Comparing Location Data From Smartphone and Dedicated Global Positioning System Devices: Implications for Epidemiologic Research

In this study, we compared location data from a dedicated Global Positioning System (GPS) device with location data from smartphones. Data from the Interventions, Equity, and Action in Cities Team (INTERACT) Study, a study examining the impact of urban-form changes on health in 4 Canadian cities (Victoria, Vancouver, Saskatoon, and Montreal), were used. A total of 337 participants contributed data collected for about 6 months from the Ethica Data smartphone application (Ethica Data Inc., Toronto, Ontario, Canada) and the SenseDoc dedicated GPS (MobySens Technologies Inc., Montreal, Quebec, Canada) during the period 2017-2019. Participants recorded an average total of 14,781 Ethica locations (standard deviation, 19,353) and 197,167 SenseDoc locations (standard deviation, 111,868). Dynamic time warping and cross-correlation were used to examine the spatial and temporal similarity of GPS points. Four activity-space measures derived from the smartphone app and the dedicated GPS device were compared. Analysis showed that cross-correlations were above 0.8 at the 125-m resolution for the survey and day levels and increased as cell size increased. At the day or survey level, there were only small differences between the activity-space measures. Based on our findings, we recommend dedicated GPS devices for studies where the exposure and the outcome are both measured at high frequency and when the analysis will not be aggregate. When the exposure and outcome are measured or will be aggregated to the day level, the dedicated GPS device and the smartphone app provide similar results.

PLASTIC BRONCHITIS: A RARE COMPLICATION FOLLOWING A MOTOR VEHICLE COLLISION

Plastic bronchitis, more appropriately termed chyloptysis, is a rare and potentially fatal condition caused by chylous coating of the airways. These cast coating can dislodge and become an obstructive mass in the patient's airway, necessitating rapid intervention. PB is well described to occur following single ventricle physiology heart disease corrective procedures, particularly following Fontan procedures. It is less commonly seen in traumatic settings. We present the youngest known case of a traumatic injury induced plastic bronchitis. A 19-year-old man was involved in a motor vehicle accident with airbag deployment. The airbags struck him in the chest; however, the patient felt well at the time and did not seek medical attention. Several months later the patient began coughing up milky white masses identified as casts. He was initially diagnosed with asthma but did not respond to therapy. He ultimately was found to have evidence of thoracic duct injury. Options for therapy were discussed, including possible thoracic duct ligation. The patient opted to continue a low-fat diet and has remained cast free. This case highlights the importance of considering plastic bronchitis in patients with cast production and a history of trauma to the chest.

A theory-based model of cumulative activity

Energy expenditure can be used to examine the health of individuals and the impact of environmental factors on physical activity. One of the more common ways to quantify energy expenditure is to process accelerometer data into some unit of measurement for this expenditure, such as Actigraph activity counts, and bin those measures into physical activity levels. However, accepted thresholds can vary between demographics, and some units of energy measurements do not currently have agreed upon thresholds. We present an approach which computes unique thresholds for each individual, using piecewise exponential functions to model the characteristics of their overall physical activity patterns corresponding to well established sedentary, light, moderate and vigorous activity levels from the literature. Models are fit using existing piecewise fitting techniques and software. Most participants’ activity intensity profile is exceptionally well modeled as piecewise exponential decay. Using this model, we find emergent groupings of participant behavior and categorize individuals into non-vigorous, consistent, moderately active, or extremely active activity intensity profiles. In the supplemental materials, we demonstrate that the parameters of the model correlate with demographics of age, household size, and level of education, inform behavior change under COVID lockdown, and are reasonably robust to signal frequency.

Using combined Global Position System and accelerometer data points to examine how built environments and gentrification are associated with physical activity in four Canadian cities

Background

Built and social environments are associated with physical activity. Global Positioning Systems (GPS) and accelerometer data can capture how people move through their environments and provide promising tools to better understand associations between environmental characteristics and physical activity. The purpose of this study is to examine the associations between GPS-derived exposure to built environment and gentrification characteristics and accelerometer-measured physical activity in a sample of adults across four cities.

Methods

We used wave 1 data from the Interventions, Research, and Action in Cities Team, a cohort of adults living in the Canadian cities of Victoria, Vancouver, Saskatoon, and Montreal. A subsample of participants wore a SenseDoc device for 10 days during May 2017–January 2019 to record GPS and accelerometry data. Two physical activity outcomes were derived from SenseDoc data: time spent in light, moderate, and vigorous physical activity; and time spent in moderate or vigorous physical activity. Using corresponding GPS coordinates, we summarized physical activity outcomes by dissemination area—a Canadian census geography that represents areas where 400 to 700 people live- and joined to built (active living space, proximity to amenities, and urban compactness) and gentrification measures. We examined the associations between environmental measures and physical activity outcomes using multi-level negative binomial regression models that were stratified by city and adjusted for covariates (weekday/weekend), home dissemination area, precipitation, temperature) and participant-level characteristics obtained from a survey (age, gender, income, race).

Results

We found that adults spent more time being physically active near their homes, and in environments that were more walkable and near parks and less time in urban compact areas, regardless of where participants lived. Our analysis also highlighted how proximity to different amenities was linked to physical activity across different cities.

Conclusions

Our study provides insights into how built environment and gentrification characteristics are associated with the amount of time adults spend being physically active in four Canadian cities. These findings enhance our understanding of the influence that environments have on physical activity over time and space, and can support policies to increase physical activity.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12966-022-01306-z.

Positron-emitting radiotracers spatially resolve unexpected biogeochemical relationships linked with methane oxidation in Arctic soils

Arctic soils are marked by cryoturbic features, which impact soil-atmosphere methane (CH₄ ) dynamics vital to global climate regulation. Cryoturbic diapirism alters C/N chemistry within frost boils by introducing soluble organic carbon and nutrients, potentially influencing microbial CH₄ oxidation. CH₄ oxidation in soils, however, requires a spatio-temporal convergence of ecological factors to occur. Spatial delineation of microbial activity with respect to these key microbial and biogeochemical factors at relevant scales is experimentally challenging in inherently complex and heterogeneous natural soil matrices. This work aims to overcome this barrier by spatially linking microbial CH₄ oxidation with C/N chemistry and metagenomic characteristics. This is achieved by using positron-emitting radiotracers to visualize millimeter-scale active CH₄ uptake areas in Arctic soils with and without diapirism. X-ray absorption spectroscopic speciation of active and inactive areas shows CH₄ uptake spatially associates with greater proportions of inorganic N in diapiric frost boils. Metagenomic analyses reveal Ralstonia pickettii associates with CH₄ uptake across soils along with pertinent CH₄ and inorganic N metabolism associated genes. This study highlights the critical relationship between CH₄ and N cycles in Arctic soils, with potential implications for better understanding future climate. Furthermore, our experimental framework presents a novel, widely applicable strategy for unraveling ecological relationships underlying greenhouse gas dynamics under global change.

Why machine learning (ML) has failed physical activity research and how we can improve

Measuring physical activity is a critical issue for our understanding of the health benefits of human movement. Machine learning (ML), using accelerometer data, has become a common way to measure physical activity. ML has failed physical activity measurement research in four important ways. First, as a field, physical activity researchers have not adopted and used principles from computer science. Benchmark datasets are common in computer science and allow the direct comparison of different ML approaches. Access to and development of benchmark datasets are critical components in advancing ML for physical activity. Second, the priority of methods development focused on ML has created blind spots in physical activity measurement. Methods, other than cut-point approaches, may be sufficient or superior to ML but these are not prioritised in our research. Third, while ML methods are common in published papers, their integration with software is rare. Physical activity researchers must continue developing and integrating ML methods into software to be fully adopted by applied researchers in the discipline. Finally, training continues to limit the uptake of ML in applied physical activity research. We must improve the development, integration and use of software that allows for ML methods’ broad training and application in the field.

Plastic bronchitis: A rare complication following a motor vehicle collision

Plastic bronchitis, more appropriately termed chyloptysis, is a rare and potentially fatal condition caused by chylous coating of the airways. These cast coating can dislodge and become an obstructive mass in the patient's airway, necessitating rapid intervention. PB is well described to occur following single ventricle physiology heart disease corrective procedures, particularly following Fontan procedures. It is less commonly seen in traumatic settings. We present the youngest known case of a traumatic injury induced plastic bronchitis. A 19-year-old man was involved in a motor vehicle accident with airbag deployment. The airbags struck him in the chest; however, the patient felt well at the time and did not seek medical attention. Several months later the patient began coughing up milky white masses identified as casts. He was initially diagnosed with asthma but did not respond to therapy. He ultimately was found to have evidence of thoracic duct injury. Options for therapy were discussed, including possible thoracic duct ligation. The patient opted to continue a lowfat diet and has remained cast free. This case highlights the importance of considering plastic bronchitis in patients with cast production and a history of trauma to the chest.

INTERACT: A comprehensive approach to assess urban form interventions through natural experiments

BACKGROUND

Urban form interventions can result in positive and negative impacts on physical activity, social participation, and well-being, and inequities in these outcomes. Natural experiment studies can advance our understanding of causal effects and processes related to urban form interventions. The INTErventions, Research, and Action in Cities Team (INTERACT) is a pan-Canadian collaboration of interdisciplinary scientists, urban planners, and public health decision makers advancing research on the design of healthy and sustainable cities for all. Our objectives are to use natural experiment studies to deliver timely evidence about how urban form interventions influence health, and to develop methods and tools to facilitate such studies going forward.

METHODS

INTERACT will evaluate natural experiments in four Canadian cities: the Arbutus Greenway in Vancouver, British Columbia; the All Ages and Abilities Cycling Network in Victoria, BC; a new Bus Rapid Transit system in Saskatoon, Saskatchewan; and components of the Sustainable Development Plan 2016-2020 in Montreal, Quebec, a plan that includes urban form changes initiated by the city and approximately 230 partnering organizations. We will recruit a cohort of between 300 and 3000 adult participants, age 18 or older, in each city and collect data at three time points. Participants will complete health and activity space surveys and provide sensor-based location and physical activity data. We will conduct qualitative interviews with a subsample of participants in each city. Our analysis methods will combine machine learning methods for detecting transportation mode use and physical activity, use temporal Geographic Information Systems to quantify changes to urban intervention exposure, and apply analytic methods for natural experiment studies including interrupted time series analysis.

DISCUSSION

INTERACT aims to advance the evidence base on population health intervention research and address challenges related to big data, knowledge mobilization and engagement, ethics, and causality. We will collect ~ 100 TB of sensor data from participants over 5 years. We will address these challenges using interdisciplinary partnerships, training of highly qualified personnel, and modern methodologies for using sensor-based data.

How many days are enough?: capturing routine human mobility

Wedding mobile phone sensor technology and human spatial behaviour has great potential. The ubiquity of Global Positioning Systems (GPS) technology has made gathering data about human mobility simpler, more precise, and with higher fidelity, providing minute-by-minute records of the locations of cohorts from dozens of participants. While this data provides a strong basis for Geographic Information Science research, it also constitutes an invasion of the participants' privacy and can provide more information than researchers require to answer their questions. As an ethical and practical consideration, researchers should gather only as much data as they need. In this paper, we take three weeks of GPS traces from over a hundred student participants in mobile phone-based tracking studies and show that fewer than 14 days of data is necessary to establish complete activity spaces. We define 'complete' as the point at which marginal information gains become negligible according to a pairwise temporal analysis of the Kullback-Leibler (KL) divergence of the spatial (bivariate) histogram through time. For the fixed level of information difference, observable in the data, impacts due to individual variability, population composition, and spatial resolution are evident. However, all populations at each level of resolution examined in the paper demonstrated convergence to low divergence levels occurred within a matter of days, and to negligible information gain in less than two weeks. The methods described in the paper represent a novel metric useful to understand the interaction between measurements and information in human mobility.

A glossary for big data in population and public health: discussion and commentary on terminology and research methods

The volume and velocity of data are growing rapidly and big data analytics are being applied to these data in many fields. Population and public health researchers may be unfamiliar with the terminology and statistical methods used in big data. This creates a barrier to the application of big data analytics. The purpose of this glossary is to define terms used in big data and big data analytics and to contextualise these terms. We define the five Vs of big data and provide definitions and distinctions for data mining, machine learning and deep learning, among other terms. We provide key distinctions between big data and statistical analysis methods applied to big data. We contextualise the glossary by providing examples where big data analysis methods have been applied to population and public health research problems and provide brief guidance on how to learn big data analysis methods.

Building Research Capacity: Results of a Feasibility Study Using a Novel mHealth Epidemiological Data Collection System Within a Gestational Diabetes Population

Public health researchers have traditionally relied on individual self-reporting when collecting much epidemiological surveillance data. Data acquisition can be costly, difficult to acquire, and the data often notoriously unreliable. An interesting option for the collection of individual health (or indicators of individual health) data is the personal smartphone. Smartphones are ubiquitous, and the required infrastructure is well-developed across Canada, including many remote areas. Researchers and health professionals are asking themselves how they might exploit increasing smartphone uptake for the purposes of data collection, hopefully leading to improved individual and public health. A novel smartphone-based epidemiological data collection and analysis system has been developed by faculty and students from the CEPHIL (Computational Epidemiology and Public Health Informatics) Lab in the Department of Computer Science at the University of Saskatchewan. A pilot feasibility study was then designed to examine possible relationships between smartphone sensor data, surveys and individual clinical data within a population of pregnant women. The study focused on the development of Gestational Diabetes (GDM), a transient condition during pregnancy, but with serious potential post-birth complications for both mother and child. The researchers questioned whether real-time smartphone data could improve the clinical management and outcomes of women at risk for developing GDM, enabling earlier treatment. The initial results from this small study did not show improved prediction of GDM, but did demonstrate that real-time individual health and sensor data may be readily collected and analyzed efficiently while maintaining confidentiality. Because the original version of the data collection software could only run on Android phones, this often meant the study participants were required to carry two phones, and this often meant the study phone was not carried, and therefore data not collected. The lessons learned will greatly inform future research.

Design and methods of a social network isolation study for reducing respiratory infection transmission: The eX-FLU cluster randomized trial

BACKGROUND

Social networks are increasingly recognized as important points of intervention, yet relatively few intervention studies of respiratory infection transmission have utilized a network design. Here we describe the design, methods, and social network structure of a randomized intervention for isolating respiratory infection cases in a university setting over a 10-week period.

METHODOLOGY/PRINCIPAL FINDINGS

590 students in six residence halls enrolled in the eX-FLU study during a chain-referral recruitment process from September 2012-January 2013. Of these, 262 joined as "seed" participants, who nominated their social contacts to join the study, of which 328 "nominees" enrolled. Participants were cluster-randomized by 117 residence halls. Participants were asked to respond to weekly surveys on health behaviors, social interactions, and influenza-like illness (ILI) symptoms. Participants were randomized to either a 3-Day dorm room isolation intervention or a control group (no isolation) upon illness onset. ILI cases reported on their isolation behavior during illness and provided throat and nasal swab specimens at onset, day-three, and day-six of illness. A subsample of individuals (N=103) participated in a sub-study using a novel smartphone application, iEpi, which collected sensor and contextually-dependent survey data on social interactions. Within the social network, participants were significantly positively assortative by intervention group, enrollment type, residence hall, iEpi participation, age, gender, race, and alcohol use (all P<0.002).

CONCLUSIONS/SIGNIFICANCE

We identified a feasible study design for testing the impact of isolation from social networks in a university setting. These data provide an unparalleled opportunity to address questions about isolation and infection transmission, as well as insights into social networks and behaviors among college-aged students. Several important lessons were learned over the course of this project, including feasible isolation durations, the need for extensive organizational efforts, as well as the need for specialized programmers and server space for managing survey and smartphone data.

Leveraging H1N1 infection transmission modeling with proximity sensor microdata

BACKGROUND

The contact networks between individuals can have a profound impact on the evolution of an infectious outbreak within a network. The impact of the interaction between contact network and disease dynamics on infection spread has been investigated using both synthetic and empirically gathered micro-contact data, establishing the utility of micro-contact data for epidemiological insight. However, the infection models tied to empirical contact data were highly stylized and were not calibrated or compared against temporally coincident infection rates, or omitted critical non-network based risk factors such as age or vaccination status.

METHODS

In this paper we present an agent-based simulation model firmly grounded in disease dynamics, incorporating a detailed characterization of the natural history of infection, and 13 weeks worth of micro-contact and participant health and risk factor information gathered during the 2009 H1N1 flu pandemic.

RESULTS

We demonstrate that the micro-contact data-based model yields results consistent with the case counts observed in the study population, derive novel metrics based on the logarithm of the time degree for evaluating individual risk based on contact dynamic properties, and present preliminary findings pertaining to the impact of internal network structures on the spread of disease at an individual level.

CONCLUSIONS

Through the analysis of detailed output of Monte Carlo ensembles of agent based simulations we were able to recreate many possible scenarios of infection transmission using an empirically grounded dynamic contact network, providing a validated and grounded simulation framework and methodology. We confirmed recent findings on the importance of contact dynamics, and extended the analysis to new measures of the relative risk of different contact dynamics. Because exponentially more time spent with others correlates to a linear increase in infection probability, we conclude that network dynamics have an important, but not dominant impact on infection transmission for H1N1 transmission in our study population.

Variant ataxia-telangiectasia presenting as primary-appearing dystonia in Canadian Mennonites

OBJECTIVE

To compare the phenotype of primary-appearing dystonia due to variant ataxia-telangiectasia (A-T) with that of other dystonia ascertained for genetics research.

METHODS

Movement disorder specialists examined 20 Canadian Mennonite adult probands with primary-appearing dystonia, as well as relatives in 4 families with parent-child transmission of dystonia. We screened for the exon 43 c.6200 C>A (p. A2067D) ATM mutation and mutations in DYT1 and DYT6. Clinical features of the individuals with dystonia who were harboring ATM mutations were compared with those of individuals without mutations.

RESULT

Genetic analysis revealed a homozygous founder mutation in ATM in 13 members from 3 of the families, and no one harbored DYT6 or DYT1 mutations. Dystonia in ATM families mimicked other forms of early-onset primary torsion dystonia, especially DYT6, with prominent cervical, cranial, and brachial involvement. Mean age at onset was markedly younger in the patients with variant A-T (n = 12) than in patients with other dystonia (n = 23), (12 years vs 40 years, p < 0.05). The patients with A-T were remarkable for the absence of notable cerebellar atrophy on MRI, lack of frank ataxia on examination, and absence of ocular telangiectasias at original presentation, as well as the presence of prominent myoclonus-dystonia in 2 patients. Many also developed malignancies.

CONCLUSION

Ataxia and telangiectasias may not be prominent features of patients with variant A-T treated for dystonia in adulthood, and variant A-T may mimic primary torsion dystonia and myoclonus-dystonia.

Olfactory dysfunction in LRRK2 G2019S mutation carriers

BACKGROUND

Olfactory dysfunction is an established nonmotor feature of idiopathic Parkinson disease (PD), which may precede disease onset. Olfaction is likely disturbed in patients with PD with leucine-rich repeat kinase (LRRK2) G2019S mutations, although the degree of impairment is debated. It is also unclear whether mutation carriers who have not yet manifested with PD have olfactory disturbances.

METHODS

Thirty-one subjects with LRRK2 G2019S mutation-related PD (PD-manifesting carriers [PD-MC]), 30 subjects with PD without mutations (PD noncarriers [PD-NC]), 28 mutation carrier family members (nonmanifesting carriers [NMC]), and 46 controls completed the University of Pennsylvania Smell Identification Test (UPSIT). Generalized estimating equations were applied to determine whether olfactory score was associated with PD and LRRK2 mutation status.

RESULTS

As expected, having PD was associated with impaired olfaction regardless of LRRK2 mutation status. More importantly, however, impaired olfaction was increased overall in LRRK2 carriers both with and without PD, though the impairment was only present in a subset of NMCs. Compared to controls, the mean score was lower among NMC (difference = -3.518, p = 0.006), MC (difference = -7.677, p < 0.0001), and idiopathic PD (PD-NC) (difference = -13.810, p < 0.0001). Olfaction was better among MC (PD-MC) than non-LRRK2 PD (PD-NC) (difference = 6.13, p = 0.0012). Group differences from the continuous analysis were maintained in dichotomous analysis stratifying at 15th percentile for age and gender.

CONCLUSION

Olfaction is impaired in LRRK2 G2019S-mutation related PD, although less overall than other PD. Further, olfaction is impaired in a subset of LRRK2 NMC, suggesting that olfaction may be a marker for development of PD in this group, and that longitudinal studies are warranted.

Cord blood telomere length, telomerase activity and inflammatory markers in pregnancies in women with diabetes or gestational diabetes

AIMS

We tested the hypothesis that diabetes during pregnancy leads to chromosomal DNA damage and telomere attrition in the feto placental unit and cord blood, and provides evidence for intrauterine programming towards a senescent phenotype in the offspring.

METHODS

We obtained cord blood from pregnant women with pregestational Type 1 diabetes (n=26), Type 2 diabetes (n=20) or gestational diabetes (n=71), and control subjects without diabetes (n=45, n=76 and n=81, respectively) matched for maternal and gestational age. We measured cord blood mononuclear cell telomere length, telomerase activity (a reverse transcriptase that limits telomere attrition), and concentrations of insulin, high-sensitivity C-reactive protein (hs-CRP) and soluble intercellular adhesion molecule-1 (sICAM-1).

RESULTS

We found no significant differences between groups in cord blood telomere length in any nucleated cell type, or in hs-CRP or sICAM-1 concentrations, but telomerase activity was higher in cord blood from Type 1 (P<0.05) and gestational diabetes pregnancies (P<0.05), but not in Type 2 diabetes pregnancies. There were no significant relationships between glycaemic control, cord blood telomere length, telomerase activity or inflammatory markers in any group.

CONCLUSIONS

We found no difference in cord blood telomere length in pregnancies of women with diabetes compared with control subjects, but higher cord blood telomerase activity in Type 1 and gestational diabetes. This may reflect upregulated telomere reverse transcriptase in response to in utero oxidative DNA and telomere damage. These observations are relevant to the hypothesis that diabetes during pregnancy leads to in utero preprogramming towards senescence in the offspring.

Human gene expression profiles of susceptibility and resistance in tuberculosis

Tuberculosis (TB) still poses a profound burden on global health, owing to significant morbidity and mortality worldwide. Although a fully functional immune system is essential for the control of Mycobacterium tuberculosis infection, the underlying mechanisms and reasons for failure in part of the infected population remain enigmatic. Here, whole-blood microarray gene expression analyses were performed in TB patients and in latently as well as uninfected healthy controls to define biomarkers predictive of susceptibility and resistance. Fc gamma receptor 1B (FCGRIB)was identified as the most differentially expressed gene, and, in combination with four other markers, produced a high degree of accuracy in discriminating TB patients and latently infected donors. We determined differentially expressed genes unique for active disease and identified profiles that correlated with susceptibility and resistance to TB. Elevated expression of innate immune-related genes in active TB and higher expression of particular gene clusters involved in apoptosis and natural killer cell activity in latently infected donors are likely to be the major distinctive factors determining failure or success in controlling M. tuberculosis infection. The gene expression profiles defined in this study provide valuable clues for better understanding of progression from latent infection to active disease and pave the way for defining predictive correlates of protection in TB.

Impact of age and sex on mycobacterial immunity in an area of high tuberculosis incidence

SETTING

The extent of immune reactivity measured by the tuberculin skin test (TST) and interferon-gamma (IFN-gamma) T-cell assays is usually not analysed.

OBJECTIVE

To determine the impact of age and sex on assay positivity and on the extent of reactivity of both TST and T-cell assays in young persons in an area of South Africa with high TB transmission.

RESULTS

Age had a strong impact on assay positivity for all seven immune phenotypes tested (P < 0.0007). Among positive responders, the extent of purified protein derivative (PPD) triggered IFN-gamma release (P < 0.003) was sensitive to age. ESAT-6 triggered IFN-gamma release (day 7, P = 0.03) and the frequency of PPD-specific IFN-gamma(+)CD4(+) (P = 0.03) and IFN-gamma(+)CD8(+) cells (P = 0.04) were weakly dependent on age. By contrast, the extent of TST induration was insensitive to age (P > 0.05), and sex had no significant impact on any phenotype measured (P > 0.05). The high proportion of positive responders in the 1-10 year age-group observed with long-term whole blood assays, but not with 3-day assays and TST, suggests that long-term whole blood assays may be confounded by bacille Calmette-Guérin vaccination in this age group.

CONCLUSION

There is a significant impact of age, but not sex, on different assays of immune reactivity in this high TB transmission setting.

Highly discordant T cell responses in individuals with recent exposure to household tuberculosis

BACKGROUND

There are limited data comparing interferon-gamma release assays (IGRAs) for the detection of Mycobacterium tuberculosis infection in highly endemic settings.

METHODS

A cross-sectional household contact study was conducted to measure the agreement of two IGRAs in relation to the tuberculin skin test (TST) to detect M tuberculosis infection and to assess the influence of M tuberculosis exposure and age.

RESULTS

In 82 individuals in household contact, 93% of children and 42% of adults had a high M tuberculosis contact score. The TST was positive in 78% of adults and 54% of children, the T-SPOT.TB was positive in 89% of children and 66% of adults and the QuantiFERON TB Gold (QTF) was positive in a similar proportion of adults and children (38.1% and 39.6%). In children there was poor agreement between the TST and T-SPOT.TB (kappa = -0.15) and the T-SPOT.TB and the QTF (kappa = -0.03), but good agreement between the TST and the QTF (kappa = 0.78) using 10 mm cut-off. In adults there was fair to moderate agreement between the TST and T-SPOT.TB (kappa = 0.38), the TST and QTF (kappa = 0.34) and T-SPOT.TB and QTF (kappa = -0.50). High levels of exposure to M tuberculosis were associated with at least a sevenfold odds of being T-SPOT.TB positive (95% CI 7.67 to 508.69) and a threefold odds of being QTF positive (95% CI 3.02 to 30.54). There was a significant difference in the magnitude of T-SPOT.TB early secretory antigenic target (ESAT)-6 and culture filtrate protein 10 kD (CFP-10) spot counts between adults and children.

CONCLUSIONS

The T-SPOT.TB may be more sensitive than the TST or QTF for detecting recent M tuberculosis infection in children. Differences between assays and the predictive utility of these findings for subsequent disease development should be prospectively assessed.

Characterization of maleuric acid derivatives on transgenic human monoclonal antibody due to post-secretional modifications in goat milk

A fully human antibody to tumor necrosis factor-alpha was expressed in the mammary glands of transgenic goats. The goat expressed antibody (gAb) is heterogeneous and has several isoforms due to typical cellular post-translational modifications. In addition, one post-secretional modification on gAb was discovered by high-resolution cation exchange chromatography (CIEX). The presence of these variants in the final product was shown to be dependent upon the initial milk storage and traditional purification methodologies used. These observations allow for the development of new sample recovery and purification processes to eliminate these variants. Various enzymatic treatments were used to characterize different gAb heavy chain C-terminal lysine and sialic acid variants. In addition, an unknown derivative with the additional mass of 140 Da was found in transgenic gAb using mass spectrometry (MS). The modification sites were identified as the N-termini of gAb light chains and heavy chains using Q-TOF MS. Characterization of transgenic gAb isoforms was facilitated by utilizing different enzymes, CIEX and MS techniques. A maleuric acid modification on the N-terminal portion of gAb was shown to be consistent with the available data characterizing this new derivative of transgenic gAb isoforms in goat milk.

Glycaemic control throughout pregnancy and risk of pre-eclampsia in women with type I diabetes

The aim of this study was to examine the influence of pre-pregnancy care and its effect on early glycaemic control and also the effect of glycaemic control in later pregnancy on risk of pre-eclampsia in women with type I diabetes. A prospective cohort study of 290 consecutive nonselected pregnancies in women with type I diabetes was performed from 1991 to 2002. We examined the relationship of monthly glycosylated haemoglobin (HbA1c) level, pre-pregnancy care, parity, diabetes duration, microvascular complications, maternal age, weight and smoking with risk of pre-eclampsia. Pre-eclampsia developed in 31/243 singleton births (12.8%). HbA1c level at 24 weeks was significantly increased in women with pre-eclampsia compared with women without pre-eclampsia (6.0 versus 5.6%, P= 0.017) and was, after nulliparity, the strongest independent predictor of increased risk (OR 1.65 for each 1% increase in HbA1c; P= 0.01). In contrast, there was no relationship between pre-pregnancy care or HbA1c level at booking and risk of pre-eclampsia.

Cattle and sheep farms as reservoirs of Campylobacter

AIM

This is a review of the natural Campylobacter colonization and transmission among ruminant livestock in the dairy farm environment.

METHODS AND RESULTS

Using cultural detection methods and enumeration techniques the distribution of Campylobacter in ruminant animals at birth, on the farm, at slaughter and in the farm environment have been examined. Colonization and shedding rates are higher among young animals while patterns of shedding in adult animals may be seasonal. Stored and land-dispersed slurries provide a reservoir for scavenging birds and flies and a source for runoff.

CONCLUSIONS

The dairy farm plays a significant role in the dissemination of Campylobacter subtypes that can cause disease in the human community.

SIGNIFICANCE AND IMPACT OF STUDY

An understanding of the role of the dairy farm in the environmental cycle of Campylobacter is required in order to devise intervention strategies.

Clinical trials in neuro-oncology

Clinical trials are prospective scientific studies involving human participants and form the basis for identifying new treatments for diseases like brain tumors. A clinical trial should be designed to provide definitive results for a study question. Therefore, investigators should understand the principles underlying the design, execution and analysis of clinical trials. In addition to the application of basic principles germane to the design of all clinical trials, studies in neuro-oncology also involve unique challenges in case definition, selection of endpoints and definition of response. This review begins with enumeration of the basic principles of clinical trial design including reduction of bias and variability, and concludes with a review of study design factors of particular relevance for neuro-oncology.

Do HIV type 1 RNA levels provide additional prognostic value to CD4(+) T lymphocyte counts in patients with advanced HIV type 1 infection?

Our objective was to assess whether HIV-1 RNA levels provide additional prognostic information beyond CD4(+) T lymphocyte counts in the prediction of subsequent HIV-1 disease progression among patients with advanced HIV-1 disease. In a nested case-control study conducted in patients with baseline CD4(+) T lymphocyte counts < 300 cells/mm(3) and receiving nucleoside reverse transcriptase inhibitors, 102 patients who progressed to an AIDS-defining event or death were matched within 10 CD4(+) T lymphocyte cells/mm(3) to patients who did not progress. The relationship between plasma HIV-1 RNA levels and HIV-1 disease progression was studied using conditional logistic regression analysis, which adjusts for the matching by baseline CD4(+) T lymphocytes. We observed a 0.10 log(10) copies/ml difference in baseline HIV-1 RNA levels between cases and their matched controls (p = 0.027). The relative risk for HIV-1 disease progression increased with increasing baseline HIV-1 RNA levels (odds ratio [OR] for a 3-fold higher HIV-1 RNA level, 1.42; 95% confidence interval [CI], 1.08--1.86), and remained important when also controlling for clinical status at baseline and CD4(+) T lymphocytes at 2 months (p = 0.038). Higher baseline HIV-1 RNA levels were associated with HIV-1 disease progression among patients with a baseline CD4(+) T lymphocyte count of 100 cells/mm(3) or greater (OR, 1.80; 95% CI, 1.15--2.81), but not among patients with a baseline CD4(+) T lymphocyte count < 100 cells/mm(3) (OR, 1.09; 95% CI, 0.73--1.63). We concluded that HIV-1 RNA levels predict subsequent HIV-1 disease progression independent of CD4(+) T lymphocyte counts. The magnitude and importance of the prognostic information contained in the HIV-1 RNA levels appear to depend on the CD4(+) T lymphocyte counts.

Use of pulsed-field gel electrophoresis and flagellin gene typing in identifying clonal groups of Campylobacter jejuni and Campylobacter coli in farm and clinical environments

Although campylobacters have been isolated from a wide range of animal hosts, the association between campylobacters isolated from humans and animals in the farm environment is unclear. We used flagellin gene typing and pulsed-field gel electrophoresis (PFGE) to investigate the genetic diversity among isolates from animals (cattle, sheep, and turkey) in farm environments and sporadic cases of campylobacteriosis in the same geographical area. Forty-eight combined fla types were seen among the 315 Campylobacter isolates studied. Six were found in isolates from all four hosts and represented 50% of the total number of isolates. Seventy-one different SmaI PFGE macrorestriction profiles (mrps) were observed, with 86% of isolates assigned to one of 29 different mrps. Fifty-seven isolates from diverse hosts, times, and sources had an identical SmaI mrp and combined fla type. Conversely, a number of genotypes were unique to a particular host. We provide molecular evidence which suggests a link between campylobacters in the farm environment with those causing disease in the community.

Combination nucleoside analog reverse transcriptase inhibitor(s) plus nevirapine, nelfinavir, or ritonavir in stable antiretroviral therapy-experienced HIV-infected children: week 24 results of a randomized controlled trial--PACTG 377. Pediatric AIDS Clinical Trials Group 377 Study Team

One hundred eighty-one antiretroviral-experienced, protease inhibitor-naive, clinically stable HIV-infected children between 4 months and 17 years of age were randomly assigned to receive one of four combination regimens to evaluate the change in plasma HIV RNA, safety, and tolerance when changing antiretroviral therapy to a protease inhibitor-containing combination regimen. All four regimens contained stavudine; in addition children received nevirapine plus ritonavir, lamivudine plus nelfinavir, nevirapine plus nelfinavir, or lamivudine plus nevirapine plus nelfinavir. Twelve additional children chose to receive stavudine plus lamivudine plus nelfinavir, with nelfinavir given bid, rather than tid as for the main regimens. Overall, 51% (89/176; 95% CI 43-58%) of the children on the randomized portion of the study had an HIV RNA response (< or =400 copies/ml) on at least two of the three HIV RNA determinations taken at Weeks 8, 12, and 16. At Week 24 the proportion of children with an HIV RNA response still on initial therapy was 47% (83/176; 95% CI 40-55%) and ranged from 41 to 61% for the four randomized treatment arms. Rash was frequently seen (27%) on the treatment arms containing nevirapine. At Week 24 64% (7/11, 95% CI 31-89%) of the children on the bid nelfinavir combination regimen were still on initial therapy with an HIV RNA response as compared with 46% (23/50; 95% CI 32-61%) on the corresponding tid nelfinavir combination regimen. A change in antiretroviral therapy to a protease inhibitor-containing regimen was associated with a virological response rate of approximately 50% for this patient population.

Activity of antibiotics used in human medicine for Campylobacter jejuni isolated from farm animals and their environment in Lancashire, UK

A retrospective study of 96 Campylobacter jejuni isolated from farm animals and the environment showed that most were less susceptible than the NCTC type strain to nalidixic acid (MICs 4-32 mg/L), ciprofloxacin (MICs 1-2 mg/L) and erythromycin (MICs 16-64 mg/L), but had similar susceptibility to tetracycline (MICs 4-8 mg/L) and kanamycin (MICs 4-8 mg/L). None had the high MICs of ciprofloxacin (>32 mg/L) or erythromycin (1024 mg/L) typically associated with clinical resistance in this species. Some farms used antimicrobial agents, but there was no obvious association between the use of agents and the susceptibility of the isolates.

Immunologic response to combination nucleoside analogue plus protease inhibitor therapy in stable antiretroviral therapy-experienced human immunodeficiency virus-infected children

The response of 40 immunologic parameters was studied for 147 clinically stable, protease inhibitor-naive, human immunodeficiency virus (HIV)-infected children aged 2-17 years when antiretroviral therapy was changed to either a dual nucleoside analogue regimen or a protease inhibitor-containing regimen. Immunologic response to therapy, as measured by lymphocyte subsets, 3-color flow cytometric measures, and lymphoproliferative assays, were investigated for changes in weeks 44 and 48. The most significant changes after baseline that were associated with the administration of a protease inhibitor-containing regimen were seen for percentages of CD8(+)/CD38(+)/HLA-DR(+), CD8(+)/CD95(+)/CD28(-), and CD8. The percentages of CD8(+)/CD38(+)/HLA-DR(+) and CD8(+)/CD95(+)/CD28(-) decreased from baseline medians of 33% and 46% to medians of 18% and 30% at week 44 (P<.0001 for both). Median CD4 cell count increased 168 cells/microL (from 694 cells/microL to 862 cells/microL; P=.02) by week 48 in this clinically stable population. Changes in lymphoproliferative responses to HIV antigens and recall antigens did not increase over time and between groups.

A member of the Hsp60 gene family from the peach potato aphid, Myzus persicae (Sulzer.)

A novel cDNA clone encoding a mitochondrial Hsp60 was isolated from a Myzus persicae cDNA library. The nucleotide sequence consisted of 2348 bp and contained an open reading frame (ORF) of 1722 bases. The putative protein encoded by this ORF consisted of 574 amino acids and was designated MPHSP60. Comparison of MPHSP60 with other Hsp60s found that it was most similar to Hsp60 from Culicoides variipennis (85.6% similarity). Phylogenetic analysis revealed that MPHSP60 is clustered together with other insect Hsp60s. Comparisons were also made between MPHSP60 and SymL, the GroEL homologue of Myzus persicae endosymbionts.