Ebolavirus diagnosis made simple, comparable and faster than molecular detection methods: preparing for the future

Background The 2014/2015 Ebolavirus outbreak resulted in more than 28,000 cases and 11,323 reported deaths, as of March 2016. Domestic transmission of the Guinea strain associated with the outbreak occurred mainly in six African countries, and international transmission was reported in four countries. Outbreak management was limited by the inability to rapidly diagnose infected cases. A further fifteen countries in Africa are predicted to be at risk of Ebolavirus outbreaks in the future as a consequence of climate change and urbanization. Early detection of cases and reduction of transmission rates is critical to prevent and manage future severe outbreaks. We designed a rapid assay for detection of Ebolavirus using recombinase polymerase amplification, a rapid isothermal amplification technology that can be combined with portable lateral flow detection technology. The developed rapid assay operates in 30 min and was comparable with real-time TaqMan™ PCR. Methods Designed, screened, selected and optimized oligonucleotides using the NP coding region from Ebola Zaire virus (Guinea strain). We determined the analytical sensitivity of our Ebola rapid molecular test by testing selected primers and probe with tenfold serial dilutions (1.34 × 1010− 1.34 × 101 copies/μL) of cloned NP gene from Mayinga strain of Zaire ebolavirus in pCAGGS vector, and serially diluted cultured Ebolavirus as established by real-time TaqMan™ PCR that was performed using ABI7500 in Fast Mode. We tested extracted and reverse transcribed RNA from cultured Zaire ebolavirus strains – Mayinga, Gueckedou C05, Gueckedou C07, Makona, Kissidougou and Kiwit. We determined the analytical specificity of our assay with related viruses: Marburg, Ebola Reston and Ebola Sudan. We further tested for Dengue virus 1–4, Plasmodium falciparum and West Nile Virus (Kunjin strain). Results The assay had a detection limit of 134 copies per μL of plasmid containing the NP gene of Ebolavirus Mayinga, and cultured Ebolavirus and was highly specific for the Zaire ebolavirus species, including the Guinea strain responsible for the 2014/2015 outbreak. The assay did not detect related viruses like Marburg, Reston, or Sudan viruses, and other pathogens likely to be isolated from clinical samples. Conclusions Our assay could be suitable for implementation in district and primary health laboratories, as only a heating block and centrifuge is required for operation. The technique could provide a pathway for rapid screening of patients and animals for improved management of outbreaks

Quantification of the whole-body burden of radiographic osteoarthritis using factor analysis

INTRODUCTION: Although osteoarthritis (OA) commonly involves multiple joints, no widely accepted method for quantifying whole-body OA burden exists. Therefore, our aim was to apply factor analytic methods to radiographic OA (rOA) grades across multiple joint sites, representing both presence and severity, to quantify the burden of rOA. METHODS: We used cross-sectional data from the Johnston County Osteoarthritis Project. The sample (n = 2092) had a mean age of 65 ± 11 years, body mass index (BMI) 31 ± 7 kg/m2, with 33% men and 34% African Americans. A single expert reader (intra-rater κ = 0.89) provided radiographic grades based on standard atlases for the hands (30 joints, including bilateral distal and proximal interphalangeal [IP], thumb IP, metacarpophalangeal [MCP] and carpometacarpal [CMC] joints), knees (patellofemoral and tibiofemoral, 4 joints), hips (2 joints), and spine (5 levels [L1/2 to L5/S1]). All grades were entered into an exploratory common factor analysis as continuous variables. Stratified factor analyses were used to look for differences by gender, race, age, and cohort subgroups. RESULTS: Four factors were identified as follows: IP/CMC factor (20 joints), MCP factor (8 joints), Knee factor (4 joints), Spine factor (5 levels). These factors had high internal consistency reliability (Cronbach's α range 0.80 to 0.95), were not collapsible into a single factor, and had moderate between-factor correlations (Pearson correlation coefficient r = 0.24 to 0.44). There were no major differences in factor structure when stratified by subgroup. CONCLUSIONS: The 4 factors obtained in this analysis indicate that the variables contained within each factor share an underlying cause, but the 4 factors are distinct, suggesting that combining these joint sites into one overall measure is not appropriate. Using such factors to reflect multi-joint rOA in statistical models can reduce the number of variables needed and increase precision

Associations of educational attainment, occupation and community poverty with knee osteoarthritis in the Johnston County (North Carolina) osteoarthritis project

Abstract: Introduction: The purpose of this study was to examine data from the Johnston County Osteoarthritis (OA) Project for independent associations of educational attainment, occupation and community poverty with tibiofemoral knee OA. Methods: A cross-sectional analysis was conducted on 3,591 individuals (66% Caucasian and 34% African American). Educational attainment ( 25%) were examined separately and together in logistic models adjusting for covariates of age, gender, race, body mass index (BMI), smoking, knee injury and occupational activity score. Outcomes were presence of radiographic knee OA (rOA), symptomatic knee OA (sxOA), bilateral rOA and bilateral sxOA. Results: When all three socioeconomic status (SES) variables were analyzed simultaneously, low educational attainment was significantly associated with rOA (odds ratio (OR) = 1.44, 95% confidence interval (CI) 1.20, 1.73), bilateral rOA (OR = 1.43, 95% CI 1.13, 1.81), and sxOA (OR = 1.66, 95% CI 1.34, 2.06), after adjusting for covariates. Independently, living in a community of high household poverty rate was associated with rOA (OR = 1.83, 95% CI 1.43, 2.36), bilateral rOA (OR = 1.56, 95% CI 1.12, 2.16), and sxOA (OR = 1.36, 95% CI 1.00, 1.83). Occupation had no significant independent association beyond educational attainment and community poverty. Conclusions: Both educational attainment and community SES were independently associated with knee OA after adjusting for primary risk factors for knee OA

Differential effects of calcium- and vitamin D-fortified milk with FOS-inulin compared to regular milk, on bone biomarkers in Chinese pre- and postmenopausal women

PURPOSE: To compare the effects of a high-calcium vitamin D-fortified milk with added FOS-inulin versus regular milk on serum parathyroid hormone, and bone turnover markers in premenopausal (Pre-M) and postmenopausal (PM) women over 12 weeks. METHODS: Premenopausal women (n = 136, mean age 41 (±5) years) and postmenopausal women [n = 121, mean age 59 (±4) years] were recruited, and each age group randomised into two groups to take two glasses per day of control = regular milk (500 mg calcium per day) or intervention (Int) = fortified milk (1000 mg calcium for pre-M women and 1200 mg calcium for PM women, 96 mg magnesium, 2.4 mg zinc, 15 µg vitamin D, 4 g FOS-inulin per day). At baseline, week 4 and week 12 serum minerals and bone biochemical markers were measured and bone density was measured at baseline. RESULTS: Mean 25-hydroxyvitamin D [25(OH) vitamin D3] levels among groups were between 49 and 65 nmol/L at baseline, and over the 12 weeks of supplementation, the fortified milk improved vitamin D status in both Int groups. CTx-1 and PINP reduced significantly in both Pre-M and PM groups over the 12 weeks, with the changes in CTx-1 being significantly different (P < 0.035) between PM control and PM Int groups at week 12. Parathyroid hormone levels were significantly reduced in all groups over time, except for control PM group where levels increased at 12 weeks. CONCLUSION: The overall pattern of responses indicates that while both regular milk and fortified milk reduce bone resorption in young and older women, fortified milk is measurably more effective

Variations in Hip Shape Are Associated with Radiographic Knee Osteoarthritis : Cross-sectional and Longitudinal Analyses of the Johnston County Osteoarthritis Project

Acknowledgment We thank our funding sources, as well as the staff and participants in the Johnston County Osteoarthritis Project, without whom this work would not be possible. Funding was provided in part by the US National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS) K23 AR061406 (Nelson); US National Institutes of Health (NIH)/NIAMS P60AR30701 (Jordan/Renner/Schwartz); US Centers for Disease Control/Association of Schools of Public Health S043 and S3486 (Jordan/Renner); K24-AR04884, P50-AR063043, and P50-AR060752 (Lane); and NIH/National Center for Advancing Translational Sciences KL2TR001109 (Golightly).Peer reviewedPostprin

Limited educational attainment and radiographic and symptomatic knee osteoarthritis: a cross-sectional analysis using data from the Johnston County (North Carolina) Osteoarthritis Project

Abstract Introduction Applying a cross-sectional analysis to a sample of 2,627 African-American and Caucasian adults aged ≥ 45 years from the Johnston County Osteoarthritis Project, we studied the association between educational attainment and prevalence of radiographic knee osteoarthritis and symptomatic knee osteoarthritis. Methods Age- and race-adjusted associations between education and osteoarthritis outcomes were assessed by gender-stratified logistic regression models, with additional models adjusting for body mass index, knee injury, smoking, alcohol use, and occupational factors. Results In an analysis of all participants, low educational attainment (<12 years) was associated with higher prevalence of four knee osteoarthritis outcomes (unilateral and bilateral radiographic and symptomatic osteoarthritis). Women with low educational attainment had 50% higher odds of having radiographic knee osteoarthritis and 65% higher odds of symptomatic knee osteoarthritis compared with those with higher educational attainment (≥ 12 years), by using fully adjusted models. In the subset of postmenopausal women, these associations tended to be weaker but little affected by adjustment for hormone replacement therapy. Men with low educational attainment had 85% higher odds of having symptomatic knee osteoarthritis by using fully adjusted models, but the association with radiographic knee osteoarthritis was explained by age. Conclusions After adjustment for known risk factors, educational attainment, as an indicator of socioeconomic status, is associated with symptomatic knee osteoarthritis in both men and women and with radiographic knee osteoarthritis in women

New Last Glacial Maximum Ice Thickness constraints for the Weddell Sea Embayment, Antarctica

We describe new Last Glacial Maximum (LGM) ice thickness constraints for three locations spanning the Weddell Sea Embayment (WSE) of Antarctica. Samples collected from the Shackleton Range, Pensacola Mountains, and the Lassiter Coast constrain the LGM thickness of the Slessor Glacier, Foundation Ice Stream, and grounded ice proximal to the modern Ronne Ice Shelf edge on the Antarctic Peninsula, respectively. Previous attempts to reconstruct LGM-to-present ice thickness changes around the WSE used measurements of long-lived cosmogenic nuclides, primarily Be-10. An absence of post-LGM apparent exposure ages at many sites led to LGM thickness reconstructions that were spatially highly variable and inconsistent with flow line modelling. Estimates for the contribution of the ice sheet occupying the WSE at the LGM to global sea level since deglaciation vary by an order of magnitude, from 1.4 to 14.1m of sea level equivalent. Here we use a short-lived cosmogenic nuclide, in situ-produced C-14, which is less susceptible to inheritance problems than Be-10 and other long-lived nuclides. We use in situ C-14 to evaluate the possibility that sites with no post-LGM exposure ages are biased by cosmogenic nuclide inheritance due to surface preservation by cold-based ice and non-deposition of LGM-aged drift. Our measurements show that the Slessor Glacier was between 310 and up to 655m thicker than present at the LGM. The Foundation Ice Stream was at least 800m thicker, and ice on the Lassiter Coast was at least 385m thicker than present at the LGM. With evidence for LGM thickening at all of our study sites, our in situ C-14 measurements indicate that the long-lived nuclide measurements of previous studies were influenced by cosmogenic nuclide inheritance. Our inferred LGM configuration, which is primarily based on minimum ice thickness constraints and thus does not constrain an upper limit, indicates a relatively modest contribution to sea level rise since the LGM of < 4.6 m, and possibly as little as < 1.5 m

Network Discovery Pipeline Elucidates Conserved Time-of-Day–Specific cis-Regulatory Modules

Correct daily phasing of transcription confers an adaptive advantage to almost all organisms, including higher plants. In this study, we describe a hypothesis-driven network discovery pipeline that identifies biologically relevant patterns in genome-scale data. To demonstrate its utility, we analyzed a comprehensive matrix of time courses interrogating the nuclear transcriptome of Arabidopsis thaliana plants grown under different thermocycles, photocycles, and circadian conditions. We show that 89% of Arabidopsis transcripts cycle in at least one condition and that most genes have peak expression at a particular time of day, which shifts depending on the environment. Thermocycles alone can drive at least half of all transcripts critical for synchronizing internal processes such as cell cycle and protein synthesis. We identified at least three distinct transcription modules controlling phase-specific expression, including a new midnight specific module, PBX/TBX/SBX. We validated the network discovery pipeline, as well as the midnight specific module, by demonstrating that the PBX element was sufficient to drive diurnal and circadian condition-dependent expression. Moreover, we show that the three transcription modules are conserved across Arabidopsis, poplar, and rice. These results confirm the complex interplay between thermocycles, photocycles, and the circadian clock on the daily transcription program, and provide a comprehensive view of the conserved genomic targets for a transcriptional network key to successful adaptation

Differences in multijoint radiographic osteoarthritis phenotypes among African Americans and Caucasians: The Johnston County Osteoarthritis Project

To define and contrast multiple joint radiographic osteoarthritis (rOA) phenotypes describing hand and whole-body rOA among African Americans and Caucasians