Diagnostic performance of line-immunoassay based algorithms for incident HIV-1 infection

Background Serologic testing algorithms for recent HIV seroconversion (STARHS) provide important information for HIV surveillance. We have previously demonstrated that a patient's antibody reaction pattern in a confirmatory line immunoassay (INNO-LIA™ HIV I/II Score) provides information on the duration of infection, which is unaffected by clinical, immunological and viral variables. In this report we have set out to determine the diagnostic performance of Inno-Lia algorithms for identifying incident infections in patients with known duration of infection and evaluated the algorithms in annual cohorts of HIV notifications. Methods Diagnostic sensitivity was determined in 527 treatment-naive patients infected for up to 12 months. Specificity was determined in 740 patients infected for longer than 12 months. Plasma was tested by Inno-Lia and classified as either incident (< = 12 m) or older infection by 26 different algorithms. Incident infection rates (IIR) were calculated based on diagnostic sensitivity and specificity of each algorithm and the rule that the total of incident results is the sum of true-incident and false-incident results, which can be calculated by means of the pre-determined sensitivity and specificity. Results The 10 best algorithms had a mean raw sensitivity of 59.4% and a mean specificity of 95.1%. Adjustment for overrepresentation of patients in the first quarter year of infection further reduced the sensitivity. In the preferred model, the mean adjusted sensitivity was 37.4%. Application of the 10 best algorithms to four annual cohorts of HIV-1 notifications totalling 2'595 patients yielded a mean IIR of 0.35 in 2005/6 (baseline) and of 0.45, 0.42 and 0.35 in 2008, 2009 and 2010, respectively. The increase between baseline and 2008 and the ensuing decreases were highly significant. Other adjustment models yielded different absolute IIR, although the relative changes between the cohorts were identical for all models. Conclusions The method can be used for comparing IIR in annual cohorts of HIV notifications. The use of several different algorithms in combination, each with its own sensitivity and specificity to detect incident infection, is advisable as this reduces the impact of individual imperfections stemming primarily from relatively low sensitivities and sampling bias.

Simple Estimation of Incident HIV Infection Rates in Notification Cohorts Based on Window Periods of Algorithms for Evaluation of Line-Immunoassay Result Patterns

Background Tests for recent infections (TRIs) are important for HIV surveillance. We have shown that a patient's antibody pattern in a confirmatory line immunoassay (Inno-Lia) also yields information on time since infection. We have published algorithms which, with a certain sensitivity and specificity, distinguish between incident (< = 12 months) and older infection. In order to use these algorithms like other TRIs, i.e., based on their windows, we now determined their window periods. Methods We classified Inno-Lia results of 527 treatment-naïve patients with HIV-1 infection < = 12 months according to incidence by 25 algorithms. The time after which all infections were ruled older, i.e. the algorithm's window, was determined by linear regression of the proportion ruled incident in dependence of time since infection. Window-based incident infection rates (IIR) were determined utilizing the relationship ‘Prevalence = Incidence x Duration’ in four annual cohorts of HIV-1 notifications. Results were compared to performance-based IIR also derived from Inno-Lia results, but utilizing the relationship ‘incident = true incident + false incident’ and also to the IIR derived from the BED incidence assay. Results Window periods varied between 45.8 and 130.1 days and correlated well with the algorithms' diagnostic sensitivity (R2 = 0.962; P<0.0001). Among the 25 algorithms, the mean window-based IIR among the 748 notifications of 2005/06 was 0.457 compared to 0.453 obtained for performance-based IIR with a model not correcting for selection bias. Evaluation of BED results using a window of 153 days yielded an IIR of 0.669. Window-based IIR and performance-based IIR increased by 22.4% and respectively 30.6% in 2008, while 2009 and 2010 showed a return to baseline for both methods. Conclusions IIR estimations by window- and performance-based evaluations of Inno-Lia algorithm results were similar and can be used together to assess IIR changes between annual HIV notification cohorts.

Timing of bacterial carriage sampling in vaccine trials: A modelling study.

BACKGROUND Pathogenic bacteria are often asymptomatically carried in the nasopharynx. Bacterial carriage can be reduced by vaccination and has been used as an alternative endpoint to clinical disease in randomised controlled trials (RCTs). Vaccine efficacy (VE) is usually calculated as 1 minus a measure of effect. Estimates of vaccine efficacy from cross-sectional carriage data collected in RCTs are usually based on prevalence odds ratios (PORs) and prevalence ratios (PRs), but it is unclear when these should be measured. METHODS We developed dynamic compartmental transmission models simulating RCTs of a vaccine against a carried pathogen to investigate how VE can best be estimated from cross-sectional carriage data, at which time carriage should optimally be assessed, and to which factors this timing is most sensitive. In the models, vaccine could change carriage acquisition and clearance rates (leaky vaccine); values for these effects were explicitly defined (facq, 1/fdur). POR and PR were calculated from model outputs. Models differed in infection source: other participants or external sources unaffected by the trial. Simulations using multiple vaccine doses were compared to empirical data. RESULTS The combined VE against acquisition and duration calculated using POR (VEˆacq.dur, (1-POR)×100) best estimates the true VE (VEacq.dur, (1-facq×fdur)×100) for leaky vaccines in most scenarios. The mean duration of carriage was the most important factor determining the time until VEˆacq.dur first approximates VEacq.dur: if the mean duration of carriage is 1-1.5 months, up to 4 months are needed; if the mean duration is 2-3 months, up to 8 months are needed. Minor differences were seen between models with different infection sources. In RCTs with shorter intervals between vaccine doses it takes longer after the last dose until VEˆacq.dur approximates VEacq.dur. CONCLUSION The timing of sample collection should be considered when interpreting vaccine efficacy against bacterial carriage measured in RCTs.

Poorly controlled type 2 diabetes mellitus is associated with a decreased risk of incident gout: a population-based case-control study

OBJECTIVE The aim of this study was to explore the risk of incident gout in patients with type 2 diabetes mellitus (T2DM) in association with diabetes duration, diabetes severity and antidiabetic drug treatment. METHODS We conducted a case-control study in patients with T2DM using the UK-based Clinical Practice Research Datalink (CPRD). We identified case patients aged ≥18 years with an incident diagnosis of gout between 1990 and 2012. We matched to each case patient one gout-free control patient. We used conditional logistic regression analysis to calculate adjusted ORs (adj. ORs) with 95% CIs and adjusted our analyses for important potential confounders. RESULTS The study encompassed 7536 T2DM cases with a first-time diagnosis of gout. Compared to a diabetes duration <1 year, prolonged diabetes duration (1-3, 3-6, 7-9 and ≥10 years) was associated with decreased adj. ORs of 0.91 (95% CI 0.79 to 1.04), 0.76 (95% CI 0.67 to 0.86), 0.70 (95% CI 0.61 to 0.86), and 0.58 (95% CI 0.51 to 0.66), respectively. Compared to a reference A1C level of <7%, the risk estimates of increasing A1C levels (7.0-7.9, 8.0-8.9 and ≥9%) steadily decreased with adj. ORs of 0.79 (95% CI 0.72 to 0.86), 0.63 (95% CI 0.55 to 0.72), and 0.46 (95% CI 0.40 to 0.53), respectively. Neither use of insulin, metformin, nor sulfonylureas was associated with an altered risk of incident gout. CONCLUSIONS Increased A1C levels, but not use of antidiabetic drugs, was associated with a decreased risk of incident gout among patients with T2DM.

Modelling susceptibility of grassland soil to macropore flow

Investigating preferential flow, including macropore flow, is crucial to predicting and preventing point sources of contamination in soil, for example in the vicinity of pumping wells. With a view to advancing groundwater protection, this study aimed (i) to quantify the strength of macropore flow in four representative natural grassland soils on the Swiss plateau, and (ii) to define the parameters that significantly control macropore flow in grassland soil. For each soil type we selected three measurement points on which three successive irrigation experiments were carried out, resulting in a total of 36 irrigations. The strength of macropore flow, parameterized as the cumulated water volume flowing from macropores at a depth of 1 m in response to an irrigation of 60 mm h−1 intensity and 1 h duration, was simulated using the dual-permeability MACRO model. The model calibration was based on the key soil parameters and fine measurements of water content at different depths. Modelling results indicate high performance of macropore flow in all investigated soil types except in gleysols. The volume of water that flowed from macropores and was hence expected to reach groundwater varied between 81% and 94% in brown soils, 59% and 67% in para-brown soils, 43% and 56% in acid brown soils, and 22% and 35% in gleysols. These results show that spreading pesticides and herbicides in pumping well protection zones poses a high risk of contamination and must be strictly prohibited. We also found that organic carbon content was not correlated with the strength of macropore flow, probably due to its very weak variation in our study, while saturated water content showed a negative correlation with macropore flow. The correlation between saturated hydraulic conductivity (Ks) and macropore flow was negative as well, but weak. Macropore flow appears to be controlled by the interaction between the bulk density of the uppermost topsoil layer (0–0.10 m) and the macroporosity of the soil below. This interaction also affects the variations in Ks and saturated water content. Further investigations are needed to better understand the combined effect of all these processes including the exchange between micropore and macropore domains.

Modelling zero-inflated count data when exposure varies: with an application to tumor counts)

This paper is concerned with the analysis of zero-inflated count data when time of exposure varies. It proposes a modified zero-inflated count data model where the probability of an extra zero is derived from an underlying duration model with Weibull hazard rate. The new model is compared to the standard Poisson model with logit zero inflation in an application to the effect of treatment with thiotepa on the number of new bladder tumors.

Association of hormone therapy and incident gout: population-based case-control study

OBJECTIVE This study aims to assess the odds of developing incident gout in association with the use of postmenopausal estrogen-progestogen therapy, according to type, timing, duration, and route of administration of estrogen-progestogen therapy. METHODS We conducted a retrospective population-based case-control analysis using the United Kingdom-based Clinical Practice Research Datalink. We identified women (aged 45 y or older) who had a first-time diagnosis of gout recorded between 1990 and 2010. We matched one female control with each case on age, general practice, calendar time, and years of active history in the database. We used multivariate conditional logistic regression to calculate odds ratios (ORs) with 95% CIs (adjusted for confounders). RESULTS The adjusted OR for gout with current use of oral formulations of opposed estrogens (estrogen-progestogen) was 0.69 (95% CI, 0.56-0.86) compared with never use. Current use was associated with a decreased OR for gout in women without renal failure (adjusted OR, 0.71; 95% CI, 0.57-0.87) and hypertension (adjusted OR, 0.62; 95% CI, 0.44-0.87) compared with never use. Tibolone was associated with a decreased OR for gout (adjusted OR, 0.77; 95% CI, 0.63-0.95) compared with never use. Estrogens alone did not alter the OR for gout. CONCLUSIONS Current use of oral opposed estrogens, but not unopposed estrogens, is associated with a decreased OR for incident gout in women without renal failure and is more pronounced in women with hypertension. Use of tibolone is associated with a decreased OR for incident gout. The decreased OR for gout may be related to the progestogen component rather than the estrogen component.

A retrospective cohort study of the duration of hepatitis B vaccine immunity and associated factors in pediatric dialysis patients

Dialysis patients are at high risk for hepatitis B infection, which is a serious but preventable disease. Prevention strategies include the administration of the hepatitis B vaccine. Dialysis patients have been noted to have a poor immune response to the vaccine and lose immunity more rapidly. The long term immunogenicity of the hepatitis B vaccine has not been well defined in pediatric dialysis patients especially if administered during infancy as a routine childhood immunization.^ Purpose. The aim of this study was to determine the median duration of hepatitis B immunity and to study the effect of vaccination timing and other cofactors on the duration of hepatitis B immunity in pediatric dialysis patients.^ Methods. Duration of hepatitis B immunity was determined by Kaplan-Meier survival analysis. Comparison of stratified survival analysis was performed using log-rank analysis. Multivariate analysis by Cox regression was used to estimate hazard ratios for the effect of timing of vaccine administration and other covariates on the duration of hepatitis B immunity.^ Results. 193 patients (163 incident patients) had complete data available for analysis. Mean age was 11.2±5.8 years and mean ESRD duration was 59.3±97.8 months. Kaplan-Meier analysis showed that the total median overall duration of immunity (since the time of the primary vaccine series) was 112.7 months (95% CI: 96.6, 124.4), whereas the median overall duration of immunity for incident patients was 106.3 months (95% CI: 93.93, 124.44). Incident patients had a median dialysis duration of hepatitis B immunity equal to 37.1 months (95% CI: 24.16, 72.26). Multivariate adjusted analysis showed that there was a significant difference between patients based on the timing of hepatitis B vaccination administration (p<0.001). Patients immunized after the start of dialysis had a hazard ratio of 6.13 (2.87, 13.08) for loss of hepatitis B immunity compared to patients immunized as infants (p<0.001).^ Conclusion. This study confirms that patients immunized after dialysis onset have an overall shorter duration of hepatitis B immunity as measured by hepatitis B antibody titers and after the start of dialysis, protective antibody titer levels in pediatric dialysis patients wane rapidly compared to healthy children.^

Leukemia and occupational exposure to electromagnetic fields: An incident case-control study

The existence of an association between leukemia and electromagnetic fields (EMF) is still controversial. The results of epidemiologic studies of leukemia in occupational groups with exposure to EMF are inconsistent. Weak associations have been seen in a few studies. EMF assessment is lacking in precision. Reported dose-response relationships have been based on qualitative levels of exposure to EMF without regard to duration of employment or EMF intensity on the jobs. Furthermore, potential confounding factors in the associations were not often well controlled. The current study is an analysis of the data collected from an incident case-control study. The primary objective was to test the hypothesis that occupational exposure to EMF is associated with leukemia, including total leukemia (TL), myelogenous leukemia (MYELOG) and acute non-lymphoid leukemia (ANLL). Potential confounding factors: occupational exposure to benzene, age, smoking, alcohol consumption, and previous medical radiation exposures were controlled in multivariate logistic regression models. Dose-response relationships were estimated by cumulative occupational exposure to EMF, taking into account duration of employment and EMF intensity on the jobs. In order to overcome weaknesses of most previous studies, special efforts were made to improve the precision of EMF assessment. Two definitions of EMF were used and result discrepancies using the two definitions were observed. These difference raised a question as to whether the workers at jobs with low EMF exposure should be considered as non-exposed in future studies. In addition, the current study suggested use of lifetime cumulative EMF exposure estimates to determine dose-response relationship. The analyses of the current study suggest an association between ANLL and employment at selected jobs with high EMF exposure. The existence of an association between three types of leukemia and broader categories of occupational EMF exposure, is still undetermined. If an association does exist between occupational EMF exposure and leukemia, the results of the current study suggest that EMF might only be a potential factor in the promotion of leukemia, but not its initiation. ^

Dive depth and dive duration data of subadult and adult, male and female southern elephant seals from Marion Island between 2004 and 2008 with links to datasets

Sexual segregation in habitat use occurs in a number of animal species, including southern elephant seals, where differences in migration localities and dive behaviour between sexes have been recorded. Due to the extreme sexual size dimorphism exhibited by southern elephant seals, it is unclear whether observed differences in dive behaviour are due to increased physiological capacity of males, compared to females, or differences in activity budgets and foraging behaviour. Here we use a mixed-effects modelling approach to investigate the effects of sex, size, age and individual variation on a number of dive parameters measured on southern elephant seals from Marion Island. Although individual variation accounted for substantial portions of total model variance for many response variables, differences in maximum and targeted dive depths were always influenced by sex, and only partly by body length. Conversely, dive durations were always influenced by body length, while sex was not identified as a significant influence. These results support hypotheses that physiological capability associated with body size is a limiting factor on dive durations. However, differences in vertical depth use appear to be the result of differences in forage selection between sexes, rather than a by-product of the size dimorphism displayed by this species. This provides further support for resource partitioning and possible avoidance of inter-sexual competition in southern elephant seals.

Seismic modelling and ava analysis of hidrocarbon traps

In this study, forward seismic modelling of four geological models with Hydrocarbon (HC) traps were performed by ray tracing method to produce synthetic seismogram of each model. The idea is to identify the Hydrocarbon Indicators (HCI‟s) such as bright spot, flat spot, dim spot and Bottom Simulating Reflector (BSR) in the synthethic seismogram. The modelling was performed in DISCO/FOCUS 5.0 seismic data processing programme. Strong positive and negative reflection amplitudes and some artifact reflection horizons were observed on produced seismograms due to rapid changes in subsurface velocity and geometry respectively Additionally, Amplitude-versus-angle (AVA) curves of each HCIs was calculated by the Crewes Zoeppritz Explorer programme. AVA curves show that how the reflection coefficients change with the density and the P and S wave velocities of each layer such as oil, gas, gas hydrate or water saturated sediments. Due to AVA curves, an increase in reflection amplitude with incident angle of seismic waves corresponds to an indicator of a hydrocarbon reservoir

Infrastructure (Resilience-oriented) Modelling Language: I®ML A proposal for modelling infrastructures and their connections

The modelling of critical infrastructures (CIs) is an important issue that needs to be properly addressed, for several reasons. It is a basic support for making decisions about operation and risk reduction. It might help in understanding high-level states at the system-of-systems layer, which are not ready evident to the organisations that manage the lower level technical systems. Moreover, it is also indispensable for setting a common reference between operator and authorities, for agreeing on the incident scenarios that might affect those infrastructures. So far, critical infrastructures have been modelled ad-hoc, on the basis of knowledge and practice derived from less complex systems. As there is no theoretical framework, most of these efforts proceed without clear guides and goals and using informally defined schemas based mostly on boxes and arrows. Different CIs (electricity grid, telecommunications networks, emergency support, etc) have been modelled using particular schemas that were not directly translatable from one CI to another. If there is a desire to build a science of CIs it is because there are some observable commonalities that different CIs share. Up until now, however, those commonalities were not adequately compiled or categorized, so building models of CIs that are rooted on such commonalities was not possible. This report explores the issue of which elements underlie every CI and how those elements can be used to develop a modelling language that will enable CI modelling and, subsequently, analysis of CI interactions, with a special focus on resilience

Efficient methodologies for system matrix modelling in iterative image reconstruction for rotating high-resolution PET

A fully 3D iterative image reconstruction algorithm has been developed for high-resolution PET cameras composed of pixelated scintillator crystal arrays and rotating planar detectors, based on the ordered subsets approach. The associated system matrix is precalculated with Monte Carlo methods that incorporate physical effects not included in analytical models, such as positron range effects and interaction of the incident gammas with the scintillator material. Custom Monte Carlo methodologies have been developed and optimized for modelling of system matrices for fast iterative image reconstruction adapted to specific scanner geometries, without redundant calculations. According to the methodology proposed here, only one-eighth of the voxels within two central transaxial slices need to be modelled in detail. The rest of the system matrix elements can be obtained with the aid of axial symmetries and redundancies, as well as in-plane symmetries within transaxial slices. Sparse matrix techniques for the non-zero system matrix elements are employed, allowing for fast execution of the image reconstruction process. This 3D image reconstruction scheme has been compared in terms of image quality to a 2D fast implementation of the OSEM algorithm combined with Fourier rebinning approaches. This work confirms the superiority of fully 3D OSEM in terms of spatial resolution, contrast recovery and noise reduction as compared to conventional 2D approaches based on rebinning schemes. At the same time it demonstrates that fully 3D methodologies can be efficiently applied to the image reconstruction problem for high-resolution rotational PET cameras by applying accurate pre-calculated system models and taking advantage of the system's symmetries.

Laser ablation modelling of aluminium, silver and crystalline silicon for applications in photovoltaic technologies

Laser material processing is being extensively used in photovoltaic applications for both the fabrication of thin film modules and the enhancement of the crystalline silicon solar cells. The two temperature model for thermal diffusion was numerically solved in this paper. Laser pulses of 1064, 532 or 248 nm with duration of 35, 26 or 10 ns were considered as the thermal source leading to the material ablation. Considering high irradiance levels (108–109 W cm−2), a total absorption of the energy during the ablation process was assumed in the model. The materials analysed in the simulation were aluminium (Al) and silver (Ag), which are commonly used as metallic electrodes in photovoltaic devices. Moreover, thermal diffusion was also simulated for crystalline silicon (c-Si). A similar trend of temperature as a function of depth and time was found for both metals and c-Si regardless of the employed wavelength. For each material, the ablation depth dependence on laser pulse parameters was determined by means of an ablation criterion. Thus, after the laser pulse, the maximum depth for which the total energy stored in the material is equal to the vaporisation enthalpy was considered as the ablation depth. For all cases, the ablation depth increased with the laser pulse fluence and did not exhibit a clear correlation with the radiation wavelength. Finally, the experimental validation of the simulation results was carried out and the ability of the model with the initial hypothesis of total energy absorption to closely fit experimental results was confirmed.

CFD modelling of the interaction between the Surface Boundary Layer and rotor wake. Comparison of results obtained with different turbulence models and mesh strategies

A simplified CFD wake model based on the actuator disk concept is used to simulate the wind turbine, represented by a disk upon which a distribution of forces, defined as axial momentum sources, are applied on the incoming non-uniform flow. The rotor is supposed to be uniformly loaded, with the exerted forces function of the incident wind speed, the thrust coefficient and the rotor diameter. The model is tested under different parameterizations of turbulence models and validated through experimental measurements downwind of a wind turbine in terms of wind speed deficit and turbulence intensity.