Synergy detection: A practical guide to statistical assessment of potential drug combinations.

Combination treatments have been of increasing importance in drug development across therapeutic areas to improve treatment response, minimize the development of resistance, and/or minimize adverse events. Pre-clinical in-vitro combination experiments aim to explore the potential of such drug combinations during drug discovery by comparing the observed effect of the combination with the expected treatment effect under the assumption of no interaction (i.e., null model). This tutorial will address important design aspects of such experiments to allow proper statistical evaluation. Additionally, it will highlight the Biochemically Intuitive Generalized Loewe methodology (BIGL R package available on CRAN) to statistically detect deviations from the expectation under different null models. A clear advantage of the methodology is the quantification of the effect sizes, together with confidence interval while controlling the directional false coverage rate. Finally, a case study will showcase the workflow in analyzing combination experiments.

Chromium Nitride Umpolung Tuned by the Locus of Oxidation.

Oxidation of a series of CrV nitride salen complexes (CrVNSalR) with different para-phenolate substituents (R = CF3, tBu, NMe2) was investigated to determine how the locus of oxidation (either metal or ligand) dictates reactivity at the nitride. Para-phenolate substituents were chosen to provide maximum variation in the electron-donating ability of the tetradentate ligand at a site remote from the metal coordination sphere. We show that one-electron oxidation affords CrVI nitrides ([CrVINSalR]+; R = CF3, tBu) and a localized CrV nitride phenoxyl radical for the more electron-donating NMe2 substituent ([CrVNSalNMe2]•+). The facile nitride homocoupling observed for the MnVI analogues was significantly attenuated for the CrVI complexes due to a smaller increase in nitride character in the M≡N π* orbitals for Cr relative to Mn. Upon oxidation, both the calculated nitride natural population analysis (NPA) charge and energy of molecular orbitals associated with the {Cr≡N} unit change to a lesser extent for the CrV ligand radical derivative ([CrVNSalNMe2]•+) in comparison to the CrVI derivatives ([CrVINSalR]+; R = CF3, tBu). As a result, [CrVNSalNMe2]•+ reacts with B(C6F5)3, thus exhibiting similar nucleophilic reactivity to the neutral CrV nitride derivatives. In contrast, the CrVI derivatives ([CrVINSalR]+; R = CF3, tBu) act as electrophiles, displaying facile reactivity with PPh3 and no reaction with B(C6F5)3. Thus, while oxidation to the ligand radical does not change the reactivity profile, metal-based oxidation to CrVI results in umpolung, a switch from nucleophilic to electrophilic reactivity at the terminal nitride.

Elaboration on the Electronics of Salen Manganese Nitrides: Investigations into Alkoxy-Substituted Ligand Scaffolds.

The ligand electronics of salen manganese nitride complexes directly influence the locus of oxidation and, thus, the reactivity of the resulting oxidized species. This work investigates the influence of tert-butoxy, isopropoxy, and methoxy substituents on the electronics of salen manganese nitride species and includes the first documentation of the para Hammett value for the tert-butoxy substituent (σpara = -0.13 ± 0.03). Each alkoxy-substituted complex undergoes metal-based oxidation to form manganese(VI), and the kinetics of bimolecular homocoupling to form N2 were assessed by cyclic voltammetry. Bis-oxidation of the manganese complexes was investigated at low temperature using cyclic voltammery and UV-vis-near-IR spectroscopy, and in combination with theoretical calculations, plausible electronic structures of the dications are provided.

The President's 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's 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's data and methodology applied to Duber's 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's nationally aggregated dataset or "may reflect a lack of data quality" in the Duber study (Duber, et al. 2010).

Omega-3 Long-Chain Polyunsaturated Fatty Acids Intake by Ethnicity, Income, and Education Level in the United States: NHANES 2003-2014.

Although there are many recognized health benefits for the consumption of omega-3 (n-3) long-chain polyunsaturated fatty acids (LCPUFA), intake in the United States remains below recommended amounts. This analysis was designed to provide an updated assessment of fish and n-3 LCPUFA intake (eicosapentaenoic (EPA), docosahexaenoic acid (DHA), and EPA+DHA) in the United States adult population, based on education, income, and race/ethnicity, using data from the 2003-2014 National Health and Nutrition Examination Survey (NHANES) (n = 44,585). Over this survey period, participants with less education and lower income had significantly lower n-3 LCPUFA intakes and fish intakes (p < 0.001 for all between group comparisons). N-3 LCPUFA intake differed significantly according to ethnicity (p < 0.001), with the highest intake of n-3 LCPUFA and fish in individuals in the "Other" category (including Asian Americans). Supplement use increased EPA + DHA intake, but only 7.4% of individuals consistently took supplements. Overall, n-3 LCPUFA intake in this study population was low, but our findings indicate that individuals with lower educational attainment and income are at even higher risk of lower n-3 LCPUFA and fish intake.

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 < 0.001) and the number of children in the home (p < 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 < 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.

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's findings and assessing the robustness of Cowan's results to alternative analytical models based on their study design. We determined how out-migration occurring during Cowan's 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.

Comparing methods for clinical investigator site inspection selection: a comparison of site selection methods of investigators in clinical trials.

Background During the past two decades, the number and complexity of clinical trials have risen dramatically increasing the difficulty of choosing sites for inspection. FDA's resources are limited and so sites should be chosen with care. Purpose To determine if data mining techniques and/or unsupervised statistical monitoring can assist with the process of identifying potential clinical sites for inspection. Methods Five summary-level clinical site datasets from four new drug applications (NDA) and one biologics license application (BLA), where the FDA had performed or had planned site inspections, were used. The number of sites inspected and the results of the inspections were blinded to the researchers. Five supervised learning models from the previous two years (2016-2017) of an on-going research project were used to predict site inspections results, i.e., No Action Indicated (NAI), Voluntary Action Indicated (VAI), or Official Action Indicated (OAI). Statistical Monitoring Applied to Research Trials (SMARTTM) software for unsupervised statistical monitoring software developed by CluePoints (Mont-Saint-Guibert, Belgium) was utilized to identify atypical centers (via a p-value approach) within a study.Finally, Clinical Investigator Site Selection Tool (CISST), developed by the Center for Drug Evaluation and Research (CDER), was used to calculate the total risk of each site thereby providing a framework for site selection. The agreement between the predictions of these methods was compared. The overall accuracy and sensitivity of the methods were graphically compared. Results Spearman's rank order correlation was used to examine the agreement between the SMARTTM analysis (CluePoints' software) and the CISST analysis. The average aggregated correlation between the p-values (SMARTTM) and total risk scores (CISST) for all five studies was 0.21, and range from -0.41 to 0.50. The Random Forest models for 2016 and 2017 showed the highest aggregated mean agreement (65.1%) amongst outcomes (NAI, VAI, OAI) for the three available studies. While there does not appear to be a single most accurate approach, the performance of methods under certain circumstances is discussed later in this paper. Limitations Classifier models based on data mining techniques require historical data (i.e., training data) to develop the model. There is a possibility that sites in the five-summary level datasets were included in the training datasets for the models from the previous year's research which could result in spurious confirmation of predictive ability. Additionally, the CISST was utilized in three of the five site selection processes, possibly biasing the data. Conclusion The agreement between methods was lower than expected and no single method emerged as the most accurate.

n-3 Docosapentaenoic Acid Intake and Relationship with Plasma Long-Chain n-3 Fatty Acid Concentrations in the United States: NHANES 2003-2014.

The long-chain n-3 fatty acids, eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), play a crucial role in health, but previous National Health and Nutrition Examination Survey (NHANES) analyses have shown that EPA and DHA intake in the United States is far below recommendations (~250-500 mg/day EPA + DHA). Less is known about docosapentaenoic acid (DPA), the metabolic intermediate of EPA and DHA; however, evidence suggests DPA may be an important contributor to long-chain n-3 fatty acid intake and impart unique benefits. We used NHANES 2003-2014 data (n = 45,347) to assess DPA intake and plasma concentrations, as well as the relationship between intake and plasma concentrations of EPA, DPA, and DHA. Mean DPA intake was 22.3 ± 0.8 mg/day from 2013 to 2014, and increased significantly over time (p < 0.001), with the lowest values from 2003 to 2004 (16.2 ± 1.2 mg/day). DPA intake was higher in adults (20-55 years) and seniors (55+ years) compared to younger individuals. In regression analyses, DPA intake was a significant predictor of plasma EPA (ß = 138.5; p < 0.001) and DHA (ß = 318.9; p < 0.001). Plasma DPA was predicted by EPA and DHA intake (ß = 13.15; p = 0.001 and ß = 7.4; p = 0.002), but not dietary DPA (p = 0.3). This indicates that DPA intake is not a good marker of plasma DPA status (or vice versa), and further research is needed to understand the factors that affect the interconversion of EPA and DPA. These findings have implications for future long-chain n-3 fatty acids dietary recommendations.

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.

Omega-3 Fatty Acid Intake by Age, Gender, and Pregnancy Status in the United States: National Health and Nutrition Examination Survey 2003⁻2014.

Despite the importance of n-3 fatty acids for health, intakes remain below recommended levels. The objective of this study was to provide an updated assessment of fish and n-3 fatty acid intake (i.e., eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA), and EPA+DHA) in the United States using the 2003⁻2014 National Health and Nutrition Examination Survey (NHANES) data (n = 45,347)). Over this survey period, toddlers, children, and adolescents (aged 1⁻19) had significantly lower n-3 fatty acid intake (p < 0.001) compared to adults and seniors, which remained significant after adjusting for caloric intake. Females demonstrated lower n-3 fatty acid intake than males (p < 0.001), with adult and senior women having significantly lower intakes compared to men in the same age categories (p < 0.001) after adjustment for energy intake. Women also consumed less fish than men (5.8 versus 6.1 servings/month, p < 0.001). The estimated intakes of n-3 fatty acids in pregnant women did not differ from non-pregnant women (p = 0.6 for EPA+DHA), although pregnant women reported consuming less high n-3 fatty acid-containing fish than non-pregnant women (1.8 versus 2.6 servings/month, p < 0.001). Our findings indicate that subgroups of the population may be at higher risk of n-3 fatty acid intakes below recommended levels.

Synthesis and Reactivity of a Low-Coordinate Iron(II) Hydride Complex: Applications in Catalytic Hydrodefluorination.

A low-coordinate iron hydride complex bearing an unsymmetrical NpN (enamido-phosphinimine) ligand scaffold was synthesized and fully characterized. Insertion reactivity with azobenzene, 3-hexyne, and 1-azidoadamantane was explored, and the isolated products were analogous to previously reported ß-diketiminate iron hydride insertion products. Surprisingly, the NpN iron hydride displays unprecedented reactivity toward hexafluorobenzene, affording an NpN iron fluoride complex and pentafluorobenzene as products. The NpN iron hydride is a precatalyst for catalytic hydro-defluorination of perfluorinated aromatics in the presence of silane. Kinetic studies indicated that the rate-determining step during catalysis involved silane.

Neoadjuvant treatment of pancreatic adenocarcinoma: a systematic review and meta-analysis of 5520 patients.

BACKGROUND: Recent years have seen standardization of the anatomic definitions of pancreatic adenocarcinoma, and increasing utilization of neoadjuvant therapy (NAT). The aim of the current review was to summarize the evidence for NAT in pancreatic adenocarcinoma since 2009, when consensus criteria for resectable (R), borderline resectable (BR), and locally advanced (LA) disease were endorsed. METHODS: PubMed search was undertaken along with extensive backward search of the references of published articles to identify studies utilizing NAT for pancreatic adenocarcinoma. Abstracts from ASCO-GI 2014 and 2015 were also searched. RESULTS: A total of 96 studies including 5520 patients were included in the final quantitative synthesis. Pooled estimates revealed 36% grade ≥ 3 toxicities, 5% biliary complications, 21% hospitalization rate and low mortality (0%, range 0-16%) during NAT. The majority of patients (59%) had stable disease. On an intention-to-treat basis, R0-resection rates varied from 63% among R patients to 23% among LA patients. R0 rates were > 80% among all patients who were resected after NAT. Among R and BR patients who underwent resection after NAT, median OS was 30 and 27.4 months, respectively. CONCLUSIONS: The current study summarizes the recent literature for NAT in pancreatic adenocarcinoma and demonstrates improving outcomes after NAT compared to those historically associated with a surgery-first approach for pancreatic adenocarcinoma.

Low coordinate iron derivatives stabilized by a ß-diketiminate mimic. Synthesis and coordination chemistry of enamidophosphinimine scaffolds to generate diiron dinitrogen complexes.

In an effort to mimic N-diaryl-ß-diketiminate ligands (Nacnac), we have converted N-arylimine phosphine ligands to enamine-phosphinimines via the Staudinger reaction. By varying the aryl azide, one can access enamine-phosphinimine ligands with the same or different N-aryl substituents on both the enamine and phosphinimine units, which allows this intrinsically unsymmetrical bidentate donor set to present variable steric effects at the metal center. The enamine-phosphinimine was deprotonated and used in metathetical reactions with Fe(ii) bromide precursors to generate low coordinate complexes of the empirical formula [(CY5)NpN(Ar,Ar')]FeBr (where CY5 = cyclopentenyl; Ar,Ar' = 2,6-diisopropylphenyl, 2,6-dimethylphenyl, 2,4,6-trimethylphenyl). Depending on the substituents, these bromide derivatives can be monomeric or dimeric via bromide bridges. Reduction under dinitrogen using potassium graphite generates the dinitrogen complexes ([(CY5)NpN(Ar,Ar')]Fe)2(µ-N2) for Ar,Ar' = 2,6-diisopropylphenyl, and Ar = 2,6-dimethylphenyl, Ar' = 2,4,6-trimethylphenyl. However, for the former, a unsymmetrical side product can be isolated that has a bridging N-2,6-diisopropylphenylimide unit with one enamido-phosphine ligand bound to one iron and the other iron stabilized with an intact enamido-phosphinimine. When the steric bulk is reduced on both nitrogen donors, a complicated product mixture is obtained after reduction from which a small amount of [(CY5)NpN(Ar,Ar')]Fe[(CY5)NP(Ar)] (Ar,Ar' = 2,6-dimethylphenyl) could be isolated. All of these complexes are paramagnetic and have been characterized by elemental analysis, magnetic studies and X-ray crystallography.

Cleavage of an aryl carbon-nitrogen bond of a phosphazido iron(II) complex promoted by hydride metathesis.

Upon reaction with KBEt3H, the pseudo tetrahedral Fe(II) complex with a bulky enamido-phosphazide ligand set undergoes elimination of N2 and 1,3-Me2C6H4 to generate the dinuclear Fe(II) derivative with bridging phosphinimido units. When the reaction is performed using KBEt3D, no deuterium is incorporated into the eliminated 1,3-Me2C6H4; all of the deuterium ends up as D2. When the reaction is performed in THF-d8, only 2-d-1,3-Me2C6H3D was detected by GCMS. These studies are consistent with a radical mechanism.