105 research outputs found
Modelling workplace contact networks: the effects of organizational structure, architecture, and reporting errors on epidemic predictions
Face-to-face social contacts are potentially important transmission routes
for acute respiratory infections, and understanding the contact network can
improve our ability to predict, contain, and control epidemics. Although
workplaces are important settings for infectious disease transmission, few
studies have collected workplace contact data and estimated workplace contact
networks. We use contact diaries, architectural distance measures, and
institutional structures to estimate social contact networks within a Swiss
research institute. Some contact reports were inconsistent, indicating
reporting errors. We adjust for this with a latent variable model, jointly
estimating the true (unobserved) network of contacts and duration-specific
reporting probabilities. We find that contact probability decreases with
distance, and research group membership, role, and shared projects are strongly
predictive of contact patterns. Estimated reporting probabilities were low only
for 0-5 minute contacts. Adjusting for reporting error changed the estimate of
the duration distribution, but did not change the estimates of covariate
effects and had little effect on epidemic predictions. Our epidemic simulation
study indicates that inclusion of network structure based on architectural and
organizational structure data can improve the accuracy of epidemic forecasting
models.Comment: 36 pages, 4 figure
A description of within-family resource exchange networks in a Malawian village
In this paper we explore patterns of economic transfers between adults within household and family networks in a village in Malawi’s Rumphi district, using data from the 2006 round of the Malawi Longitudinal Study of Families and Health. We fit Exponential-family Random Graph Models (ERGMs) to assess individual, relational, and higher-order network effects. The network effects of cyclic giving, reciprocity, and in-degree and out-degree distribution suggest a network with a tendency away from the formation of hierarchies or "hubs." Effects of age, sex, working status, education, health status, and kinship relation are also considered.Malawi, Malawi Longitudinal Study of Families and Health, networks, resource exchange, social network
Estimating within-household contact networks from egocentric data
Acute respiratory diseases are transmitted over networks of social contacts.
Large-scale simulation models are used to predict epidemic dynamics and
evaluate the impact of various interventions, but the contact behavior in these
models is based on simplistic and strong assumptions which are not informed by
survey data. These assumptions are also used for estimating transmission
measures such as the basic reproductive number and secondary attack rates.
Development of methodology to infer contact networks from survey data could
improve these models and estimation methods. We contribute to this area by
developing a model of within-household social contacts and using it to analyze
the Belgian POLYMOD data set, which contains detailed diaries of social
contacts in a 24-hour period. We model dependency in contact behavior through a
latent variable indicating which household members are at home. We estimate
age-specific probabilities of being at home and age-specific probabilities of
contact conditional on two members being at home. Our results differ from the
standard random mixing assumption. In addition, we find that the probability
that all members contact each other on a given day is fairly low: 0.49 for
households with two 0--5 year olds and two 19--35 year olds, and 0.36 for
households with two 12--18 year olds and two 36+ year olds. We find higher
contact rates in households with 2--3 members, helping explain the higher
influenza secondary attack rates found in households of this size.Comment: Published in at http://dx.doi.org/10.1214/11-AOAS474 the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
Estimating within-school contact networks to understand influenza transmission
Many epidemic models approximate social contact behavior by assuming random
mixing within mixing groups (e.g., homes, schools and workplaces). The effect
of more realistic social network structure on estimates of epidemic parameters
is an open area of exploration. We develop a detailed statistical model to
estimate the social contact network within a high school using friendship
network data and a survey of contact behavior. Our contact network model
includes classroom structure, longer durations of contacts to friends than
nonfriends and more frequent contacts with friends, based on reports in the
contact survey. We performed simulation studies to explore which network
structures are relevant to influenza transmission. These studies yield two key
findings. First, we found that the friendship network structure important to
the transmission process can be adequately represented by a dyad-independent
exponential random graph model (ERGM). This means that individual-level sampled
data is sufficient to characterize the entire friendship network. Second, we
found that contact behavior was adequately represented by a static rather than
dynamic contact network.Comment: Published in at http://dx.doi.org/10.1214/11-AOAS505 the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
Chloroquine as weekly chemoprophylaxis or intermittent treatment to prevent malaria in pregnancy in Malawi: a randomised controlled trial.
BACKGROUND: Sulfadoxine-pyrimethamine resistance threatens efficacy of intermittent preventive treatment of malaria during pregnancy, and alternative regimens need to be identified. With the return of chloroquine efficacy in southern Africa, we postulated that chloroquine either as an intermittent therapy or as weekly chemoprophylaxis would be more efficacious than intermittent sulfadoxine-pyrimethamine for prevention of malaria in pregnancy and associated maternal and newborn adverse outcomes. METHODS: We did an open-label, single-centre, randomised controlled trial at Ndirande Health Centre, Blantyre, in southern Malawi. We enrolled pregnant women (first or second pregnancy) at 20-28 weeks' gestation who were HIV negative. Participants were randomly assigned in a 1:1:1 ratio using a computer-generated list to either intermittent sulfadoxine-pyrimethamine (two doses of 1500 mg sulfadoxine and 75 mg pyrimethamine, 4 weeks apart), intermittent chloroquine (two doses of 600 mg on day 1, 600 mg on day 2, and 300 mg on day 3), or chloroquine prophylaxis (600 mg on day 1 then 300 mg every week). The primary endpoint was placental malaria in the modified intent-to-treat population, which consisted of participants who contributed placental histopathology data at birth. Secondary outcomes included clinical malaria, maternal anaemia, low birthweight, and safety. This trial is registered with ClinicalTrials.gov, number NCT01443130. FINDINGS: Between February, 2012, and May, 2014, we enrolled and randomly allocated 900 women, of whom 765 contributed histopathological data and were included in the primary analysis. 108 (14%) women had placental malaria, which was lower than the anticipated prevalence of placental malaria infection. Protection from placental malaria was not improved by chloroquine as either prophylaxis (30 [12%] of 259 had positive histopathology; relative risk [RR] 0·75, 95% CI 0·48-1·17) or intermittent therapy (39 [15%] of 253; RR 1·00, 0·67-1·50) compared with intermittent sulfadoxine-pyrimethamine (39 [15%] of 253). In protocol-specified analyses adjusted for maternal age, gestational age at enrolment, bednet use the night before enrolment, anaemia at enrolment, and malaria infection at enrolment, women taking chloroquine as prophylaxis had 34% lower placental infections than did those allocated intermittent sulfadoxine-pyrimethamine (RR 0·66, 95% CI 0·46-0·95). Clinical malaria was reported in nine women assigned intermittent sulfadoxine-pyrimethamine, four allocated intermittent chloroquine (p=0·26), and two allocated chloroquine prophylaxis (p=0·063). Maternal anaemia was noted in five women assigned intermittent sulfadoxine-pyrimethamine, 15 allocated intermittent chloroquine (p=0·038), and six assigned chloroquine prophylaxis (p>0·99). Low birthweight was recorded for 31 babies born to women allocated intermittent sulfadoxine-pyrimethamine, 29 assigned intermittent chloroquine (p=0·78), and 41 allocated chloroquine prophylaxis (p=0·28). Four women assigned intermittent sulfadoxine-pyrimethamine had adverse events possibly related to study product compared with 94 women allocated intermittent chloroquine (p<0·0001) and 26 allocated chloroquine prophylaxis (p<0·0001). Three women had severe or life-threatening adverse events related to study product, of whom all were assigned intermittent chloroquine (p=0·25). INTERPRETATION: Chloroquine administered as intermittent therapy did not provide better protection from malaria and related adverse effects compared with intermittent sulfadoxine-pyrimethamine in a setting of high resistance to sulfadoxine-pyrimethamine. Chloroquine chemoprophylaxis might provide benefit in protecting against malaria during pregnancy, but studies with larger sample sizes are needed to confirm these results. FUNDING: US National Institutes of Health
Social contact patterns and implications for infectious disease transmission: a systematic review and meta-analysis of contact surveys
Background: Transmission of respiratory pathogens such as SARS-CoV-2 depends on patterns of contact and mixing across populations. Understanding this is crucial to predict pathogen spread and the effectiveness of control efforts. Most analyses of contact patterns to date have focussed on high-income settings. Methods: Here, we conduct a systematic review and individual-participant meta-analysis of surveys carried out in low- and middle-income countries and compare patterns of contact in these settings to surveys previously carried out in high-income countries. Using individual-level data from 28,503 participants and 413,069 contacts across 27 surveys we explored how contact characteristics (number, location, duration and whether physical) vary across income settings. Results: Contact rates declined with age in high- and upper-middle-income settings, but not in low-income settings, where adults aged 65+ made similar numbers of contacts as younger individuals and mixed with all age-groups. Across all settings, increasing household size was a key determinant of contact frequency and characteristics, but low-income settings were characterised by the largest, most intergenerational households. A higher proportion of contacts were made at home in low-income settings, and work/school contacts were more frequent in high-income strata. We also observed contrasting effects of gender across income-strata on the frequency, duration and type of contacts individuals made. Conclusions: These differences in contact patterns between settings have material consequences for both spread of respiratory pathogens, as well as the effectiveness of different non-pharmaceutical interventions
Towards an integrated model for breast cancer etiology: The lifelong interplay of genes, lifestyle, and hormones
While the association of a number of risk factors, such as family history and reproductive patterns, with breast cancer has been well established for many years, work in the past 10–15 years also has added substantially to our understanding of disease etiology. Contributions of particular note include the delineation of the role of endogenous and exogenous estrogens to breast cancer risk, and the discovery and quantification of risk associated with several gene mutations (e.g. BRCA1). Although it is difficult to integrate all epidemiologic data into a single biologic model, it is clear that several important components or pathways exist. Early life events probably determine both the number of susceptible breast cells at risk and whether mutations occur in these cells. High endogenous estrogens are well established as an important cause of breast cancer, and many known risk factors appear to operate through this pathway. Estrogens (and probably other growth factors) appear to accelerate the development of breast cancer at many points along the progression from early mutation to tumor metastasis, and appear to be influential at many points in a woman's life. These data now provide a basis for a number of strategies that can reduce risk of breast cancer, although some strategies represent complex decision-making. Together, the modification of nutritional and lifestyle risk factors and the judicious use of chemopreventive agents could have a major impact on breast cancer incidence. Further research is needed in many areas, but a few specific arenas are given particular mention
Combining Asian and European genome-wide association studies of colorectal cancer improves risk prediction across racial and ethnic populations
Polygenic risk scores (PRS) have great potential to guide precision colorectal cancer (CRC) prevention by identifying those at higher risk to undertake targeted screening. However, current PRS using European ancestry data have sub-optimal performance in non-European ancestry populations, limiting their utility among these populations. Towards addressing this deficiency, we expand PRS development for CRC by incorporating Asian ancestry data (21,731 cases; 47,444 controls) into European ancestry training datasets (78,473 cases; 107,143 controls). The AUC estimates (95% CI) of PRS are 0.63(0.62-0.64), 0.59(0.57-0.61), 0.62(0.60-0.63), and 0.65(0.63-0.66) in independent datasets including 1681-3651 cases and 8696-115,105 controls of Asian, Black/African American, Latinx/Hispanic, and non-Hispanic White, respectively. They are significantly better than the European-centric PRS in all four major US racial and ethnic groups (p-values < 0.05). Further inclusion of non-European ancestry populations, especially Black/African American and Latinx/Hispanic, is needed to improve the risk prediction and enhance equity in applying PRS in clinical practice
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