Beta Regression Models for Repeated-Measures Data Analysis

Bounded data often give rise to uncorrectable skew and heteroscedasticity. Bounded data are a relatively frequent occurrence in clinical and research settings. For example, in neuropsychology, most neurocognitive tests are bounded, and subjects are repeatedly measured over time. The statistician needs to choose a model that accounts for the correlated nature of the repeated measures. The Beta distribution is a natural choice for modeling bounded data. Currently, generalized linear mixed models (GLMM) and generalized estimating equations (GEE) are two methods that can be used to model Beta distributed data with repeated measures. However, GLMMs and GEEs have limitations, i.e., GLMMs require numerical integration and GEEs are not based on a joint likelihood making model selection more ambiguous. Therefore, we present two alternative models (LNMVB and SLMVB) that are based on a joint likelihood and do not require numerical integration for the estimation of the model parameters. We compare our proposed models to the Beta GLMM and the Beta GEE using simulated data and a real dataset from the National NeuroAIDS Tissue Consortium. Through simulation, we found the LNMVB and the Beta GEE were the only models that produced unbiased estimates of the location parameter for all scenarios considered. The LNMVB tended to have better control of the Type I error rate compared to the Beta GEE, especially for smaller sample sizes (i.e., N \u3c 30). The coverage probabilities for both the LNMVB and the Beta GEE tended towards 95% as sample size increased with the LNMVB generally closer to the desired 95% coverage probability. Lastly, the Beta GEE was the only model that consistently had a mean bias near zero when estimating the correlation parameter. Based on simulated data, we conclude that the LNMVB is preferred for analyzing small sample (i.e., \u3c 30), repeatedly-measured proportional data. Either the LNMVB or the Beta GEE is sufficient to analyze large sample (i.e., \u3e 50), correlated Beta distributed data. Furthermore, if the correlation is the parameter of interest, the Beta GEE is the preferred model

The President\u27s Emergency Plan for AIDS Relief and Adult Mortality: A Replication Study of HIV Development Assistance Effects in Sub-Saharan African Countries

The US budget for global health funding, which was by far the largest of similar funding in the world, increased from US $1.3 billion in 2001 to more than US$10 billion in recent years. More than 54% of this funding was allocated to the Global Fund to Fight HIV/AIDS through the US President\u27s Emergency Plan for AIDS Relief (PEPFAR) in Africa. However, recent studies indicate contradictory results regarding the effectiveness of PEPFAR. One by Bendavid, Holmes, Bhattacharya, and Miller shows positive effects of PEPFAR in reducing adult mortality in Africa, while another by Duber, Coates, Szekeras, Kaji, and Lewis finds that there are no significant differences in reducing adult mortality in countries that received PEPFAR funding vs countries that did not. Due to their potential impact on policy decisions regarding critical global health funding, we wanted to assess why the results are discrepant. To do this, we replicated the Bendavid study. The replication provides verification that the study replicable and that the analytic choices of the authors are robust to different assumptions or restrictions. This allows us to assess the different choices and data available to the two research groups and draw some conclusions about why the results may be different. Then, focusing on two of the prominently discrepant studies, i.e., the Bendavid study (1998-2008) and the Duber study (2000-2006), we establish why the two studies are in disagreement. We apply appropriate individual-level and country-level analytical methodology as used by Bendavid over the analytical time period used for the Duber study (2000-2006), which originally focused on nationally aggregated data and differed in some key focus countries. For our first objective, we replicated the original Bendavid study findings and our findings support their conclusion that between 1998-2008 all-cause mortality decreased significantly more (OR = 0.84, CI, 0.72-0.99) in countries that implemented PEPFAR. For our second objective (Bendavid\u27s data and methodology applied to Duber\u27s study period), we found reduction in all cause adult mortality to be borderline insignificant (OR = 0.87 CI, 0.75-1.01, p = 0.06), most possibly reflecting the abbreviated fewer number of events and sample size over a shorter period. Therefore, our overall analyses are consistent with the conclusion of positive impact of the PEPFAR program in reducing adult mortality. We believe that the discrepancy observed in the original studies mainly a reflection of shortcomings in the analytical approach necessitated by the Duber study\u27s nationally aggregated dataset or may reflect a lack of data quality in the Duber study (Duber, et al. 2010)

Cash Transfers and HIV/HSV-2 Prevalence: A Replication of a Cluster Randomized Trial in Malawi

INTRODUCTION: In this paper we perform a replication analysis of Effect of a cash transfer programme for schooling on prevalence of HIV and herpes simplex type 2 in Malawi: a cluster randomised trial by Sarah Baird and others published in The Lancet in 2012. The original study was a two-year cluster randomized intervention trial of never married girls aged 13-22 in Malawi. Enumeration areas were randomized to either an intervention involving cash transfer (conditional or unconditional of school enrollment) or control. The study included 1708 Malawian girls, who were enrolled at baseline and had biological testing for HIV and herpes simplex virus type 2 (HSV-2) at 18 months. The original findings showed that in the cohort of girls enrolled in school at baseline, the intervention had an effect on school enrollment, sexual outcomes, and HIV and HSV-2 prevalence. However, in the baseline school dropout cohort, the original study showed no intervention effect on HIV and HSV-2 prevalence. METHODS: We performed a replication of the study to investigate the consistency and robustness of key results reported. A pre-specified replication plan was approved and published online. Cleaned data was obtained from the original authors. A pure replication was conducted by reading the methods section and reproducing the results and tables found in the original paper. Robustness of the results were examined with alternative analysis methods in a measurement and estimation analysis (MEA) approach. A theory of change analysis was performed testing a causal pathway, the effect of intervention on HIV awareness, and whether the intervention effect depended on the wealth of the individual. RESULTS: The pure replication found that other than a few minor discrepancies, the original study was well replicated. However, the randomization and sampling weights could not be verified due to the lack of access to raw data and a detailed sample selection plan. Therefore, we are unable to determine how sampling influenced the results, which could be highly dependent on the sample. In MEA it was found that the intervention effect on HIV prevalence in the baseline schoolgirls cohort was somewhat sensitive to model choice, with a non-significant intervention effect for HIV depending on the statistical model used. The intervention effect on HSV-2 prevalence was more robust in terms of statistical significance, however, the odds ratios and confidence intervals differed from the original result by more than 10%. A theory of change analysis showed no effect of intervention on HIV awareness. In a causal pathway analysis, several variables were partial mediators, or potential mediators, indicating that the intervention could be working through its effect on school enrollment or selected sexual behaviors. CONCLUSIONS: The effect of intervention on HIV prevalence in the baseline schoolgirls was sensitive to the model choice; however, HSV-2 prevalence results were confirmed. We recommend that the results from the original published analysis indicating the impact of cash transfers on HIV prevalence be treated with caution

Preventing HIV and HSV-2 Through Knowledge and Attitudes: A Replication Study of a Multi-Component Community-Based Intervention in Zimbabwe

INTRODUCTION: Approximately two-thirds of HIV-infected individuals reside in sub-Saharan Africa. The region accounts for 68% of the new HIV infections occurring worldwide with almost one-half of these infections being among young adults aged 12-24 years. Cowan and colleagues conducted a community-based, multi-component HIV intervention aimed at youth in rural Zimbabwe. Despite some changes in knowledge and attitudes, the community-based intervention did not affect the prevalence of HIV or HSV-2. We selected this frequently cited study for replication since it incorporates individual-, community-, and structural- level intervention components that are often considered in global HIV/AIDS prevention programs. Additionally, the intervention could be easily scaled-up, which is especially important in the context of limited resources. Although this study indicated no intervention effects in reducing HIV, the authors acknowledged some key methodological challenges. Our replication analysis provided important insights regarding the impact of these challenges to the interpretation of the results of this study. METHODS: Our replication study focused on replicating Cowan\u27s findings and assessing the robustness of Cowan\u27s results to alternative analytical models based on their study design. We determined how out-migration occurring during Cowan\u27s study may have affected the population characteristics, the intervention exposure level, and the study findings. While the original intervention targeted knowledge and attitudes as a mechanism to decrease HIV/HSV-2, the Cowan study evaluated the intervention effects on knowledge, attitudes, and prevalence of HIV or HSV-2 separately. To better identify the pathway describing the interrelationship among the intervention and knowledge, attitudes, and prevalence of HIV or HSV-2, we assessed whether increases in knowledge or attitudes were associated with decreased HIV or HSV-2 prevalence. RESULTS: We replicated the original findings with minor discrepancies during the pure replication. Our additional analyses revealed that the study population characteristics changed over time in ways that may have affected outcomes. These changes also affected the levels of intervention exposure, with 48.7% males and 75.5% females of the intervention group receiving low-level exposure. Both genders with higher level intervention exposure experienced higher increments in multiple knowledge, attitude, and sexual risk behavior outcomes. Unfortunately, these did not translate to a significant reduction in HIV or HSV-2 regardless of the level and combination of knowledge and attitude domains. However, males receiving high-level intervention exposure compared to control indicated significantly lower odds of having HIV or HSV-2 under a Bayesian modeling paradigm. CONCLUSIONS: Our findings suggest a more robust conclusion on the study intervention effects. Further study based on a design that more consistently maximizes the exposure level of the intervention is necessary and should ideally be an evaluated goal in similar studies. Evaluation of the intervention impact for key subgroups of the target population is important and would better advise the use and scale-up of the evaluated interventions in various contexts. Our observation of a consistent lack of relationship between knowledge/attitudes and HIV/HSV-2 suggests a need to explore and include relevant additional and or complementary interventions, e.g., promoting effective skills in reducing risky sexual behaviors and addressing cultural and structural bottlenecks that may reduce HIV/HSV-2 risk among youth

Assessing the continuity of the blue ice climate record at Patriot Hills, Horseshoe Valley, West Antarctica

We use high resolution Ground Penetrating Radar (GPR) to assess the continuity of the Blue Ice Area (BIA) horizontal climate record at Patriot Hills, Horseshoe Valley, West Antarctica. The sequence contains three pronounced changes in deuterium isotopic values at ~18 cal ka, ~12 cal ka and ~8 cal ka. GPR surveys along the climate sequence reveal continuous, conformable dipping isochrones, separated by two unconformities in the isochrone layers, which correlate with the two older deuterium shifts. We interpret these incursions as discontinuities in the sequence, rather than direct measures of climate change. Ice-sheet models and Internal Layer Continuity Index plots suggest that the unconformities represent periods of erosion occurring as the former ice surface was scoured by katabatic winds in front of mountains at the head of Horseshoe Valley. This study demonstrates the importance of high resolution GPR surveys for investigating both paleo-flow dynamics and interpreting BIA climate records

Towards a North Sea ecosystem component of GOOS for assessment and management: report from a strategic workshop in Bergen 5-7 September 2001

ICES and IOC have established a joint Steering Group on GOOS (SGGOOS), which also involves the European component of GOOS (EuroGOOS). To increase the efficiency and effectiveness of the use of data products from current relevant national and international monitoring of the North Sea, the workshop invited the national agencies responsible for monitoring of the North Sea to: - establish a coordinated mechanism that could add value to existing activities by integrating data from various sources (physical, chemical, biological) to aid development of an ecosystem approach, - collaborate by means of a pilot project sponsored by ICES and EuroGOOS to demonstrate the usefulness of this approach by integrating data on oceanography and fisheries

Introductions over introductions: the genomic adulteration of an early genetically valuable alien species in the United Kingdom.

Invasive alien species are a major cause of biodiversity loss. Nevertheless, non-native species can also contribute to conservation objectives. In 1673, the red-legged partridge (Alectoris rufa), a galliform native to southwest Europe, was introduced from France (A. r. rufa) into the UK for hunting purposes. Nowadays, hunters constantly supplement natural populations of A. rufa in its native range with stocks of captive-bred individuals. Such birds are usually genetically unscreened, and human-mediated hybridization with the exotic chukar (Alectoris chukar) has undermined genomic integrity of the species. Alectoris rufa in the UK has never been genetically investigated, and birds from East Anglian estates with no modern history of supplementation offer a potential genomic backup for the highly polluted native-range A. r. rufa. We genotyped modern and ancient (1824–1934) birds at the mitochondrial DNA (mtDNA) level to determine present and past kinship between East Anglian and native-range A. rufa. We used Short Tandem Repeats (STR) and Random Amplified Polymorphic DNA (RAPD) markers to identify A. rufa × A. chukar hybrids. The kinship of East Anglian birds with A. r. rufa was confirmed. No A. chukar introgression was found in ancient East Anglian A. rufa. Among modern partridges, we found birds with A. chukar mtDNA, and both STRs and RAPDs disclosed many A. rufa × A. chukar hybrids. While the genetic analysis pointed to the increase of diversity and decline of disparity over time within and among A. rufa populations, respectively, the conservation value of the resource historically introduced to the UK proved to have been quashed by three decades of recent releases of A. chukar and its A. rufa hybrids. © 2014, Springer International Publishing Switzerland

Intelligence in offspring born to women exposed to intimate partner violence: a population-based cohort study

Background: Intimate partner violence (IPV) is a risk factor for developmental problems in offspring. Despite a high prevalence of IPV in the UK and elsewhere, the longer-term outcomes of offspring born to exposed mothers remain under-researched. Methods: Population-based cohort study. We assessed IPV prevalence by type and timing for 3,153 mother-child pairs with complete data within our study population and examined associations between IPV and offspring IQ. We used multiple-imputation to evaluate bias due to our exclusion of observations with missing covariate data. Results: Nearly one in five mothers reported IPV during the study period, with 17.6% reporting emotional violence and 6.8% reporting physical violence. Taking into account potential confounders, the IQ scores of children born to mothers exposed to physical violence remained lower than those of maternally unexposed children (full-scale IQ = −2.8 points [95%CI −4.9 to −0.7], verbal IQ = −2.2 [95%CI −4.4 to −0.1], performance IQ = −2.7 [95%CI  −5.0 to −0.5]) and odds of below-average intelligence (IQ<90) remained increased for full-scale (OR 1.48 [95%CI 1.03 to 2.14] and performance IQ (OR 1.48 [95%CI 1.08 to 2.04]) but not verbal IQ (OR 1.06 [95%CI 0.69 to 1.64]). Most physical violence occurred postnatally, and relative odds were most substantial when mothers were exposed to violence across pre-/perinatal and postnatal study periods (OR performance IQ<90 = 2.97 [95%CI 1.30 to 6.82]). Conclusions: Maternal exposure to physical IPV is associated with lower offspring IQ at age 8. Associations persisted after adjusting for potential confounders and were driven by violence occurring postnatally

The Impact of Body Mass Index and Sociodemographic Factors on Moderate-to-Vigorous Physical Activity and Sedentary Behaviors of Women With Young Children: A Cross-Sectional Examination

OBJECTIVES: Moderate-to-vigorous physical activity provides multiple benefits to women after childbirth. To achieve these benefits, the recommendation that adults obtain, 150 min of moderate-to-vigorous physical activity per week and reduce sedentary behaviors, also applies to women in the post-partum phase of the life span. However, research examining the moderate-to-vigorous physical activity and sedentary behaviors of women with young children (0-2 years) is limited. A greater understanding of these behaviors from a nationally representative sample is needed. Therefore, the primary objective of this study was to determine the levels of moderate-to-vigorous physical activity and sedentary behaviors of a nationally representative sample of women with young children within the United States. A secondary objective was to examine the influence of body mass index and sociodemographic factors on these behaviors. METHODS: Cross-sectional data from four cycles of the National Health and Nutrition Examination Survey (2007-2008, 2009-2010, 2011-2012, and 2013-2014) were used for analysis. Descriptive statistics were calculated and a generalized linear model was used to investigate associations between mean minutes of moderate-to-vigorous physical activity, sedentary activity, body mass index, and sociodemographic variables. DISCUSSION: Women with young children (n = 477) obtained 634 min in moderate-to-vigorous physical activity per week and this was positively associated with having a higher income (p \u3c 0.001) and the number of children in the home (p \u3c 0.001). In total, 62% of women were meeting the World Health Organization guidelines for aerobic activity. Lower odds of achieving guidelines was associated with being Black (p = 0.004), Mexican American (p = 0.009), or married (p = 0.042) compared with being White or not married. Finally, women accumulated ~5 h of sedentary activity per day, with higher levels associated with race (p = 0.005), education (p = 0.022), and number of children within the home (p \u3c 0.001). Research efforts should continue to focus on strategies to help non-adhering women with young children achieve the physical activity recommendations and reduce time spent in sedentary behaviors