Multivariate modelling of responses to conditional items: New possibilities for latent class analysis

Questionnaire data may contain missing values because certain questions do not apply to all respondents. For instance, questions addressing particular attributes of a symptom, such as frequency, triggers or seasonality, are only applicable to those who have experienced the symptom, while for those who have not, responses to these items will be missing. This missing information does not fall into the category 'missing by design', rather the features of interest do not exist and cannot be measured regardless of survey design. Analysis of responses to such conditional items is therefore typically restricted to the subpopulation in which they apply. This article is concerned with joint multivariate modelling of responses to both unconditional and conditional items without restricting the analysis to this subpopulation. Such an approach is of interest when the distributions of both types of responses are thought to be determined by common parameters affecting the whole population. By integrating the conditional item structure into the model, inference can be based both on unconditional data from the entire population and on conditional data from subjects for whom they exist. This approach opens new possibilities for multivariate analysis of such data. We apply this approach to latent class modelling and provide an example using data on respiratory symptoms (wheeze and cough) in children. Conditional data structures such as that considered here are common in medical research settings and, although our focus is on latent class models, the approach can be applied to other multivariate models.

Predicting the population impact of chlamydia screening programmes: comparative mathematical modelling study

BACKGROUND: Published individual-based, dynamic sexual network modelling studies reach different conclusions about the population impact of screening for Chlamydia trachomatis. The objective of this study was to conduct a direct comparison of the effect of organised chlamydia screening in different models. METHODS: Three models simulating population-level sexual behaviour, chlamydia transmission, screening and partner notification were used. Parameters describing a hypothetical annual opportunistic screening program in 16-24 year olds were standardised, whereas other parameters from the three original studies were retained. Model predictions of the change in chlamydia prevalence were compared under a range of scenarios. RESULTS: Initial overall chlamydia prevalence rates were similar in women but not men and there were age and sex-specific differences between models. The number of screening tests carried out was comparable in all models but there were large differences in the predicted impact of screening. After 10 years of screening, the predicted reduction in chlamydia prevalence in women aged 16-44 years ranged from 4% to 85%. Screening men and women had a greater impact than screening women alone in all models. There were marked differences between models in assumptions about treatment seeking and sexual behaviour before the start of the screening intervention. CONCLUSIONS: Future models of chlamydia transmission should be fitted to both incidence and prevalence data. This meta-modelling study provides essential information for explaining differences between published studies and increasing the utility of individual-based chlamydia transmission models for policy making.

Explaining the Ditransitive Person-Role Constraint

This paper proposes a frequency-based explanation of the Ditransitive Person-Role Constraint, a cross-linguistic generalization that can be formulated as follows: "Combinations of bound pronouns with the roles Recipient and Theme are disfavored if the Theme pronoun is first or second person and the Recipient pronoun is third person."

Towards an Open Source Framework for Collaborative Problem-Based Learning Environments

This paper presents our research works in the domain of Collaborative Environments centred on Problem Based Learning (PBL) and taking advantage of existing Electronic Documents. We first present the modelling and engineering problems that we want to address; then we discuss technological issues of such a research particularly the use of OpenUSS and of the Enterprise Java Open Source Architecture (EJOSA) to implement such collaborative PBL environments.

Monitoring of antiretroviral therapy and mortality in HIV programmes in Malawi, South Africa and Zambia: mathematical modelling study

OBJECTIVES Mortality in patients starting antiretroviral therapy (ART) is higher in Malawi and Zambia than in South Africa. We examined whether different monitoring of ART (viral load [VL] in South Africa and CD4 count in Malawi and Zambia) could explain this mortality difference. DESIGN Mathematical modelling study based on data from ART programmes. METHODS We used a stochastic simulation model to study the effect of VL monitoring on mortality over 5 years. In baseline scenario A all parameters were identical between strategies except for more timely and complete detection of treatment failure with VL monitoring. Additional scenarios introduced delays in switching to second-line ART (scenario B) or higher virologic failure rates (due to worse adherence) when monitoring was based on CD4 counts only (scenario C). Results are presented as relative risks (RR) with 95% prediction intervals and percent of observed mortality difference explained. RESULTS RRs comparing VL with CD4 cell count monitoring were 0.94 (0.74-1.03) in scenario A, 0.94 (0.77-1.02) with delayed switching (scenario B) and 0.80 (0.44-1.07) when assuming a 3-times higher rate of failure (scenario C). The observed mortality at 3 years was 10.9% in Malawi and Zambia and 8.6% in South Africa (absolute difference 2.3%). The percentage of the mortality difference explained by VL monitoring ranged from 4% (scenario A) to 32% (scenarios B and C combined, assuming a 3-times higher failure rate). Eleven percent was explained by non-HIV related mortality. CONCLUSIONS VL monitoring reduces mortality moderately when assuming improved adherence and decreased failure rates.

Cost-effectiveness of point-of-care viral load monitoring of antiretroviral therapy in resource-limited settings: mathematical modelling study

BACKGROUND Monitoring of HIV viral load in patients on combination antiretroviral therapy (ART) is not generally available in resource-limited settings. We examined the cost-effectiveness of qualitative point-of-care viral load tests (POC-VL) in sub-Saharan Africa. DESIGN Mathematical model based on longitudinal data from the Gugulethu and Khayelitsha township ART programmes in Cape Town, South Africa. METHODS Cohorts of patients on ART monitored by POC-VL, CD4 cell count or clinically were simulated. Scenario A considered the more accurate detection of treatment failure with POC-VL only, and scenario B also considered the effect on HIV transmission. Scenario C further assumed that the risk of virologic failure is halved with POC-VL due to improved adherence. We estimated the change in costs per quality-adjusted life-year gained (incremental cost-effectiveness ratios, ICERs) of POC-VL compared with CD4 and clinical monitoring. RESULTS POC-VL tests with detection limits less than 1000 copies/ml increased costs due to unnecessary switches to second-line ART, without improving survival. Assuming POC-VL unit costs between US$5 and US$20 and detection limits between 1000 and 10,000 copies/ml, the ICER of POC-VL was US$4010-US$9230 compared with clinical and US$5960-US$25540 compared with CD4 cell count monitoring. In Scenario B, the corresponding ICERs were US$2450-US$5830 and US$2230-US$10380. In Scenario C, the ICER ranged between US$960 and US$2500 compared with clinical monitoring and between cost-saving and US$2460 compared with CD4 monitoring. CONCLUSION The cost-effectiveness of POC-VL for monitoring ART is improved by a higher detection limit, by taking the reduction in new HIV infections into account and assuming that failure of first-line ART is reduced due to targeted adherence counselling.

Solute transport in crystalline rocks at Äspö — II: Blind predictions, inverse modelling and lessons learnt from test STT1

Based on the results from detailed structural and petrological characterisation and on up-scaled laboratory values for sorption and diffusion, blind predictions were made for the STT1 dipole tracer test performed in the Swedish A¨ spo¨ Hard Rock Laboratory. The tracers used were nonsorbing, such as uranine and tritiated water, weakly sorbing 22Na+, 85Sr2 +, 47Ca2 +and more strongly sorbing 86Rb+, 133Ba2 +, 137Cs+. Our model consists of two parts: (1) a flow part based on a 2D-streamtube formalism accounting for the natural background flow field and with an underlying homogeneous and isotropic transmissivity field and (2) a transport part in terms of the dual porosity medium approach which is linked to the flow part by the flow porosity. The calibration of the model was done using the data from one single uranine breakthrough (PDT3). The study clearly showed that matrix diffusion into a highly porous material, fault gouge, had to be included in our model evidenced by the characteristic shape of the breakthrough curve and in line with geological observations. After the disclosure of the measurements, it turned out that, in spite of the simplicity of our model, the prediction for the nonsorbing and weakly sorbing tracers was fairly good. The blind prediction for the more strongly sorbing tracers was in general less accurate. The reason for the good predictions is deemed to be the result of the choice of a model structure strongly based on geological observation. The breakthrough curves were inversely modelled to determine in situ values for the transport parameters and to draw consequences on the model structure applied. For good fits, only one additional fracture family in contact with cataclasite had to be taken into account, but no new transport mechanisms had to be invoked. The in situ values for the effective diffusion coefficient for fault gouge are a factor of 2–15 larger than the laboratory data. For cataclasite, both data sets have values comparable to laboratory data. The extracted Kd values for the weakly sorbing tracers are larger than Swedish laboratory data by a factor of 25–60, but agree within a factor of 3–5 for the more strongly sorbing nuclides. The reason for the inconsistency concerning Kds is the use of fresh granite in the laboratory studies, whereas tracers in the field experiments interact only with fracture fault gouge and to a lesser extent with cataclasite both being mineralogically very different (e.g. clay-bearing) from the intact wall rock.

Diffusion of HTO, Br-, I-, Cs+, Sr-85(2+) and Co-60(2+) in a clay formation: Results and modelling from an in situ experiment in Opalinus Clay

The migration of radioactive and chemical contaminants in clay materials and argillaceous host rocks is characterised by diffusion and retention processes. Valuable information on such processes can be gained by combining diffusion studies at laboratory scale with field migration tests. In this work, the outcome of a multi-tracer in situ migration test performed in the Opalinus Clay formation in the Mont Terri underground rock laboratory (Switzerland) is presented. Thus, 1.16 x 10(5) Bq/L of HTO, 3.96 x 10(3) Bq/L of Sr-85, 6.29 x 10(2) Bq/L of Co-60, 2.01 x 10(-3) mol/L Cs, 9.10 x 10(-4) mol/L I and 1.04 x 10(-3) mol/L Br were injected into the borehole. The decrease of the radioisotope concentrations in the borehole was monitored using in situ gamma-spectrometry. The other tracers were analyzed with state-of-the-art laboratory procedures after sampling of small water aliquots from the reservoir. The diffusion experiment was carried out over a period of one year after which the interval section was overcored and analyzed. Based on the experimental data from the tracer evolution in the borehole and the tracer profiles in the rock, the diffusion of tracers was modelled with the numerical code CRUNCH. The results obtained for HTO (H-3), I- and Br- confirm previous lab and in situ diffusion data. Anionic fluxes into the formation were smaller compared to HTO because of anion exclusion effects. The migration of the cations Sr-85(2+), Cs+ and Co-60(2+) was found to be governed by both diffusion and sorption processes. For Sr-85(2+), the slightly higher diffusivity relative to HTO and the low sorption value are consistent with laboratory diffusion measurements on small-scale samples. In the case of Cs+, the numerically deduced high diffusivity and the Freundlich-type sorption behaviour is also supported by ongoing laboratory data. For Co, no laboratory diffusion data were yet available for comparison; however, the modelled data suggests that Co-60(2+) sorption was weaker than would be expected from available batch sorption data. Overall, the results demonstrate the feasibility of the experimental setup for obtaining high-quality diffusion data for conservative and sorbing tracers. (C) 2007 Elsevier Ltd. All rights reserved.

Present state of global wetland extent and wetland methane modelling: methodology of a model inter-comparison project (WETCHIMP)

The Wetland and Wetland CH4 Intercomparison of Models Project (WETCHIMP) was created to evaluate our present ability to simulate large-scale wetland characteristics and corresponding methane (CH4) emissions. A multi-model comparison is essential to evaluate the key uncertainties in the mechanisms and parameters leading to methane emissions. Ten modelling groups joined WETCHIMP to run eight global and two regional models with a common experimental protocol using the same climate and atmospheric carbon dioxide (CO2) forcing datasets. We reported the main conclusions from the intercomparison effort in a companion paper (Melton et al., 2013). Here we provide technical details for the six experiments, which included an equilibrium, a transient, and an optimized run plus three sensitivity experiments (temperature, precipitation, and atmospheric CO2 concentration). The diversity of approaches used by the models is summarized through a series of conceptual figures, and is used to evaluate the wide range of wetland extent and CH4 fluxes predicted by the models in the equilibrium run. We discuss relationships among the various approaches and patterns in consistencies of these model predictions. Within this group of models, there are three broad classes of methods used to estimate wetland extent: prescribed based on wetland distribution maps, prognostic relationships between hydrological states based on satellite observations, and explicit hydrological mass balances. A larger variety of approaches was used to estimate the net CH4 fluxes from wetland systems. Even though modelling of wetland extent and CH4 emissions has progressed significantly over recent decades, large uncertainties still exist when estimating CH4 emissions: there is little consensus on model structure or complexity due to knowledge gaps, different aims of the models, and the range of temporal and spatial resolutions of the models.

REST-based sensor networks with OData

RESTful services gained a lot of attention recently, even in the enterprise world, which is traditionally more web-service centric. Data centric RESfFul services, as previously mainly known in web environments, established themselves as a second paradigm complementing functional WSDL-based SOA. In the Internet of Things, and in particular when talking about sensor motes, the Constraint Application Protocol (CoAP) is currently in the focus of both research and industry. In the enterprise world a protocol called OData (Open Data Protocol) is becoming the future RESTful data access standard. To integrate sensor motes seamlessly into enterprise networks, an embedded OData implementation on top of CoAP is desirable, not requiring an intermediary gateway device. In this paper we introduce and evaluate an embedded OData implementation. We evaluate the OData protocol in terms of performance and energy consumption, considering different data encodings, and compare it to a pure CoAP implementation. We were able to demonstrate that the additional resources needed for an OData/JSON implementation are reasonable when aiming for enterprise interoperability, where OData is suggested to solve both the semantic and technical interoperability problems we have today when connecting systems

Modelling the effects of land use and climate changes on hydrology in the Ursern Valley, Switzerland

While many studies have been conducted in mountainous catchments to examine the impact of climate change on hydrology, the interactions between climate changes and land use components have largely unknown impacts on hydrology in alpine regions. They need to be given special attention in order to devise possible strategies concerning general development in these regions. Thus, the main aim was to examine the impact of land use (i.e. bushland expansion) and climate changes (i.e. increase of temperature) on hydrology by model simulations. For this purpose, the physically based WaSiM-ETH model was applied to the catchment of Ursern Valley in the central Alps (191 km2) over the period of 1983−2005. Modelling results showed that the reduction of the mean monthly discharge during the summer period is due primarily to the retreat of snow discharge in time and secondarily to the reduction in the glacier surface area together with its retreat in time, rather than the increase in the evapotranspiration due to the expansion of the “green alder” on the expense of grassland. The significant decrease in summer discharge during July, August and September shows a change in the regime from b-glacio-nival to nivo-glacial. These changes are confirmed by the modeling results that attest to a temporal shift in snowmelt and glacier discharge towards earlier in the year: March, April and May for snowmelt and May and June for glacier discharge. It is expected that the yearly total discharge due to the land use changes will be reduced by 0.6% in the near future, whereas, it will be reduced by about 5% if climate change is also taken into account. Copyright © 2013 John Wiley & Sons, Ltd.

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.

A community-based geological reconstruction of Antarctic Ice Sheet deglaciation since the Last Glacial Maximum

A robust understanding of Antarctic Ice Sheet deglacial history since the Last Glacial Maximum is important in order to constrain ice sheet and glacial-isostatic adjustment models, and to explore the forcing mechanisms responsible for ice sheet retreat. Such understanding can be derived from a broad range of geological and glaciological datasets and recent decades have seen an upsurge in such data gathering around the continent and Sub-Antarctic islands. Here, we report a new synthesis of those datasets, based on an accompanying series of reviews of the geological data, organised by sector. We present a series of timeslice maps for 20 ka, 15 ka, 10 ka and 5 ka, including grounding line position and ice sheet thickness changes, along with a clear assessment of levels of confidence. The reconstruction shows that the Antarctic Ice sheet did not everywhere reach the continental shelf edge at its maximum, that initial retreat was asynchronous, and that the spatial pattern of deglaciation was highly variable, particularly on the inner shelf. The deglacial reconstruction is consistent with a moderate overall excess ice volume and with a relatively small Antarctic contribution to meltwater pulse 1a. We discuss key areas of uncertainty both around the continent and by time interval, and we highlight potential priorities for future work. The synthesis is intended to be a resource for the modelling and glacial geological community.

Prospective memory, executive functions, and metacognition are already differentiated in young elementary school children: Evidence from latent factor modelling

This study investigated the empirical differentiation of prospective memory, executive functions, and metacognition and their structural relationships in 119 elementary school children (M = 95 months, SD = 4.8 months). These cognitive abilities share many characteristics on the theoretical level and are all highly relevant in many everyday contexts when intentions must be executed. Nevertheless, their empirical relationships have not been examined on the latent level, although an empirical approach would contribute to our knowledge concerning the differentiation of cognitive abilities during childhood. We administered a computerized event-based prospective memory task, three executive function tasks (updating, inhibition, shifting), and a metacognitive control task in the context of spelling. Confirmatory factor analysis revealed that the three cognitive abilities are already empirically differentiable in young elementary school children. At the same time, prospective memory and executive functions were found to be strongly related, and there was also a close link between prospective memory and metacognitive control. Furthermore, executive functions and metacognitive control were marginally significantly related. The findings are discussed within a framework of developmental differentiation and conceptual similarities and differences.

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.