A convenient sample of 101 women living in a rural area. MEASUREMENTS: Demographic characteristics, semistructured questions and Chinese Adult Health Promotion scale were used in this study. RESULTS: The mode of the duration of their marriages was 20 years. Nearly 14% were diagnosed as precancerous and underwent further treatment. 24 percent of the women took no action during the 3 months after receiving the results. As many as 96% of the participants were not aware of the 90% 5-year survival rate for localized cervical cancer. From semistructured interviews, 4 behavioral responses and 5 actions were identified. Notably, many women in this study practiced health-promoting behaviors for health responsibility, regular exercise and stress management with low frequency. CONCLUSIONS: These analytical results may prove useful in developing intervention strategies to assist women with positive Papanicolaou test results to choose treatment modalities and adopt healthy behaviors.