Coverage Proportions Research Articles

Confidence interval comparison: Precision of maximum likelihood estimates in LLOQ affected data.

When data is derived under a single or multiple lower limits of quantification (LLOQ), estimation of distribution parameters as well as precision of these estimates appear to be challenging, as the way to account for unquantifiable observations due to LLOQs needs particular attention. The aim of this investigation is to characterize the precision of censored sample maximum likelihood estimates of the mean for normal, exponential and Poisson distribution affected by one or two LLOQs using confidence intervals (CI). In a simulation study, asymptotic and bias-corrected accelerated bootstrap CIs for the location parameter mean are compared with respect to coverage proportion and interval width. To enable this examination, we derived analytical expressions of the maximum likelihood location parameter estimate for the assumption of exponentially and Poisson distributed data, where the censored sample method and simple imputation method are used to account for LLOQs. Additionally, we vary the proportion of observations below the LLOQs. When based on the censored sample estimate, the bootstrap CI led to higher coverage proportions and narrower interval width than the asymptotic CI. The results differed by underlying distribution. Under the assumption of normality, the CI's coverage proportion and width suffered most from high proportions of unquantifiable observations. For exponentially and Poisson distributed data, both CI approaches delivered similar results. To derive the CIs, the point estimates from the censored sample method are preferable, because the point estimate of the simple imputation method leads to higher bias for all investigated distributions. This biased simple imputation estimate impairs the coverage proportion of the respective CI. The bootstrap CI surpassed the asymptotic CIs with respect to coverage proportion for the investigated choice of distributional assumptions. The variety of distributions for which the methods are suitable gives the applicant a widely usable tool to handle LLOQ affected data with appropriate approaches.

Spatial Accessibility Models of the Efficient Network of Secondary Healthcare Providers in Slovenia

The main purpose of our research was to assess the accessibility of existing providers of secondary healthcare using established theoretical models of spatial accessibility. In the study, we analyzed the optimal locations and the optimal number of healthcare providers needed for an efficient network of secondary healthcare providers in Slovenia. We used four different location–allocation models and found that the MA-model is the most suitable for planning a potentially efficient network of general hospitals in Slovenia. We showed various scenarios for the development of the general hospital network based on three distinct accessibility travel time intervals, while also taking into account various population coverage proportions that can access hospital services within a given travel time interval. The key finding is that the same coverage of the population with hospital services could be achieved with a smaller number of general hospitals, if the hospitals were optimally located.

Meningococcal A conjugate vaccine coverage in the meningitis belt of Africa from 2010 to 2021: a modelling study

As of the end of 2021, twenty-four countries in the African meningitis belt have rolled out mass campaigns of MenAfriVac®, a meningococcal A conjugate vaccine (MACV) first introduced in 2010. Twelve have completed introduction of MACV into routine immunisation (RI) schedules. Although select post-campaign coverage data are published, no study currently comprehensively estimates MACV coverage from both routine and campaign sources in the meningitis belt across age, country, and time. In this modelling study, we assembled campaign data from the twenty-four countries that had introduced any immunisation activity during or before the year 2021 (Benin, Burkina Faso, Burundi, Cameroon, Central African Republic, Chad, Côte d'Ivoire, Democratic Republic of the Congo, Ethiopia, Eritrea, the Gambia, Ghana, Guinea, Guinea Bissau, Kenya, Mali, Mauritania, Niger, Nigeria, Senegal, South Sudan, Sudan, Togo and Uganda) via WHO reports and RI data via systematic review. Next, we modelled RI coverage using Spatiotemporal Gaussian Process Regression. Then, we synthesized these estimates with campaign data into a cohort model, tracking coverage for each age cohort from age 1 to 29 years over time for each country. Coverage in high-risk locations amongst children aged 1-4 in 2021 was estimated to be highest in Togo with 96.0% (95% uncertainty interval [UI] 92.0-99.0), followed by Niger with 87.2% (95% UI 85.3-89.0) and Burkina Faso, with 86.4% (95% UI 85.1-87.6). These countries had high coverage values driven by an initial successful mass immunisation campaign, followed by a catch-up campaign, followed by introduction of RI. Due to the influence of older mass vaccination campaigns, coverage proportions skewed higher in the 1-29 age group than the 1-4 group, with a median coverage of 82.9% in 2021 in the broader age group compared to 45.6% in the narrower age group. These estimates highlight where gaps in immunisation remain and emphasise the need for broader efforts to strengthen RI systems. This methodological framework can be applied to estimate coverage for any vaccine that has been delivered in both routine and supplemental immunisation activities. Bill and Melinda Gates Foundation.

Vaccination coverage in Italian children and antimicrobial resistance: an ecological analysis

BackgroundAlthough a general consensus that vaccines could be a complementary strategy against antimicrobial resistance (AMR), there is still the need for studies investigating the relationship between childhood vaccination coverage and AMR proportions in the overall population.MethodsWe performed an ecological analysis of available Italian data (vaccination coverages, AMR proportions, number of isolates tested, and antibiotic use) to evaluate the relationships between vaccination coverages in children and AMR proportions in the last 2 decades.ResultsAfter adjusting for covariates, we showed that AMR proportions decreased with increasing vaccination coverages, especially for some combinations of vaccines, pathogens, and antimicrobials. Vaccination coverages for pertussis, diphtheria, and tetanus were inversely related to proportions of E. coli resistant to fluoroquinolones and third generation cephalosporins, K. pneumoniae resistant to carbapenems and third generation cephalosporins, and P. aeruginosa resistant to piperacillin and tazobactam. Polio vaccination coverage was inversely related to proportions of E. coli and K. pneumoniae resistant to third generation cephalosporins.ConclusionsThese results, however, should be interpreted cautiously due to the ecological nature of our analysis. For this reason, further studies designed ad hoc should be encouraged to measure the impact of increasing childhood vaccination coverage on AMR.

National and subnational short-term forecasting of COVID-19 in Germany and Poland during early 2021

BackgroundDuring the COVID-19 pandemic there has been a strong interest in forecasts of the short-term development of epidemiological indicators to inform decision makers. In this study we evaluate probabilistic real-time predictions of confirmed cases and deaths from COVID-19 in Germany and Poland for the period from January through April 2021.MethodsWe evaluate probabilistic real-time predictions of confirmed cases and deaths from COVID-19 in Germany and Poland. These were issued by 15 different forecasting models, run by independent research teams. Moreover, we study the performance of combined ensemble forecasts. Evaluation of probabilistic forecasts is based on proper scoring rules, along with interval coverage proportions to assess calibration. The presented work is part of a pre-registered evaluation study.ResultsWe find that many, though not all, models outperform a simple baseline model up to four weeks ahead for the considered targets. Ensemble methods show very good relative performance. The addressed time period is characterized by rather stable non-pharmaceutical interventions in both countries, making short-term predictions more straightforward than in previous periods. However, major trend changes in reported cases, like the rebound in cases due to the rise of the B.1.1.7 (Alpha) variant in March 2021, prove challenging to predict.ConclusionsMulti-model approaches can help to improve the performance of epidemiological forecasts. However, while death numbers can be predicted with some success based on current case and hospitalization data, predictability of case numbers remains low beyond quite short time horizons. Additional data sources including sequencing and mobility data, which were not extensively used in the present study, may help to improve performance.

Nanosized Janus AuNR-Pt Motor for Enhancing NIR-II Photoacoustic Imaging of Deep Tumor and Pt2+ Ion-Based Chemotherapy

Synthetic micro/nanomotors have great potential in deep tissue imaging and in vivo drug delivery because of their active motion ability. However, applying nanomotors with a size less than 100 nm to in vivo imaging and therapy is one of the core changes in this field. Herein, a nanosized hydrogen peroxide (H2O2)-driven Janus gold nanorod-platinum (JAuNR-Pt) nanomotor is developed for enhancing the second near-infrared region (NIR-II) photoacoustic (PA) imaging of deep tissues of tumors and for effective tumor treatment. The JAuNR-Pt nanomotor is prepared by depositing platinum (Pt) on one end of a gold nanorod with varying proportions of Pt shell coverage, including 10%, 25%, 50%, 75%, and 100%. The JAuNR-Pt nanomotor with Pt shell coverage proportions of 50% exhibits the highest diffusion coefficient (De), and it can rapidly move in the presence of H2O2. The self-propulsion of JAuNR-Pt nanomotor enhances cellular uptake, accelerates lysosomal escape, and facilitates continuous release of cytotoxic Pt2+ ions to the nucleus, causing DNA damage and cell apoptosis. The JAuNR-Pt nanomotor presents deep penetration and enhanced accumulation in tumors as well as high tumor treatment effect. Therefore, this work displays deep tumor imaging and an excellent antitumor effect, providing an effective tool for accurate diagnosis and treatment of diseases.

The Inverse Relationship between Influenza Vaccination and Antimicrobial Resistance: An Ecological Analysis of Italian Data.

Antimicrobial resistance (AMR) is one of the key threats to global health and requires sustainable and effective actions to reduce its consequences in the near future worldwide. There are several well-documented and epidemiologically supported examples that both bacterial and viral vaccines might have an impact on AMR. Here, we conducted an ecological analysis of Italian data to evaluate the relationship between influenza vaccination coverage and AMR proportions over the last two decades. We found significant negative correlations between influenza vaccination coverage in the population over 64 years and AMR in Escherichia coli and Klebsiella pneumoniae isolates. The observed inverse relationships were confirmed by linear regression analysis. Similar results were obtained for the vaccination coverage in the overall population. Despite the main limitations of our study, its findings suggested an inverse relationship between influenza vaccination coverage and AMR proportions over the years, which was in accordance with previous theories illustrating how influenza vaccination reduced antibiotic prescriptions. However, since our study did not allow for us to elucidate the mechanisms underpinning the observed relationship, more and better data on confounding and mediating factors should be considered in future research.

Gender differentials in spatial distribution of immunisation status in children aged 12-23 months by district in Punjab - Results from Pakistan Social and Living Standards Measurements Survey 2014-15.

In Pakistan routine immunisation for children is offered free of cost in the public sector and several studies have been conducted analysing coverage at the village, city, district, and provincial levels that show wide variation in immunisation coverage rates. Using the district level Pakistan Bureau of Statistics 'Pakistan Social and Living Standards Measurements' survey data for 2014-15, various immunisation indices were analysed and mapped for Punjab province. The mapping of gender disaggregated, three immunisation indices at the district level illustrate that immunisation of 12-to-23-month children is wide spread in the Punjab province. In the southern and central districts, immunisation coverage was not at par with the northern districts. Gender-based immunisation coverage proportions does show differentials that is a cause of concern. Disease mapping brings out these immunisation coverage and differences in an easily understandable format that could help better plan, target, and deliver childhood routine immunisations in the province.

Reliability analysis for accelerated degradation data based on the Wiener process with random effects

AbstractOn the basis of the principle of degradation mechanism invariance, a Wiener degradation process with random drift parameter is used to model the data collected from the constant stress accelerated degradation test. Small‐sample statistical inference method for this model is proposed. On the basis of Fisher's method, a test statistic is proposed to test if there is unit‐to‐unit variability in the population. For reliability inference, the quantities of interest are the quantile function, the reliability function, and the mean time to failure at the designed stress level. Because it is challenging to obtain exact confidence intervals (CIs) for these quantities, a regression type of model is used to construct pivotal quantities, and we develop generalized confidence intervals (GCIs) procedure for those quantities of interest. Generalized prediction interval for future degradation value at designed stress level is also discussed. A Monte Carlo simulation study is used to demonstrate the benefits of our procedures. Through simulation comparison, it is found that the coverage proportions of the proposed GCIs are better than that of the Wald CIs and GCIs have good properties even when there are only a small number of test samples available. Finally, a real example is used to illustrate the developed procedures.

Decreased prevalence of Moraxella catarrhalis in addition to Streptococcus pneumoniae in children with upper respiratory tract infection after introduction of conjugated pneumococcal vaccine: a retrospective cohort study

ObjectivesTo study effects of the introduction of pneumococcal conjugate vaccines (PCV) on the interspecies dynamics of Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis in preschool children with respiratory tract infection. MethodsNasopharyngeal samples from children aged ≤6 years with upper respiratory tract infection (n = 14 473) in South Sweden were analysed during 14 consecutive years, 5 years before and 9 years after PCV introduction. The yearly prevalence was calculated, and multivariate count regressions between prevalence and estimated yearly proportions of vaccinated children were performed. Associations between pneumococcal serotypes and the other pathogens were assessed. ResultsWhen comparing the prevaccine period with the years after introduction, the prevalence of S. pneumoniae decreased by 65.2% (16.4 to 5.7 per 1000 individuals; p < 0.001), whereas M. catarrhalis and H. influenzae decreased by 52.1% (21.5 to 10.3 per 1000 individuals; p < 0.001) and 46.6% (13.6 to 7.3 per 1000 individuals; p < 0.001), respectively. In multivariate negative binomial regressions adjusted for yearly numbers of samples taken, S. pneumoniae and M. catarrhalis were significantly negatively associated with increasing vaccine coverage proportions (adjusted prevalence ratio (aPR) = 0.17; p < 0.001 and aPR = 0.48; p < 0.001, respectively), whereas H. influenzae (aPR = 0.75; p = 0.17) was not. In addition, the proportion of cultures positive for S. pneumoniae as well as M. catarrhalis was significantly lower in the postvaccine period compared to the prevaccine period, while this was not the case for H. influenzae. A significant positive association between certain PCV serotypes and simultaneous growth with M. catarrhalis was observed. ConclusionsAfter introduction of PCV, the prevalence of M. catarrhalis in addition to S. pneumoniae in children with respiratory tract infection decreased; this was also the case after adjusting for reduced numbers of samples taken. This may partly be attributed to a positive association between PCV serotypes and M. catarrhalis.

An evaluation of sequencing coverage and genotyping strategies to assess neutral and adaptive diversity.

Whole genome sequences (WGS) greatly increase our ability to precisely infer population genetic parameters, demographic processes, and selection signatures. However, WGS may still be not affordable for a representative number of individuals/populations. In this context, our goal was to assess the efficiency of several SNP genotyping strategies by testing their ability to accurately estimate parameters describing neutral diversity and to detect signatures of selection. We analysed 110 WGS at 12× coverage for four different species, i.e., sheep, goats and their wild counterparts. From these data we generated 946 data sets corresponding to random panels of 1K to 5M variants, commercial SNP chips and exome capture, for sample sizes of five to 48 individuals. We also extracted low-coverage genome resequencing of 1×, 2× and 5× by randomly subsampling reads from the 12× resequencing data. Globally, 5K to 10K random variants were enough for an accurate estimation of genome diversity. Conversely, commercial panels and exome capture displayed strong ascertainment biases. Besides the characterization of neutral diversity, the detection of the signature of selection and the accurate estimation of linkage disequilibrium (LD) required high-density panels of at least 1M variants. Finally, genotype likelihoods increased the quality of variant calling from low coverage resequencing but proportions of incorrect genotypes remained substantial, especially for heterozygote sites. Whole genome resequencing coverage of at least 5× appeared to be necessary for accurate assessment of genomic variations. These results have implications for studies seeking to deploy low-density SNP collections or genome scans across genetically diverse populations/species showing similar genetic characteristics and patterns of LD decay for a wide variety of purposes.

Hybrid prevalence estimation: Method to improve intervention coverage estimations

Delivering excellent health services requires accurate health information systems (HIS) data. Poor-quality data can lead to poor judgments and outcomes. Unlike probability surveys, which are representative of the population and carry accuracy estimates, HIS do not, but in many countries the HIS is the primary source of data used for administrative estimates. However, HIS are not structured to detect gaps in service coverage and leave communities exposed to unnecessary health risks. Here we propose a method to improve informatics by combining HIS and probability survey data to construct a hybrid estimator. This technique provides a more accurate estimator than either data source alone and facilitates informed decision-making. We use data from vitamin A and polio vaccination campaigns in children from Madagascar and Benin to demonstrate the effect. The hybrid estimator is a weighted average of two measurements and produces SEs and 95% confidence intervals (CIs) for the hybrid and HIS estimators. The estimates of coverage proportions using the combined data and the survey estimates differ by no more than 3%, while decreasing the SE by 1-6%; the administrative estimates from the HIS and combined data estimates are very different, with 3-25 times larger CI, questioning the value of administrative estimates. Estimators of unknown accuracy may lead to poorly formulated policies and wasted resources. The hybrid estimator technique can be applied to disease prevention services for which population coverages are measured. This methodology creates more accurate estimators, alongside measured HIS errors, to improve tracking the public's health.

A Combined Approach to Classifying Land Surface Cover of Urban Domestic Gardens Using Citizen Science Data and High Resolution Image Analysis

Domestic gardens are an important component of cities, contributing significantly to urban green infrastructure (GI) and its associated ecosystem services. However, domestic gardens are incredibly heterogeneous which presents challenges for quantifying their GI contribution and associated benefits for sustainable urban development. This study applies an innovative methodology that combines citizen science data with high resolution image analysis to create a garden dataset in the case study city of Manchester, UK. An online Citizen Science Survey (CSS) collected estimates of proportional coverage for 10 garden land surface types from 1031 city residents. High resolution image analysis was conducted to validate the CSS estimates, and to classify 7 land surface cover categories for all garden parcels in the city. Validation of the CSS land surface estimations revealed a mean accuracy of 76.63% (s = 15.24%), demonstrating that citizens are able to provide valid estimates of garden surface coverage proportions. An Object Based Image Analysis (OBIA) classification achieved an estimated overall accuracy of 82%, with further processing required to classify shadow objects. CSS land surface estimations were then extrapolated across the entire classification through calculation of within image class proportions, to provide the proportional coverage of 10 garden land surface types (buildings, hard impervious surfaces, hard pervious surfaces, bare soil, trees, shrubs, mown grass, rough grass, cultivated land, water) within every garden parcel in the city. The final dataset provides a better understanding of the composition of GI in domestic gardens and how this varies across the city. An average garden in Manchester has 50.23% GI, including trees (16.54%), mown grass (14.46%), shrubs (9.19%), cultivated land (7.62%), rough grass (1.97%) and water (0.45%). At the city scale, Manchester has 49.0% GI, and around one fifth (20.94%) of this GI is contained within domestic gardens. This is useful evidence to inform local urban development policies.

Immunization Coverage in Migrant School Children Along the Thailand-Myanmar Border.

The objective of this project was to document and increase vaccine coverage in migrant school children on the Thailand-Myanmar border. Migrant school children (n = 12,277) were enrolled in a school-based immunization program in four Thai border districts. The children were evaluated for vaccination completion and timing, for six different vaccines: Bacille Calmette-Guerin (BCG); Oral Polio vaccine (OPV); Hepatitis B vaccine (HepB); Diphtheria, Pertussis and Tetanus vaccine (DTP); Measles Containing Vaccine or Measles, Mumps and Rubella vaccine (MMR); Tetanus and Diphtheria containing vaccine (Td). Vaccine coverage proportions for BCG, OPV3, DTP3, HepB3 and measles containing vaccine were 92.3, 85.3, 63.8, 72.2, and 90.9 % respectively. Most children were able to receive vaccines in a time appropriate manner. School-based immunization programs offer a suitable vaccine delivery mechanism for hard-to-reach populations. However, these data suggest overall low vaccine coverage in migrant populations. Further efforts toward improving appropriate vaccine coverage and methods of retaining documentation of vaccination in mobile migrant populations are necessary for improved health.

Optimizing HIV pre-exposure prophylaxis implementation among men who have sex with men in a large urban centre: a dynamic modelling study.

IntroductionOnce-daily tenofovir/emtricitabine-based pre-exposure prophylaxis (PrEP) can reduce HIV acquisition in men who have sex with men (MSM), by 44% in the iPrEx trial, and reaching up to 99% with high adherence. We examined the potential population-level impact and cost-effectiveness of different PrEP implementation strategies.MethodsWe developed a dynamic, stochastic compartmental model of HIV transmission among the estimated 57,400 MSM in Toronto, Canada. Parameterization was performed using local epidemiologic data. Strategies examined included (1) uniform PrEP delivery versus targeting the highest risk decile of MSM (with varying coverage proportions); (2) increasing PrEP efficacy as a surrogate of adherence (44% to 99%); and (3) varying HIV test frequency (once monthly to once yearly). Outcomes included HIV infections averted and the incremental cost ($CAD) per incremental quality-adjusted-life-year (QALY) gained over 20 years.ResultsUse of PrEP among all HIV-uninfected MSM at 25, 50, 75 and 100% coverage prevented 1970, 3427, 4317, and 4581 infections, respectively, with cost/QALY increasing from $500,000 to $800,000 CAD. Targeted PrEP for the highest risk MSM at 25, 50, 75 and 100% coverage prevented 1166, 2154, 2816, and 3012 infections, respectively, with cost/QALY ranging from $35,000 to $70,000 CAD. Maximizing PrEP efficacy, in a scenario of 25% coverage of high-risk MSM with PrEP, prevented 1540 infections with a cost/QALY of $15,000 CAD. HIV testing alone (Q3 months) averted 898 of infections with a cost savings of $4,000 CAD per QALY.ConclusionsThe optimal implementation strategy for PrEP over the next 20 years at this urban centre is to target high-risk MSM and to maximize efficacy by supporting PrEP adherence. A large health benefit of PrEP implementation could come from engaging undiagnosed HIV-infected individuals into care.

Meta-analysis of multiple outcomes: a multilevel approach.

In meta-analysis, dependent effect sizes are very common. An example is where in one or more studies the effect of an intervention is evaluated on multiple outcome variables for the same sample of participants. In this paper, we evaluate a three-level meta-analytic model to account for this kind of dependence, extending the simulation results of Van den Noortgate, López-López, Marín-Martínez, and Sánchez-Meca Behavior Research Methods, 45, 576-594 (2013) by allowing for a variation in the number of effect sizes per study, in the between-study variance, in the correlations between pairs of outcomes, and in the sample size of the studies. At the same time, we explore the performance of the approach if the outcomes used in a study can be regarded as a random sample from a population of outcomes. We conclude that although this approach is relatively simple and does not require prior estimates of the sampling covariances between effect sizes, it gives appropriate mean effect size estimates, standard error estimates, and confidence interval coverage proportions in a variety of realistic situations.

Block Bootstrap Calibration with Application to the Fire Weather Index

This article presents an analysis of Ontario Fire Weather Index (FWI) data†The data used is ©1963–2004, Queen’s Printer for Ontario, Canada, and was referenced under agreement with the Ontario Ministry of Natural Resources.Color versions of one or more of the figures in the article can be found online at www.tandfonline.com/lssp. using the block bootstrap for time series. Confidence intervals for parameters such as the first lag autocorrelation can have low coverage relative to the nominal level. Therefore, adjustments to the confidence intervals are necessary in order to achieve reasonable accuracy. We introduce a confidence interval calibration method in which the length of the confidence interval is adjusted according to an amount determined from a double bootstrap. We compare this method with the α-level adjustment method, and we find that the length-adjustment method is superior under scenarios similar to that of the FWI data: coverage proportions are slightly higher for the length-adjustment approach, and confidence interval widths are markedly smaller. Applying the length-adjustment method to the Ontario FWI data gives different results than would be obtained without adjustment.

Abstract P1-02-05: Identification of HER-2/neu amplification using amplicon based benchtop next generation sequencing

Abstract Introduction Aplicon based next generation sequencing (NGS) assays have the potential to incorporate simultaneous assessment of somatic mutations and copy number variation into a single platform. Although not specifically designed for this purpose, we noted numerous examples of apparent HER-2/neu gene amplification in analyzing results from our mutation profiling 46-gene cancer NGS panel (Life Technologies, South San Francisco, CA). Material and Methods Existing amplicon coverage data from the TorrentSuite 2.0 (Life Technologies) pipeline was accessed and used to generate a HER-2/neu coverage proportion (ratio between all HER-2/neu amplicon reads and all other amplicon reads). This ratio was calculated for 170 unique cases of breast carcinoma. A total of 4 cases were eliminated from analysis due to indeterminate IHC/FISH results. Using a total of 166 cases, we performed ROC curve analysis to determine the sensitivity and specificity of NGS based HER-2/neu amplification compared to that of traditional IHC and FISH testing (MedCalc v8.0). Results The NGS based HER-2/neu coverage proportions in the 166 cases showed a clearly non-normal distribution with an outlier cluster of cases with an elevated NGS HER-2/neu ratio (6 cases with ratios &amp;gt;0.045). The distribution of NGS based HER-2/neu ratios for the entire population ranged from 0.01 to a maximum of 0.34. ROC curve analysis of NGS HER-2/neu proportions compared to IHC/FISH data showed a maximal sensitivity of 75.0% and specificity of 100% at an NGS ratio cut off of ≥0.045. In the 166 cases, 6 showed a HER-2/neu coverage proportion of &amp;gt; 0.045 (range 0.045-0.34). Utilizing the 0.045 NGS ratio cut off value, the population frequency of cases positive for HER2 expression was 3.4%. Of the 160 samples with NGS coverage proportion &amp;lt; 0.045, only two cases were positive by IHC/FISH testing. The correlation between NGS HER-2/neu coverage proportion and IHC/FISH testing was highly significant (Spearman rank correlation r = 0.67, p &amp;lt; 0.0001 CI: 0.58-0.75). Conclusions Even utilizing a limited somatic cancer panel that includes less than 200 amplicons in 46 genes, clinically significant HER-2/neu amplification can be readily identified. This is the first study to describe the functional utility of HER-2/neu amplification detection using a NGS based amplicon assay. This study shows that in addition to mutation analysis, amplification data can be simultaneously obtained, which has striking implications for potential clinical utility and HER-2/neu amplification detection outside of traditional IHC and HER2 testing modalities. Furthermore, utilizing this assay as a primary screening modality could limit the additional expense of multiple single gene testing. Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P1-02-05.

Improving the collection of knowledge, attitude and practice data with community surveys: a comparison of two second-stage sampling methods

Second-stage sampling techniques, including spatial segmentation, are widely used in community health surveys when reliable household sampling frames are not available. In India, an unresearched technique for household selection is used in eight states, which samples the house with the last marriage or birth as the starting point. Users question whether this last-birth or last-marriage (LBLM) approach introduces bias affecting survey results. We conducted two simultaneous population-based surveys. One used segmentation sampling; the other used LBLM. LBLM sampling required modification before assessment was possible and a more systematic approach was tested using last birth only. We compared coverage proportions produced by the two independent samples for six malaria indicators and demographic variables (education, wealth and caste). We then measured the level of agreement between the caste of the selected participant and the caste of the health worker making the selection. No significant difference between methods was found for the point estimates of six malaria indicators, education, caste or wealth of the survey participants (range of P: 0.06 to >0.99). A poor level of agreement occurred between the caste of the health worker used in household selection and the caste of the final participant, (Κ = 0.185), revealing little association between the two, and thereby indicating that caste was not a source of bias. Although LBLM was not testable, a systematic last-birth approach was tested. If documented concerns of last-birth sampling are addressed, this new method could offer an acceptable alternative to segmentation in India. However, inter-state caste variation could affect this result. Therefore, additional assessment of last birth is required before wider implementation is recommended.

Reflectance indices as a diagnostic tool for weed control performed by multipurpose equipment in precision agriculture

Several tools of precision agriculture have been developed for specific uses. However, this specificity may hinder the implementation of precision agriculture due to an increasing in costs and operational complexity. The use of vegetation index sensors which are traditionally developed for crop fertilization, for site-specific weed management can provide multiple utilizations of these sensors and result in the optimization of precision agriculture. The aim of this study was to evaluate the relationship between reflectance indices of weeds obtained by the GreenSeekerTM sensor and conventional parameters used for weed interference quantification. Two experiments were conducted with soybean and corn by establishing a gradient of weed interference through the use of pre- and post-emergence herbicides. The weed quantification was evaluated by the normalized difference vegetation index (NDVI) and the ratio of red to near infrared (Red/NIR) obtained using the GreenSeekerTM sensor, the visual weed control, the weed dry matter, and digital photographs, which supplied information about the leaf area coverage proportions of weed and straw. The weed leaf coverage obtained using digital photography was highly associated with the NDVI (r = 0.78) and the Red/NIR (r = -0.74). The weed dry matter also positively correlated with the NDVI obtained in 1 m linear (r = 0.66). The results indicated that the GreenSeekerTM sensor originally used for crop fertilization could also be used to obtain reflectance indices in the area between rows of crops to support decision-making programs for weed control.